Starting phenix.real_space_refine on Thu Feb 22 11:06:52 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5l_26354/02_2024/7u5l_26354.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5l_26354/02_2024/7u5l_26354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.67 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5l_26354/02_2024/7u5l_26354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5l_26354/02_2024/7u5l_26354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5l_26354/02_2024/7u5l_26354.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7u5l_26354/02_2024/7u5l_26354.pdb" } resolution = 2.67 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= 0.133 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: 5 Type Number sf(0) Gaussians Fe 24 7.16 5 S 192 5.16 5 C 21288 2.51 5 N 6048 2.21 5 O 6552 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 28": "OE1" <-> "OE2" Residue "B GLU 28": "OE1" <-> "OE2" Residue "C GLU 28": "OE1" <-> "OE2" Residue "D GLU 28": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "F GLU 28": "OE1" <-> "OE2" Residue "G GLU 28": "OE1" <-> "OE2" Residue "H GLU 28": "OE1" <-> "OE2" Residue "I GLU 28": "OE1" <-> "OE2" Residue "J GLU 28": "OE1" <-> "OE2" Residue "K GLU 28": "OE1" <-> "OE2" Residue "L GLU 28": "OE1" <-> "OE2" Residue "M GLU 28": "OE1" <-> "OE2" Residue "N GLU 28": "OE1" <-> "OE2" Residue "O GLU 28": "OE1" <-> "OE2" Residue "P GLU 28": "OE1" <-> "OE2" Residue "Q GLU 28": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "S GLU 28": "OE1" <-> "OE2" Residue "T GLU 28": "OE1" <-> "OE2" Residue "U GLU 28": "OE1" <-> "OE2" Residue "V GLU 28": "OE1" <-> "OE2" Residue "W GLU 28": "OE1" <-> "OE2" Residue "X GLU 28": "OE1" <-> "OE2" Time to flip residues: 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 34104 Number of models: 1 Model: "" Number of chains: 48 Chain: "A" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "B" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "C" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "D" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "E" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "F" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "G" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "H" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "I" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "J" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "K" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "L" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "M" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "N" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "O" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "P" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "Q" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "R" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "S" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "T" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "U" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "V" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "W" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "X" Number of atoms: 1420 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1420 Classifications: {'peptide': 173} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 168} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "U" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "V" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' FE': 1} Classifications: {'undetermined': 1} Time building chain proxies: 16.84, per 1000 atoms: 0.49 Number of scatterers: 34104 At special positions: 0 Unit cell: (129.47, 129.47, 129.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Fe 24 26.01 S 192 16.00 O 6552 8.00 N 6048 7.00 C 21288 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: 13.27 Conformation dependent library (CDL) restraints added in 5.7 seconds 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7920 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.42 Creating SS restraints... Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 49 through 77 Processing helix chain 'A' and resid 96 through 125 Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 96 through 125 Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 49 through 77 Processing helix chain 'C' and resid 96 through 125 Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 49 through 77 Processing helix chain 'D' and resid 96 through 125 Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 49 through 77 Processing helix chain 'E' and resid 96 through 125 Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 Processing helix chain 'F' and resid 49 through 77 Processing helix chain 'F' and resid 96 through 125 Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 Processing helix chain 'G' and resid 49 through 77 Processing helix chain 'G' and resid 96 through 125 Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 Processing helix chain 'G' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 Processing helix chain 'H' and resid 49 through 77 Processing helix chain 'H' and resid 96 through 125 Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 Processing helix chain 'H' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 Processing helix chain 'I' and resid 49 through 77 Processing helix chain 'I' and resid 96 through 125 Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 Processing helix chain 'I' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 Processing helix chain 'J' and resid 49 through 77 Processing helix chain 'J' and resid 96 through 125 Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 Processing helix chain 'J' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 Processing helix chain 'K' and resid 49 through 77 Processing helix chain 'K' and resid 96 through 125 Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 Processing helix chain 'K' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 Processing helix chain 'L' and resid 49 through 77 Processing helix chain 'L' and resid 96 through 125 Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 Processing helix chain 'M' and resid 49 through 77 Processing helix chain 'M' and resid 96 through 125 Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 Processing helix chain 'M' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 Processing helix chain 'N' and resid 49 through 77 Processing helix chain 'N' and resid 96 through 125 Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 Processing helix chain 'N' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 Processing helix chain 'O' and resid 49 through 77 Processing helix chain 'O' and resid 96 through 125 Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 Processing helix chain 'O' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 Processing helix chain 'P' and resid 49 through 77 Processing helix chain 'P' and resid 96 through 125 Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 Processing helix chain 'P' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 Processing helix chain 'Q' and resid 49 through 77 Processing helix chain 'Q' and resid 96 through 125 Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 Processing helix chain 'Q' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 77 Processing helix chain 'R' and resid 96 through 125 Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 Processing helix chain 'R' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 Processing helix chain 'S' and resid 49 through 77 Processing helix chain 'S' and resid 96 through 125 Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 Processing helix chain 'S' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 Processing helix chain 'T' and resid 49 through 77 Processing helix chain 'T' and resid 96 through 125 Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 42 Processing helix chain 'U' and resid 49 through 77 Processing helix chain 'U' and resid 96 through 125 Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 Processing