Starting phenix.real_space_refine on Thu Mar 14 17:50:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/03_2024/6hqe_0252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/03_2024/6hqe_0252.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/03_2024/6hqe_0252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/03_2024/6hqe_0252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/03_2024/6hqe_0252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/03_2024/6hqe_0252.pdb" } resolution = 4.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 3 Type Number sf(0) Gaussians C 5668 2.51 5 N 1976 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 22": "NH1" <-> "NH2" Residue "B ARG 22": "NH1" <-> "NH2" Residue "C ARG 22": "NH1" <-> "NH2" Residue "D ARG 22": "NH1" <-> "NH2" Residue "E ARG 22": "NH1" <-> "NH2" Residue "F ARG 22": "NH1" <-> "NH2" Residue "G ARG 22": "NH1" <-> "NH2" Residue "H ARG 22": "NH1" <-> "NH2" Residue "I ARG 22": "NH1" <-> "NH2" Residue "J ARG 22": "NH1" <-> "NH2" Residue "K ARG 22": "NH1" <-> "NH2" Residue "L ARG 22": "NH1" <-> "NH2" Residue "M ARG 22": "NH1" <-> "NH2" Residue "N ARG 22": "NH1" <-> "NH2" Residue "O ARG 22": "NH1" <-> "NH2" Residue "P ARG 22": "NH1" <-> "NH2" Residue "Q ARG 22": "NH1" <-> "NH2" Residue "R ARG 22": "NH1" <-> "NH2" Residue "S ARG 22": "NH1" <-> "NH2" Residue "T ARG 22": "NH1" <-> "NH2" Residue "U ARG 22": "NH1" <-> "NH2" Residue "V ARG 22": "NH1" <-> "NH2" Residue "W ARG 22": "NH1" <-> "NH2" Residue "X ARG 22": "NH1" <-> "NH2" Residue "Y ARG 22": "NH1" <-> "NH2" Residue "Z ARG 22": "NH1" <-> "NH2" Residue "a ARG 22": "NH1" <-> "NH2" Residue "b ARG 22": "NH1" <-> "NH2" Residue "c ARG 22": "NH1" <-> "NH2" Residue "d ARG 22": "NH1" <-> "NH2" Residue "e ARG 22": "NH1" <-> "NH2" Residue "f ARG 22": "NH1" <-> "NH2" Residue "g ARG 22": "NH1" <-> "NH2" Residue "h ARG 22": "NH1" <-> "NH2" Residue "i ARG 22": "NH1" <-> "NH2" Residue "j ARG 22": "NH1" <-> "NH2" Residue "k ARG 22": "NH1" <-> "NH2" Residue "l ARG 22": "NH1" <-> "NH2" Residue "m ARG 22": "NH1" <-> "NH2" Residue "n ARG 22": "NH1" <-> "NH2" Residue "o ARG 22": "NH1" <-> "NH2" Residue "p ARG 22": "NH1" <-> "NH2" Residue "q ARG 22": "NH1" <-> "NH2" Residue "r ARG 22": "NH1" <-> "NH2" Residue "s ARG 22": "NH1" <-> "NH2" Residue "t ARG 22": "NH1" <-> "NH2" Residue "u ARG 22": "NH1" <-> "NH2" Residue "v ARG 22": "NH1" <-> "NH2" Residue "w ARG 22": "NH1" <-> "NH2" Residue "x ARG 22": "NH1" <-> "NH2" Residue "y ARG 22": "NH1" <-> "NH2" Residue "z ARG 22": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 9360 Number of models: 1 Model: "" Number of chains: 52 Chain: "A" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "B" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "C" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "D" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "E" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "F" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "G" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "H" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "I" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "J" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "K" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "L" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "M" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "N" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "O" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "P" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Q" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "R" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "S" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "T" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "U" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "V" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "W" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "X" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Y" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "Z" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "a" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "b" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "c" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "d" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "e" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "f" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "g" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "h" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "i" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "j" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "k" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "l" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "m" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "n" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "o" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "p" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "q" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "r" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "s" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "t" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "u" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "v" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "w" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "x" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "y" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Chain: "z" Number of atoms: 180 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 180 Classifications: {'peptide': 23} Link IDs: {'PTRANS': 1, 'TRANS': 21} Time building chain proxies: 4.79, per 1000 atoms: 0.51 Number of scatterers: 9360 At special positions: 0 Unit cell: (91.08, 91.08, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 1716 8.00 N 1976 7.00 C 5668 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: 3.59 Conformation dependent library (CDL) restraints added in 1.8 seconds 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2392 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 0 sheets defined 78.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 2 through 7 Processing helix chain 'A' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG A 16 " --> pdb=" O ASP A 12 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 7 Processing helix chain 'B' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG B 16 " --> pdb=" O ASP B 12 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 7 Processing helix chain 'C' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG C 16 " --> pdb=" O ASP C 12 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 7 Processing helix chain 'D' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG D 16 " --> pdb=" O ASP D 12 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 7 Processing helix chain 'E' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG E 16 " --> pdb=" O ASP E 12 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 7 Processing helix chain 'F' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG F 16 " --> pdb=" O ASP F 12 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 7 Processing helix chain 'G' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG G 16 " --> pdb=" O ASP G 12 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 7 Processing helix chain 'H' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG H 16 " --> pdb=" O ASP H 12 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 7 Processing helix chain 'I' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG I 16 " --> pdb=" O ASP I 12 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 7 Processing helix chain 'J' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG J 16 " --> pdb=" O ASP J 12 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 7 Processing helix