Starting phenix.real_space_refine on Fri Dec 8 23:17:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/12_2023/6hqe_0252.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/12_2023/6hqe_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_0252/12_2023/6hqe_0252.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/12_2023/6hqe_0252.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/12_2023/6hqe_0252.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6hqe_0252/12_2023/6hqe_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-1.21rc1-5172/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: 4.95, per 1000 atoms: 0.53 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: 3.73 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: 0.97 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: 2.17 Time building geometry restraints manager: 4.01 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: 0.000 Extract box with map and model: 1.080 Check model and map are aligned: 0.140 Set scattering table: 0.100 Process input model: 26.550 Find NCS groups from input model: 0.710 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.520 ------------------------------------------------------------------------------- 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 : 1.076 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.3514 time to fit residues: 234.8170 Evaluate side-chains 380 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 380 time to evaluate : 1.180 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5448 ------------------------------------------------------------------------------- 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: 6.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 60 optimal weight: 6.9990 chunk 94 optimal weight: 3.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.8521 moved from start: 0.4832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9412 Z= 0.293 Angle : 0.627 6.158 12636 Z= 0.329 Chirality : 0.041 0.122 1456 Planarity : 0.010 0.057 1716 Dihedral : 4.425 14.666 1404 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 18.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -2.69 (0.26), residues: 1092 helix: -1.52 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -2.05 (0.56), residues: 208 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 525 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 525 time to evaluate : 1.242 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 525 average time/residue: 0.3762 time to fit residues: 240.0041 Evaluate side-chains 483 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 483 time to evaluate : 1.126 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.6153 ------------------------------------------------------------------------------- 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: 0.5980 chunk 29 optimal weight: 10.0000 chunk 78 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 94 optimal weight: 10.0000 chunk 102 optimal weight: 3.9990 chunk 84 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 32 optimal weight: 10.0000 chunk 75 optimal weight: 20.0000 overall best weight: 5.3188 ------------------------------------------------------------------------------- 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: 0.8516 moved from start: 0.5488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 9412 Z= 0.265 Angle : 0.630 5.172 12636 Z= 0.318 Chirality : 0.040 0.131 1456 Planarity : 0.008 0.051 1716 Dihedral : 3.968 12.926 1404 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 17.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % 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: -1.50 (0.25), residues: 1092 helix: -0.60 (0.16), residues: 884 sheet: None (None), residues: 0 loop : -2.12 (0.53), 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 535 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 535 time to evaluate : 1.084 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 535 average time/residue: 0.3810 time to fit residues: 247.0992 Evaluate side-chains 491 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 491 time to evaluate : 1.101 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5590 ------------------------------------------------------------------------------- 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: 3.9990 chunk 71 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 63 optimal weight: 0.8980 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 83 optimal weight: 6.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- 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: 0.8456 moved from start: 0.5900 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= 0.200 Angle : 0.584 3.865 12636 Z= 0.299 Chirality : 0.039 0.170 1456 Planarity : 0.007 0.045 1716 Dihedral : 3.653 12.859 1404 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.21 % Favored : 96.79 % Rotamer: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % 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: -0.30 (0.26), residues: 1092 helix: 0.31 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -2.03 (0.54), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG f 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 539 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 539 time to evaluate : 1.077 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 539 average time/residue: 0.3671 time to fit residues: 239.8748 Evaluate side-chains 490 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 490 time to evaluate : 1.318 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5495 ------------------------------------------------------------------------------- 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: 2.9990 chunk 1 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 41 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 69 optimal weight: 0.6980 chunk 0 optimal weight: 9.9990 chunk 51 optimal weight: 9.9990 chunk 90 optimal weight: 7.9990 chunk 25 optimal weight: 0.9990 chunk 33 optimal weight: 6.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- 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: 0.8419 moved from start: 0.6196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 9412 Z= 0.215 Angle : 0.615 7.826 12636 Z= 0.309 Chirality : 0.039 0.159 1456 Planarity : 0.008 0.047 1716 Dihedral : 3.587 14.272 1404 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % 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: 0.38 (0.27), residues: 1092 helix: 0.82 (0.17), residues: 884 sheet: None (None), residues: 0 loop : -2.02 (0.53), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 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 517 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 517 time to evaluate : 1.234 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 517 average time/residue: 0.3692 time to fit residues: 231.8541 Evaluate side-chains 480 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 480 time to evaluate : 1.176 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3996 ------------------------------------------------------------------------------- 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: 0.2980 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 100 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 97 optimal weight: 0.8980 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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: 0.8346 moved from start: 0.6468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 9412 Z= 0.186 Angle : 0.604 8.032 12636 Z= 0.304 Chirality : 0.038 0.147 1456 Planarity : 0.007 0.047 1716 Dihedral : 3.419 11.834 1404 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 15.