Starting phenix.real_space_refine on Thu Feb 15 22:06:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd2_10146/02_2024/6sd2_10146.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd2_10146/02_2024/6sd2_10146.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd2_10146/02_2024/6sd2_10146.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd2_10146/02_2024/6sd2_10146.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd2_10146/02_2024/6sd2_10146.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6sd2_10146/02_2024/6sd2_10146.pdb" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 21 5.16 5 C 8442 2.51 5 N 2415 2.21 5 O 2688 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 128": "OE1" <-> "OE2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "A ARG 154": "NH1" <-> "NH2" Residue "C PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 128": "OE1" <-> "OE2" Residue "C ARG 134": "NH1" <-> "NH2" Residue "C ARG 154": "NH1" <-> "NH2" Residue "D PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 128": "OE1" <-> "OE2" Residue "D ARG 134": "NH1" <-> "NH2" Residue "D ARG 154": "NH1" <-> "NH2" Residue "F PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 128": "OE1" <-> "OE2" Residue "F ARG 134": "NH1" <-> "NH2" Residue "F ARG 154": "NH1" <-> "NH2" Residue "G PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ARG 134": "NH1" <-> "NH2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "I PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 128": "OE1" <-> "OE2" Residue "I ARG 134": "NH1" <-> "NH2" Residue "I ARG 154": "NH1" <-> "NH2" Residue "J PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 128": "OE1" <-> "OE2" Residue "J ARG 134": "NH1" <-> "NH2" Residue "J ARG 154": "NH1" <-> "NH2" Residue "L PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 128": "OE1" <-> "OE2" Residue "L ARG 134": "NH1" <-> "NH2" Residue "L ARG 154": "NH1" <-> "NH2" Residue "N PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 128": "OE1" <-> "OE2" Residue "N ARG 134": "NH1" <-> "NH2" Residue "N ARG 154": "NH1" <-> "NH2" Residue "O PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 128": "OE1" <-> "OE2" Residue "O ARG 134": "NH1" <-> "NH2" Residue "O ARG 154": "NH1" <-> "NH2" Residue "Q PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 128": "OE1" <-> "OE2" Residue "Q ARG 134": "NH1" <-> "NH2" Residue "Q ARG 154": "NH1" <-> "NH2" Residue "R PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 128": "OE1" <-> "OE2" Residue "R ARG 134": "NH1" <-> "NH2" Residue "R ARG 154": "NH1" <-> "NH2" Residue "T PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T GLU 128": "OE1" <-> "OE2" Residue "T ARG 134": "NH1" <-> "NH2" Residue "T ARG 154": "NH1" <-> "NH2" Residue "U PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 128": "OE1" <-> "OE2" Residue "U ARG 134": "NH1" <-> "NH2" Residue "U ARG 154": "NH1" <-> "NH2" Residue "W PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 128": "OE1" <-> "OE2" Residue "W ARG 134": "NH1" <-> "NH2" Residue "W ARG 154": "NH1" <-> "NH2" Residue "Y PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 128": "OE1" <-> "OE2" Residue "Y ARG 134": "NH1" <-> "NH2" Residue "Y ARG 154": "NH1" <-> "NH2" Residue "Z PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 128": "OE1" <-> "OE2" Residue "Z ARG 134": "NH1" <-> "NH2" Residue "Z ARG 154": "NH1" <-> "NH2" Residue "b PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 128": "OE1" <-> "OE2" Residue "b ARG 134": "NH1" <-> "NH2" Residue "b ARG 154": "NH1" <-> "NH2" Residue "c PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 128": "OE1" <-> "OE2" Residue "c ARG 134": "NH1" <-> "NH2" Residue "c ARG 154": "NH1" <-> "NH2" Residue "e PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 128": "OE1" <-> "OE2" Residue "e ARG 134": "NH1" <-> "NH2" Residue "e ARG 154": "NH1" <-> "NH2" Residue "f PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "f GLU 128": "OE1" <-> "OE2" Residue "f ARG 134": "NH1" <-> "NH2" Residue "f ARG 154": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13566 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "C" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "D" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "G" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "I" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "J" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "L" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "N" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "O" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "Q" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "R" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "T" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "U" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "W" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "Y" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "Z" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "b" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "c" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "e" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Chain: "f" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 646 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain breaks: 1 Time building chain proxies: 7.31, per 1000 atoms: 0.54 Number of scatterers: 13566 At special positions: 0 Unit cell: (166.866, 166.044, 38.634, 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 21 16.00 O 2688 8.00 N 2415 7.00 C 8442 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: 5.16 Conformation dependent library (CDL) restraints added in 2.6 seconds 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3402 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 21 sheets defined 40.9% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'A' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA A 135 " --> pdb=" O ASN A 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 138 " --> pdb=" O ARG A 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG A 142 " --> pdb=" O GLY A 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR A 146 " --> pdb=" O ARG A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER A 192 " --> pdb=" O GLU A 188 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 208 No H-bonds generated for 'chain 'A' and resid 206 through 208' Processing helix chain 'C' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG C 142 " --> pdb=" O GLY C 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR C 146 " --> pdb=" O ARG C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER C 192 " --> pdb=" O GLU C 188 " (cutoff:3.500A) Processing helix chain 'C' and resid 206 through 208 No H-bonds generated for 'chain 'C' and resid 206 through 208' Processing helix chain 'D' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY D 138 " --> pdb=" O ARG D 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG D 142 " --> pdb=" O GLY D 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR D 146 " --> pdb=" O ARG D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER D 192 " --> pdb=" O GLU D 188 " (cutoff:3.500A) Processing helix chain 'D' and resid 206 through 208 No H-bonds generated for 'chain 'D' and resid 206 through 208' Processing helix chain 'F' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA F 135 " --> pdb=" O ASN F 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY F 138 " --> pdb=" O ARG F 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG F 142 " --> pdb=" O GLY F 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR F 146 " --> pdb=" O ARG F 142 " (cutoff:3.500A) Processing helix chain 'F' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER F 192 " --> pdb=" O GLU F 188 " (cutoff:3.500A) Processing helix chain 'F' and resid 206 through 208 No H-bonds generated for 'chain 'F' and resid 206 through 208' Processing helix chain 'G' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA G 135 " --> pdb=" O ASN G 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY G 138 " --> pdb=" O ARG G 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG G 142 " --> pdb=" O GLY G 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER G 192 " --> pdb=" O GLU G 188 " (cutoff:3.500A) Processing helix chain 'G' and resid 206 through 208 No H-bonds generated for 'chain 'G' and resid 206 through 208' Processing helix chain 'I' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA I 135 " --> pdb=" O ASN I 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY I 138 " --> pdb=" O ARG I 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG I 142 " --> pdb=" O GLY I 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR I 146 " --> pdb=" O ARG I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER I 192 " --> pdb=" O GLU I 188 " (cutoff:3.500A) Processing helix chain 'I' and resid 206 through 208 No H-bonds generated for 'chain 'I' and resid 206 through 208' Processing helix chain 'J' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA J 135 " --> pdb=" O ASN J 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY J 138 " --> pdb=" O ARG J 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG J 142 " --> pdb=" O GLY J 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR J 146 " --> pdb=" O ARG J 142 " (cutoff:3.500A) Processing helix chain 'J' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER J 192 " --> pdb=" O GLU J 188 " (cutoff:3.500A) Processing helix chain 'J' and resid 206 through 208 No H-bonds generated for 'chain 'J' and resid 206 through 208' Processing helix chain 'L' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA L 135 " --> pdb=" O ASN L 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY L 138 " --> pdb=" O ARG L 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG L 142 " --> pdb=" O GLY L 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR L 146 " --> pdb=" O ARG L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER L 192 " --> pdb=" O GLU L 188 " (cutoff:3.500A) Processing helix chain 'L' and resid 206 through 208 No H-bonds generated for 'chain 'L' and resid 206 through 208' Processing helix chain 'N' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA N 135 " --> pdb=" O ASN N 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY N 138 " --> pdb=" O ARG N 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG N 142 " --> pdb=" O GLY N 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR N 146 " --> pdb=" O ARG N 142 " (cutoff:3.500A) Processing helix chain 'N' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER N 192 " --> pdb=" O GLU N 188 " (cutoff:3.500A) Processing helix chain 'N' and resid 206 through 208 No H-bonds generated for 'chain 'N' and resid 206 through 208' Processing helix chain 'O' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA O 135 " --> pdb=" O ASN O 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY O 138 " --> pdb=" O ARG O 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG O 142 " --> pdb=" O GLY O 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR O 146 " --> pdb=" O ARG O 142 " (cutoff:3.500A) Processing helix chain 'O' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER O 192 " --> pdb=" O GLU O 188 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 208 No H-bonds generated for 'chain 'O' and resid 206 through 208' Processing helix chain 'Q' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA Q 135 " --> pdb=" O ASN Q 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY Q 138 " --> pdb=" O ARG Q 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Q 142 " --> pdb=" O GLY Q 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR Q 146 " --> pdb=" O ARG Q 142 " (cutoff:3.500A) Processing helix chain 'Q' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER Q 192 " --> pdb=" O GLU Q 188 " (cutoff:3.500A) Processing helix chain 'Q' and resid 206 through 208 No H-bonds generated for 'chain 'Q' and resid 206 through 208' Processing helix chain 'R' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA R 135 " --> pdb=" O ASN R 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY R 138 " --> pdb=" O ARG R 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG R 142 " --> pdb=" O GLY R 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR R 146 " --> pdb=" O ARG R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER R 192 " --> pdb=" O GLU R 188 " (cutoff:3.500A) Processing helix chain 'R' and resid 206 through 208 No H-bonds generated for 'chain 'R' and resid 206 through 208' Processing helix chain 'T' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA T 135 " --> pdb=" O ASN T 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY T 138 " --> pdb=" O ARG T 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG T 142 " --> pdb=" O GLY T 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR T 146 " --> pdb=" O ARG T 142 " (cutoff:3.500A) Processing helix chain 'T' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER T 192 " --> pdb=" O GLU T 188 " (cutoff:3.500A) Processing helix chain 'T' and resid 206 through 208 No H-bonds generated for 'chain 'T' and resid 206 through 208' Processing helix chain 'U' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA U 135 " --> pdb=" O ASN U 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY U 138 " --> pdb=" O ARG U 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG U 142 " --> pdb=" O GLY U 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR U 146 " --> pdb=" O ARG U 142 " (cutoff:3.500A) Processing helix chain 'U' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER U 192 " --> pdb=" O GLU U 188 " (cutoff:3.500A) Processing helix chain 'U' and resid 206 through 208 No H-bonds generated for 'chain 'U' and resid 206 through 208' Processing helix chain 'W' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA W 135 " --> pdb=" O ASN W 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY W 138 " --> pdb=" O ARG W 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG W 142 " --> pdb=" O GLY W 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR W 146 " --> pdb=" O ARG W 142 " (cutoff:3.500A) Processing helix chain 'W' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) Processing helix chain 'W' and resid 206 through 208 No H-bonds generated for 'chain 'W' and resid 206 through 208' Processing helix chain 'Y' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA Y 135 " --> pdb=" O ASN Y 131 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLY Y 138 " --> pdb=" O ARG Y 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Y 142 " --> pdb=" O GLY Y 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR Y 146 " --> pdb=" O ARG Y 142 " (cutoff:3.500A) Processing helix chain 'Y' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER Y 192 " --> pdb=" O GLU Y 188 " (cutoff:3.500A) Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Z' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA Z 135 " --> pdb=" O ASN Z 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY Z 138 " --> pdb=" O ARG Z 134 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ARG Z 142 " --> pdb=" O GLY Z 138 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N THR Z 146 " --> pdb=" O ARG Z 142 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER Z 192 " --> pdb=" O GLU Z 188 " (cutoff:3.500A) Processing helix chain 'Z' and resid 206 through 208 No H-bonds generated for 'chain 'Z' and resid 206 through 208' Processing helix chain 'b' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA b 135 " --> pdb=" O ASN b 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY b 138 " --> pdb=" O ARG b 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG b 142 " --> pdb=" O GLY b 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR b 146 " --> pdb=" O ARG b 142 " (cutoff:3.500A) Processing helix chain 'b' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER b 192 " --> pdb=" O GLU b 188 " (cutoff:3.500A) Processing helix chain 'b' and resid 206 through 208 No H-bonds generated for 'chain 'b' and resid 206 through 208' Processing helix chain 'c' and resid 128 through 146 removed outlier: 3.704A pdb=" N ALA c 135 " --> pdb=" O ASN c 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY c 138 " --> pdb=" O ARG c 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG c 142 " --> pdb=" O GLY c 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR c 146 " --> pdb=" O ARG c 142 " (cutoff:3.500A) Processing helix chain 'c' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER c 192 " --> pdb=" O GLU c 188 " (cutoff:3.500A) Processing helix chain 'c' and resid 206 through 208 No H-bonds generated for 'chain 'c' and resid 206 through 208' Processing helix chain 'e' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA e 135 " --> pdb=" O ASN e 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY e 138 " --> pdb=" O ARG e 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG e 142 " --> pdb=" O GLY e 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR e 146 " --> pdb=" O ARG e 142 " (cutoff:3.500A) Processing helix chain 'e' and resid 187 through 200 removed outlier: 3.969A pdb=" N SER e 192 " --> pdb=" O GLU e 188 " (cutoff:3.500A) Processing helix chain 'e' and resid 206 through 208 No H-bonds generated for 'chain 'e' and resid 206 through 208' Processing helix chain 'f' and resid 128 through 146 removed outlier: 3.703A pdb=" N ALA f 135 " --> pdb=" O ASN f 131 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY f 138 " --> pdb=" O ARG f 134 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG f 142 " --> pdb=" O GLY f 138 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N THR f 146 " --> pdb=" O ARG f 142 " (cutoff:3.500A) Processing helix chain 'f' and resid 187 through 200 removed outlier: 3.970A pdb=" N SER f 192 " --> pdb=" O GLU f 188 " (cutoff:3.500A) Processing helix chain 'f' and resid 206 through 208 No H-bonds generated for 'chain 'f' and resid 206 through 208' Processing sheet with id=AA1, first strand: chain 'A' and resid 152 through 158 Processing sheet with id=AA2, first strand: chain 'C' and resid 152 through 158 Processing sheet with id=AA3, first strand: chain 'D' and resid 152 through 158 Processing sheet with id=AA4, first strand: chain 'F' and resid 152 through 158 Processing sheet with id=AA5, first strand: chain 'G' and resid 152 through 158 Processing sheet with id=AA6, first strand: chain 'I' and resid 152 through 158 Processing sheet with id=AA7, first strand: chain 'J' and resid 152 through 158 Processing sheet with id=AA8, first strand: chain 'L' and resid 152 through 158 Processing sheet with id=AA9, first strand: chain 'N' and resid 152 through 158 Processing sheet with id=AB1, first strand: chain 'O' and resid 152 through 158 Processing sheet with id=AB2, first strand: chain 'Q' and resid 152 through 158 Processing sheet with id=AB3, first strand: chain 'R' and resid 152 through 158 Processing sheet with id=AB4, first strand: chain 'T' and resid 152 through 158 Processing sheet with id=AB5, first strand: chain 'U' and resid 152 through 158 Processing sheet with id=AB6, first strand: chain 'W' and resid 152 through 158 Processing sheet with id=AB7, first strand: chain 'Y' and resid 152 through 158 Processing sheet with id=AB8, first strand: chain 'Z' and resid 152 through 158 Processing sheet with id=AB9, first strand: chain 'b' and resid 152 through 158 Processing sheet with id=AC1, first strand: chain 'c' and resid 152 through 158 Processing sheet with id=AC2, first strand: chain 'e' and resid 152 through 158 Processing sheet with id=AC3, first strand: chain 'f' and resid 152 through 158 672 hydrogen bonds defined for protein. 1890 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: 3.68 Time building geometry restraints manager: 5.56 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: 4685 1.34 - 1.46: 1832 1.46 - 1.57: 7196 1.57 - 1.69: 0 1.69 - 1.80: 42 Bond restraints: 13755 Sorted by residual: bond pdb=" CA HIS Q 218 " pdb=" C HIS Q 218 " ideal model delta sigma weight residual 1.532 1.518 0.014 9.60e-03 1.09e+04 2.11e+00 bond pdb=" CA HIS C 218 " pdb=" C HIS C 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.05e+00 bond pdb=" CA HIS F 218 " pdb=" C HIS F 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 2.01e+00 bond pdb=" CA HIS b 218 " pdb=" C HIS b 218 " ideal model delta sigma weight residual 1.532 1.519 0.014 9.60e-03 1.09e+04 1.99e+00 bond pdb=" CA HIS W 218 " pdb=" C HIS W 218 " ideal model delta sigma weight residual 1.532 1.519 0.013 9.60e-03 1.09e+04 1.95e+00 ... (remaining 13750 not shown) Histogram of bond angle deviations from ideal: 100.74 - 106.86: 605 106.86 - 112.97: 7875 112.97 - 119.08: 3442 119.08 - 125.20: 6663 125.20 - 131.31: 168 Bond angle restraints: 18753 Sorted by residual: angle pdb=" N VAL F 198 " pdb=" CA VAL F 198 " pdb=" C VAL F 198 " ideal model delta sigma weight residual 112.12 108.68 3.44 8.40e-01 1.42e+00 1.68e+01 angle pdb=" N VAL U 198 " pdb=" CA VAL U 198 " pdb=" C VAL U 198 " ideal model delta sigma weight residual 112.12 108.69 3.43 8.40e-01 1.42e+00 1.67e+01 angle pdb=" N VAL W 198 " pdb=" CA VAL W 198 " pdb=" C VAL W 198 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.66e+01 angle pdb=" N VAL A 198 " pdb=" CA VAL A 198 " pdb=" C VAL A 198 " ideal model delta sigma weight residual 112.12 108.70 3.42 8.40e-01 1.42e+00 1.65e+01 angle pdb=" N VAL J 198 " pdb=" CA VAL J 198 " pdb=" C VAL J 198 " ideal model delta sigma weight residual 112.12 108.71 3.41 8.40e-01 1.42e+00 1.65e+01 ... (remaining 18748 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.35: 7082 13.35 - 26.71: 751 26.71 - 40.06: 399 40.06 - 53.42: 105 53.42 - 66.77: 63 Dihedral angle restraints: 8400 sinusoidal: 3171 harmonic: 5229 Sorted by residual: dihedral pdb=" CA GLU R 128 " pdb=" C GLU R 128 " pdb=" N GLN R 129 " pdb=" CA GLN R 129 " ideal model delta harmonic sigma weight residual 180.00 161.10 18.90 0 5.00e+00 4.00e-02 1.43e+01 dihedral pdb=" CA GLU A 128 " pdb=" C GLU A 128 " pdb=" N GLN A 129 " pdb=" CA GLN A 129 " ideal model delta harmonic sigma weight residual 180.00 161.13 18.87 0 5.00e+00 4.00e-02 1.42e+01 dihedral pdb=" CA GLU O 128 " pdb=" C GLU O 128 " pdb=" N GLN O 129 " pdb=" CA GLN O 129 " ideal model delta harmonic sigma weight residual 180.00 161.14 18.86 0 5.00e+00 4.00e-02 1.42e+01 ... (remaining 8397 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1230 0.032 - 0.064: 678 0.064 - 0.096: 297 0.096 - 0.128: 84 0.128 - 0.160: 42 Chirality restraints: 2331 Sorted by residual: chirality pdb=" CB THR U 179 " pdb=" CA THR U 179 " pdb=" OG1 THR U 179 " pdb=" CG2 THR U 179 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.38e-01 chirality pdb=" CB THR W 179 " pdb=" CA THR W 179 " pdb=" OG1 THR W 179 " pdb=" CG2 THR W 179 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CB THR e 179 " pdb=" CA THR e 179 " pdb=" OG1 THR e 179 " pdb=" CG2 THR e 179 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.35e-01 ... (remaining 2328 not shown) Planarity restraints: 2457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR I 179 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C THR I 179 " 0.022 2.00e-02 2.50e+03 pdb=" O THR I 179 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU I 180 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR c 179 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.69e+00 pdb=" C THR c 179 " 0.022 2.00e-02 2.50e+03 pdb=" O THR c 179 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU c 180 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 179 " -0.006 2.00e-02 2.50e+03 1.30e-02 1.68e+00 pdb=" C THR C 179 " 0.022 2.00e-02 2.50e+03 pdb=" O THR C 179 " -0.008 2.00e-02 2.50e+03 pdb=" N LEU C 180 " -0.008 2.00e-02 2.50e+03 ... (remaining 2454 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.86: 4697 2.86 - 3.37: 12576 3.37 - 3.88: 21040 3.88 - 4.39: 26350 4.39 - 4.90: 45117 Nonbonded interactions: 109780 Sorted by model distance: nonbonded pdb=" O THR U 146 " pdb=" OG1 THR U 146 " model vdw 2.355 2.440 nonbonded pdb=" O THR I 146 " pdb=" OG1 THR I 146 " model vdw 2.355 2.440 nonbonded pdb=" O THR W 146 " pdb=" OG1 THR W 146 " model vdw 2.355 2.440 nonbonded pdb=" O THR A 146 " pdb=" OG1 THR A 146 " model vdw 2.355 2.440 nonbonded pdb=" O THR R 146 " pdb=" OG1 THR R 146 " model vdw 2.355 2.440 ... (remaining 109775 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 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'I' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'O' selection = chain 'Q' selection = chain 'R' selection = chain 'T' selection = chain 'U' selection = chain 'W' selection = chain 'Y' selection = chain 'Z' selection = chain 'b' selection = chain 'c' selection = chain 'e' selection = chain 'f' } 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: 0.010 Normalize map: mean=0, sd=1: 3.