Starting phenix.real_space_refine on Tue Mar 19 01:10:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjs_29246/03_2024/8fjs_29246.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjs_29246/03_2024/8fjs_29246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjs_29246/03_2024/8fjs_29246.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjs_29246/03_2024/8fjs_29246.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjs_29246/03_2024/8fjs_29246.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fjs_29246/03_2024/8fjs_29246.pdb" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.100 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 14300 2.51 5 N 3600 2.21 5 O 4625 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 122": "OE1" <-> "OE2" Residue "B GLU 122": "OE1" <-> "OE2" Residue "C GLU 122": "OE1" <-> "OE2" Residue "D GLU 122": "OE1" <-> "OE2" Residue "E GLU 122": "OE1" <-> "OE2" Residue "F GLU 122": "OE1" <-> "OE2" Residue "G GLU 122": "OE1" <-> "OE2" Residue "H GLU 122": "OE1" <-> "OE2" Residue "I GLU 122": "OE1" <-> "OE2" Residue "J GLU 122": "OE1" <-> "OE2" Residue "K GLU 122": "OE1" <-> "OE2" Residue "L GLU 122": "OE1" <-> "OE2" Residue "M GLU 122": "OE1" <-> "OE2" Residue "N GLU 122": "OE1" <-> "OE2" Residue "O GLU 122": "OE1" <-> "OE2" Residue "P GLU 122": "OE1" <-> "OE2" Residue "Q GLU 122": "OE1" <-> "OE2" Residue "R GLU 122": "OE1" <-> "OE2" Residue "S GLU 122": "OE1" <-> "OE2" Residue "T GLU 122": "OE1" <-> "OE2" Residue "U GLU 122": "OE1" <-> "OE2" Residue "V GLU 122": "OE1" <-> "OE2" Residue "W GLU 122": "OE1" <-> "OE2" Residue "X GLU 122": "OE1" <-> "OE2" Residue "Y GLU 122": "OE1" <-> "OE2" Time to flip residues: 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 22550 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "B" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "D" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "F" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "H" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "I" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "J" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "K" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "L" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "M" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "N" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "O" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "P" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "Q" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "R" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "S" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "T" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "U" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "V" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "W" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "X" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Chain: "Y" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 902 Classifications: {'peptide': 132} Modifications used: {'COO': 1} Link IDs: {'TRANS': 131} Time building chain proxies: 11.77, per 1000 atoms: 0.52 Number of scatterers: 22550 At special positions: 0 Unit cell: (90.72, 91.8, 219.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 4625 8.00 N 3600 7.00 C 14300 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: 8.19 Conformation dependent library (CDL) restraints added in 4.4 seconds 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5750 Finding SS restraints... Secondary structure from input PDB file: 50 helices and 50 sheets defined 29.6% alpha, 47.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.20 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 3.603A pdb=" N VAL A 5 " --> pdb=" O LEU A 1 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY A 106 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL A 108 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY B 106 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 108 " --> pdb=" O ARG B 105 " (cutoff:3.500A) Processing helix chain 'C' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY C 106 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL C 108 " --> pdb=" O ARG C 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY D 106 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL D 108 " --> pdb=" O ARG D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY E 106 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL E 108 " --> pdb=" O ARG E 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY F 106 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL F 108 " --> pdb=" O ARG F 105 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY G 106 " --> pdb=" O THR G 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL G 108 " --> pdb=" O ARG G 105 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY H 106 " --> pdb=" O THR H 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL H 108 " --> pdb=" O ARG H 105 " (cutoff:3.500A) Processing helix chain 'I' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY I 106 " --> pdb=" O THR I 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL I 108 " --> pdb=" O ARG I 105 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY J 106 " --> pdb=" O THR J 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL J 108 " --> pdb=" O ARG J 105 " (cutoff:3.500A) Processing helix chain 'K' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY K 106 " --> pdb=" O THR K 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL K 108 " --> pdb=" O ARG K 105 " (cutoff:3.500A) Processing helix chain 'L' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY L 106 " --> pdb=" O THR L 103 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N VAL L 108 " --> pdb=" O ARG L 105 " (cutoff:3.500A) Processing helix chain 'M' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY M 106 " --> pdb=" O THR M 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL M 108 " --> pdb=" O ARG M 105 " (cutoff:3.500A) Processing helix chain 'N' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY N 106 " --> pdb=" O THR N 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL N 108 " --> pdb=" O ARG N 105 " (cutoff:3.500A) Processing helix chain 'O' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY O 106 " --> pdb=" O THR O 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL O 108 " --> pdb=" O ARG O 105 " (cutoff:3.500A) Processing helix chain 'P' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY P 34 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY P 106 " --> pdb=" O THR P 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL P 108 " --> pdb=" O ARG P 105 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY Q 106 " --> pdb=" O THR Q 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL Q 108 " --> pdb=" O ARG Q 105 " (cutoff:3.500A) Processing helix chain 'R' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY R 106 " --> pdb=" O THR R 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL R 108 " --> pdb=" O ARG R 105 " (cutoff:3.500A) Processing helix chain 'S' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY S 106 " --> pdb=" O THR S 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL S 108 " --> pdb=" O ARG S 105 " (cutoff:3.500A) Processing helix chain 'T' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY T 106 " --> pdb=" O THR T 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL T 108 " --> pdb=" O ARG T 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY U 106 " --> pdb=" O THR U 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL U 108 " --> pdb=" O ARG U 105 " (cutoff:3.500A) Processing helix chain 'V' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY V 34 " --> pdb=" O GLY V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY V 106 " --> pdb=" O THR V 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL V 108 " --> pdb=" O ARG V 105 " (cutoff:3.500A) Processing helix chain 'W' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY W 34 " --> pdb=" O GLY W 30 " (cutoff:3.500A) Processing helix chain 'W' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY W 106 " --> pdb=" O THR W 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL W 108 " --> pdb=" O ARG W 105 " (cutoff:3.500A) Processing helix chain 'X' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY X 34 " --> pdb=" O GLY X 30 " (cutoff:3.500A) Processing helix chain 'X' and resid 103 through 108 removed outlier: 3.963A pdb=" N GLY X 106 " --> pdb=" O THR X 103 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL X 108 " --> pdb=" O ARG X 105 " (cutoff:3.500A) Processing helix chain 'Y' and resid 2 through 34 removed outlier: 3.517A pdb=" N GLY Y 34 " --> pdb=" O GLY Y 30 " (cutoff:3.500A) Processing helix chain 'Y' and resid 103 through 108 removed outlier: 3.964A pdb=" N GLY Y 106 " --> pdb=" O THR Y 103 " (cutoff:3.500A) removed outlier: 4.047A pdb=" N VAL Y 108 " --> pdb=" O ARG Y 105 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR A 52 " --> pdb=" O SER A 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 64 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER A 77 " --> pdb=" O SER A 96 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N VAL A 78 " --> pdb=" O THR A 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR A 67 " --> pdb=" O VAL A 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR A 64 " --> pdb=" O ILE A 84 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR B 52 " --> pdb=" O SER B 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 64 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 removed outlier: 3.701A pdb=" N SER B 77 " --> pdb=" O SER B 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL B 78 " --> pdb=" O THR B 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR B 67 " --> pdb=" O VAL B 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 64 " --> pdb=" O ILE B 84 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR C 52 " --> pdb=" O SER C 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 64 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER C 77 " --> pdb=" O SER C 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL C 78 " --> pdb=" O THR C 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR C 67 " --> pdb=" O VAL C 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 64 " --> pdb=" O ILE C 84 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR D 52 " --> pdb=" O SER D 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER D 77 " --> pdb=" O SER D 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL D 78 " --> pdb=" O THR D 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR D 67 " --> pdb=" O VAL D 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR D 64 " --> pdb=" O ILE D 84 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR E 52 " --> pdb=" O SER E 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER E 77 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL E 78 " --> pdb=" O THR E 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR E 67 " --> pdb=" O VAL E 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR E 64 " --> pdb=" O ILE E 84 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR F 52 " --> pdb=" O SER F 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 64 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER F 77 " --> pdb=" O SER F 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL F 78 " --> pdb=" O THR F 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR F 67 " --> pdb=" O VAL F 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR F 64 " --> pdb=" O ILE F 84 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR G 52 " --> pdb=" O SER G 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 64 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'G' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER G 77 " --> pdb=" O SER G 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL G 78 " --> pdb=" O THR G 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR G 67 " --> pdb=" O VAL G 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR G 64 " --> pdb=" O ILE G 84 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR H 52 " --> pdb=" O SER H 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER H 77 " --> pdb=" O SER H 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL H 78 " --> pdb=" O THR H 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR H 67 " --> pdb=" O VAL H 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR H 64 " --> pdb=" O ILE H 84 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR I 52 " --> pdb=" O SER I 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'I' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER I 77 " --> pdb=" O SER I 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL I 78 " --> pdb=" O THR I 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR I 67 " --> pdb=" O VAL I 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR I 64 " --> pdb=" O ILE I 84 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR J 52 " --> pdb=" O SER J 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER J 77 " --> pdb=" O SER J 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL J 78 " --> pdb=" O THR J 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR J 67 " --> pdb=" O VAL J 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR J 64 " --> pdb=" O ILE J 84 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR K 52 " --> pdb=" O SER K 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 64 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'K' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER K 77 " --> pdb=" O SER K 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL K 78 " --> pdb=" O THR K 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR K 67 " --> pdb=" O VAL K 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR K 64 " --> pdb=" O ILE K 84 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR L 52 " --> pdb=" O SER L 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR L 64 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER L 77 " --> pdb=" O SER L 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL L 78 " --> pdb=" O THR L 67 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N THR L 67 " --> pdb=" O VAL L 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR L 64 " --> pdb=" O ILE L 84 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR M 52 " --> pdb=" O SER M 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR M 64 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'M' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER M 77 " --> pdb=" O SER M 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL M 78 " --> pdb=" O THR M 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR M 67 " --> pdb=" O VAL M 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR M 64 " --> pdb=" O ILE M 84 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'N' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR N 52 " --> pdb=" O SER N 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR N 64 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'N' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER N 77 " --> pdb=" O SER N 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL N 78 " --> pdb=" O THR N 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR N 67 " --> pdb=" O VAL N 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR N 64 " --> pdb=" O ILE N 84 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR O 52 " --> pdb=" O SER O 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR O 64 " --> pdb=" O ILE O 84 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER O 77 " --> pdb=" O SER O 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL O 78 " --> pdb=" O THR O 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR O 67 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR O 64 " --> pdb=" O ILE O 84 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR P 52 " --> pdb=" O SER P 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR P 64 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'P' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER P 77 " --> pdb=" O SER P 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL P 78 " --> pdb=" O THR P 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR P 67 " --> pdb=" O VAL P 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR P 64 " --> pdb=" O ILE P 84 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Q' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR Q 52 " --> pdb=" O SER Q 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Q 64 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'Q' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER Q 77 " --> pdb=" O SER Q 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL Q 78 " --> pdb=" O THR Q 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR Q 67 " --> pdb=" O VAL Q 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Q 64 " --> pdb=" O ILE Q 84 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR R 52 " --> pdb=" O SER R 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR R 64 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'R' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER R 77 " --> pdb=" O SER R 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL R 78 " --> pdb=" O THR R 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR R 67 " --> pdb=" O VAL R 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR R 64 " --> pdb=" O ILE R 84 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR S 52 " --> pdb=" O SER S 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 64 " --> pdb=" O ILE S 84 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'S' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER S 77 " --> pdb=" O SER S 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL S 78 " --> pdb=" O THR S 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR S 67 " --> pdb=" O VAL S 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR S 64 " --> pdb=" O ILE S 84 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'T' and resid 38 through 40 removed outlier: 3.777A pdb=" N THR T 52 " --> pdb=" O SER T 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR T 64 " --> pdb=" O ILE T 84 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'T' and resid 38 through 40 removed outlier: 3.701A pdb=" N SER T 77 " --> pdb=" O SER T 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL T 78 " --> pdb=" O THR T 67 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N THR T 67 " --> pdb=" O VAL T 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR T 64 " --> pdb=" O ILE T 84 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'U' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR U 52 " --> pdb=" O SER U 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR U 64 " --> pdb=" O ILE U 84 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'U' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER U 77 " --> pdb=" O SER U 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL U 78 " --> pdb=" O THR U 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR U 67 " --> pdb=" O VAL U 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR U 64 " --> pdb=" O ILE U 84 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'V' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR V 52 " --> pdb=" O SER V 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR V 64 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'V' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER V 77 " --> pdb=" O SER V 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL V 78 " --> pdb=" O THR V 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR V 67 " --> pdb=" O VAL V 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR V 64 " --> pdb=" O ILE V 84 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'W' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR W 52 " --> pdb=" O SER W 47 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR W 64 " --> pdb=" O ILE W 84 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'W' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER W 77 " --> pdb=" O SER W 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL W 78 " --> pdb=" O THR W 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR W 67 " --> pdb=" O VAL W 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N THR W 64 " --> pdb=" O ILE W 84 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'X' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR X 52 " --> pdb=" O SER X 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR X 64 " --> pdb=" O ILE X 84 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'X' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER X 77 " --> pdb=" O SER X 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL X 78 " --> pdb=" O THR X 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR X 67 " --> pdb=" O VAL X 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR X 64 " --> pdb=" O ILE X 84 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Y' and resid 38 through 40 removed outlier: 3.776A pdb=" N THR Y 52 " --> pdb=" O SER Y 47 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 64 " --> pdb=" O ILE Y 84 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Y' and resid 38 through 40 removed outlier: 3.702A pdb=" N SER Y 77 " --> pdb=" O SER Y 96 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N VAL Y 78 " --> pdb=" O THR Y 67 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N THR Y 67 " --> pdb=" O VAL Y 78 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR Y 64 " --> pdb=" O ILE Y 84 " (cutoff:3.500A) 1575 hydrogen bonds defined for protein. 