chain 'K' and resid 12 through 23 removed outlier: 3.590A pdb=" N ARG K 16 " --> pdb=" O ASP K 12 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 7 Processing helix chain 'L' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG L 16 " --> pdb=" O ASP L 12 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 7 Processing helix chain 'M' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG M 16 " --> pdb=" O ASP M 12 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 7 Processing helix chain 'N' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG N 16 " --> pdb=" O ASP N 12 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 7 Processing helix chain 'O' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG O 16 " --> pdb=" O ASP O 12 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 7 Processing helix chain 'P' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG P 16 " --> pdb=" O ASP P 12 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 7 Processing helix chain 'Q' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG Q 16 " --> pdb=" O ASP Q 12 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 7 Processing helix chain 'R' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG R 16 " --> pdb=" O ASP R 12 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 7 Processing helix chain 'S' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 7 Processing helix chain 'T' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG T 16 " --> pdb=" O ASP T 12 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 7 Processing helix chain 'U' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG U 16 " --> pdb=" O ASP U 12 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 7 Processing helix chain 'V' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG V 16 " --> pdb=" O ASP V 12 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 7 Processing helix chain 'W' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG W 16 " --> pdb=" O ASP W 12 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 7 Processing helix chain 'X' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG X 16 " --> pdb=" O ASP X 12 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 7 Processing helix chain 'Y' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG Y 16 " --> pdb=" O ASP Y 12 " (cutoff:3.500A) Processing helix chain 'Z' and resid 2 through 7 Processing helix chain 'Z' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG Z 16 " --> pdb=" O ASP Z 12 " (cutoff:3.500A) Processing helix chain 'a' and resid 2 through 7 Processing helix chain 'a' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG a 16 " --> pdb=" O ASP a 12 " (cutoff:3.500A) Processing helix chain 'b' and resid 2 through 7 Processing helix chain 'b' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG b 16 " --> pdb=" O ASP b 12 " (cutoff:3.500A) Processing helix chain 'c' and resid 2 through 7 Processing helix chain 'c' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG c 16 " --> pdb=" O ASP c 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 2 through 7 Processing helix chain 'd' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'e' and resid 2 through 7 Processing helix chain 'e' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG e 16 " --> pdb=" O ASP e 12 " (cutoff:3.500A) Processing helix chain 'f' and resid 2 through 7 Processing helix chain 'f' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG f 16 " --> pdb=" O ASP f 12 " (cutoff:3.500A) Processing helix chain 'g' and resid 2 through 7 Processing helix chain 'g' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG g 16 " --> pdb=" O ASP g 12 " (cutoff:3.500A) Processing helix chain 'h' and resid 2 through 7 Processing helix chain 'h' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG h 16 " --> pdb=" O ASP h 12 " (cutoff:3.500A) Processing helix chain 'i' and resid 2 through 7 Processing helix chain 'i' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG i 16 " --> pdb=" O ASP i 12 " (cutoff:3.500A) Processing helix chain 'j' and resid 2 through 7 Processing helix chain 'j' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG j 16 " --> pdb=" O ASP j 12 " (cutoff:3.500A) Processing helix chain 'k' and resid 2 through 7 Processing helix chain 'k' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG k 16 " --> pdb=" O ASP k 12 " (cutoff:3.500A) Processing helix chain 'l' and resid 2 through 7 Processing helix chain 'l' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG l 16 " --> pdb=" O ASP l 12 " (cutoff:3.500A) Processing helix chain 'm' and resid 2 through 7 Processing helix chain 'm' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG m 16 " --> pdb=" O ASP m 12 " (cutoff:3.500A) Processing helix chain 'n' and resid 2 through 7 Processing helix chain 'n' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG n 16 " --> pdb=" O ASP n 12 " (cutoff:3.500A) Processing helix chain 'o' and resid 2 through 7 Processing helix chain 'o' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG o 16 " --> pdb=" O ASP o 12 " (cutoff:3.500A) Processing helix chain 'p' and resid 2 through 7 Processing helix chain 'p' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG p 16 " --> pdb=" O ASP p 12 " (cutoff:3.500A) Processing helix chain 'q' and resid 2 through 7 Processing helix chain 'q' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG q 16 " --> pdb=" O ASP q 12 " (cutoff:3.500A) Processing helix chain 'r' and resid 2 through 7 Processing helix chain 'r' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG r 16 " --> pdb=" O ASP r 12 " (cutoff:3.500A) Processing helix chain 's' and resid 2 through 7 Processing helix chain 's' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG s 16 " --> pdb=" O ASP s 12 " (cutoff:3.500A) Processing helix chain 't' and resid 2 through 7 Processing helix chain 't' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG t 16 " --> pdb=" O ASP t 12 " (cutoff:3.500A) Processing helix chain 'u' and resid 2 through 7 Processing helix chain 'u' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG u 16 " --> pdb=" O ASP u 12 " (cutoff:3.500A) Processing helix chain 'v' and resid 2 through 7 Processing helix chain 'v' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG v 16 " --> pdb=" O ASP v 12 " (cutoff:3.500A) Processing helix chain 'w' and resid 2 through 7 Processing helix chain 'w' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG w 16 " --> pdb=" O ASP w 12 " (cutoff:3.500A) Processing helix chain 'x' and resid 2 through 7 Processing helix chain 'x' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG x 16 " --> pdb=" O ASP x 12 " (cutoff:3.500A) Processing helix chain 'y' and resid 2 through 7 Processing helix chain 'y' and resid 12 through 23 removed outlier: 3.591A pdb=" N ARG y 16 " --> pdb=" O ASP y 12 " (cutoff:3.500A) Processing helix chain 'z' and resid 2 through 7 Processing helix chain 'z' and resid 12 through 23 removed outlier: 3.592A pdb=" N ARG z 16 " --> pdb=" O ASP z 12 " (cutoff:3.500A) 468 hydrogen bonds defined for protein. 