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 16.280 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 37.040 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8250 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 13755 Z= 0.573 Angle : 0.880 5.207 18753 Z= 0.514 Chirality : 0.050 0.160 2331 Planarity : 0.003 0.014 2457 Dihedral : 16.062 66.772 4998 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 5.56 % Allowed : 4.17 % Favored : 90.28 % 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: -4.71 (0.17), residues: 1764 helix: -4.00 (0.13), residues: 693 sheet: -1.49 (0.22), residues: 504 loop : -3.06 (0.22), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 156 PHE 0.007 0.002 PHE Q 126 TYR 0.009 0.002 TYR W 132 ARG 0.002 0.000 ARG c 142 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 464 time to evaluate : 1.639 Fit side-chains REVERT: A 151 LYS cc_start: 0.8418 (ttmt) cc_final: 0.7934 (tttm) REVERT: A 184 ARG cc_start: 0.7820 (mtt-85) cc_final: 0.6763 (mtp85) REVERT: C 151 LYS cc_start: 0.8570 (ttmt) cc_final: 0.8088 (tttm) REVERT: D 151 LYS cc_start: 0.8525 (ttmt) cc_final: 0.7904 (tttm) REVERT: F 151 LYS cc_start: 0.8577 (ttmt) cc_final: 0.7990 (tttm) REVERT: G 151 LYS cc_start: 0.8749 (ttmt) cc_final: 0.8076 (tttm) REVERT: G 218 HIS cc_start: 0.7715 (m-70) cc_final: 0.7486 (m170) REVERT: I 151 LYS cc_start: 0.8596 (ttmt) cc_final: 0.8014 (tttm) REVERT: J 151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7900 (tttm) REVERT: L 139 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7165 (mm-30) REVERT: L 151 LYS cc_start: 0.8555 (ttmt) cc_final: 0.7835 (tttm) REVERT: N 151 LYS cc_start: 0.8563 (ttmt) cc_final: 0.7916 (tttm) REVERT: O 134 ARG cc_start: 0.7992 (mtp180) cc_final: 0.7716 (ttp-170) REVERT: O 139 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.7224 (mm-30) REVERT: O 151 LYS cc_start: 0.8645 (ttmt) cc_final: 0.7950 (tttm) REVERT: O 218 HIS cc_start: 0.7659 (m-70) cc_final: 0.7426 (m170) REVERT: Q 151 LYS cc_start: 0.8670 (ttmt) cc_final: 0.8066 (tttm) REVERT: R 151 LYS cc_start: 0.8547 (ttmt) cc_final: 0.7868 (tttm) REVERT: R 184 ARG cc_start: 0.7698 (mtt-85) cc_final: 0.6790 (mtp85) REVERT: R 218 HIS cc_start: 0.7724 (m-70) cc_final: 0.7504 (m170) REVERT: T 134 ARG cc_start: 0.7958 (mtp180) cc_final: 0.7707 (ttp-170) REVERT: T 151 LYS cc_start: 0.8519 (ttmt) cc_final: 0.7870 (tttm) REVERT: T 197 LEU cc_start: 0.8504 (tp) cc_final: 0.8262 (tt) REVERT: U 151 LYS cc_start: 0.8551 (ttmt) cc_final: 0.7809 (tttm) REVERT: W 151 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7895 (tttm) REVERT: Y 151 LYS cc_start: 0.8656 (ttmt) cc_final: 0.7978 (tttm) REVERT: Z 151 LYS cc_start: 0.8554 (ttmt) cc_final: 0.7851 (tttm) REVERT: Z 184 ARG cc_start: 0.7692 (mtt-85) cc_final: 0.6683 (mtp85) REVERT: b 151 LYS cc_start: 0.8571 (ttmt) cc_final: 0.7858 (tttm) REVERT: b 177 THR cc_start: 0.8315 (OUTLIER) cc_final: 0.8110 (m) REVERT: b 218 HIS cc_start: 0.7752 (m-70) cc_final: 0.7547 (m170) REVERT: c 151 LYS cc_start: 0.8538 (ttmt) cc_final: 0.7934 (tttm) REVERT: c 218 HIS cc_start: 0.7781 (m-70) cc_final: 0.7563 (m170) REVERT: e 151 LYS cc_start: 0.8604 (ttmt) cc_final: 0.8022 (tttm) REVERT: f 151 LYS cc_start: 0.8607 (ttmt) cc_final: 0.8072 (tttm) outliers start: 84 outliers final: 25 residues processed: 494 average time/residue: 0.3192 time to fit residues: 209.2048 Evaluate side-chains 397 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 369 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 GLU Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain C residue 139 GLU Chi-restraints excluded: chain D residue 139 GLU Chi-restraints excluded: chain D residue 177 THR Chi-restraints excluded: chain F residue 139 GLU Chi-restraints excluded: chain F residue 177 THR Chi-restraints excluded: chain G residue 139 GLU Chi-restraints excluded: chain I residue 139 GLU Chi-restraints excluded: chain I residue 177 THR Chi-restraints excluded: chain J residue 139 GLU Chi-restraints excluded: chain L residue 139 GLU Chi-restraints excluded: chain N residue 139 GLU Chi-restraints excluded: chain O residue 139 GLU Chi-restraints excluded: chain Q residue 139 GLU Chi-restraints excluded: chain Q residue 177 THR Chi-restraints excluded: chain R residue 139 GLU Chi-restraints excluded: chain T residue 139 GLU Chi-restraints excluded: chain U residue 139 GLU Chi-restraints excluded: chain W residue 139 GLU Chi-restraints excluded: chain Y residue 139 GLU Chi-restraints excluded: chain Z residue 139 GLU Chi-restraints excluded: chain b residue 139 GLU Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain c residue 139 GLU Chi-restraints excluded: chain e residue 139 GLU Chi-restraints excluded: chain f residue 139 GLU Chi-restraints excluded: chain f residue 177 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 141 optimal weight: 0.6980 chunk 127 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 85 optimal weight: 0.7980 chunk 68 optimal weight: 0.7980 chunk 131 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 chunk 98 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS C 196 HIS D 196 HIS F 196 HIS G 196 HIS I 196 HIS J 196 HIS L 196 HIS N 196 HIS O 196 HIS Q 196 HIS R 196 HIS T 196 HIS U 190 GLN U 196 HIS W 196 HIS Y 196 HIS Z 196 HIS b 196 HIS c 196 HIS e 196 HIS f 196 HIS Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13755 Z= 0.270 Angle : 0.635 9.280 18753 Z= 0.313 Chirality : 0.044 0.130 2331 Planarity : 0.004 0.026 2457 Dihedral : 5.627 32.718 1981 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 9.13 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.78 (0.19), residues: 1764 helix: -2.45 (0.16), residues: 714 sheet: 0.10 (0.27), residues: 462 loop : -2.42 (0.25), residues: 588 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 156 PHE 0.002 0.001 PHE c 126 TYR 0.011 0.001 TYR D 132 ARG 0.003 0.000 ARG N 154 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 387 time to evaluate : 1.544 Fit side-chains REVERT: A 151 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7900 (tttm) REVERT: A 184 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.6789 (mtp85) REVERT: A 192 SER cc_start: 0.8919 (m) cc_final: 0.8713 (t) REVERT: C 131 ASN cc_start: 0.7992 (t0) cc_final: 0.7717 (t0) REVERT: C 151 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7906 (tttm) REVERT: C 184 ARG cc_start: 0.7760 (mtt-85) cc_final: 0.6651 (mtp85) REVERT: D 151 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7760 (tttm) REVERT: F 151 LYS cc_start: 0.8500 (ttmt) cc_final: 0.7952 (tttm) REVERT: F 152 SER cc_start: 0.9078 (p) cc_final: 0.8857 (p) REVERT: F 222 GLN cc_start: 0.5923 (mm110) cc_final: 0.5664 (mm110) REVERT: G 151 LYS cc_start: 0.8472 (ttmt) cc_final: 0.7923 (tttm) REVERT: G 173 SER cc_start: 0.8295 (p) cc_final: 0.8029 (m) REVERT: I 151 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7884 (tttm) REVERT: I 173 SER cc_start: 0.8301 (p) cc_final: 0.8036 (m) REVERT: J 151 LYS cc_start: 0.8447 (ttmt) cc_final: 0.7932 (tttm) REVERT: L 131 ASN cc_start: 0.7862 (t0) cc_final: 0.7532 (t0) REVERT: L 151 LYS cc_start: 0.8410 (ttmt) cc_final: 0.7743 (tttm) REVERT: N 151 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7890 (tttm) REVERT: O 151 LYS cc_start: 0.8467 (ttmt) cc_final: 0.7838 (tttm) REVERT: Q 151 LYS cc_start: 0.8493 (ttmt) cc_final: 0.7840 (tttm) REVERT: R 151 LYS cc_start: 0.8428 (ttmt) cc_final: 0.7790 (tttm) REVERT: T 131 ASN cc_start: 0.7794 (t0) cc_final: 0.7436 (t0) REVERT: T 134 ARG cc_start: 0.7851 (mtp180) cc_final: 0.7607 (ttp-170) REVERT: T 151 LYS cc_start: 0.8464 (ttmt) cc_final: 0.7828 (tttm) REVERT: U 151 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7861 (tttm) REVERT: W 151 LYS cc_start: 0.8437 (ttmt) cc_final: 0.7896 (tttm) REVERT: Y 151 LYS cc_start: 0.8478 (ttmt) cc_final: 0.7893 (tttm) REVERT: Z 151 LYS cc_start: 0.8433 (ttmt) cc_final: 0.7799 (tttm) REVERT: Z 184 ARG cc_start: 0.7625 (mtt-85) cc_final: 0.6721 (mtp85) REVERT: b 151 LYS cc_start: 0.8492 (ttmt) cc_final: 0.7887 (tttm) REVERT: b 177 THR cc_start: 0.8262 (OUTLIER) cc_final: 0.8018 (m) REVERT: c 151 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7848 (tttm) REVERT: e 151 LYS cc_start: 0.8395 (ttmt) cc_final: 0.7879 (tttm) REVERT: e 216 SER cc_start: 0.8949 (m) cc_final: 0.8571 (p) REVERT: f 151 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7809 (tttm) REVERT: f 184 ARG cc_start: 0.7552 (mtt-85) cc_final: 0.6583 (mtp85) outliers start: 23 outliers final: 13 residues processed: 409 average time/residue: 0.3619 time to fit residues: 191.7175 Evaluate side-chains 336 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 322 time to evaluate : 1.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 VAL Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain F residue 130 VAL Chi-restraints excluded: chain G residue 130 VAL Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 130 VAL Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain T residue 192 SER Chi-restraints excluded: chain U residue 130 VAL Chi-restraints excluded: chain b residue 130 VAL Chi-restraints excluded: chain b residue 177 THR Chi-restraints excluded: chain c residue 130 VAL Chi-restraints excluded: chain e residue 130 VAL Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 84 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 126 optimal weight: 0.9980 chunk 103 optimal weight: 0.8980 chunk 42 optimal weight: 0.7980 chunk 152 optimal weight: 1.9990 chunk 165 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 151 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 122 optimal weight: 0.4980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 190 GLN O 218 HIS T 190 GLN U 190 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13755 Z= 0.256 Angle : 0.584 8.562 18753 Z= 0.282 Chirality : 0.043 0.120 2331 Planarity : 0.004 0.026 2457 Dihedral : 4.567 14.323 1912 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.58 % Allowed : 11.71 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.21), residues: 1764 helix: -1.94 (0.17), residues: 777 sheet: -0.06 (0.26), residues: 504 loop : -2.39 (0.30), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS T 196 PHE 0.003 0.001 PHE b 126 TYR 0.006 0.001 TYR f 132 ARG 0.007 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 385 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 346 time to evaluate : 1.694 Fit side-chains REVERT: A 151 LYS cc_start: 0.8374 (ttmt) cc_final: 0.7935 (tttm) REVERT: A 184 ARG cc_start: 0.7734 (mtt-85) cc_final: 0.6793 (mtp85) REVERT: A 222 GLN cc_start: 0.6207 (mm110) cc_final: 0.5809 (mm110) REVERT: C 131 ASN cc_start: 0.7848 (t0) cc_final: 0.7605 (t0) REVERT: C 151 LYS cc_start: 0.8392 (ttmt) cc_final: 0.7968 (tttm) REVERT: C 154 ARG cc_start: 0.8137 (mtp85) cc_final: 0.7867 (mtp85) REVERT: C 184 ARG cc_start: 0.7752 (mtt-85) cc_final: 0.6697 (mtp85) REVERT: D 131 ASN cc_start: 0.7914 (t0) cc_final: 0.7613 (t0) REVERT: D 151 LYS cc_start: 0.8122 (ttmt) cc_final: 0.7638 (tttm) REVERT: D 152 SER cc_start: 0.9114 (p) cc_final: 0.8878 (p) REVERT: F 151 LYS cc_start: 0.8408 (ttmt) cc_final: 0.7877 (tttm) REVERT: F 222 GLN cc_start: 0.6057 (mm110) cc_final: 0.5834 (mm110) REVERT: G 151 LYS cc_start: 0.8399 (ttmt) cc_final: 0.7853 (tttm) REVERT: G 154 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7985 (mtp85) REVERT: G 173 SER cc_start: 0.8236 (p) cc_final: 0.8029 (m) REVERT: I 151 LYS cc_start: 0.8400 (ttmt) cc_final: 0.7880 (tttm) REVERT: I 173 SER cc_start: 0.8250 (p) cc_final: 0.8025 (m) REVERT: J 151 LYS cc_start: 0.8393 (ttmt) cc_final: 0.7903 (tttm) REVERT: L 131 ASN cc_start: 0.7855 (t0) cc_final: 0.7558 (t0) REVERT: L 151 LYS cc_start: 0.8383 (ttmt) cc_final: 0.7811 (tttm) REVERT: N 151 LYS cc_start: 0.8267 (ttmt) cc_final: 0.7787 (tttm) REVERT: O 151 LYS cc_start: 0.8424 (ttmt) cc_final: 0.7850 (tttm) REVERT: Q 151 LYS cc_start: 0.8417 (ttmt) cc_final: 0.7770 (tttm) REVERT: Q 184 ARG cc_start: 0.7570 (mtt90) cc_final: 0.6598 (mtp85) REVERT: R 151 LYS cc_start: 0.8412 (ttmt) cc_final: 0.7800 (tttm) REVERT: T 131 ASN cc_start: 0.7759 (t0) cc_final: 0.7516 (t0) REVERT: T 134 ARG cc_start: 0.7800 (mtp180) cc_final: 0.7585 (ttp-170) REVERT: T 151 LYS cc_start: 0.8398 (ttmt) cc_final: 0.7872 (tttm) REVERT: U 151 LYS cc_start: 0.8309 (ttmt) cc_final: 0.7754 (tttm) REVERT: U 154 ARG cc_start: 0.8336 (mtp-110) cc_final: 0.8058 (mtp85) REVERT: W 151 LYS cc_start: 0.8286 (ttmt) cc_final: 0.7710 (tttm) REVERT: Y 151 LYS cc_start: 0.8445 (ttmt) cc_final: 0.7860 (tttm) REVERT: Z 151 LYS cc_start: 0.8370 (ttmt) cc_final: 0.7764 (tttm) REVERT: Z 184 ARG cc_start: 0.7621 (mtt-85) cc_final: 0.6728 (mtp85) REVERT: b 151 LYS cc_start: 0.8422 (ttmt) cc_final: 0.7803 (tttm) REVERT: c 151 LYS cc_start: 0.8318 (ttmt) cc_final: 0.7806 (tttm) REVERT: e 151 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7764 (tttm) REVERT: e 216 SER cc_start: 0.8932 (m) cc_final: 0.8627 (p) REVERT: f 151 LYS cc_start: 0.8315 (ttmt) cc_final: 0.7800 (tttm) REVERT: f 184 ARG cc_start: 0.7634 (mtt-85) cc_final: 0.6736 (mtp85) outliers start: 39 outliers final: 23 residues processed: 368 average time/residue: 0.3953 time to fit residues: 185.9911 Evaluate side-chains 345 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 322 time to evaluate : 1.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 151 optimal weight: 0.6980 chunk 114 optimal weight: 0.9990 chunk 79 optimal weight: 0.0010 chunk 16 optimal weight: 0.9980 chunk 72 optimal weight: 3.9990 chunk 102 optimal weight: 0.7980 chunk 153 optimal weight: 1.9990 chunk 162 optimal weight: 0.8980 chunk 80 optimal weight: 0.0770 chunk 145 optimal weight: 1.9990 chunk 43 optimal weight: 0.9990 overall best weight: 0.