4500 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: 9.25 Time building geometry restraints manager: 8.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7125 1.34 - 1.46: 3774 1.46 - 1.57: 11701 1.57 - 1.69: 0 1.69 - 1.80: 50 Bond restraints: 22650 Sorted by residual: bond pdb=" CB ILE U 17 " pdb=" CG2 ILE U 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.23e-01 bond pdb=" CB ILE B 17 " pdb=" CG2 ILE B 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.18e-01 bond pdb=" CB ILE P 17 " pdb=" CG2 ILE P 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.14e-01 bond pdb=" CB ILE Q 17 " pdb=" CG2 ILE Q 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.14e-01 bond pdb=" CB ILE O 17 " pdb=" CG2 ILE O 17 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.04e-01 ... (remaining 22645 not shown) Histogram of bond angle deviations from ideal: 100.79 - 106.07: 50 106.07 - 111.34: 12554 111.34 - 116.61: 5301 116.61 - 121.89: 7902 121.89 - 127.16: 5243 Bond angle restraints: 31050 Sorted by residual: angle pdb=" N THR C 60 " pdb=" CA THR C 60 " pdb=" C THR C 60 " ideal model delta sigma weight residual 112.59 110.24 2.35 1.22e+00 6.72e-01 3.72e+00 angle pdb=" N THR M 60 " pdb=" CA THR M 60 " pdb=" C THR M 60 " ideal model delta sigma weight residual 112.59 110.24 2.35 1.22e+00 6.72e-01 3.70e+00 angle pdb=" N THR W 60 " pdb=" CA THR W 60 " pdb=" C THR W 60 " ideal model delta sigma weight residual 112.59 110.25 2.34 1.22e+00 6.72e-01 3.69e+00 angle pdb=" N THR N 60 " pdb=" CA THR N 60 " pdb=" C THR N 60 " ideal model delta sigma weight residual 112.59 110.25 2.34 1.22e+00 6.72e-01 3.69e+00 angle pdb=" N THR T 60 " pdb=" CA THR T 60 " pdb=" C THR T 60 " ideal model delta sigma weight residual 112.59 110.25 2.34 1.22e+00 6.72e-01 3.67e+00 ... (remaining 31045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 9.37: 11400 9.37 - 18.74: 1050 18.74 - 28.12: 300 28.12 - 37.49: 225 37.49 - 46.86: 50 Dihedral angle restraints: 13025 sinusoidal: 3975 harmonic: 9050 Sorted by residual: dihedral pdb=" CA GLN T 65 " pdb=" CB GLN T 65 " pdb=" CG GLN T 65 " pdb=" CD GLN T 65 " ideal model delta sinusoidal sigma weight residual -60.00 -90.33 30.33 3 1.50e+01 4.44e-03 4.82e+00 dihedral pdb=" CA GLN J 65 " pdb=" CB GLN J 65 " pdb=" CG GLN J 65 " pdb=" CD GLN J 65 " ideal model delta sinusoidal sigma weight residual -60.00 -90.32 30.32 3 1.50e+01 4.44e-03 4.82e+00 dihedral pdb=" CA GLN W 65 " pdb=" CB GLN W 65 " pdb=" CG GLN W 65 " pdb=" CD GLN W 65 " ideal model delta sinusoidal sigma weight residual -60.00 -90.31 30.31 3 1.50e+01 4.44e-03 4.82e+00 ... (remaining 13022 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 2679 0.026 - 0.052: 1039 0.052 - 0.078: 332 0.078 - 0.104: 366 0.104 - 0.130: 184 Chirality restraints: 4600 Sorted by residual: chirality pdb=" CA ILE C 129 " pdb=" N ILE C 129 " pdb=" C ILE C 129 " pdb=" CB ILE C 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.25e-01 chirality pdb=" CA ILE K 129 " pdb=" N ILE K 129 " pdb=" C ILE K 129 " pdb=" CB ILE K 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.19e-01 chirality pdb=" CA ILE L 129 " pdb=" N ILE L 129 " pdb=" C ILE L 129 " pdb=" CB ILE L 129 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 4597 not shown) Planarity restraints: 3675 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE S 29 " -0.006 2.00e-02 2.50e+03 4.67e-03 3.82e-01 pdb=" CG PHE S 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE S 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE S 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE S 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE S 29 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE S 29 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE W 29 " -0.006 2.00e-02 2.50e+03 4.66e-03 3.81e-01 pdb=" CG PHE W 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE W 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE W 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE W 29 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE W 29 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE W 29 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 29 " -0.006 2.00e-02 2.50e+03 4.64e-03 3.77e-01 pdb=" CG PHE B 29 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 29 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 PHE B 29 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 PHE B 29 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 29 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE B 29 " -0.001 2.00e-02 2.50e+03 ... (remaining 3672 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 8336 2.87 - 3.38: 20122 3.38 - 3.88: 39184 3.88 - 4.39: 40997 4.39 - 4.90: 75447 Nonbonded interactions: 184086 Sorted by model distance: nonbonded pdb=" OD1 ASN T 74 " pdb=" OG SER T 99 " model vdw 2.362 2.440 nonbonded pdb=" OD1 ASN I 74 " pdb=" OG SER I 99 " model vdw 2.362 2.440 nonbonded pdb=" OD1 ASN F 74 " pdb=" OG SER F 99 " model vdw 2.362 2.440 nonbonded pdb=" OD1 ASN B 74 " pdb=" OG SER B 99 " model vdw 2.362 2.440 nonbonded pdb=" OD1 ASN P 74 " pdb=" OG SER P 99 " model vdw 2.362 2.440 ... (remaining 184081 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 12.330 Check model and map are aligned: 0.360 Set scattering table: 0.230 Process input model: 60.810 Find NCS groups from input model: 1.750 Set up NCS constraints: 0.220 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 92.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7897 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 : 0.002 0.021 22650 Z= 0.148 Angle : 0.454 3.526 31050 Z= 0.259 Chirality : 0.044 0.130 4600 Planarity : 0.001 0.005 3675 Dihedral : 10.151 46.859 7275 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % 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: 0.15 (0.15), residues: 3250 helix: 2.67 (0.17), residues: 1025 sheet: -0.62 (0.16), residues: 1125 loop : -1.57 (0.17), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.010 0.002 PHE W 29 TYR 0.002 0.001 TYR G 91 ARG 0.001 0.000 ARG R 105 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 2.245 Fit side-chains REVERT: B 89 ASN cc_start: 0.8648 (m110) cc_final: 0.8432 (m110) REVERT: E 45 THR cc_start: 0.8707 (m) cc_final: 0.8414 (m) REVERT: E 89 ASN cc_start: 0.8811 (m110) cc_final: 0.8423 (m110) REVERT: F 89 ASN cc_start: 0.8933 (m110) cc_final: 0.8726 (m110) REVERT: H 45 THR cc_start: 0.8755 (m) cc_final: 0.8494 (m) REVERT: H 89 ASN cc_start: 0.8740 (m110) cc_final: 0.8229 (m-40) REVERT: I 89 ASN cc_start: 0.8782 (m110) cc_final: 0.8497 (m110) REVERT: J 89 ASN cc_start: 0.8878 (m110) cc_final: 0.8427 (m110) REVERT: O 89 ASN cc_start: 0.8867 (m110) cc_final: 0.8555 (m-40) REVERT: P 45 THR cc_start: 0.8693 (m) cc_final: 0.8433 (m) REVERT: Q 45 THR cc_start: 0.8842 (m) cc_final: 0.8603 (m) REVERT: S 89 ASN cc_start: 0.8842 (m110) cc_final: 0.8482 (m110) REVERT: T 79 SER cc_start: 0.7676 (t) cc_final: 0.7462 (p) REVERT: T 89 ASN cc_start: 0.8898 (m110) cc_final: 0.8696 (m-40) REVERT: V 89 ASN cc_start: 0.8845 (m110) cc_final: 0.8481 (m110) REVERT: X 45 THR cc_start: 0.8714 (m) cc_final: 0.8416 (m) REVERT: Y 89 ASN cc_start: 0.8848 (m110) cc_final: 0.8298 (m-40) outliers start: 0 outliers final: 0 residues processed: 269 average time/residue: 0.4557 time to fit residues: 172.6746 Evaluate side-chains 187 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 274 optimal weight: 3.9990 chunk 246 optimal weight: 2.9990 chunk 136 optimal weight: 0.4980 chunk 84 optimal weight: 6.9990 chunk 166 optimal weight: 7.9990 chunk 131 optimal weight: 0.6980 chunk 254 optimal weight: 0.0770 chunk 98 optimal weight: 0.8980 chunk 154 optimal weight: 2.9990 chunk 189 optimal weight: 0.8980 chunk 295 optimal weight: 3.9990 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.1029 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 22650 Z= 0.142 Angle : 0.483 7.687 31050 Z= 0.264 Chirality : 0.045 0.207 4600 Planarity : 0.002 0.014 3675 Dihedral : 3.596 9.647 3350 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.43 % Allowed : 4.08 % Favored : 95.50 % 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: 0.48 (0.15), residues: 3250 helix: 2.78 (0.17), residues: 1025 sheet: -0.33 (0.15), residues: 1200 loop : -1.40 (0.18), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.008 0.001 PHE M 29 TYR 0.003 0.001 TYR C 91 ARG 0.000 0.000 ARG X 105 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 229 time to evaluate : 2.316 Fit side-chains REVERT: C 79 SER cc_start: 0.7644 (p) cc_final: 0.7099 (t) REVERT: E 45 THR cc_start: 0.8649 (m) cc_final: 0.8372 (m) REVERT: E 120 ASN cc_start: 0.8408 (p0) cc_final: 0.8139 (p0) REVERT: F 89 ASN cc_start: 0.8835 (m110) cc_final: 0.8583 (m110) REVERT: H 89 ASN cc_start: 0.8625 (m110) cc_final: 0.8154 (m-40) REVERT: J 120 ASN cc_start: 0.8497 (p0) cc_final: 0.8296 (p0) REVERT: O 89 ASN cc_start: 0.8737 (m110) cc_final: 0.8358 (m-40) REVERT: T 79 SER cc_start: 0.7493 (t) cc_final: 0.7285 (t) REVERT: T 89 ASN cc_start: 0.8784 (m110) cc_final: 0.8547 (m110) REVERT: U 81 MET cc_start: 0.7302 (mtp) cc_final: 0.7042 (mtt) REVERT: X 45 THR cc_start: 0.8830 (m) cc_final: 0.8553 (m) outliers start: 11 outliers final: 6 residues processed: 238 average time/residue: 0.5428 time to fit residues: 177.4503 Evaluate side-chains 181 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 175 time to evaluate : 2.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 164 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 245 optimal weight: 3.9990 chunk 200 optimal weight: 7.9990 chunk 81 optimal weight: 0.8980 chunk 295 optimal weight: 1.9990 chunk 319 optimal weight: 8.9990 chunk 263 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 chunk 100 optimal weight: 3.9990 chunk 237 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22650 Z= 0.393 Angle : 0.657 9.006 31050 Z= 0.338 Chirality : 0.051 0.233 4600 Planarity : 0.003 0.018 3675 Dihedral : 4.753 16.343 3350 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 3.07 % Allowed : 6.14 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.15), residues: 3250 helix: 1.87 (0.16), residues: 1025 sheet: -0.34 (0.15), residues: 1200 loop : -1.79 (0.16), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE V 29 TYR 0.009 0.003 TYR K 91 ARG 0.002 0.001 ARG J 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 239 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 160 time to evaluate : 2.541 Fit side-chains REVERT: D 45 THR cc_start: 0.8648 (OUTLIER) cc_final: 0.8305 (t) REVERT: D 79 SER cc_start: 0.8192 (OUTLIER) cc_final: 0.7692 (t) REVERT: E 45 THR cc_start: 0.8760 (m) cc_final: 0.8442 (m) REVERT: F 79 SER cc_start: 0.7934 (t) cc_final: 0.7690 (t) REVERT: F 89 ASN cc_start: 0.8762 (m110) cc_final: 0.8511 (m110) REVERT: H 45 THR cc_start: 0.8964 (OUTLIER) cc_final: 0.8427 (m) REVERT: H 89 ASN cc_start: 0.8616 (m110) cc_final: 0.8220 (m-40) REVERT: I 41 VAL cc_start: 0.8439 (m) cc_final: 0.8236 (t) REVERT: K 45 THR cc_start: 0.8979 (OUTLIER) cc_final: 0.8733 (t) REVERT: K 79 SER cc_start: 0.8052 (t) cc_final: 0.7721 (t) REVERT: L 79 SER cc_start: 0.8062 (OUTLIER) cc_final: 0.7642 (t) REVERT: O 41 VAL cc_start: 0.8597 (m) cc_final: 0.8191 (t) REVERT: O 65 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7059 (mp10) REVERT: O 79 SER cc_start: 0.8072 (p) cc_final: 0.7517 (t) REVERT: O 89 ASN cc_start: 0.8718 (m110) cc_final: 0.8403 (m-40) REVERT: R 45 THR cc_start: 0.8810 (OUTLIER) cc_final: 0.8539 (t) REVERT: R 79 SER cc_start: 0.8082 (OUTLIER) cc_final: 0.7726 (t) REVERT: S 120 ASN cc_start: 0.8701 (p0) cc_final: 0.8478 (p0) REVERT: T 79 SER cc_start: 0.7664 (t) cc_final: 0.7385 (t) REVERT: U 41 VAL cc_start: 0.8478 (m) cc_final: 0.8171 (t) REVERT: V 122 GLU cc_start: 0.8804 (tt0) cc_final: 0.8601 (tt0) REVERT: W 45 THR cc_start: 0.8990 (OUTLIER) cc_final: 0.8715 (t) outliers start: 79 outliers final: 46 residues processed: 220 average time/residue: 0.5032 time to fit residues: 152.4791 Evaluate side-chains 195 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 140 time to evaluate : 2.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain G residue 45 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain J residue 45 THR Chi-restraints excluded: chain K residue 45 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain M residue 103 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 103 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 45 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 45 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 292 optimal weight: 3.9990 chunk 222 optimal weight: 1.9990 chunk 153 optimal weight: 2.9990 chunk 32 optimal weight: 0.3980 chunk 141 optimal weight: 0.8980 chunk 198 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 314 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 281 optimal weight: 0.6980 chunk 84 optimal weight: 4.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: T 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.1786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 22650 Z= 0.184 Angle : 0.505 7.835 31050 Z= 0.270 Chirality : 0.046 0.181 4600 Planarity : 0.002 0.018 3675 Dihedral : 4.192 16.452 3350 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.33 % Allowed : 8.62 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.15), residues: 3250 helix: 2.20 (0.17), residues: 1025 sheet: -0.33 (0.15), residues: 1200 loop : -1.55 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.001 PHE Q 29 TYR 0.004 0.001 TYR K 91 ARG 0.001 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 160 time to evaluate : 2.150 Fit side-chains REVERT: C 79 SER cc_start: 0.7521 (p) cc_final: 0.7046 (t) REVERT: D 79 SER cc_start: 0.8147 (p) cc_final: 0.7623 (t) REVERT: E 45 THR cc_start: 0.8664 (m) cc_final: 0.8319 (m) REVERT: F 79 SER cc_start: 0.7941 (t) cc_final: 0.7657 (t) REVERT: F 89 ASN cc_start: 0.8801 (m110) cc_final: 0.8566 (m110) REVERT: H 89 ASN cc_start: 0.8630 (m110) cc_final: 0.8218 (m-40) REVERT: I 41 VAL cc_start: 0.8252 (m) cc_final: 0.8028 (t) REVERT: J 120 ASN cc_start: 0.8613 (p0) cc_final: 0.8348 (p0) REVERT: K 79 SER cc_start: 0.7896 (t) cc_final: 0.7592 (t) REVERT: L 79 SER cc_start: 0.7994 (OUTLIER) cc_final: 0.7556 (t) REVERT: O 79 SER cc_start: 0.7763 (OUTLIER) cc_final: 0.7286 (t) REVERT: O 89 ASN cc_start: 0.8685 (m110) cc_final: 0.8337 (m110) REVERT: R 79 SER cc_start: 0.8018 (OUTLIER) cc_final: 0.7657 (t) REVERT: T 79 SER cc_start: 0.7652 (t) cc_final: 0.7386 (t) REVERT: W 79 SER cc_start: 0.7943 (OUTLIER) cc_final: 0.7514 (t) REVERT: Y 65 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.7435 (mp10) outliers start: 60 outliers final: 33 residues processed: 205 average time/residue: 0.5177 time to fit residues: 144.6518 Evaluate side-chains 185 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 147 time to evaluate : 2.543 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 37 THR Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 261 optimal weight: 0.8980 chunk 178 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 233 optimal weight: 10.0000 chunk 129 optimal weight: 0.8980 chunk 268 optimal weight: 4.9990 chunk 217 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 160 optimal weight: 4.9990 chunk 281 optimal weight: 7.9990 chunk 79 optimal weight: 0.8980 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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: 0.8091 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 22650 Z= 0.337 Angle : 0.617 8.520 31050 Z= 0.320 Chirality : 0.050 0.196 4600 Planarity : 0.002 0.014 3675 Dihedral : 4.656 20.777 3350 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.07 % Allowed : 9.83 % Favored : 87.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.14), residues: 3250 helix: 1.83 (0.16), residues: 1025 sheet: -0.44 (0.14), residues: 1225 loop : -1.95 (0.16), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.018 0.002 PHE O 29 TYR 0.007 0.002 TYR K 91 ARG 0.002 0.001 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 137 time to evaluate : 2.549 Fit side-chains REVERT: C 79 SER cc_start: 0.7596 (OUTLIER) cc_final: 0.7124 (t) REVERT: D 29 PHE cc_start: 0.8289 (m-80) cc_final: 0.8036 (m-80) REVERT: D 79 SER cc_start: 0.8214 (OUTLIER) cc_final: 0.7697 (t) REVERT: E 45 THR cc_start: 0.8720 (m) cc_final: 0.8382 (m) REVERT: F 79 SER cc_start: 0.7962 (t) cc_final: 0.7637 (t) REVERT: F 89 ASN cc_start: 0.8771 (m110) cc_final: 0.8525 (m110) REVERT: H 45 THR cc_start: 0.8959 (OUTLIER) cc_final: 0.8421 (m) REVERT: H 89 ASN cc_start: 0.8580 (m110) cc_final: 0.8179 (m-40) REVERT: K 79 SER cc_start: 0.7880 (t) cc_final: 0.7573 (t) REVERT: L 79 SER cc_start: 0.7933 (OUTLIER) cc_final: 0.7498 (t) REVERT: O 41 VAL cc_start: 0.8558 (m) cc_final: 0.8189 (t) REVERT: O 65 GLN cc_start: 0.8574 (OUTLIER) cc_final: 0.7072 (mp10) REVERT: O 79 SER cc_start: 0.8048 (OUTLIER) cc_final: 0.7515 (t) REVERT: O 89 ASN cc_start: 0.8700 (m110) cc_final: 0.8378 (m110) REVERT: R 79 SER cc_start: 0.8067 (OUTLIER) cc_final: 0.7732 (t) REVERT: T 79 SER cc_start: 0.7622 (t) cc_final: 0.7325 (t) REVERT: Y 65 GLN cc_start: 0.8759 (OUTLIER) cc_final: 0.7453 (mp10) outliers start: 79 outliers final: 54 residues processed: 197 average time/residue: 0.5662 time to fit residues: 149.6183 Evaluate side-chains 187 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 125 time to evaluate : 2.492 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 45 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 45 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 81 MET Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 45 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 105 optimal weight: 0.8980 chunk 282 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 184 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 314 optimal weight: 0.9990 chunk 261 optimal weight: 0.9980 chunk 145 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 165 optimal weight: 6.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8017 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 22650 Z= 0.174 Angle : 0.499 6.946 31050 Z= 0.265 Chirality : 0.046 0.177 4600 Planarity : 0.002 0.013 3675 Dihedral : 4.125 18.247 3350 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.82 % Favored : 96.18 % Rotamer: Outliers : 1.90 % Allowed : 12.62 % Favored : 85.48 % 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: 0.12 (0.15), residues: 3250 helix: 2.20 (0.17), residues: 1025 sheet: -0.34 (0.14), residues: 1200 loop : -1.53 (0.17), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.001 PHE O 29 TYR 0.004 0.001 TYR K 91 ARG 0.001 0.000 ARG U 105 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 163 time to evaluate : 2.246 Fit side-chains REVERT: C 79 SER cc_start: 0.7510 (OUTLIER) cc_final: 0.7042 (t) REVERT: D 79 SER cc_start: 0.8052 (OUTLIER) cc_final: 0.7559 (t) REVERT: E 45 THR cc_start: 0.8653 (m) cc_final: 0.8309 (m) REVERT: F 89 ASN cc_start: 0.8808 (m110) cc_final: 0.8583 (m110) REVERT: H 79 SER cc_start: 0.7706 (OUTLIER) cc_final: 0.7128 (t) REVERT: H 89 ASN cc_start: 0.8592 (m110) cc_final: 0.8146 (m-40) REVERT: J 120 ASN cc_start: 0.8617 (p0) cc_final: 0.8355 (p0) REVERT: K 79 SER cc_start: 0.7776 (t) cc_final: 0.7458 (t) REVERT: L 79 SER cc_start: 0.7965 (OUTLIER) cc_final: 0.7519 (t) REVERT: O 79 SER cc_start: 0.7870 (OUTLIER) cc_final: 0.7393 (t) REVERT: O 89 ASN cc_start: 0.8678 (m110) cc_final: 0.8344 (m110) REVERT: R 79 SER cc_start: 0.7849 (OUTLIER) cc_final: 0.7471 (t) REVERT: T 79 SER cc_start: 0.7573 (t) cc_final: 0.7301 (t) REVERT: W 79 SER cc_start: 0.7947 (OUTLIER) cc_final: 0.7503 (t) REVERT: Y 65 GLN cc_start: 0.8621 (OUTLIER) cc_final: 0.7376 (mp10) REVERT: Y 79 SER cc_start: 0.7883 (OUTLIER) cc_final: 0.7395 (t) outliers start: 49 outliers final: 34 residues processed: 198 average time/residue: 0.6636 time to fit residues: 170.7460 Evaluate side-chains 193 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 150 time to evaluate : 2.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 303 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 179 optimal weight: 0.9990 chunk 229 optimal weight: 4.9990 chunk 177 optimal weight: 3.9990 chunk 264 optimal weight: 4.9990 chunk 175 optimal weight: 6.9990 chunk 313 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 190 optimal weight: 6.9990 chunk 144 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8104 moved from start: 0.2188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22650 Z= 0.370 Angle : 0.629 8.382 31050 Z= 0.327 Chirality : 0.051 0.187 4600 Planarity : 0.002 0.016 3675 Dihedral : 4.771 21.984 3350 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 3.11 % Allowed : 12.43 % Favored : 84.47 % 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 (0.14), residues: 3250 helix: 1.77 (0.16), residues: 1025 sheet: -0.47 (0.14), residues: 1225 loop : -2.04 (0.16), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.011 0.002 PHE Y 32 TYR 0.008 0.003 TYR K 91 ARG 0.002 0.001 ARG G 105 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 123 time to evaluate : 1.919 Fit side-chains REVERT: D 79 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7698 (t) REVERT: E 45 THR cc_start: 0.8732 (m) cc_final: 0.8357 (m) REVERT: F 79 SER cc_start: 0.7931 (t) cc_final: 0.7598 (t) REVERT: F 89 ASN cc_start: 0.8805 (m110) cc_final: 0.8566 (m110) REVERT: H 89 ASN cc_start: 0.8575 (m110) cc_final: 0.8170 (m-40) REVERT: J 65 GLN cc_start: 0.8783 (OUTLIER) cc_final: 0.8135 (mt0) REVERT: K 79 SER cc_start: 