helix chain 'U' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 42 Processing helix chain 'V' and resid 49 through 77 Processing helix chain 'V' and resid 96 through 125 Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 Processing helix chain 'V' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 42 Processing helix chain 'W' and resid 49 through 77 Processing helix chain 'W' and resid 96 through 125 Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 Processing helix chain 'W' and resid 164 through 175 removed outlier: 3.656A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 42 Processing helix chain 'X' and resid 49 through 77 Processing helix chain 'X' and resid 96 through 125 Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 Processing helix chain 'X' and resid 164 through 175 removed outlier: 3.657A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) 2640 hydrogen bonds defined for protein. 7920 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: 11.50 Time building geometry restraints manager: 14.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 7053 1.32 - 1.44: 8486 1.44 - 1.57: 18925 1.57 - 1.69: 0 1.69 - 1.81: 312 Bond restraints: 34776 Sorted by residual: bond pdb=" CA ALA O 67 " pdb=" C ALA O 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA V 67 " pdb=" C ALA V 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA D 67 " pdb=" C ALA D 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA C 67 " pdb=" C ALA C 67 " ideal model delta sigma weight residual 1.524 1.482 0.041 1.29e-02 6.01e+03 1.02e+01 bond pdb=" CA ALA Q 67 " pdb=" C ALA Q 67 " ideal model delta sigma weight residual 1.524 1.483 0.040 1.29e-02 6.01e+03 9.77e+00 ... (remaining 34771 not shown) Histogram of bond angle deviations from ideal: 100.39 - 107.11: 775 107.11 - 113.84: 19003 113.84 - 120.56: 14703 120.56 - 127.28: 11983 127.28 - 134.01: 360 Bond angle restraints: 46824 Sorted by residual: angle pdb=" N VAL C 143 " pdb=" CA VAL C 143 " pdb=" C VAL C 143 " ideal model delta sigma weight residual 111.00 106.80 4.20 1.09e+00 8.42e-01 1.49e+01 angle pdb=" N VAL M 143 " pdb=" CA VAL M 143 " pdb=" C VAL M 143 " ideal model delta sigma weight residual 111.00 106.82 4.18 1.09e+00 8.42e-01 1.47e+01 angle pdb=" N VAL U 143 " pdb=" CA VAL U 143 " pdb=" C VAL U 143 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 angle pdb=" N VAL L 143 " pdb=" CA VAL L 143 " pdb=" C VAL L 143 " ideal model delta sigma weight residual 111.00 106.83 4.17 1.09e+00 8.42e-01 1.46e+01 angle pdb=" N VAL Q 143 " pdb=" CA VAL Q 143 " pdb=" C VAL Q 143 " ideal model delta sigma weight residual 111.00 106.84 4.16 1.09e+00 8.42e-01 1.45e+01 ... (remaining 46819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.69: 19416 14.69 - 29.39: 1176 29.39 - 44.08: 336 44.08 - 58.78: 48 58.78 - 73.47: 120 Dihedral angle restraints: 21096 sinusoidal: 8832 harmonic: 12264 Sorted by residual: dihedral pdb=" CA ASP J 172 " pdb=" CB ASP J 172 " pdb=" CG ASP J 172 " pdb=" OD1 ASP J 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.94 59.94 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP E 172 " pdb=" CB ASP E 172 " pdb=" CG ASP E 172 " pdb=" OD1 ASP E 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.93 59.93 1 2.00e+01 2.50e-03 1.20e+01 dihedral pdb=" CA ASP T 172 " pdb=" CB ASP T 172 " pdb=" CG ASP T 172 " pdb=" OD1 ASP T 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.92 59.92 1 2.00e+01 2.50e-03 1.20e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.062: 4206 0.062 - 0.124: 459 0.124 - 0.185: 87 0.185 - 0.247: 72 0.247 - 0.309: 48 Chirality restraints: 4872 Sorted by residual: chirality pdb=" CA GLN G 142 " pdb=" N GLN G 142 " pdb=" C GLN G 142 " pdb=" CB GLN G 142 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA GLN V 142 " pdb=" N GLN V 142 " pdb=" C GLN V 142 " pdb=" CB GLN V 142 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 chirality pdb=" CA GLN O 142 " pdb=" N GLN O 142 " pdb=" C GLN O 142 " pdb=" CB GLN O 142 " both_signs ideal model delta sigma weight residual