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.00 % Allowed : 1.02 % Favored : 98.98 % 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: 0.83 (0.28), residues: 1092 helix: 0.85 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -0.80 (0.68), 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 520 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 520 time to evaluate : 1.156 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 520 average time/residue: 0.3750 time to fit residues: 235.3080 Evaluate side-chains 471 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 471 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5551 ------------------------------------------------------------------------------- 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: 0.0980 chunk 57 optimal weight: 7.9990 chunk 73 optimal weight: 7.9990 chunk 56 optimal weight: 10.0000 chunk 84 optimal weight: 4.9990 chunk 100 optimal weight: 8.9990 chunk 62 optimal weight: 1.9990 chunk 61 optimal weight: 6.9990 chunk 46 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 overall best weight: 3.4188 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.6645 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= 0.227 Angle : 0.659 8.118 12636 Z= 0.329 Chirality : 0.039 0.129 1456 Planarity : 0.007 0.056 1716 Dihedral : 3.466 12.314 1404 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 18.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.27), residues: 1092 helix: 1.33 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.73 (0.53), 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 494 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 494 time to evaluate : 1.208 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 494 average time/residue: 0.3891 time to fit residues: 234.2103 Evaluate side-chains 463 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 463 time to evaluate : 1.189 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5604 ------------------------------------------------------------------------------- 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: 6.9990 chunk 19 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 49 optimal weight: 6.9990 chunk 9 optimal weight: 5.9990 chunk 78 optimal weight: 0.0570 chunk 91 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 87 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 overall best weight: 2.2104 ------------------------------------------------------------------------------- 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: 0.8325 moved from start: 0.6837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9412 Z= 0.213 Angle : 0.673 8.304 12636 Z= 0.334 Chirality : 0.038 0.125 1456 Planarity : 0.007 0.057 1716 Dihedral : 3.414 11.526 1404 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 16.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.45 % Favored : 99.55 % 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: 1.16 (0.28), residues: 1092 helix: 1.06 (0.18), residues: 936 sheet: None (None), residues: 0 loop : -0.59 (0.67), 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 484 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 484 time to evaluate : 1.295 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 484 average time/residue: 0.3711 time to fit residues: 217.2703 Evaluate side-chains 453 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 453 time to evaluate : 1.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.5418 ------------------------------------------------------------------------------- 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: 10.0000 chunk 56 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 0.0870 chunk 84 optimal weight: 0.9990 chunk 88 optimal weight: 0.0870 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 98 optimal weight: 20.0000 chunk 60 optimal weight: 1.9990 overall best weight: 0.8140 ------------------------------------------------------------------------------- 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: 0.8251 moved from start: 0.7076 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= 0.222 Angle : 0.705 8.362 12636 Z= 0.350 Chirality : 0.038 0.131 1456 Planarity : 0.008 0.063 1716 Dihedral : 3.385 13.441 1404 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % 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: 1.13 (0.28), residues: 1092 helix: 1.28 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.45 (0.52), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 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 475 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 475 time to evaluate : 1.278 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 475 average time/residue: 0.3891 time to fit residues: 223.2897 Evaluate side-chains 442 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 442 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4160 ------------------------------------------------------------------------------- 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: 3.9990 chunk 68 optimal weight: 6.9990 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 50 optimal weight: 3.9990 chunk 65 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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: 0.8336 moved from start: 0.7075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9412 Z= 0.255 Angle : 0.751 8.810 12636 Z= 0.368 Chirality : 0.040 0.128 1456 Planarity : 0.008 0.067 1716 Dihedral : 3.514 14.874 1404 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % 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: 1.14 (0.28), residues: 1092 helix: 1.28 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.39 (0.52), residues: 208 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 459 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 459 time to evaluate : 1.170 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 459 average time/residue: 0.3822 time to fit residues: 213.6368 Evaluate side-chains 441 residues out of total 884 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 441 time to evaluate : 1.117 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.4444 ------------------------------------------------------------------------------- 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: 20.0000 chunk 12 optimal weight: 0.3980 chunk 22 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 84 optimal weight: 8.9990 chunk 10 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 chunk 59 optimal weight: 0.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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 = 0.3285 r_free = 0.3285 target = 0.095943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.088248 restraints weight = 20279.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.090527 restraints weight = 10116.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.092069 restraints weight = 5859.764| |-----------------------------------------------------------------------------| r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.7114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 9412 Z= 0.239 Angle : 0.744 8.541 12636 Z= 0.366 Chirality : 0.039 0.159 1456 Planarity : 0.008 0.068 1716 Dihedral : 3.463 14.388 1404 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 1.18 (0.28), residues: 1092 helix: 1.27 (0.18), residues: 884 sheet: None (None), residues: 0 loop : -1.20 (0.53), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG m 6 =============================================================================== Job complete usr+sys time: 3430.61 seconds wall clock time: 61 minutes 13.34 seconds (3673.34 seconds total)