1404 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: 2.20 Time building geometry restraints manager: 3.88 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 1716 1.29 - 1.35: 1924 1.35 - 1.41: 0 1.41 - 1.48: 1602 1.48 - 1.54: 4170 Bond restraints: 9412 Sorted by residual: bond pdb=" CG LEU c 23 " pdb=" CD1 LEU c 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.40e+00 bond pdb=" CG LEU e 23 " pdb=" CD1 LEU e 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU v 23 " pdb=" CD1 LEU v 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.39e+00 bond pdb=" CG LEU r 23 " pdb=" CD1 LEU r 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 bond pdb=" CG LEU R 23 " pdb=" CD1 LEU R 23 " ideal model delta sigma weight residual 1.521 1.482 0.039 3.30e-02 9.18e+02 1.38e+00 ... (remaining 9407 not shown) Histogram of bond angle deviations from ideal: 102.27 - 107.06: 416 107.06 - 111.86: 4310 111.86 - 116.65: 1618 116.65 - 121.44: 4245 121.44 - 126.23: 2047 Bond angle restraints: 12636 Sorted by residual: angle pdb=" CA LEU U 4 " pdb=" CB LEU U 4 " pdb=" CG LEU U 4 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.70e+00 angle pdb=" CA LEU E 4 " pdb=" CB LEU E 4 " pdb=" CG LEU E 4 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 angle pdb=" CA LEU L 4 " pdb=" CB LEU L 4 " pdb=" CG LEU L 4 " ideal model delta sigma weight residual 116.30 124.65 -8.35 3.50e+00 8.16e-02 5.69e+00 angle pdb=" CA LEU p 4 " pdb=" CB LEU p 4 " pdb=" CG LEU p 4 " ideal model delta sigma weight residual 116.30 124.64 -8.34 3.50e+00 8.16e-02 5.68e+00 angle pdb=" CA LEU T 4 " pdb=" CB LEU T 4 " pdb=" CG LEU T 4 " ideal model delta sigma weight residual 116.30 124.63 -8.33 3.50e+00 8.16e-02 5.67e+00 ... (remaining 12631 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.46: 4147 5.46 - 10.93: 1157 10.93 - 16.39: 572 16.39 - 21.86: 208 21.86 - 27.32: 156 Dihedral angle restraints: 6240 sinusoidal: 2704 harmonic: 3536 Sorted by residual: dihedral pdb=" CA ALA o 20 " pdb=" C ALA o 20 " pdb=" N ARG o 21 " pdb=" CA ARG o 21 " ideal model delta harmonic sigma weight residual 180.00 166.99 13.01 0 5.00e+00 4.00e-02 6.77e+00 dihedral pdb=" CA ALA z 20 " pdb=" C ALA z 20 " pdb=" N ARG z 21 " pdb=" CA ARG z 21 " ideal model delta harmonic sigma weight residual 180.00 166.99 13.01 0 5.00e+00 4.00e-02 6.77e+00 dihedral pdb=" CA ALA Q 20 " pdb=" C ALA Q 20 " pdb=" N ARG Q 21 " pdb=" CA ARG Q 21 " ideal model delta harmonic sigma weight residual 180.00 167.00 13.00 0 5.00e+00 4.00e-02 6.76e+00 ... (remaining 6237 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 526 0.029 - 0.059: 491 0.059 - 0.088: 225 0.088 - 0.118: 110 0.118 - 0.147: 104 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CA LEU Z 23 " pdb=" N LEU Z 23 " pdb=" C LEU Z 23 " pdb=" CB LEU Z 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA LEU m 23 " pdb=" N LEU m 23 " pdb=" C LEU m 23 " pdb=" CB LEU m 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.34e-01 chirality pdb=" CA LEU g 23 " pdb=" N LEU g 23 " pdb=" C LEU g 23 " pdb=" CB LEU g 23 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 1453 not shown) Planarity restraints: 1716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP o 10 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.47e+00 pdb=" N PRO o 11 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO o 11 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO o 11 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP X 10 " -0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO X 11 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO X 11 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO X 11 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP n 10 " 0.039 5.00e-02 4.00e+02 5.84e-02 5.46e+00 pdb=" N PRO n 11 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO n 11 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO n 11 " 0.032 5.00e-02 4.00e+02 ... (remaining 1713 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 2964 2.83 - 3.34: 9236 3.34 - 3.86: 16004 3.86 - 4.38: 18566 4.38 - 4.90: 27403 Nonbonded interactions: 74173 Sorted by model distance: nonbonded pdb=" OD2 ASP b 10 " pdb=" NE ARG d 16 " model vdw 2.307 2.520 nonbonded pdb=" OD2 ASP v 10 " pdb=" NE ARG x 16 " model vdw 2.338 2.520 nonbonded pdb=" OD2 ASP L 10 " pdb=" NE ARG N 16 " model vdw 2.350 2.520 nonbonded pdb=" NE ARG e 16 " pdb=" OD2 ASP g 10 " model vdw 2.372 2.520 nonbonded pdb=" NE ARG M 16 " pdb=" OD2 ASP O 10 " model vdw 2.394 2.520 ... (remaining 74168 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' selection = chain 'Y' selection = chain 'Z' selection = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.080 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: 0.950 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 25.710 Find NCS groups from input model: 0.740 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 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 : 0.009 0.039 9412 Z= 0.618 Angle : 1.254 8.355 12636 Z= 0.667 Chirality : 0.061 0.147 1456 Planarity : 0.011 0.058 1716 Dihedral : 9.670 27.320 3848 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % 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: -7.05 (0.13), residues: 1092 helix: -4.24 (0.08), residues: 988 sheet: None (None), residues: 0 loop : -4.94 (0.43), residues: 104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG v 22 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 545 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 6 ARG cc_start: 0.8755 (mtm-85) cc_final: 0.8373 (ttp-110) REVERT: E 10 ASP cc_start: 0.8970 (t0) cc_final: 0.8706 (t0) REVERT: F 6 ARG cc_start: 0.8632 (mtm-85) cc_final: 0.8415 (ttp-110) REVERT: G 10 ASP cc_start: 0.9236 (t0) cc_final: 0.8943 (t0) REVERT: K 15 VAL cc_start: 0.9481 (t) cc_final: 0.9242 (p) REVERT: N 10 ASP cc_start: 0.9197 (t0) cc_final: 0.8935 (t0) REVERT: P 10 ASP cc_start: 0.8947 (t0) cc_final: 0.8717 (t0) REVERT: Q 6 ARG cc_start: 0.8685 (mtm-85) cc_final: 0.8416 (ttm110) REVERT: S 6 ARG cc_start: 0.8645 (mtm-85) cc_final: 0.8306 (ttm-80) REVERT: T 6 ARG cc_start: 0.8914 (mtm-85) cc_final: 0.8596 (ttm110) REVERT: Y 10 ASP cc_start: 0.9088 (t0) cc_final: 0.8808 (t0) REVERT: Z 6 ARG cc_start: 0.8756 (mtm-85) cc_final: 0.8509 (ttm-80) REVERT: b 10 ASP cc_start: 0.9091 (t0) cc_final: 0.8881 (t0) REVERT: c 15 VAL cc_start: 0.9502 (t) cc_final: 0.9168 (p) REVERT: c 19 VAL cc_start: 0.9375 (t) cc_final: 0.9107 (t) REVERT: c 22 ARG cc_start: 0.8568 (mmt-90) cc_final: 0.8137 (mmt-90) REVERT: d 10 ASP cc_start: 0.9044 (t0) cc_final: 0.8794 (t0) REVERT: f 10 ASP cc_start: 0.9147 (t0) cc_final: 0.8944 (t0) REVERT: g 10 ASP cc_start: 0.9048 (t0) cc_final: 0.8729 (t0) REVERT: i 10 ASP cc_start: 0.8748 (t0) cc_final: 0.8503 (t0) REVERT: k 10 ASP cc_start: 0.9057 (t0) cc_final: 0.8788 (t0) REVERT: l 5 GLU cc_start: 0.8968 (mp0) cc_final: 0.8660 (mp0) REVERT: l 10 ASP cc_start: 0.9094 (t0) cc_final: 0.8872 (t0) REVERT: n 6 ARG cc_start: 0.8883 (mtm-85) cc_final: 0.8649 (ttp-110) REVERT: o 15 VAL cc_start: 0.9438 (t) cc_final: 0.9215 (p) REVERT: p 10 ASP cc_start: 0.9110 (t0) cc_final: 0.8802 (t0) REVERT: q 10 ASP cc_start: 0.9142 (t0) cc_final: 0.8909 (t0) REVERT: u 10 ASP cc_start: 0.9032 (t0) cc_final: 0.8695 (t0) REVERT: v 10 ASP cc_start: 0.9113 (t0) cc_final: 0.8682 (t0) REVERT: x 10 ASP cc_start: 0.9008 (t0) cc_final: 0.8775 (t0) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3414 time to fit residues: 227.9388 Evaluate side-chains 396 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 396 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 9.9990 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 81 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 94 optimal weight: 3.