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 190 GLN U 190 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13755 Z= 0.201 Angle : 0.533 7.556 18753 Z= 0.256 Chirality : 0.042 0.114 2331 Planarity : 0.003 0.027 2457 Dihedral : 4.326 13.299 1911 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 1.85 % Allowed : 12.04 % Favored : 86.11 % 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: -1.43 (0.22), residues: 1764 helix: -1.18 (0.18), residues: 714 sheet: 0.25 (0.25), residues: 504 loop : -1.51 (0.34), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS Z 156 PHE 0.002 0.001 PHE T 126 TYR 0.013 0.001 TYR F 132 ARG 0.004 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 328 time to evaluate : 1.675 Fit side-chains REVERT: A 151 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7697 (tttm) REVERT: C 151 LYS cc_start: 0.8352 (ttmt) cc_final: 0.7912 (tttm) REVERT: C 184 ARG cc_start: 0.7736 (mtt-85) cc_final: 0.6681 (mtp85) REVERT: D 151 LYS cc_start: 0.8091 (ttmt) cc_final: 0.7693 (tttm) REVERT: D 152 SER cc_start: 0.9104 (p) cc_final: 0.8837 (p) REVERT: F 151 LYS cc_start: 0.8324 (ttmt) cc_final: 0.7843 (tttm) REVERT: G 151 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7795 (tttm) REVERT: I 151 LYS cc_start: 0.8268 (ttmt) cc_final: 0.7829 (tttm) REVERT: J 151 LYS cc_start: 0.8357 (ttmt) cc_final: 0.7938 (tttm) REVERT: L 131 ASN cc_start: 0.7542 (t0) cc_final: 0.7285 (t0) REVERT: L 151 LYS cc_start: 0.8305 (ttmt) cc_final: 0.7743 (tttm) REVERT: N 151 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7704 (tttm) REVERT: O 151 LYS cc_start: 0.8364 (ttmt) cc_final: 0.7795 (tttm) REVERT: Q 151 LYS cc_start: 0.8355 (ttmt) cc_final: 0.7720 (tttm) REVERT: R 151 LYS cc_start: 0.8278 (ttmt) cc_final: 0.7683 (tttm) REVERT: T 131 ASN cc_start: 0.7711 (t0) cc_final: 0.7437 (t0) REVERT: T 134 ARG cc_start: 0.7780 (mtp180) cc_final: 0.7562 (ttp-170) REVERT: T 151 LYS cc_start: 0.8244 (ttmt) cc_final: 0.7714 (tttm) REVERT: U 151 LYS cc_start: 0.8245 (ttmt) cc_final: 0.7738 (tttm) REVERT: W 151 LYS cc_start: 0.8158 (ttmt) cc_final: 0.7761 (tttm) REVERT: Y 151 LYS cc_start: 0.8385 (ttmt) cc_final: 0.7805 (tttm) REVERT: Z 151 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7651 (tttm) REVERT: b 151 LYS cc_start: 0.8414 (ttmt) cc_final: 0.7800 (tttm) REVERT: c 151 LYS cc_start: 0.8251 (ttmt) cc_final: 0.7826 (tttm) REVERT: e 151 LYS cc_start: 0.8163 (ttmt) cc_final: 0.7778 (tttm) REVERT: e 216 SER cc_start: 0.8928 (m) cc_final: 0.8700 (p) REVERT: f 151 LYS cc_start: 0.8246 (ttmt) cc_final: 0.7712 (tttm) REVERT: f 184 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.6752 (mtp85) outliers start: 28 outliers final: 25 residues processed: 339 average time/residue: 0.4233 time to fit residues: 182.7354 Evaluate side-chains 335 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 310 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 135 optimal weight: 2.9990 chunk 92 optimal weight: 2.9990 chunk 2 optimal weight: 0.0060 chunk 120 optimal weight: 0.9990 chunk 67 optimal weight: 0.0040 chunk 138 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 82 optimal weight: 0.9980 chunk 145 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.5808 ------------------------------------------------------------------------------- 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: 0.8138 moved from start: 0.3223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 13755 Z= 0.214 Angle : 0.525 7.001 18753 Z= 0.251 Chirality : 0.041 0.117 2331 Planarity : 0.003 0.024 2457 Dihedral : 4.199 12.911 1911 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.98 % Allowed : 12.96 % Favored : 85.05 % 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: -0.92 (0.22), residues: 1764 helix: -0.69 (0.18), residues: 714 sheet: 0.44 (0.25), residues: 504 loop : -1.28 (0.35), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS I 156 PHE 0.003 0.001 PHE c 126 TYR 0.012 0.001 TYR F 132 ARG 0.007 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 308 time to evaluate : 1.830 Fit side-chains REVERT: A 151 LYS cc_start: 0.8167 (ttmt) cc_final: 0.7711 (tttm) REVERT: C 151 LYS cc_start: 0.8371 (ttmt) cc_final: 0.7909 (tttm) REVERT: D 151 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7763 (tttm) REVERT: F 151 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7823 (tttm) REVERT: G 151 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7876 (tttm) REVERT: I 151 LYS cc_start: 0.8201 (ttmt) cc_final: 0.7752 (tttm) REVERT: J 151 LYS cc_start: 0.8386 (ttmt) cc_final: 0.7957 (tttm) REVERT: L 131 ASN cc_start: 0.7492 (t0) cc_final: 0.7237 (t0) REVERT: L 151 LYS cc_start: 0.8308 (ttmt) cc_final: 0.7840 (tttm) REVERT: N 151 LYS cc_start: 0.8115 (ttmt) cc_final: 0.7665 (tttm) REVERT: O 151 LYS cc_start: 0.8341 (ttmt) cc_final: 0.7759 (tttm) REVERT: Q 151 LYS cc_start: 0.8347 (ttmt) cc_final: 0.7832 (tttm) REVERT: Q 184 ARG cc_start: 0.7353 (mtt90) cc_final: 0.6603 (mtp85) REVERT: R 151 LYS cc_start: 0.8284 (ttmt) cc_final: 0.7757 (tttm) REVERT: T 131 ASN cc_start: 0.7718 (t0) cc_final: 0.7507 (t0) REVERT: T 134 ARG cc_start: 0.7794 (mtp180) cc_final: 0.7592 (ttp-170) REVERT: T 151 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7748 (tttm) REVERT: U 151 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7752 (tttm) REVERT: W 151 LYS cc_start: 0.8161 (ttmt) cc_final: 0.7723 (tttm) REVERT: Y 151 LYS cc_start: 0.8316 (ttmt) cc_final: 0.7723 (tttm) REVERT: Z 151 LYS cc_start: 0.8177 (ttmt) cc_final: 0.7650 (tttm) REVERT: b 151 LYS cc_start: 0.8346 (ttmt) cc_final: 0.7798 (tttm) REVERT: c 151 LYS cc_start: 0.8232 (ttmt) cc_final: 0.7813 (tttm) REVERT: e 151 LYS cc_start: 0.8170 (ttmt) cc_final: 0.7770 (tttm) REVERT: e 216 SER cc_start: 0.8925 (m) cc_final: 0.8705 (p) REVERT: f 134 ARG cc_start: 0.7969 (ttp80) cc_final: 0.7757 (ttp-170) REVERT: f 151 LYS cc_start: 0.8280 (ttmt) cc_final: 0.7722 (tttm) outliers start: 30 outliers final: 29 residues processed: 318 average time/residue: 0.4350 time to fit residues: 174.8955 Evaluate side-chains 330 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 301 time to evaluate : 1.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain G residue 180 LEU Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 173 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 173 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 218 HIS Chi-restraints excluded: chain O residue 173 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain W residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 180 LEU Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 54 optimal weight: 0.5980 chunk 146 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 162 optimal weight: 0.0570 chunk 134 optimal weight: 0.0770 chunk 75 optimal weight: 2.9990 chunk 13 optimal weight: 0.1980 chunk 53 optimal weight: 0.6980 chunk 85 optimal weight: 0.0570 overall best weight: 0.0952 ------------------------------------------------------------------------------- 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: 0.8040 moved from start: 0.3695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 13755 Z= 0.141 Angle : 0.477 6.504 18753 Z= 0.228 Chirality : 0.040 0.129 2331 Planarity : 0.003 0.019 2457 Dihedral : 3.877 12.395 1911 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 0.73 % Allowed : 14.48 % Favored : 84.79 % 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: 0.39 (0.22), residues: 1764 helix: 0.77 (0.18), residues: 693 sheet: 0.69 (0.24), residues: 504 loop : -0.63 (0.34), residues: 567 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 156 PHE 0.000 0.000 PHE L 126 TYR 0.012 0.000 TYR F 132 ARG 0.007 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 316 time to evaluate : 1.555 Fit side-chains REVERT: A 151 LYS cc_start: 0.8041 (ttmt) cc_final: 0.7609 (tttm) REVERT: C 151 LYS cc_start: 0.8133 (ttmt) cc_final: 0.7669 (tttm) REVERT: D 151 LYS cc_start: 0.8074 (ttmt) cc_final: 0.7666 (tttm) REVERT: F 151 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7747 (tttm) REVERT: G 151 LYS cc_start: 0.8138 (ttmt) cc_final: 0.7716 (tttm) REVERT: I 151 LYS cc_start: 0.7852 (ttmt) cc_final: 0.7461 (tttm) REVERT: J 151 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7668 (tttm) REVERT: L 151 LYS cc_start: 0.8039 (ttmt) cc_final: 0.7606 (tttm) REVERT: L 188 GLU cc_start: 0.7058 (mt-10) cc_final: 0.6799 (mt-10) REVERT: N 151 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7572 (tttm) REVERT: O 151 LYS cc_start: 0.8043 (ttmt) cc_final: 0.7618 (tttm) REVERT: Q 151 LYS cc_start: 0.8127 (ttmt) cc_final: 0.7707 (tttm) REVERT: Q 184 ARG cc_start: 0.7186 (mtt90) cc_final: 0.6521 (mtp85) REVERT: R 151 LYS cc_start: 0.8055 (ttmt) cc_final: 0.7648 (tttm) REVERT: T 151 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7534 (tttm) REVERT: U 151 LYS cc_start: 0.8059 (ttmt) cc_final: 0.7519 (tttm) REVERT: W 151 LYS cc_start: 0.7936 (ttmt) cc_final: 0.7539 (tttm) REVERT: Y 151 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7618 (tttm) REVERT: Z 151 LYS cc_start: 0.7962 (ttmt) cc_final: 0.7581 (tttm) REVERT: b 151 LYS cc_start: 0.8112 (ttmt) cc_final: 0.7603 (tttm) REVERT: c 151 LYS cc_start: 0.8065 (ttmt) cc_final: 0.7661 (tttm) REVERT: e 151 LYS cc_start: 0.7888 (ttmt) cc_final: 0.7600 (tttm) REVERT: f 151 LYS cc_start: 0.8193 (ttmt) cc_final: 0.7649 (tttm) outliers start: 11 outliers final: 6 residues processed: 318 average time/residue: 0.4379 time to fit residues: 175.5390 Evaluate side-chains 309 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 303 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 156 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 92 optimal weight: 2.9990 chunk 118 optimal weight: 0.8980 chunk 91 optimal weight: 0.5980 chunk 136 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 161 optimal weight: 0.9980 chunk 101 optimal weight: 0.0980 chunk 98 optimal weight: 3.9990 chunk 74 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.8120 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13755 Z= 0.215 Angle : 0.503 6.493 18753 Z= 0.239 Chirality : 0.041 0.118 2331 Planarity : 0.003 0.018 2457 Dihedral : 3.958 12.133 1911 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 1.65 % Allowed : 13.69 % Favored : 84.