0.7850 (t) cc_final: 0.7525 (t) REVERT: L 79 SER cc_start: 0.7919 (OUTLIER) cc_final: 0.7484 (t) REVERT: O 65 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7013 (mp10) REVERT: O 79 SER cc_start: 0.8081 (OUTLIER) cc_final: 0.7548 (t) REVERT: O 89 ASN cc_start: 0.8722 (m110) cc_final: 0.8432 (m-40) REVERT: Q 65 GLN cc_start: 0.8743 (OUTLIER) cc_final: 0.8256 (mt0) REVERT: R 65 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7374 (mt0) REVERT: R 79 SER cc_start: 0.8065 (OUTLIER) cc_final: 0.7719 (t) REVERT: T 45 THR cc_start: 0.8967 (OUTLIER) cc_final: 0.8757 (t) REVERT: T 79 SER cc_start: 0.7598 (t) cc_final: 0.7321 (t) REVERT: V 122 GLU cc_start: 0.8728 (tt0) cc_final: 0.8494 (pt0) REVERT: W 65 GLN cc_start: 0.8584 (OUTLIER) cc_final: 0.7401 (mt0) REVERT: Y 65 GLN cc_start: 0.8741 (OUTLIER) cc_final: 0.7462 (mp10) REVERT: Y 79 SER cc_start: 0.7768 (OUTLIER) cc_final: 0.7337 (t) outliers start: 80 outliers final: 57 residues processed: 182 average time/residue: 0.6137 time to fit residues: 147.4263 Evaluate side-chains 183 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 114 time to evaluate : 2.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain I residue 45 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 45 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain L residue 123 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 45 THR Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 43 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain R residue 81 MET Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain T residue 45 THR Chi-restraints excluded: chain T residue 103 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 43 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 65 GLN Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 45 THR Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 193 optimal weight: 0.8980 chunk 125 optimal weight: 0.6980 chunk 187 optimal weight: 2.9990 chunk 94 optimal weight: 0.7980 chunk 61 optimal weight: 3.9990 chunk 60 optimal weight: 0.8980 chunk 199 optimal weight: 8.9990 chunk 213 optimal weight: 4.9990 chunk 154 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 246 optimal weight: 5.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.8051 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 22650 Z= 0.219 Angle : 0.529 7.159 31050 Z= 0.281 Chirality : 0.047 0.189 4600 Planarity : 0.002 0.014 3675 Dihedral : 4.398 20.645 3350 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 2.33 % Allowed : 13.63 % Favored : 84.04 % 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: -0.08 (0.14), residues: 3250 helix: 2.01 (0.17), residues: 1025 sheet: -0.35 (0.14), residues: 1200 loop : -1.76 (0.16), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE K 29 TYR 0.005 0.001 TYR K 91 ARG 0.001 0.000 ARG E 105 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 142 time to evaluate : 2.283 Fit side-chains REVERT: C 79 SER cc_start: 0.7513 (OUTLIER) cc_final: 0.7052 (t) REVERT: D 79 SER cc_start: 0.8033 (OUTLIER) cc_final: 0.7561 (t) REVERT: E 45 THR cc_start: 0.8702 (m) cc_final: 0.8320 (m) REVERT: F 89 ASN cc_start: 0.8813 (m110) cc_final: 0.8576 (m110) REVERT: H 79 SER cc_start: 0.7762 (OUTLIER) cc_final: 0.7184 (t) REVERT: H 89 ASN cc_start: 0.8596 (m110) cc_final: 0.8172 (m-40) REVERT: J 65 GLN cc_start: 0.8702 (OUTLIER) cc_final: 0.8178 (mt0) REVERT: K 79 SER cc_start: 0.7643 (t) cc_final: 0.7343 (t) REVERT: L 79 SER cc_start: 0.7872 (OUTLIER) cc_final: 0.7429 (t) REVERT: O 65 GLN cc_start: 0.8519 (OUTLIER) cc_final: 0.6911 (mp10) REVERT: O 79 SER cc_start: 0.7700 (OUTLIER) cc_final: 0.7266 (t) REVERT: O 89 ASN cc_start: 0.8692 (m110) cc_final: 0.8360 (m110) REVERT: Q 65 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8363 (mt0) REVERT: R 65 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.7408 (mt0) REVERT: R 79 SER cc_start: 0.7957 (OUTLIER) cc_final: 0.7599 (t) REVERT: T 79 SER cc_start: 0.7553 (t) cc_final: 0.7286 (t) REVERT: V 122 GLU cc_start: 0.8708 (tt0) cc_final: 0.8444 (pt0) REVERT: W 45 THR cc_start: 0.8836 (OUTLIER) cc_final: 0.8464 (t) REVERT: W 79 SER cc_start: 0.7936 (OUTLIER) cc_final: 0.7501 (t) REVERT: Y 65 GLN cc_start: 0.8611 (OUTLIER) cc_final: 0.7365 (mp10) REVERT: Y 79 SER cc_start: 0.7831 (OUTLIER) cc_final: 0.7402 (t) outliers start: 60 outliers final: 41 residues processed: 184 average time/residue: 0.6512 time to fit residues: 155.9541 Evaluate side-chains 191 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 136 time to evaluate : 2.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 43 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain L residue 79 SER Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 65 GLN Chi-restraints excluded: chain O residue 79 SER Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain R residue 79 SER Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain W residue 79 SER Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 284 optimal weight: 5.9990 chunk 300 optimal weight: 0.8980 chunk 273 optimal weight: 0.9990 chunk 291 optimal weight: 1.9990 chunk 175 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 chunk 229 optimal weight: 1.9990 chunk 89 optimal weight: 0.5980 chunk 263 optimal weight: 3.9990 chunk 276 optimal weight: 0.6980 chunk 290 optimal weight: 4.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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: 0.8032 moved from start: 0.2047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 22650 Z= 0.191 Angle : 0.508 6.879 31050 Z= 0.271 Chirality : 0.047 0.184 4600 Planarity : 0.002 0.013 3675 Dihedral : 4.156 17.891 3350 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.14 % Allowed : 14.21 % Favored : 83.65 % 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: 0.05 (0.15), residues: 3250 helix: 2.15 (0.17), residues: 1025 sheet: -0.33 (0.14), residues: 1200 loop : -1.67 (0.16), residues: 1025 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.017 0.001 PHE O 29 TYR 0.004 0.001 TYR K 91 ARG 0.001 0.000 ARG B 105 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 148 time to evaluate : 2.312 Fit side-chains REVERT: E 45 THR cc_start: 0.8705 (m) cc_final: 0.8322 (m) REVERT: F 79 SER cc_start: 0.7833 (t) cc_final: 0.7494 (t) REVERT: F 89 ASN cc_start: 0.8806 (m110) cc_final: 0.8568 (m110) REVERT: H 65 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7049 (mp-120) REVERT: H 79 SER cc_start: 0.7725 (OUTLIER) cc_final: 0.7143 (t) REVERT: H 89 ASN cc_start: 0.8591 (m110) cc_final: 0.8158 (m-40) REVERT: J 65 GLN cc_start: 0.8604 (OUTLIER) cc_final: 0.8150 (mt0) REVERT: K 79 SER cc_start: 0.7608 (t) cc_final: 0.7296 (t) REVERT: O 89 ASN cc_start: 0.8680 (m110) cc_final: 0.8347 (m110) REVERT: Q 65 GLN cc_start: 0.8630 (OUTLIER) cc_final: 0.8023 (mp10) REVERT: R 65 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7453 (mt0) REVERT: T 79 SER cc_start: 0.7569 (t) cc_final: 0.7286 (t) REVERT: V 122 GLU cc_start: 0.8672 (tt0) cc_final: 0.8402 (pt0) REVERT: X 65 GLN cc_start: 0.8632 (OUTLIER) cc_final: 0.7960 (mt0) REVERT: Y 65 GLN cc_start: 0.8560 (OUTLIER) cc_final: 0.7349 (mp10) REVERT: Y 79 SER cc_start: 0.7756 (OUTLIER) cc_final: 0.7317 (t) outliers start: 55 outliers final: 43 residues processed: 185 average time/residue: 0.6866 time to fit residues: 163.1513 Evaluate side-chains 196 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 145 time to evaluate : 2.