False 2.51 2.20 0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 4869 not shown) Planarity restraints: 6216 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN T 140 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASN T 140 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN T 140 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU T 141 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN K 140 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASN K 140 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN K 140 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU K 141 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN I 140 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ASN I 140 " -0.036 2.00e-02 2.50e+03 pdb=" O ASN I 140 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU I 141 " 0.012 2.00e-02 2.50e+03 ... (remaining 6213 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.37: 96 2.37 - 3.00: 17766 3.00 - 3.63: 56434 3.63 - 4.27: 89980 4.27 - 4.90: 141307 Nonbonded interactions: 305583 Sorted by model distance: nonbonded pdb=" ND1 HIS V 66 " pdb="FE FE V 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS D 66 " pdb="FE FE D 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS O 66 " pdb="FE FE O 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS G 66 " pdb="FE FE G 201 " model vdw 1.737 2.340 nonbonded pdb=" ND1 HIS A 66 " pdb="FE FE A 201 " model vdw 1.737 2.340 ... (remaining 305578 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.890 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: 0.030 Extract box with map and model: 5.420 Check model and map are aligned: 0.490 Set scattering table: 0.300 Process input model: 83.000 Find NCS groups from input model: 2.930 Set up NCS constraints: 0.540 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 105.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.005 0.041 34776 Z= 0.311 Angle : 0.579 7.048 46824 Z= 0.358 Chirality : 0.057 0.309 4872 Planarity : 0.003 0.021 6216 Dihedral : 12.292 73.471 13176 Min Nonbonded Distance : 1.737 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.39 (0.13), residues: 4104 helix: 3.40 (0.09), residues: 3264 sheet: None (None), residues: 0 loop : 0.75 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP U 94 HIS 0.003 0.001 HIS F 66 PHE 0.012 0.001 PHE K 133 TYR 0.011 0.001 TYR L 40 ARG 0.004 0.001 ARG O 109 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1425 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 1425 time to evaluate : 3.859 Fit side-chains REVERT: A 18 GLU cc_start: 0.8333 (tt0) cc_final: 0.8057 (tt0) REVERT: A 63 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6781 (mm-30) REVERT: A 64 ARG cc_start: 0.8099 (tpp80) cc_final: 0.7311 (ttp-170) REVERT: A 68 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8135 (mt-10) REVERT: A 91 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7942 (mtp85) REVERT: A 93 ASP cc_start: 0.7911 (t0) cc_final: 0.7669 (t70) REVERT: A 113 GLN cc_start: 0.8718 (tp40) cc_final: 0.8438 (tp40) REVERT: A 125 LYS cc_start: 0.8852 (mmtt) cc_final: 0.8641 (mmtm) REVERT: A 135 GLU cc_start: 0.7609 (mt-10) cc_final: 0.7325 (mt-10) REVERT: A 148 GLU cc_start: 0.8334 (tt0) cc_final: 0.8118 (tt0) REVERT: A 173 LYS cc_start: 0.8678 (mptp) cc_final: 0.8367 (mptp) REVERT: B 16 ASP cc_start: 0.8858 (m-30) cc_final: 0.8549 (m-30) REVERT: B 18 GLU cc_start: 0.8314 (tt0) cc_final: 0.8038 (tt0) REVERT: B 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6784 (mm-30) REVERT: B 91 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7939 (mtp85) REVERT: B 93 ASP cc_start: 0.7878 (t0) cc_final: 0.7632 (t70) REVERT: B 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8412 (tp40) REVERT: B 125 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8599 (mmtm) REVERT: B 135 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7276 (mt-10) REVERT: B 141 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7532 (tm-30) REVERT: B 148 GLU cc_start: 0.8339 (tt0) cc_final: 0.7930 (tt0) REVERT: C 18 GLU cc_start: 0.8293 (tt0) cc_final: 0.8007 (tt0) REVERT: C 63 GLU cc_start: 0.7580 (mm-30) cc_final: 0.6765 (mm-30) REVERT: C 64 ARG cc_start: 0.8074 (tpp80) cc_final: 0.7236 (ttp-170) REVERT: C 91 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7929 (mtp85) REVERT: C 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7644 (t70) REVERT: C 113 GLN cc_start: 0.8706 (tp40) cc_final: 0.8418 (tp40) REVERT: C 125 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8645 (mmtm) REVERT: C 135 GLU cc_start: 0.7570 (mt-10) cc_final: 0.7279 (mt-10) REVERT: C 141 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7477 (tm-30) REVERT: C 148 GLU cc_start: 0.8275 (tt0) cc_final: 0.8045 (tt0) REVERT: D 18 GLU cc_start: 0.8291 (tt0) cc_final: 0.8009 (tt0) REVERT: D 63 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6773 (mm-30) REVERT: D 91 ARG cc_start: 0.8236 (mtp85) cc_final: 0.7931 (mtp85) REVERT: D 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7646 (t70) REVERT: D 113 GLN cc_start: 0.8708 (tp40) cc_final: 0.8425 (tp40) REVERT: D 125 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8645 (mmtm) REVERT: D 135 GLU cc_start: 0.7576 (mt-10) cc_final: 0.7281 (mt-10) REVERT: D 141 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7477 (tm-30) REVERT: D 148 GLU cc_start: 0.8287 (tt0) cc_final: 0.8058 (tt0) REVERT: E 16 ASP cc_start: 0.8850 (m-30) cc_final: 0.8531 (m-30) REVERT: E 18 GLU cc_start: 0.8317 (tt0) cc_final: 0.8043 (tt0) REVERT: E 63 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6775 (mm-30) REVERT: E 64 ARG cc_start: 0.8091 (tpp80) cc_final: 0.7226 (ttp-170) REVERT: E 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7933 (mtp85) REVERT: E 93 ASP cc_start: 0.7892 (t0) cc_final: 0.7656 (t70) REVERT: E 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8407 (tp40) REVERT: E 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8598 (mmtm) REVERT: E 135 GLU cc_start: 0.7578 (mt-10) cc_final: 0.7285 (mt-10) REVERT: E 148 GLU cc_start: 0.8363 (tt0) cc_final: 0.8117 (tt0) REVERT: E 173 LYS cc_start: 0.8706 (mptp) cc_final: 0.8374 (mptp) REVERT: F 18 GLU cc_start: 0.8317 (tt0) cc_final: 0.8045 (tt0) REVERT: F 63 GLU cc_start: 0.7593 (mm-30) cc_final: 0.6782 (mm-30) REVERT: F 64 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7238 (ttp-170) REVERT: F 91 ARG cc_start: 0.8239 (mtp85) cc_final: 0.7932 (mtp85) REVERT: F 93 ASP cc_start: 0.7901 (t0) cc_final: 0.7663 (t70) REVERT: F 113 GLN cc_start: 0.8727 (tp40) cc_final: 0.8443 (tp40) REVERT: F 120 LYS cc_start: 0.8553 (tttm) cc_final: 0.8216 (ttpt) REVERT: F 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8641 (mmtm) REVERT: F 135 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7281 (mt-10) REVERT: F 141 GLU cc_start: 0.7727 (mm-30) cc_final: 0.7495 (tm-30) REVERT: F 148 GLU cc_start: 0.8336 (tt0) cc_final: 0.8116 (tt0) REVERT: F 173 LYS cc_start: 0.8686 (mptp) cc_final: 0.8374 (mptp) REVERT: G 64 ARG cc_start: 0.8071 (tpp80) cc_final: 0.7229 (ttp-170) REVERT: G 68 GLU cc_start: 0.8400 (mt-10) cc_final: 0.8193 (mt-10) REVERT: G 91 ARG cc_start: 0.8227 (mtp85) cc_final: 0.7899 (mtp85) REVERT: G 93 ASP cc_start: 0.7901 (t0) cc_final: 0.7638 (t70) REVERT: G 120 LYS cc_start: 0.8532 (tttm) cc_final: 0.8175 (ttmp) REVERT: G 124 GLU cc_start: 0.7961 (tm-30) cc_final: 0.7746 (tm-30) REVERT: G 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8623 (mmtm) REVERT: G 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7254 (mp0) REVERT: G 148 GLU cc_start: 0.8280 (tt0) cc_final: 0.8040 (tt0) REVERT: G 173 LYS cc_start: 0.8710 (mptp) cc_final: 0.8396 (mptp) REVERT: H 16 ASP cc_start: 0.8856 (m-30) cc_final: 0.8536 (m-30) REVERT: H 18 GLU cc_start: 0.8335 (tt0) cc_final: 0.8055 (tt0) REVERT: H 63 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6790 (mm-30) REVERT: H 91 ARG cc_start: 0.8254 (mtp85) cc_final: 0.7954 (mtp85) REVERT: H 93 ASP cc_start: 0.7867 (t0) cc_final: 0.7641 (t70) REVERT: H 113 GLN cc_start: 0.8712 (tp40) cc_final: 0.8434 (tp40) REVERT: H 125 