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.22), residues: 1764 helix: 0.69 (0.18), residues: 735 sheet: 0.74 (0.24), residues: 504 loop : -1.07 (0.34), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 196 PHE 0.003 0.001 PHE Z 126 TYR 0.014 0.001 TYR F 132 ARG 0.005 0.000 ARG F 154 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 292 time to evaluate : 1.712 Fit side-chains REVERT: A 151 LYS cc_start: 0.8152 (ttmt) cc_final: 0.7696 (tttm) REVERT: C 151 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7839 (tttm) REVERT: D 151 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7749 (tttm) REVERT: F 151 LYS cc_start: 0.8272 (ttmt) cc_final: 0.7769 (tttm) REVERT: G 151 LYS cc_start: 0.8298 (ttmt) cc_final: 0.7825 (tttm) REVERT: I 151 LYS cc_start: 0.8085 (ttmt) cc_final: 0.7675 (tttm) REVERT: J 151 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7850 (tttm) REVERT: L 151 LYS cc_start: 0.8120 (ttmt) cc_final: 0.7658 (tttm) REVERT: L 188 GLU cc_start: 0.7116 (mt-10) cc_final: 0.6843 (mt-10) REVERT: N 151 LYS cc_start: 0.8023 (ttmt) cc_final: 0.7576 (tttm) REVERT: O 151 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7771 (tttm) REVERT: Q 151 LYS cc_start: 0.8292 (ttmt) cc_final: 0.7837 (tttm) REVERT: Q 184 ARG cc_start: 0.7255 (mtt90) cc_final: 0.6534 (mtp85) REVERT: R 151 LYS cc_start: 0.8147 (ttmt) cc_final: 0.7618 (tttm) REVERT: T 151 LYS cc_start: 0.8099 (ttmt) cc_final: 0.7715 (tttm) REVERT: U 151 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7585 (tttm) REVERT: W 151 LYS cc_start: 0.8095 (ttmt) cc_final: 0.7641 (tttm) REVERT: W 154 ARG cc_start: 0.8317 (mtp85) cc_final: 0.8104 (mtp85) REVERT: Y 151 LYS cc_start: 0.8293 (ttmt) cc_final: 0.7740 (tttm) REVERT: Z 151 LYS cc_start: 0.8060 (ttmt) cc_final: 0.7617 (tttm) REVERT: b 151 LYS cc_start: 0.8208 (ttmt) cc_final: 0.7702 (tttm) REVERT: c 151 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7744 (tttm) REVERT: e 151 LYS cc_start: 0.8068 (ttmt) cc_final: 0.7666 (tttm) REVERT: f 151 LYS cc_start: 0.8317 (ttmt) cc_final: 0.7725 (tttm) outliers start: 25 outliers final: 20 residues processed: 302 average time/residue: 0.5258 time to fit residues: 202.8890 Evaluate side-chains 312 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 292 time to evaluate : 1.603 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain I residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 100 optimal weight: 3.9990 chunk 64 optimal weight: 0.4980 chunk 96 optimal weight: 0.2980 chunk 48 optimal weight: 0.0570 chunk 31 optimal weight: 2.9990 chunk 102 optimal weight: 0.6980 chunk 110 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 127 optimal weight: 2.9990 chunk 147 optimal weight: 2.9990 overall best weight: 0.4498 ------------------------------------------------------------------------------- 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: 0.8102 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13755 Z= 0.186 Angle : 0.490 6.412 18753 Z= 0.233 Chirality : 0.041 0.112 2331 Planarity : 0.002 0.017 2457 Dihedral : 3.923 12.347 1911 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.19 % Allowed : 14.02 % Favored : 84.79 % 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: 0.82 (0.22), residues: 1764 helix: 1.25 (0.18), residues: 714 sheet: 0.79 (0.24), residues: 504 loop : -0.55 (0.35), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 196 PHE 0.002 0.001 PHE I 126 TYR 0.014 0.001 TYR F 132 ARG 0.005 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 292 time to evaluate : 1.547 Fit side-chains REVERT: A 151 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7669 (tttm) REVERT: C 151 LYS cc_start: 0.8222 (ttmt) cc_final: 0.7749 (tttm) REVERT: D 151 LYS cc_start: 0.8114 (ttmt) cc_final: 0.7744 (tttm) REVERT: F 151 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7763 (tttm) REVERT: G 151 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7812 (tttm) REVERT: I 151 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7634 (tttm) REVERT: J 151 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7834 (tttm) REVERT: L 151 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7618 (tttm) REVERT: L 188 GLU cc_start: 0.7091 (mt-10) cc_final: 0.6822 (mt-10) REVERT: N 151 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7573 (tttm) REVERT: O 151 LYS cc_start: 0.8214 (ttmt) cc_final: 0.7731 (tttm) REVERT: Q 151 LYS cc_start: 0.8204 (ttmt) cc_final: 0.7742 (tttm) REVERT: Q 184 ARG cc_start: 0.7247 (mtt90) cc_final: 0.6512 (mtp85) REVERT: R 151 LYS cc_start: 0.8164 (ttmt) cc_final: 0.7735 (tttm) REVERT: T 151 LYS cc_start: 0.8094 (ttmt) cc_final: 0.7603 (tttm) REVERT: U 151 LYS cc_start: 0.8162 (ttmt) cc_final: 0.7595 (tttm) REVERT: W 151 LYS cc_start: 0.8070 (ttmt) cc_final: 0.7596 (tttm) REVERT: Y 151 LYS cc_start: 0.8255 (ttmt) cc_final: 0.7688 (tttm) REVERT: Z 151 LYS cc_start: 0.8057 (ttmt) cc_final: 0.7611 (tttm) REVERT: b 151 LYS cc_start: 0.8220 (ttmt) cc_final: 0.7705 (tttm) REVERT: b 184 ARG cc_start: 0.7482 (mtt-85) cc_final: 0.6690 (mtp85) REVERT: c 151 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7714 (tttm) REVERT: e 151 LYS cc_start: 0.8040 (ttmt) cc_final: 0.7679 (tttm) REVERT: f 151 LYS cc_start: 0.8296 (ttmt) cc_final: 0.7707 (tttm) outliers start: 18 outliers final: 15 residues processed: 300 average time/residue: 0.4494 time to fit residues: 168.5747 Evaluate side-chains 305 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 290 time to evaluate : 1.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain T residue 173 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 155 optimal weight: 0.5980 chunk 141 optimal weight: 0.9980 chunk 150 optimal weight: 0.5980 chunk 90 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 136 optimal weight: 0.8980 chunk 142 optimal weight: 0.8980 chunk 99 optimal weight: 2.9990 chunk 159 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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: 0.8124 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 13755 Z= 0.221 Angle : 0.503 6.449 18753 Z= 0.240 Chirality : 0.041 0.133 2331 Planarity : 0.003 0.017 2457 Dihedral : 3.990 12.504 1911 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.52 % Allowed : 13.36 % Favored : 85.