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 191 optimal weight: 4.9990 chunk 308 optimal weight: 3.9990 chunk 188 optimal weight: 0.9990 chunk 146 optimal weight: 5.9990 chunk 214 optimal weight: 0.0770 chunk 323 optimal weight: 3.9990 chunk 298 optimal weight: 5.9990 chunk 257 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 199 optimal weight: 4.9990 chunk 158 optimal weight: 0.7980 overall best weight: 1.9744 ------------------------------------------------------------------------------- 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: 0.8084 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 22650 Z= 0.314 Angle : 0.592 8.108 31050 Z= 0.309 Chirality : 0.049 0.190 4600 Planarity : 0.002 0.012 3675 Dihedral : 4.609 20.064 3350 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 2.25 % Allowed : 14.17 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.14), residues: 3250 helix: 1.85 (0.16), residues: 1025 sheet: -0.45 (0.14), residues: 1225 loop : -2.02 (0.16), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.015 0.002 PHE S 29 TYR 0.007 0.002 TYR K 91 ARG 0.002 0.001 ARG B 105 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6500 Ramachandran restraints generated. 3250 Oldfield, 0 Emsley, 3250 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 129 time to evaluate : 2.389 Fit side-chains REVERT: C 79 SER cc_start: 0.7553 (OUTLIER) cc_final: 0.7098 (t) REVERT: D 79 SER cc_start: 0.8207 (OUTLIER) cc_final: 0.7677 (t) REVERT: E 45 THR cc_start: 0.8731 (m) cc_final: 0.8330 (m) REVERT: F 79 SER cc_start: 0.7797 (t) cc_final: 0.7456 (t) REVERT: F 89 ASN cc_start: 0.8827 (m110) cc_final: 0.8591 (m110) REVERT: H 65 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.7304 (mp-120) REVERT: H 79 SER cc_start: 0.7798 (OUTLIER) cc_final: 0.7259 (t) REVERT: H 89 ASN cc_start: 0.8573 (m110) cc_final: 0.8157 (m-40) REVERT: J 65 GLN cc_start: 0.8722 (OUTLIER) cc_final: 0.8170 (mt0) REVERT: K 79 SER cc_start: 0.7655 (t) cc_final: 0.7361 (t) REVERT: O 79 SER cc_start: 0.7698 (p) cc_final: 0.7275 (t) REVERT: O 89 ASN cc_start: 0.8696 (m110) cc_final: 0.8373 (m110) REVERT: Q 65 GLN cc_start: 0.8754 (OUTLIER) cc_final: 0.8398 (mt0) REVERT: R 65 GLN cc_start: 0.8567 (OUTLIER) cc_final: 0.7482 (mt0) REVERT: R 79 SER cc_start: 0.7966 (p) cc_final: 0.7604 (t) REVERT: T 79 SER cc_start: 0.7576 (t) cc_final: 0.7294 (t) REVERT: V 122 GLU cc_start: 0.8724 (tt0) cc_final: 0.8441 (pt0) REVERT: W 45 THR cc_start: 0.8932 (OUTLIER) cc_final: 0.8580 (t) REVERT: X 65 GLN cc_start: 0.8740 (OUTLIER) cc_final: 0.7923 (mt0) REVERT: Y 65 GLN cc_start: 0.8623 (OUTLIER) cc_final: 0.7368 (mp10) REVERT: Y 79 SER cc_start: 0.7796 (OUTLIER) cc_final: 0.7399 (t) outliers start: 58 outliers final: 46 residues processed: 171 average time/residue: 0.6520 time to fit residues: 145.8416 Evaluate side-chains 181 residues out of total 2575 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 124 time to evaluate : 2.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain B residue 123 THR Chi-restraints excluded: chain C residue 79 SER Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 79 SER Chi-restraints excluded: chain D residue 122 GLU Chi-restraints excluded: chain D residue 123 THR Chi-restraints excluded: chain E residue 37 THR Chi-restraints excluded: chain E residue 43 THR Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 123 THR Chi-restraints excluded: chain H residue 37 THR Chi-restraints excluded: chain H residue 43 THR Chi-restraints excluded: chain H residue 65 GLN Chi-restraints excluded: chain H residue 79 SER Chi-restraints excluded: chain H residue 123 THR Chi-restraints excluded: chain I residue 37 THR Chi-restraints excluded: chain I residue 43 THR Chi-restraints excluded: chain J residue 37 THR Chi-restraints excluded: chain J residue 65 GLN Chi-restraints excluded: chain K residue 37 THR Chi-restraints excluded: chain K residue 43 THR Chi-restraints excluded: chain L residue 37 THR Chi-restraints excluded: chain L residue 43 THR Chi-restraints excluded: chain M residue 37 THR Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 37 THR Chi-restraints excluded: chain O residue 123 THR Chi-restraints excluded: chain P residue 8 LEU Chi-restraints excluded: chain P residue 43 THR Chi-restraints excluded: chain P residue 123 THR Chi-restraints excluded: chain Q residue 37 THR Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 GLN Chi-restraints excluded: chain Q residue 123 THR Chi-restraints excluded: chain R residue 37 THR Chi-restraints excluded: chain R residue 65 GLN Chi-restraints excluded: chain S residue 37 THR Chi-restraints excluded: chain S residue 43 THR Chi-restraints excluded: chain S residue 123 THR Chi-restraints excluded: chain T residue 37 THR Chi-restraints excluded: chain T residue 43 THR Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 37 THR Chi-restraints excluded: chain U residue 45 THR Chi-restraints excluded: chain U residue 123 THR Chi-restraints excluded: chain V residue 37 THR Chi-restraints excluded: chain V residue 45 THR Chi-restraints excluded: chain W residue 37 THR Chi-restraints excluded: chain W residue 45 THR Chi-restraints excluded: chain X residue 65 GLN Chi-restraints excluded: chain X residue 123 THR Chi-restraints excluded: chain Y residue 37 THR Chi-restraints excluded: chain Y residue 65 GLN Chi-restraints excluded: chain Y residue 79 SER Chi-restraints excluded: chain Y residue 123 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 325 random chunks: chunk 204 optimal weight: 5.9990 chunk 274 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 chunk 237 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 71 optimal weight: 0.9990 chunk 258 optimal weight: 1.9990 chunk 108 optimal weight: 4.9990 chunk 265 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 47 optimal weight: 7.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 65 GLN W 65 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3218 r_free = 0.3218 target = 0.115126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.095683 restraints weight = 26060.640| |-----------------------------------------------------------------------------| r_work (start): 0.2966 rms_B_bonded: 1.45 r_work: 0.2891 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.2100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 22650 Z= 0.192 Angle : 0.510 6.932 31050 Z= 0.271 Chirality : 0.047 0.184 4600 Planarity : 0.002 0.021 3675 Dihedral : 4.197 18.109 3350 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.21 % Allowed : 14.25 % Favored : 83.53 % 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: 0.20 (0.14), residues: 3250 helix: 2.13 (0.17), residues: 1025 sheet: 0.16 (0.15), residues: 1100 loop : -1.82 (0.15), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE K 29 TYR 0.004 0.001 TYR K 91 ARG 0.001 0.000 ARG E 105 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4334.81 seconds wall clock time: 79 minutes 46.94 seconds (4786.94 seconds total)