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.4608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 9412 Z= 0.244 Angle : 0.571 5.685 12636 Z= 0.305 Chirality : 0.041 0.120 1456 Planarity : 0.010 0.056 1716 Dihedral : 4.349 11.913 1404 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.94 (0.26), residues: 1092 helix: -1.78 (0.16), residues: 936 sheet: None (None), residues: 0 loop : -1.40 (0.71), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 22 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 534 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 534 time to evaluate : 1.161 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7716 (t70) cc_final: 0.7514 (t70) REVERT: B 6 ARG cc_start: 0.8757 (ttp-110) cc_final: 0.8453 (ttm110) REVERT: D 5 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8855 (mm-30) REVERT: D 12 ASP cc_start: 0.7611 (t70) cc_final: 0.7370 (t70) REVERT: E 5 GLU cc_start: 0.9177 (mp0) cc_final: 0.8902 (mm-30) REVERT: E 10 ASP cc_start: 0.9137 (t0) cc_final: 0.8757 (t0) REVERT: E 21 ARG cc_start: 0.8993 (mmm-85) cc_final: 0.8789 (mmm-85) REVERT: F 12 ASP cc_start: 0.7704 (t70) cc_final: 0.7471 (t70) REVERT: G 10 ASP cc_start: 0.9180 (t0) cc_final: 0.8841 (t0) REVERT: G 21 ARG cc_start: 0.9061 (mmm-85) cc_final: 0.8802 (mmm-85) REVERT: K 22 ARG cc_start: 0.9060 (tpp-160) cc_final: 0.8849 (ttm110) REVERT: N 10 ASP cc_start: 0.9189 (t0) cc_final: 0.8807 (t0) REVERT: S 22 ARG cc_start: 0.9270 (tpp80) cc_final: 0.8990 (tpp-160) REVERT: V 5 GLU cc_start: 0.9218 (mm-30) cc_final: 0.8711 (mm-30) REVERT: W 21 ARG cc_start: 0.8884 (mmm-85) cc_final: 0.8465 (mmm-85) REVERT: X 5 GLU cc_start: 0.9097 (mp0) cc_final: 0.8841 (mm-30) REVERT: Y 10 ASP cc_start: 0.9133 (t0) cc_final: 0.8817 (t0) REVERT: b 10 ASP cc_start: 0.9144 (t0) cc_final: 0.8816 (t0) REVERT: c 12 ASP cc_start: 0.8312 (t70) cc_final: 0.7919 (t0) REVERT: d 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8939 (t0) REVERT: f 10 ASP cc_start: 0.9071 (t0) cc_final: 0.8743 (t0) REVERT: f 21 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8604 (mmm-85) REVERT: g 10 ASP cc_start: 0.8986 (t0) cc_final: 0.8588 (t0) REVERT: h 12 ASP cc_start: 0.8198 (t70) cc_final: 0.7980 (t70) REVERT: i 10 ASP cc_start: 0.8785 (t0) cc_final: 0.8397 (t0) REVERT: j 12 ASP cc_start: 0.7681 (t70) cc_final: 0.7370 (t70) REVERT: k 10 ASP cc_start: 0.9208 (t0) cc_final: 0.8774 (t0) REVERT: l 6 ARG cc_start: 0.8885 (ttm110) cc_final: 0.8607 (ttm110) REVERT: l 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8964 (t0) REVERT: m 21 ARG cc_start: 0.8927 (mmm-85) cc_final: 0.8578 (mmm-85) REVERT: o 5 GLU cc_start: 0.9188 (mm-30) cc_final: 0.8967 (mm-30) REVERT: o 12 ASP cc_start: 0.7924 (t70) cc_final: 0.7720 (t70) REVERT: p 10 ASP cc_start: 0.9170 (t0) cc_final: 0.8677 (t0) REVERT: q 10 ASP cc_start: 0.9066 (t0) cc_final: 0.8706 (t0) REVERT: s 19 VAL cc_start: 0.9604 (t) cc_final: 0.9390 (t) REVERT: u 10 ASP cc_start: 0.9076 (t0) cc_final: 0.8587 (t0) REVERT: v 12 ASP cc_start: 0.7891 (t70) cc_final: 0.7520 (t70) REVERT: y 5 GLU cc_start: 0.8822 (mp0) cc_final: 0.8588 (mm-30) REVERT: z 5 GLU cc_start: 0.9178 (mm-30) cc_final: 0.8838 (mm-30) outliers start: 0 outliers final: 0 residues processed: 534 average time/residue: 0.3545 time to fit residues: 229.4352 Evaluate side-chains 498 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 20.0000 chunk 29 optimal weight: 0.9980 chunk 78 optimal weight: 9.9990 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 94 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 4.9990 chunk 93 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 75 optimal weight: 7.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 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 0.023 9412 Z= 0.183 Angle : 0.545 4.979 12636 Z= 0.282 Chirality : 0.038 0.114 1456 Planarity : 0.008 0.049 1716 Dihedral : 3.833 10.592 1404 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.42 (0.26), residues: 1092 helix: -0.50 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -2.31 (0.52), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 6 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 547 time to evaluate : 1.003 Fit side-chains revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8711 (ttp-110) cc_final: 0.8400 (ttm110) REVERT: E 10 ASP cc_start: 0.9070 (t0) cc_final: 0.8661 (t0) REVERT: H 21 ARG cc_start: 0.8881 (mmm-85) cc_final: 0.8495 (mmm-85) REVERT: J 5 GLU cc_start: 0.9114 (mm-30) cc_final: 0.8606 (mm-30) REVERT: J 6 ARG cc_start: 0.8602 (ttm110) cc_final: 0.8211 (ttm110) REVERT: K 5 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8658 (mm-30) REVERT: K 10 ASP cc_start: 0.9329 (t0) cc_final: 0.9033 (t0) REVERT: L 7 LEU cc_start: 0.9224 (mt) cc_final: 0.8954 (mt) REVERT: N 10 ASP cc_start: 0.9181 (t0) cc_final: 0.8746 (t0) REVERT: N 21 ARG cc_start: 0.8823 (mmm-85) cc_final: 0.8487 (mmm-85) REVERT: S 21 ARG cc_start: 0.9151 (mmm-85) cc_final: 0.8913 (mmm-85) REVERT: S 22 ARG cc_start: 0.9117 (tpp80) cc_final: 0.8810 (tpp-160) REVERT: V 5 GLU cc_start: 0.9025 (mm-30) cc_final: 0.8655 (mm-30) REVERT: W 21 ARG cc_start: 0.8792 (mmm-85) cc_final: 0.8418 (mmm-85) REVERT: X 5 GLU cc_start: 0.9084 (mp0) cc_final: 0.8796 (mm-30) REVERT: Y 10 ASP cc_start: 0.9210 (t0) cc_final: 0.8848 (t0) REVERT: Z 10 ASP cc_start: 0.9280 (t0) cc_final: 0.8898 (t0) REVERT: Z 21 ARG cc_start: 0.8981 (mmm-85) cc_final: 0.8775 (mmm-85) REVERT: Z 23 LEU cc_start: 0.8779 (mm) cc_final: 0.7771 (pp) REVERT: a 22 ARG cc_start: 0.9309 (tpp80) cc_final: 0.8929 (tpp80) REVERT: b 6 ARG cc_start: 0.8714 (ttm110) cc_final: 0.8433 (ttm110) REVERT: b 10 ASP cc_start: 0.9135 (t0) cc_final: 0.8821 (t0) REVERT: d 10 ASP cc_start: 0.9264 (t0) cc_final: 0.9023 (t0) REVERT: d 23 LEU cc_start: 0.8391 (mm) cc_final: 0.8061 (mt) REVERT: f 10 ASP cc_start: 0.9056 (t0) cc_final: 0.8803 (t0) REVERT: g 10 ASP cc_start: 0.8936 (t0) cc_final: 0.8493 (t0) REVERT: i 6 ARG cc_start: 0.8661 (ttm110) cc_final: 0.8459 (ttm110) REVERT: j 12 ASP cc_start: 0.7481 (t70) cc_final: 0.7266 (t70) REVERT: k 10 ASP cc_start: 0.9196 (t0) cc_final: 0.8702 (t0) REVERT: l 7 LEU cc_start: 0.9394 (mt) cc_final: 0.9176 (mp) REVERT: l 23 LEU cc_start: 0.7885 (mm) cc_final: 0.6720 (pp) REVERT: n 21 ARG cc_start: 0.8878 (mmm-85) cc_final: 0.8537 (mmm-85) REVERT: n 23 LEU cc_start: 0.8247 (mm) cc_final: 0.7200 (pp) REVERT: p 10 ASP cc_start: 0.9083 (t0) cc_final: 0.8593 (t0) REVERT: p 23 LEU cc_start: 0.8342 (mm) cc_final: 0.7540 (pp) REVERT: q 10 ASP cc_start: 0.9089 (t0) cc_final: 0.8753 (t0) REVERT: t 6 ARG cc_start: 0.8956 (ttm110) cc_final: 0.8756 (ttm110) REVERT: u 10 ASP cc_start: 0.9147 (t0) cc_final: 0.8567 (t0) REVERT: v 6 ARG cc_start: 0.8675 (ttm-80) cc_final: 0.8332 (ttm-80) REVERT: v 12 ASP cc_start: 0.7791 (t70) cc_final: 0.7397 (t70) REVERT: x 6 ARG cc_start: 0.8746 (ttm-80) cc_final: 0.8463 (ttm110) REVERT: y 5 GLU cc_start: 0.8744 (mp0) cc_final: 0.8514 (mm-30) REVERT: z 5 GLU cc_start: 0.9068 (mm-30) cc_final: 0.8826 (mm-30) outliers start: 0 outliers final: 0 residues processed: 547 average time/residue: 0.3477 time to fit residues: 231.4619 Evaluate side-chains 504 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 2.9990 chunk 71 optimal weight: 8.9990 chunk 49 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 63 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 100 optimal weight: 10.0000 chunk 89 optimal weight: 3.9990 chunk 27 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.5744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9412 Z= 0.180 Angle : 0.550 4.135 12636 Z= 0.280 Chirality : 0.038 0.113 1456 Planarity : 0.008 0.045 1716 Dihedral : 3.641 14.017 1404 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.45 (0.26), residues: 1092 helix: 0.24 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -2.28 (0.51), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 6 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 538 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8759 (mm-30) REVERT: B 6 ARG cc_start: 0.8648 (ttp-110) cc_final: 0.8391 (ttm110) REVERT: C 5 GLU cc_start: 0.8928 (mp0) cc_final: 0.8620 (mp0) REVERT: C 6 ARG cc_start: 0.8466 (ttm-80) cc_final: 0.8238 (ttm-80) REVERT: E 10 ASP cc_start: 0.9133 (t0) cc_final: 0.8688 (t0) REVERT: F 12 ASP cc_start: 0.7516 (t70) cc_final: 0.7287 (t70) REVERT: H 21 ARG cc_start: 0.8869 (mmm-85) cc_final: 0.8593 (mmm-85) REVERT: I 5 GLU cc_start: 0.8970 (mp0) cc_final: 0.8760 (mm-30) REVERT: J 6 ARG cc_start: 0.8704 (ttm110) cc_final: 0.8275 (ttm110) REVERT: J 22 ARG cc_start: 0.9160 (tpp80) cc_final: 0.8597 (tpp-160) REVERT: K 5 GLU cc_start: 0.9041 (mm-30) cc_final: 0.8713 (mm-30) REVERT: K 10 