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.22), residues: 1764 helix: 1.02 (0.18), residues: 735 sheet: 0.86 (0.24), residues: 504 loop : -1.00 (0.34), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS J 196 PHE 0.003 0.001 PHE Y 126 TYR 0.013 0.001 TYR F 132 ARG 0.004 0.000 ARG Q 184 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 288 time to evaluate : 1.654 Fit side-chains REVERT: A 151 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7720 (tttm) REVERT: C 151 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7847 (tttm) REVERT: D 151 LYS cc_start: 0.8179 (ttmt) cc_final: 0.7778 (tttm) REVERT: F 151 LYS cc_start: 0.8300 (ttmt) cc_final: 0.7786 (tttm) REVERT: G 151 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7856 (tttm) REVERT: I 151 LYS cc_start: 0.8190 (ttmt) cc_final: 0.7728 (tttm) REVERT: J 151 LYS cc_start: 0.8304 (ttmt) cc_final: 0.7865 (tttm) REVERT: L 131 ASN cc_start: 0.7545 (t0) cc_final: 0.7326 (t0) REVERT: L 151 LYS cc_start: 0.8206 (ttmt) cc_final: 0.7725 (tttm) REVERT: L 188 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6844 (mt-10) REVERT: N 151 LYS cc_start: 0.8082 (ttmt) cc_final: 0.7619 (tttm) REVERT: O 151 LYS cc_start: 0.8311 (ttmt) cc_final: 0.7808 (tttm) REVERT: Q 151 LYS cc_start: 0.8354 (ttmt) cc_final: 0.7829 (tttm) REVERT: R 151 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7713 (tttm) REVERT: T 151 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7676 (tttm) REVERT: U 151 LYS cc_start: 0.8242 (ttmt) cc_final: 0.7666 (tttm) REVERT: W 151 LYS cc_start: 0.8129 (ttmt) cc_final: 0.7618 (tttm) REVERT: Y 151 LYS cc_start: 0.8271 (ttmt) cc_final: 0.7724 (tttm) REVERT: Z 151 LYS cc_start: 0.8100 (ttmt) cc_final: 0.7651 (tttm) REVERT: b 151 LYS cc_start: 0.8250 (ttmt) cc_final: 0.7721 (tttm) REVERT: b 184 ARG cc_start: 0.7449 (mtt-85) cc_final: 0.6634 (mtp85) REVERT: c 151 LYS cc_start: 0.8253 (ttmt) cc_final: 0.7833 (tttm) REVERT: e 151 LYS cc_start: 0.8165 (ttmt) cc_final: 0.7732 (tttm) REVERT: e 188 GLU cc_start: 0.7430 (mt-10) cc_final: 0.7202 (mt-10) REVERT: f 151 LYS cc_start: 0.8344 (ttmt) cc_final: 0.7740 (tttm) outliers start: 23 outliers final: 22 residues processed: 298 average time/residue: 0.4503 time to fit residues: 167.9684 Evaluate side-chains 309 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 287 time to evaluate : 1.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain F residue 175 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 175 SER Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain O residue 175 SER Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain T residue 173 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 173 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 97 optimal weight: 0.7980 chunk 75 optimal weight: 1.9990 chunk 110 optimal weight: 0.8980 chunk 167 optimal weight: 0.5980 chunk 154 optimal weight: 0.5980 chunk 133 optimal weight: 0.2980 chunk 13 optimal weight: 0.2980 chunk 102 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 105 optimal weight: 0.6980 chunk 141 optimal weight: 0.4980 overall best weight: 0.4580 ------------------------------------------------------------------------------- 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: 0.8105 moved from start: 0.3689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13755 Z= 0.190 Angle : 0.492 6.411 18753 Z= 0.234 Chirality : 0.041 0.123 2331 Planarity : 0.002 0.017 2457 Dihedral : 3.928 12.633 1911 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.52 % Allowed : 13.49 % Favored : 84.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.01 (0.22), residues: 1764 helix: 1.44 (0.18), residues: 714 sheet: 0.91 (0.24), residues: 504 loop : -0.51 (0.35), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS T 196 PHE 0.002 0.001 PHE I 126 TYR 0.016 0.001 TYR F 132 ARG 0.004 0.000 ARG Q 184 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3528 Ramachandran restraints generated. 1764 Oldfield, 0 Emsley, 1764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 294 time to evaluate : 1.598 Fit side-chains REVERT: A 151 LYS cc_start: 0.8186 (ttmt) cc_final: 0.7670 (tttm) REVERT: C 151 LYS cc_start: 0.8265 (ttmt) cc_final: 0.7768 (tttm) REVERT: D 151 LYS cc_start: 0.8189 (ttmt) cc_final: 0.7758 (tttm) REVERT: F 151 LYS cc_start: 0.8290 (ttmt) cc_final: 0.7779 (tttm) REVERT: G 151 LYS cc_start: 0.8221 (ttmt) cc_final: 0.7790 (tttm) REVERT: I 151 LYS cc_start: 0.8117 (ttmt) cc_final: 0.7666 (tttm) REVERT: J 151 LYS cc_start: 0.8283 (ttmt) cc_final: 0.7855 (tttm) REVERT: L 151 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7665 (tttm) REVERT: N 151 LYS cc_start: 0.8004 (ttmt) cc_final: 0.7548 (tttm) REVERT: O 151 LYS cc_start: 0.8274 (ttmt) cc_final: 0.7770 (tttm) REVERT: Q 151 LYS cc_start: 0.8264 (ttmt) cc_final: 0.7789 (tttm) REVERT: R 151 LYS cc_start: 0.8241 (ttmt) cc_final: 0.7692 (tttm) REVERT: T 151 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7661 (tttm) REVERT: U 151 LYS cc_start: 0.8218 (ttmt) cc_final: 0.7643 (tttm) REVERT: W 151 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7622 (tttm) REVERT: Y 151 LYS cc_start: 0.8266 (ttmt) cc_final: 0.7696 (tttm) REVERT: Z 151 LYS cc_start: 0.8089 (ttmt) cc_final: 0.7630 (tttm) REVERT: b 151 LYS cc_start: 0.8237 (ttmt) cc_final: 0.7718 (tttm) REVERT: b 184 ARG cc_start: 0.7466 (mtt-85) cc_final: 0.6672 (mtp85) REVERT: c 151 LYS cc_start: 0.8185 (ttmt) cc_final: 0.7748 (tttm) REVERT: e 151 LYS cc_start: 0.8146 (ttmt) cc_final: 0.7778 (tttm) REVERT: e 188 GLU cc_start: 0.7442 (mt-10) cc_final: 0.7212 (mt-10) REVERT: f 151 LYS cc_start: 0.8334 (ttmt) cc_final: 0.7730 (tttm) outliers start: 23 outliers final: 23 residues processed: 301 average time/residue: 0.4377 time to fit residues: 164.9845 Evaluate side-chains 315 residues out of total 1512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 292 time to evaluate : 1.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 173 SER Chi-restraints excluded: chain A residue 175 SER Chi-restraints excluded: chain C residue 179 THR Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain F residue 173 SER Chi-restraints excluded: chain G residue 175 SER Chi-restraints excluded: chain J residue 175 SER Chi-restraints excluded: chain L residue 175 SER Chi-restraints excluded: chain N residue 222 GLN Chi-restraints excluded: chain Q residue 175 SER Chi-restraints excluded: chain R residue 159 MET Chi-restraints excluded: chain R residue 175 SER Chi-restraints excluded: chain T residue 173 SER Chi-restraints excluded: chain U residue 173 SER Chi-restraints excluded: chain W residue 175 SER Chi-restraints excluded: chain Y residue 175 SER Chi-restraints excluded: chain Z residue 175 SER Chi-restraints excluded: chain b residue 175 SER Chi-restraints excluded: chain c residue 173 SER Chi-restraints excluded: chain c residue 175 SER Chi-restraints excluded: chain e residue 175 SER Chi-restraints excluded: chain f residue 175 SER Chi-restraints excluded: chain f residue 179 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 168 random chunks: chunk 40 optimal weight: 1.9990 chunk 122 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 37 optimal weight: 0.6980 chunk 133 optimal weight: 0.5980 chunk 55 optimal weight: 0.0980 chunk 137 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 117 optimal weight: 0.0070 chunk 7 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.138984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.113376 restraints weight = 15602.485| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.36 r_work: 0.3094 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.3729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13755 Z= 0.191 Angle : 0.491 6.449 18753 Z= 0.234 Chirality : 0.041 0.120 2331 Planarity : 0.002 0.019 2457 Dihedral : 3.908 12.450 1911 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 9.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.92 % Allowed : 13.16 % Favored : 84.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.22), residues: 1764 helix: 1.55 (0.18), residues: 714 sheet: 0.96 (0.24), residues: 504 loop : -0.52 (0.34), residues: 546 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS C 196 PHE 0.002 0.001 PHE I 126 TYR 0.015 0.001 TYR F 132 ARG 0.004 0.000 ARG Q 184 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3935.65 seconds wall clock time: 71 minutes 31.00 seconds (4291.00 seconds total)