ASP cc_start: 0.9270 (t0) cc_final: 0.8927 (t0) REVERT: L 7 LEU cc_start: 0.9189 (mt) cc_final: 0.8881 (mt) REVERT: L 10 ASP cc_start: 0.9125 (t0) cc_final: 0.8859 (t0) REVERT: N 6 ARG cc_start: 0.8705 (ttm110) cc_final: 0.8273 (ttm110) REVERT: N 10 ASP cc_start: 0.9110 (t0) cc_final: 0.8813 (t0) REVERT: Q 21 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8639 (mmm-85) REVERT: S 21 ARG cc_start: 0.9140 (mmm-85) cc_final: 0.8933 (mmm-85) REVERT: S 22 ARG cc_start: 0.8951 (tpp80) cc_final: 0.8719 (ttm-80) REVERT: V 5 GLU cc_start: 0.8814 (mm-30) cc_final: 0.8535 (mm-30) REVERT: W 21 ARG cc_start: 0.8996 (mmm-85) cc_final: 0.8710 (mmm-85) REVERT: X 21 ARG cc_start: 0.8902 (mmm-85) cc_final: 0.8605 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9179 (t0) cc_final: 0.8861 (t0) REVERT: Z 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8779 (t0) REVERT: Z 23 LEU cc_start: 0.8377 (mm) cc_final: 0.8106 (mt) REVERT: a 22 ARG cc_start: 0.9244 (tpp80) cc_final: 0.8967 (tpp80) REVERT: b 10 ASP cc_start: 0.9051 (t0) cc_final: 0.8750 (t0) REVERT: d 10 ASP cc_start: 0.9314 (t0) cc_final: 0.8982 (t0) REVERT: e 13 ARG cc_start: 0.8348 (ttp80) cc_final: 0.7775 (ttm170) REVERT: f 10 ASP cc_start: 0.9070 (t0) cc_final: 0.8852 (t0) REVERT: f 23 LEU cc_start: 0.8132 (mm) cc_final: 0.7505 (pp) REVERT: g 10 ASP cc_start: 0.9034 (t0) cc_final: 0.8605 (t0) REVERT: i 5 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8442 (mm-30) REVERT: i 10 ASP cc_start: 0.9009 (t0) cc_final: 0.8466 (t0) REVERT: i 21 ARG cc_start: 0.8602 (mmm-85) cc_final: 0.8376 (mmm-85) REVERT: k 10 ASP cc_start: 0.9237 (t0) cc_final: 0.8702 (t0) REVERT: k 21 ARG cc_start: 0.8880 (mmm-85) cc_final: 0.8577 (mmm-85) REVERT: n 21 ARG cc_start: 0.8822 (mmm-85) cc_final: 0.8509 (mmm-85) REVERT: p 5 GLU cc_start: 0.9141 (mm-30) cc_final: 0.8700 (mm-30) REVERT: p 10 ASP cc_start: 0.9046 (t0) cc_final: 0.8530 (t0) REVERT: p 21 ARG cc_start: 0.8960 (mmm-85) cc_final: 0.8685 (mmm-85) REVERT: p 23 LEU cc_start: 0.8282 (mm) cc_final: 0.7470 (pp) REVERT: q 10 ASP cc_start: 0.9114 (t0) cc_final: 0.8762 (t0) REVERT: r 15 VAL cc_start: 0.9023 (p) cc_final: 0.8816 (p) REVERT: t 10 ASP cc_start: 0.8913 (t0) cc_final: 0.8593 (t0) REVERT: u 10 ASP cc_start: 0.9262 (t0) cc_final: 0.8684 (t0) REVERT: v 6 ARG cc_start: 0.8671 (ttm-80) cc_final: 0.8405 (ttm-80) REVERT: v 12 ASP cc_start: 0.7705 (t70) cc_final: 0.7355 (t70) REVERT: w 12 ASP cc_start: 0.7948 (t70) cc_final: 0.7745 (t70) REVERT: x 6 ARG cc_start: 0.8717 (ttm-80) cc_final: 0.8484 (ttm110) REVERT: y 5 GLU cc_start: 0.8826 (mp0) cc_final: 0.8540 (mm-30) REVERT: y 22 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8463 (ttm110) REVERT: z 5 GLU cc_start: 0.9003 (mm-30) cc_final: 0.8795 (mm-30) outliers start: 0 outliers final: 0 residues processed: 538 average time/residue: 0.3538 time to fit residues: 230.7761 Evaluate side-chains 513 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 513 time to evaluate : 1.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 74 optimal weight: 10.0000 chunk 41 optimal weight: 8.9990 chunk 85 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 2.9990 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.5940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 9412 Z= 0.205 Angle : 0.579 4.333 12636 Z= 0.292 Chirality : 0.038 0.116 1456 Planarity : 0.008 0.057 1716 Dihedral : 3.527 14.340 1404 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 15.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 0.11 (0.27), residues: 1092 helix: 0.38 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -1.14 (0.65), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG k 6 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 1.107 Fit side-chains revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8652 (ttp-110) cc_final: 0.8417 (ttm110) REVERT: B 10 ASP cc_start: 0.9280 (t0) cc_final: 0.8924 (t0) REVERT: C 5 GLU cc_start: 0.8956 (mp0) cc_final: 0.8637 (mp0) REVERT: C 6 ARG cc_start: 0.8471 (ttm-80) cc_final: 0.8212 (ttm-80) REVERT: C 21 ARG cc_start: 0.9028 (mmm-85) cc_final: 0.8789 (mmm-85) REVERT: E 10 ASP cc_start: 0.9157 (t0) cc_final: 0.8668 (t0) REVERT: F 12 ASP cc_start: 0.7638 (t70) cc_final: 0.7351 (t70) REVERT: G 10 ASP cc_start: 0.9214 (t0) cc_final: 0.8813 (t0) REVERT: H 21 ARG cc_start: 0.8865 (mmm-85) cc_final: 0.8648 (mmm-85) REVERT: J 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8961 (t0) REVERT: J 22 ARG cc_start: 0.8915 (tpp80) cc_final: 0.8683 (tpp-160) REVERT: K 5 GLU cc_start: 0.9081 (mm-30) cc_final: 0.8612 (mm-30) REVERT: K 10 ASP cc_start: 0.9315 (t0) cc_final: 0.8973 (t0) REVERT: L 6 ARG cc_start: 0.8631 (ttm110) cc_final: 0.8405 (ttm110) REVERT: L 7 LEU cc_start: 0.9208 (mt) cc_final: 0.8946 (mt) REVERT: L 10 ASP cc_start: 0.9140 (t0) cc_final: 0.8885 (t0) REVERT: L 22 ARG cc_start: 0.9111 (tpp-160) cc_final: 0.8862 (tpp-160) REVERT: M 6 ARG cc_start: 0.8796 (ttm110) cc_final: 0.8536 (ttm110) REVERT: N 6 ARG cc_start: 0.8706 (ttm110) cc_final: 0.8227 (ttm110) REVERT: N 10 ASP cc_start: 0.9147 (t0) cc_final: 0.8845 (t0) REVERT: Q 21 ARG cc_start: 0.8952 (mmm-85) cc_final: 0.8706 (mmm-85) REVERT: S 22 ARG cc_start: 0.9011 (tpp80) cc_final: 0.8804 (ttm-80) REVERT: T 10 ASP cc_start: 0.9198 (t0) cc_final: 0.8849 (t0) REVERT: V 5 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8507 (mm-30) REVERT: V 10 ASP cc_start: 0.9236 (t0) cc_final: 0.8847 (t0) REVERT: V 23 LEU cc_start: 0.7743 (mt) cc_final: 0.7514 (mt) REVERT: W 21 ARG cc_start: 0.8889 (mmm-85) cc_final: 0.8641 (mmm-85) REVERT: W 22 ARG cc_start: 0.8974 (tpp-160) cc_final: 0.8730 (ttm-80) REVERT: X 10 ASP cc_start: 0.9058 (t0) cc_final: 0.8851 (t0) REVERT: X 21 ARG cc_start: 0.8963 (mmm-85) cc_final: 0.8614 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9181 (t0) cc_final: 0.8856 (t0) REVERT: Z 10 ASP cc_start: 0.9262 (t0) cc_final: 0.8858 (t0) REVERT: b 10 ASP cc_start: 0.9049 (t0) cc_final: 0.8704 (t0) REVERT: c 12 ASP cc_start: 0.8335 (t70) cc_final: 0.8131 (t70) REVERT: d 10 ASP cc_start: 0.9317 (t0) cc_final: 0.9001 (t0) REVERT: f 10 ASP cc_start: 0.9046 (t0) cc_final: 0.8831 (t0) REVERT: f 23 LEU cc_start: 0.8343 (mm) cc_final: 0.7859 (pp) REVERT: g 10 ASP cc_start: 0.9100 (t0) cc_final: 0.8660 (t0) REVERT: i 10 ASP cc_start: 0.9158 (t0) cc_final: 0.8678 (t0) REVERT: i 15 VAL cc_start: 0.9515 (p) cc_final: 0.9310 (p) REVERT: j 6 ARG cc_start: 0.8897 (ttm110) cc_final: 0.8535 (ttm110) REVERT: j 10 ASP cc_start: 0.9068 (t0) cc_final: 0.8740 (t0) REVERT: k 10 ASP cc_start: 0.9236 (t0) cc_final: 0.8727 (t0) REVERT: l 10 ASP cc_start: 0.9410 (t0) cc_final: 0.9081 (t0) REVERT: n 21 ARG cc_start: 0.8846 (mmm-85) cc_final: 0.8583 (mmm-85) REVERT: p 5 GLU cc_start: 0.9159 (mm-30) cc_final: 0.8731 (mm-30) REVERT: p 6 ARG cc_start: 0.8924 (ttm-80) cc_final: 0.8714 (ttm110) REVERT: p 10 ASP cc_start: 0.9129 (t0) cc_final: 0.8621 (t0) REVERT: q 10 ASP cc_start: 0.9156 (t0) cc_final: 0.8741 (t0) REVERT: t 10 ASP cc_start: 0.8896 (t0) cc_final: 0.8652 (t0) REVERT: u 10 ASP cc_start: 0.9190 (t0) cc_final: 0.8690 (t0) REVERT: v 6 ARG cc_start: 0.8734 (ttm-80) cc_final: 0.8456 (ttm-80) REVERT: v 10 ASP cc_start: 0.8934 (t0) cc_final: 0.8711 (t0) REVERT: x 6 ARG cc_start: 0.8745 (ttm-80) cc_final: 0.8521 (ttm110) REVERT: y 22 ARG cc_start: 0.9213 (tpp80) cc_final: 0.8473 (ttm110) outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.3547 time to fit residues: 230.1865 Evaluate side-chains 515 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 515 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 3.9990 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 6.9990 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 7.9990 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 5.9990 chunk 8 optimal weight: 20.0000 chunk 33 optimal weight: 7.9990 chunk 52 optimal weight: 1.9990 chunk 97 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.6093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9412 Z= 0.202 Angle : 0.590 5.957 12636 Z= 0.298 Chirality : 0.038 0.123 1456 Planarity : 0.008 0.052 1716 Dihedral : 3.454 12.420 1404 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % 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: 0.60 (0.27), residues: 1092 helix: 0.73 (0.17), residues: 936 sheet: None (None), residues: 0 loop : -1.10 (0.65), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG m 6 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 529 time to evaluate : 1.082 Fit side-chains revert: symmetry clash REVERT: B 6 ARG cc_start: 0.8656 (ttp-110) cc_final: 0.8390 (ttm110) REVERT: B 10 ASP cc_start: 0.9275 (t0) cc_final: 0.8896 (t0) REVERT: C 5 GLU cc_start: 0.9016 (mp0) cc_final: 0.8637 (mp0) REVERT: E 5 GLU cc_start: 0.8943 (mm-30) cc_final: 0.8727 (mm-30) REVERT: E 10 ASP cc_start: 0.9141 (t0) cc_final: 0.8721 (t0) REVERT: F 12 ASP cc_start: 0.7657 (t70) cc_final: 0.7285 (t70) REVERT: G 10 ASP cc_start: 0.9187 (t0) cc_final: 0.8807 (t0) REVERT: H 12 ASP cc_start: 0.8202 (t70) cc_final: 0.7958 (t70) REVERT: J 10 ASP cc_start: 0.9163 (t0) cc_final: 0.8916 (t0) REVERT: K 5 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8640 (mm-30) REVERT: K 10 ASP cc_start: 0.9335 (t0) cc_final: 0.8999 (t0) REVERT: K 21 ARG cc_start: 0.8925 (mmm-85) cc_final: 0.8344 (tmm-80) REVERT: K 23 LEU cc_start: 0.8590 (mm) cc_final: 0.8341 (mm) REVERT: L 6 ARG cc_start: 0.8648 (ttm110) cc_final: 0.8424 (ttm110) REVERT: L 10 ASP cc_start: 0.9168 (t0) cc_final: 0.8870 (t0) REVERT: N 6 ARG cc_start: 0.8686 (ttm110) cc_final: 0.8276 (ttm110) REVERT: N 10 ASP cc_start: 0.9122 (t0) cc_final: 0.8815 (t0) REVERT: Q 5 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8794 (mm-30) REVERT: Q 21 ARG cc_start: 0.8929 (mmm-85) cc_final: 0.8673 (mmm-85) REVERT: R 14 GLU cc_start: 0.8929 (tp30) cc_final: 0.8699 (tp30) REVERT: T 10 ASP cc_start: 0.9218 (t0) cc_final: 0.8904 (t0) REVERT: V 5 GLU cc_start: 0.8765 (mm-30) cc_final: 0.8556 (mm-30) REVERT: V 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8868 (t0) REVERT: V 23 LEU cc_start: 0.7711 (mt) cc_final: 0.7491 (mt) REVERT: W 21 ARG cc_start: 0.8876 (mmm-85) cc_final: 0.8645 (mmm-85) REVERT: X 10 ASP cc_start: 0.9114 (t0) cc_final: 0.8817 (t0) REVERT: X 21 ARG cc_start: 0.8966 (mmm-85) cc_final: 0.8623 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9204 (t0) cc_final: 0.8903 (t0) REVERT: Z 10 ASP cc_start: 0.9272 (t0) cc_final: 0.8883 (t0) REVERT: b 10 ASP cc_start: 0.9044 (t0) cc_final: 0.8697 (t0) REVERT: d 10 ASP cc_start: 0.9327 (t0) cc_final: 0.9016 (t0) REVERT: d 23 LEU cc_start: 0.8543 (mm) cc_final: 0.8287 (mt) REVERT: f 2 GLU cc_start: 0.8399 (mp0) cc_final: 0.7983 (mm-30) REVERT: f 10 ASP cc_start: 0.9092 (t0) cc_final: 0.8860 (t0) REVERT: g 10 ASP cc_start: 0.9163 (t0) cc_final: 0.8825 (t0) REVERT: h 12 ASP cc_start: 0.7916 (t70) cc_final: 0.7660 (t70) REVERT: i 10 ASP cc_start: 0.9166 (t0) cc_final: 0.8682 (t0) REVERT: i 15 VAL cc_start: 0.9493 (p) cc_final: 0.9279 (p) REVERT: j 6 ARG cc_start: 0.8898 (ttm110) cc_final: 0.8554 (ttm110) REVERT: j 10 ASP cc_start: 0.9035 (t0) cc_final: 0.8764 (t0) REVERT: k 10 ASP cc_start: 0.9289 (t0) cc_final: 0.8769 (t0) REVERT: l 6 ARG cc_start: 0.8779 (ttm110) cc_final: 0.8258 (ttm110) REVERT: l 10 ASP cc_start: 0.9390 (t0) cc_final: 0.9102 (t0) REVERT: n 21 ARG cc_start: 0.8852 (mmm-85) cc_final: 0.8566 (mmm-85) REVERT: p 10 ASP cc_start: 0.9122 (t0) cc_final: 0.8614 (t0) REVERT: q 10 ASP cc_start: 0.9161 (t0) cc_final: 0.8771 (t0) REVERT: t 10 ASP cc_start: 0.8862 (t0) cc_final: 0.8594 (t0) REVERT: u 10 ASP cc_start: 0.9280 (t0) cc_final: 0.8846 (t0) REVERT: v 6 ARG cc_start: 0.8666 (ttm-80) cc_final: 0.8384 (ttm-80) REVERT: w 12 ASP cc_start: 0.7929 (t70) cc_final: 0.7674 (t70) REVERT: z 15 VAL cc_start: 0.8780 (p) cc_final: 0.8410 (m) outliers start: 0 outliers final: 0 residues processed: 529 average time/residue: 0.3570 time to fit residues: 229.0768 Evaluate side-chains 506 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 506 time to evaluate : 1.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 6.9990 chunk 84 optimal weight: 0.0170 chunk 100 optimal weight: 5.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 overall best weight: 2.4026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.6293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9412 Z= 0.201 Angle : 0.608 8.136 12636 Z= 0.306 Chirality : 0.038 0.132 1456 Planarity : 0.008 0.056 1716 Dihedral : 3.418 14.242 1404 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 16.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 1.13 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.27), residues: 1092 helix: 1.25 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -2.08 (0.50), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG m 6 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 527 time to evaluate : 1.044 Fit side-chains revert: symmetry clash REVERT: A 12 ASP cc_start: 0.7735 (t70) cc_final: 0.7500 (t0) REVERT: B 6 ARG cc_start: 0.8643 (ttp-110) cc_final: 0.8392 (ttm110) REVERT: B 10 ASP cc_start: 0.9266 (t0) cc_final: 0.8881 (t0) REVERT: B 15 VAL cc_start: 0.9126 (p) cc_final: 0.8908 (p) REVERT: C 5 GLU cc_start: 0.8935 (mp0) cc_final: 0.8664 (mp0) REVERT: E 5 GLU cc_start: 0.8922 (mm-30) cc_final: 0.8709 (mm-30) REVERT: E 10 ASP cc_start: 0.9144 (t0) cc_final: 0.8679 (t0) REVERT: G 5 GLU cc_start: 0.8956 (mm-30) cc_final: 0.8688 (mm-30) REVERT: G 10 ASP cc_start: 0.9205 (t0) cc_final: 0.8824 (t0) REVERT: H 23 LEU cc_start: 0.8180 (mm) cc_final: 0.7860 (mm) REVERT: I 5 GLU cc_start: 0.8947 (mp0) cc_final: 0.8596 (mm-30) REVERT: J 10 ASP cc_start: 0.9103 (t0) cc_final: 0.8868 (t0) REVERT: K 5 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8646 (mm-30) REVERT: K 10 ASP cc_start: 0.9355 (t0) cc_final: 0.9006 (t0) REVERT: K 21 ARG cc_start: 0.8937 (mmm-85) cc_final: 0.8297 (tmm-80) REVERT: L 6 ARG cc_start: 0.8659 (ttm110) cc_final: 0.8404 (ttm110) REVERT: L 10 ASP cc_start: 0.9185 (t0) cc_final: 0.8881 (t0) REVERT: L 22 ARG cc_start: 0.9005 (tpp-160) cc_final: 0.8677 (tpp-160) REVERT: M 10 ASP cc_start: 0.9208 (t0) cc_final: 0.8882 (t0) REVERT: N 6 ARG cc_start: 0.8689 (ttm110) cc_final: 0.8263 (ttm110) REVERT: N 10 ASP cc_start: 0.9163 (t0) cc_final: 0.8860 (t0) REVERT: Q 21 ARG cc_start: 0.8995 (mmm-85) cc_final: 0.8773 (mmm-85) REVERT: S 10 ASP cc_start: 0.9302 (t0) cc_final: 0.8787 (t0) REVERT: S 15 VAL cc_start: 0.9022 (p) cc_final: 0.8780 (p) REVERT: T 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8901 (t0) REVERT: T 15 VAL cc_start: 0.9158 (p) cc_final: 0.8936 (m) REVERT: V 10 ASP cc_start: 0.9228 (t0) cc_final: 0.8853 (t0) REVERT: W 21 ARG cc_start: 0.8803 (mmm-85) cc_final: 0.8507 (mmm-85) REVERT: X 10 ASP cc_start: 0.9081 (t0) cc_final: 0.8860 (t0) REVERT: X 21 ARG cc_start: 0.8949 (mmm-85) cc_final: 0.8628 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9209 (t0) cc_final: 0.8961 (t0) REVERT: Z 10 ASP cc_start: 0.9235 (t0) cc_final: 0.8847 (t0) REVERT: b 10 ASP cc_start: 0.9053 (t0) cc_final: 0.8654 (t0) REVERT: d 10 ASP cc_start: 0.9307 (t0) cc_final: 0.9013 (t0) REVERT: f 2 GLU cc_start: 0.8336 (mp0) cc_final: 0.8016 (mm-30) REVERT: f 10 ASP cc_start: 0.9060 (t0) cc_final: 0.8786 (t0) REVERT: f 23 LEU cc_start: 0.8112 (mm) cc_final: 0.7706 (pp) REVERT: g 10 ASP cc_start: 0.9153 (t0) cc_final: 0.8852 (t0) REVERT: h 12 ASP cc_start: 0.7875 (t70) cc_final: 0.7578 (t70) REVERT: i 10 ASP cc_start: 0.9171 (t0) cc_final: 0.8710 (t0) REVERT: i 15 VAL cc_start: 0.9440 (p) cc_final: 0.9235 (p) REVERT: j 6 ARG cc_start: 0.8783 (ttm110) cc_final: 0.8517 (ttm110) REVERT: j 10 ASP cc_start: 0.9002 (t0) cc_final: 0.8736 (t0) REVERT: k 10 ASP cc_start: 0.9274 (t0) cc_final: 0.8781 (t0) REVERT: l 6 ARG cc_start: 0.8745 (ttm110) cc_final: 0.8468 (ttm110) REVERT: l 23 LEU cc_start: 0.8063 (mm) cc_final: 0.7786 (mt) REVERT: n 21 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8542 (mmm-85) REVERT: p 10 ASP cc_start: 0.9102 (t0) cc_final: 0.8611 (t0) REVERT: p 23 LEU cc_start: 0.7859 (mm) cc_final: 0.7050 (pp) REVERT: q 10 ASP cc_start: 0.9149 (t0) cc_final: 0.8775 (t0) REVERT: r 10 ASP cc_start: 0.9199 (t0) cc_final: 0.8915 (t0) REVERT: t 6 ARG cc_start: 0.8728 (ttm-80) cc_final: 0.8402 (ttm110) REVERT: u 10 ASP cc_start: 0.9292 (t0) cc_final: 0.8864 (t0) REVERT: v 12 ASP cc_start: 0.7968 (t70) cc_final: 0.7566 (t70) REVERT: v 23 LEU cc_start: 0.8040 (mt) cc_final: 0.7826 (mt) REVERT: z 14 GLU cc_start: 0.8945 (tp30) cc_final: 0.8586 (mt-10) REVERT: z 15 VAL cc_start: 0.8853 (p) cc_final: 0.8652 (m) outliers start: 0 outliers final: 0 residues processed: 527 average time/residue: 0.3515 time to fit residues: 224.4941 Evaluate side-chains 501 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 501 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 9 optimal weight: 8.9990 chunk 78 optimal weight: 7.9990 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 0.8980 chunk 87 optimal weight: 5.9990 chunk 93 optimal weight: 0.3980 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.6360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9412 Z= 0.224 Angle : 0.641 7.406 12636 Z= 0.324 Chirality : 0.039 0.130 1456 Planarity : 0.008 0.060 1716 Dihedral : 3.466 13.537 1404 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 18.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % 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: 0.92 (0.27), residues: 1092 helix: 0.93 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -0.92 (0.65), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG Q 6 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 514 time to evaluate : 1.077 Fit side-chains REVERT: A 12 ASP cc_start: 0.7686 (t70) cc_final: 0.7478 (t70) REVERT: B 6 ARG cc_start: 0.8670 (ttp-110) cc_final: 0.8431 (ttm110) REVERT: B 10 ASP cc_start: 0.9068 (t0) cc_final: 0.8810 (t0) REVERT: C 5 GLU cc_start: 0.8984 (mp0) cc_final: 0.8681 (mp0) REVERT: D 10 ASP cc_start: 0.9052 (t0) cc_final: 0.8782 (t0) REVERT: E 10 ASP cc_start: 0.9123 (t0) cc_final: 0.8712 (t0) REVERT: F 12 ASP cc_start: 0.7648 (t70) cc_final: 0.7170 (t70) REVERT: G 10 ASP cc_start: 0.9225 (t0) cc_final: 0.8836 (t0) REVERT: H 12 ASP cc_start: 0.8188 (t70) cc_final: 0.7968 (t70) REVERT: I 5 GLU cc_start: 0.8983 (mp0) cc_final: 0.8585 (mm-30) REVERT: K 5 GLU cc_start: 0.9082 (mm-30) cc_final: 0.8690 (mm-30) REVERT: K 10 ASP cc_start: 0.9321 (t0) cc_final: 0.9047 (t0) REVERT: L 10 ASP cc_start: 0.9099 (t0) cc_final: 0.8841 (t0) REVERT: M 10 ASP cc_start: 0.9267 (t0) cc_final: 0.8901 (t0) REVERT: N 6 ARG cc_start: 0.8726 (ttm110) cc_final: 0.8286 (ttm110) REVERT: N 10 ASP cc_start: 0.9047 (t0) cc_final: 0.8817 (t0) REVERT: O 10 ASP cc_start: 0.9052 (t0) cc_final: 0.8726 (t0) REVERT: T 10 ASP cc_start: 0.9192 (t0) cc_final: 0.8959 (t0) REVERT: U 6 ARG cc_start: 0.8712 (ttm-80) cc_final: 0.8492 (ttm110) REVERT: V 10 ASP cc_start: 0.9232 (t0) cc_final: 0.8762 (t0) REVERT: W 21 ARG cc_start: 0.8848 (mmm-85) cc_final: 0.8611 (mmm-85) REVERT: X 10 ASP cc_start: 0.9119 (t0) cc_final: 0.8838 (t0) REVERT: X 21 ARG cc_start: 0.8921 (mmm-85) cc_final: 0.8717 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9217 (t0) cc_final: 0.8989 (t0) REVERT: Z 10 ASP cc_start: 0.9240 (t0) cc_final: 0.8861 (t0) REVERT: b 10 ASP cc_start: 0.9045 (t0) cc_final: 0.8705 (t0) REVERT: c 12 ASP cc_start: 0.8563 (t70) cc_final: 0.8282 (t70) REVERT: d 10 ASP cc_start: 0.9318 (t0) cc_final: 0.9000 (t0) REVERT: f 2 GLU cc_start: 0.8528 (mp0) cc_final: 0.8214 (mm-30) REVERT: f 10 ASP cc_start: 0.9067 (t0) cc_final: 0.8800 (t0) REVERT: g 10 ASP cc_start: 0.9142 (t0) cc_final: 0.8839 (t0) REVERT: h 21 ARG cc_start: 0.8683 (mmm-85) cc_final: 0.8418 (mmm-85) REVERT: i 10 ASP cc_start: 0.9109 (t0) cc_final: 0.8668 (t0) REVERT: j 6 ARG cc_start: 0.8801 (ttm110) cc_final: 0.8539 (ttm110) REVERT: k 10 ASP cc_start: 0.9277 (t0) cc_final: 0.8809 (t0) REVERT: l 6 ARG cc_start: 0.8711 (ttm110) cc_final: 0.8433 (ttm110) REVERT: l 12 ASP cc_start: 0.7933 (t70) cc_final: 0.7553 (t70) REVERT: n 21 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8515 (mmm-85) REVERT: o 10 ASP cc_start: 0.9380 (t0) cc_final: 0.9004 (t0) REVERT: p 5 GLU cc_start: 0.9017 (mm-30) cc_final: 0.8746 (mm-30) REVERT: p 6 ARG cc_start: 0.8903 (ttm110) cc_final: 0.8694 (ttm110) REVERT: p 10 ASP cc_start: 0.9149 (t0) cc_final: 0.8616 (t0) REVERT: q 10 ASP cc_start: 0.9150 (t0) cc_final: 0.8787 (t0) REVERT: r 10 ASP cc_start: 0.9234 (t0) cc_final: 0.8833 (t0) REVERT: s 10 ASP cc_start: 0.9248 (t0) cc_final: 0.8997 (t0) REVERT: t 6 ARG cc_start: 0.8716 (ttm-80) cc_final: 0.8482 (ttm110) REVERT: u 10 ASP cc_start: 0.9293 (t0) cc_final: 0.8866 (t0) REVERT: v 12 ASP cc_start: 0.7754 (t70) cc_final: 0.7508 (t70) REVERT: w 12 ASP cc_start: 0.8124 (t70) cc_final: 0.7885 (t70) REVERT: z 5 GLU cc_start: 0.8775 (mm-30) cc_final: 0.8541 (mm-30) REVERT: z 12 ASP cc_start: 0.7756 (t70) cc_final: 0.7549 (t0) REVERT: z 14 GLU cc_start: 0.8958 (tp30) cc_final: 0.8546 (mt-10) REVERT: z 15 VAL cc_start: 0.8860 (p) cc_final: 0.8658 (m) outliers start: 0 outliers final: 0 residues processed: 514 average time/residue: 0.3539 time to fit residues: 220.3657 Evaluate side-chains 493 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 493 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 9.9990 chunk 56 optimal weight: 9.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 28 optimal weight: 0.0370 chunk 84 optimal weight: 9.9990 chunk 88 optimal weight: 0.0170 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 8.9990 chunk 60 optimal weight: 6.9990 overall best weight: 2.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.6514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9412 Z= 0.221 Angle : 0.662 6.993 12636 Z= 0.334 Chirality : 0.038 0.130 1456 Planarity : 0.008 0.065 1716 Dihedral : 3.483 13.270 1404 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 1.13 (0.27), residues: 1092 helix: 1.36 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.82 (0.50), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG m 6 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 504 time to evaluate : 1.001 Fit side-chains REVERT: B 6 ARG cc_start: 0.8672 (ttp-110) cc_final: 0.8459 (ttm110) REVERT: B 10 ASP cc_start: 0.9007 (t0) cc_final: 0.8798 (t0) REVERT: C 5 GLU cc_start: 0.8993 (mp0) cc_final: 0.8705 (mp0) REVERT: E 10 ASP cc_start: 0.9088 (t0) cc_final: 0.8723 (t0) REVERT: F 12 ASP cc_start: 0.7502 (t70) cc_final: 0.7138 (t70) REVERT: G 10 ASP cc_start: 0.9214 (t0) cc_final: 0.8839 (t0) REVERT: I 5 GLU cc_start: 0.8925 (mp0) cc_final: 0.8575 (mm-30) REVERT: K 5 GLU cc_start: 0.9055 (mm-30) cc_final: 0.8665 (mm-30) REVERT: K 10 ASP cc_start: 0.9328 (t0) cc_final: 0.9058 (t0) REVERT: L 10 ASP cc_start: 0.9100 (t0) cc_final: 0.8843 (t0) REVERT: M 6 ARG cc_start: 0.8703 (ttm110) cc_final: 0.8490 (ttm110) REVERT: M 10 ASP cc_start: 0.9242 (t0) cc_final: 0.8935 (t0) REVERT: N 6 ARG cc_start: 0.8707 (ttm110) cc_final: 0.8283 (ttm110) REVERT: N 10 ASP cc_start: 0.8994 (t0) cc_final: 0.8740 (t0) REVERT: O 10 ASP cc_start: 0.9030 (t0) cc_final: 0.8715 (t0) REVERT: P 12 ASP cc_start: 0.8326 (t0) cc_final: 0.7990 (t0) REVERT: R 5 GLU cc_start: 0.8809 (mm-30) cc_final: 0.8602 (mm-30) REVERT: S 10 ASP cc_start: 0.9254 (t0) cc_final: 0.8849 (t0) REVERT: T 10 ASP cc_start: 0.9240 (t0) cc_final: 0.8944 (t0) REVERT: V 10 ASP cc_start: 0.9247 (t0) cc_final: 0.8743 (t0) REVERT: W 21 ARG cc_start: 0.8839 (mmm-85) cc_final: 0.8635 (mmm-85) REVERT: X 10 ASP cc_start: 0.9086 (t0) cc_final: 0.8851 (t0) REVERT: X 21 ARG cc_start: 0.8913 (mmm-85) cc_final: 0.8705 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9218 (t0) cc_final: 0.9009 (t0) REVERT: Z 10 ASP cc_start: 0.9227 (t0) cc_final: 0.8855 (t0) REVERT: b 10 ASP cc_start: 0.9022 (t0) cc_final: 0.8685 (t0) REVERT: c 12 ASP cc_start: 0.8721 (t70) cc_final: 0.8433 (t70) REVERT: d 10 ASP cc_start: 0.9306 (t0) cc_final: 0.9006 (t0) REVERT: d 23 LEU cc_start: 0.7634 (mt) cc_final: 0.7381 (mt) REVERT: f 2 GLU cc_start: 0.8551 (mp0) cc_final: 0.8233 (mm-30) REVERT: f 10 ASP cc_start: 0.9036 (t0) cc_final: 0.8729 (t0) REVERT: g 10 ASP cc_start: 0.9164 (t0) cc_final: 0.8831 (t0) REVERT: i 5 GLU cc_start: 0.8609 (mm-30) cc_final: 0.8382 (mm-30) REVERT: i 10 ASP cc_start: 0.9187 (t0) cc_final: 0.8727 (t0) REVERT: k 10 ASP cc_start: 0.9281 (t0) cc_final: 0.8843 (t0) REVERT: l 6 ARG cc_start: 0.8709 (ttm110) cc_final: 0.8250 (ttm110) REVERT: l 12 ASP cc_start: 0.7751 (t70) cc_final: 0.7533 (t70) REVERT: n 21 ARG cc_start: 0.8767 (mmm-85) cc_final: 0.8527 (mmm-85) REVERT: o 10 ASP cc_start: 0.9376 (t0) cc_final: 0.9003 (t0) REVERT: p 5 GLU cc_start: 0.9022 (mm-30) cc_final: 0.8808 (mm-30) REVERT: p 10 ASP cc_start: 0.9114 (t0) cc_final: 0.8641 (t0) REVERT: q 10 ASP cc_start: 0.9132 (t0) cc_final: 0.8801 (t0) REVERT: r 21 ARG cc_start: 0.9046 (mmm-85) cc_final: 0.8637 (mmm-85) REVERT: s 10 ASP cc_start: 0.9215 (t0) cc_final: 0.8923 (t0) REVERT: t 12 ASP cc_start: 0.7786 (t70) cc_final: 0.7562 (t0) REVERT: u 10 ASP cc_start: 0.9202 (t0) cc_final: 0.8895 (t0) REVERT: v 12 ASP cc_start: 0.7947 (t70) cc_final: 0.7565 (t70) REVERT: w 12 ASP cc_start: 0.8100 (t70) cc_final: 0.7836 (t70) REVERT: y 5 GLU cc_start: 0.8801 (mm-30) cc_final: 0.8516 (mm-30) REVERT: z 15 VAL cc_start: 0.8929 (p) cc_final: 0.8726 (m) outliers start: 0 outliers final: 0 residues processed: 504 average time/residue: 0.3459 time to fit residues: 211.8541 Evaluate side-chains 489 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 489 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 8.9990 chunk 68 optimal weight: 9.9990 chunk 103 optimal weight: 20.0000 chunk 95 optimal weight: 0.5980 chunk 82 optimal weight: 3.9990 chunk 8 optimal weight: 0.0010 chunk 63 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 65 optimal weight: 0.0670 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 2.9990 overall best weight: 0.9326 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.6714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 9412 Z= 0.213 Angle : 0.663 6.319 12636 Z= 0.335 Chirality : 0.038 0.138 1456 Planarity : 0.008 0.063 1716 Dihedral : 3.410 12.423 1404 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 1092 helix: 0.90 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -0.65 (0.65), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG m 6 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2184 Ramachandran restraints generated. 1092 Oldfield, 0 Emsley, 1092 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 498 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 498 time to evaluate : 1.120 Fit side-chains revert: symmetry clash REVERT: B 10 ASP cc_start: 0.9002 (t0) cc_final: 0.8799 (t0) REVERT: C 5 GLU cc_start: 0.8983 (mp0) cc_final: 0.8685 (mp0) REVERT: E 6 ARG cc_start: 0.8649 (ttm-80) cc_final: 0.8174 (ttm110) REVERT: E 10 ASP cc_start: 0.9063 (t0) cc_final: 0.8679 (t0) REVERT: F 12 ASP cc_start: 0.7324 (t70) cc_final: 0.6939 (t70) REVERT: G 10 ASP cc_start: 0.9147 (t0) cc_final: 0.8793 (t0) REVERT: I 5 GLU cc_start: 0.8924 (mp0) cc_final: 0.8637 (mm-30) REVERT: K 5 GLU cc_start: 0.9062 (mm-30) cc_final: 0.8607 (mm-30) REVERT: K 10 ASP cc_start: 0.9319 (t0) cc_final: 0.9056 (t0) REVERT: L 10 ASP cc_start: 0.9062 (t0) cc_final: 0.8807 (t0) REVERT: L 21 ARG cc_start: 0.8758 (mmm-85) cc_final: 0.8303 (tpp80) REVERT: M 10 ASP cc_start: 0.9238 (t0) cc_final: 0.8900 (t0) REVERT: N 6 ARG cc_start: 0.8669 (ttm110) cc_final: 0.8235 (ttm-80) REVERT: N 10 ASP cc_start: 0.8980 (t0) cc_final: 0.8736 (t0) REVERT: P 12 ASP cc_start: 0.8117 (t0) cc_final: 0.7833 (t0) REVERT: S 6 ARG cc_start: 0.8349 (ttm-80) cc_final: 0.8049 (ttm-80) REVERT: V 10 ASP cc_start: 0.9130 (t0) cc_final: 0.8685 (t0) REVERT: W 5 GLU cc_start: 0.8746 (mm-30) cc_final: 0.8475 (mm-30) REVERT: W 21 ARG cc_start: 0.8814 (mmm-85) cc_final: 0.8546 (mmm-85) REVERT: X 21 ARG cc_start: 0.8896 (mmm-85) cc_final: 0.8625 (mmm-85) REVERT: Y 10 ASP cc_start: 0.9240 (t0) cc_final: 0.9038 (t0) REVERT: Z 10 ASP cc_start: 0.9178 (t0) cc_final: 0.8765 (t0) REVERT: b 10 ASP cc_start: 0.9009 (t0) cc_final: 0.8719 (t0) REVERT: b 14 GLU cc_start: 0.9010 (tp30) cc_final: 0.8797 (mm-30) REVERT: d 10 ASP cc_start: 0.9310 (t0) cc_final: 0.9013 (t0) REVERT: d 23 LEU cc_start: 0.7580 (mt) cc_final: 0.7314 (mt) REVERT: f 2 GLU cc_start: 0.8555 (mp0) cc_final: 0.8247 (mm-30) REVERT: f 10 ASP cc_start: 0.8979 (t0) cc_final: 0.8697 (t0) REVERT: g 10 ASP cc_start: 0.9122 (t0) cc_final: 0.8831 (t0) REVERT: h 12 ASP cc_start: 0.7970 (t70) cc_final: 0.7763 (t70) REVERT: i 5 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8393 (mm-30) REVERT: i 10 ASP cc_start: 0.9171 (t0) cc_final: 0.8719 (t0) REVERT: i 15 VAL cc_start: 0.9428 (p) cc_final: 0.9217 (p) REVERT: j 12 ASP cc_start: 0.7854 (t0) cc_final: 0.7595 (t70) REVERT: j 23 LEU cc_start: 0.7869 (mt) cc_final: 0.7650 (mt) REVERT: k 10 ASP cc_start: 0.9265 (t0) cc_final: 0.8890 (t0) REVERT: l 6 ARG cc_start: 0.8620 (ttm110) cc_final: 0.8340 (ttm110) REVERT: l 12 ASP cc_start: 0.7735 (t70) cc_final: 0.7397 (t70) REVERT: n 23 LEU cc_start: 0.8025 (mm) cc_final: 0.7404 (pp) REVERT: p 5 GLU cc_start: 0.8964 (mm-30) cc_final: 0.8633 (mm-30) REVERT: p 10 ASP cc_start: 0.9051 (t0) cc_final: 0.8563 (t0) REVERT: q 10 ASP cc_start: 0.9132 (t0) cc_final: 0.8801 (t0) REVERT: q 14 GLU cc_start: 0.8841 (tp30) cc_final: 0.8634 (tp30) REVERT: u 10 ASP cc_start: 0.9196 (t0) cc_final: 0.8882 (t0) REVERT: u 21 ARG cc_start: 0.8828 (mmm-85) cc_final: 0.8421 (tpt-90) REVERT: v 12 ASP cc_start: 0.7713 (t70) cc_final: 0.7452 (t70) REVERT: w 12 ASP cc_start: 0.8001 (t70) cc_final: 0.7765 (t70) REVERT: z 12 ASP cc_start: 0.7789 (t70) cc_final: 0.7444 (t0) REVERT: z 15 VAL cc_start: 0.8863 (p) cc_final: 0.8624 (m) outliers start: 0 outliers final: 0 residues processed: 498 average time/residue: 0.3518 time to fit residues: 213.7553 Evaluate side-chains 465 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 0.0270 chunk 12 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 34 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 72 optimal weight: 0.0270 chunk 4 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 overall best weight: 0.7900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096757 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.089264 restraints weight = 19444.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.091562 restraints weight = 9773.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.093043 restraints weight = 5584.616| |-----------------------------------------------------------------------------| r_work (final): 0.3217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.6934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9412 Z= 0.221 Angle : 0.696 8.462 12636 Z= 0.347 Chirality : 0.038 0.152 1456 Planarity : 0.008 0.065 1716 Dihedral : 3.455 12.517 1404 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 16.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.27), residues: 1092 helix: 1.16 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.56 (0.51), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG M 6 =============================================================================== Job complete usr+sys time: 3350.02 seconds wall clock time: 59 minutes 29.65 seconds (3569.65 seconds total)