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8596 (mmtm) REVERT: H 135 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7279 (mt-10) REVERT: H 148 GLU cc_start: 0.8380 (tt0) cc_final: 0.8161 (tt0) REVERT: I 18 GLU cc_start: 0.8314 (tt0) cc_final: 0.8036 (tt0) REVERT: I 63 GLU cc_start: 0.7587 (mm-30) cc_final: 0.6768 (mm-30) REVERT: I 64 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7228 (ttp-170) REVERT: I 91 ARG cc_start: 0.8234 (mtp85) cc_final: 0.7929 (mtp85) REVERT: I 93 ASP cc_start: 0.7891 (t0) cc_final: 0.7619 (t70) REVERT: I 113 GLN cc_start: 0.8722 (tp40) cc_final: 0.8437 (tp40) REVERT: I 125 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8641 (mmtm) REVERT: I 135 GLU cc_start: 0.7567 (mt-10) cc_final: 0.7277 (mt-10) REVERT: I 148 GLU cc_start: 0.8279 (tt0) cc_final: 0.8036 (tt0) REVERT: J 18 GLU cc_start: 0.8311 (tt0) cc_final: 0.8035 (tt0) REVERT: J 63 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6780 (mm-30) REVERT: J 91 ARG cc_start: 0.8238 (mtp85) cc_final: 0.7938 (mtp85) REVERT: J 93 ASP cc_start: 0.7892 (t0) cc_final: 0.7621 (t70) REVERT: J 113 GLN cc_start: 0.8725 (tp40) cc_final: 0.8443 (tp40) REVERT: J 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8642 (mmtm) REVERT: J 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7276 (mt-10) REVERT: J 148 GLU cc_start: 0.8281 (tt0) cc_final: 0.8043 (tt0) REVERT: K 16 ASP cc_start: 0.8821 (m-30) cc_final: 0.8503 (m-30) REVERT: K 18 GLU cc_start: 0.8319 (tt0) cc_final: 0.8032 (tt0) REVERT: K 63 GLU cc_start: 0.7590 (mm-30) cc_final: 0.6777 (mm-30) REVERT: K 64 ARG cc_start: 0.8083 (tpp80) cc_final: 0.7236 (ttp-170) REVERT: K 91 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7908 (mtp85) REVERT: K 93 ASP cc_start: 0.7881 (t0) cc_final: 0.7643 (t70) REVERT: K 95 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7592 (mm-30) REVERT: K 113 GLN cc_start: 0.8721 (tp40) cc_final: 0.8430 (tp40) REVERT: K 117 GLU cc_start: 0.8072 (mm-30) cc_final: 0.7855 (mm-30) REVERT: K 125 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8612 (mmtm) REVERT: K 135 GLU cc_start: 0.7568 (mt-10) cc_final: 0.7283 (mt-10) REVERT: K 141 GLU cc_start: 0.7688 (mm-30) cc_final: 0.7256 (mp0) REVERT: K 148 GLU cc_start: 0.8349 (tt0) cc_final: 0.7930 (tt0) REVERT: L 64 ARG cc_start: 0.8072 (tpp80) cc_final: 0.7229 (ttp-170) REVERT: L 68 GLU cc_start: 0.8404 (mt-10) cc_final: 0.8201 (mt-10) REVERT: L 91 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7901 (mtp85) REVERT: L 93 ASP cc_start: 0.7896 (t0) cc_final: 0.7633 (t70) REVERT: L 113 GLN cc_start: 0.8721 (tp40) cc_final: 0.8436 (tp40) REVERT: L 120 LYS cc_start: 0.8531 (tttm) cc_final: 0.8177 (ttmp) REVERT: L 124 GLU cc_start: 0.7955 (tm-30) cc_final: 0.7742 (tm-30) REVERT: L 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8622 (mmtm) REVERT: L 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7256 (mp0) REVERT: L 148 GLU cc_start: 0.8279 (tt0) cc_final: 0.8040 (tt0) REVERT: L 173 LYS cc_start: 0.8707 (mptp) cc_final: 0.8391 (mptp) REVERT: M 16 ASP cc_start: 0.8844 (m-30) cc_final: 0.8517 (m-30) REVERT: M 18 GLU cc_start: 0.8314 (tt0) cc_final: 0.8041 (tt0) REVERT: M 63 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6771 (mm-30) REVERT: M 64 ARG cc_start: 0.8079 (tpp80) cc_final: 0.7324 (ttp-170) REVERT: M 68 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8146 (mt-10) REVERT: M 91 ARG cc_start: 0.8230 (mtp85) cc_final: 0.7913 (mtp85) REVERT: M 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7662 (t70) REVERT: M 113 GLN cc_start: 0.8706 (tp40) cc_final: 0.8422 (tp40) REVERT: M 120 LYS cc_start: 0.8517 (tttm) cc_final: 0.8233 (tttp) REVERT: M 125 LYS cc_start: 0.8850 (mmtt) cc_final: 0.8605 (mmtm) REVERT: M 135 GLU cc_start: 0.7604 (mt-10) cc_final: 0.7319 (mt-10) REVERT: M 141 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7506 (tm-30) REVERT: M 148 GLU cc_start: 0.8317 (tt0) cc_final: 0.8081 (tt0) REVERT: N 16 ASP cc_start: 0.8852 (m-30) cc_final: 0.8531 (m-30) REVERT: N 18 GLU cc_start: 0.8317 (tt0) cc_final: 0.8043 (tt0) REVERT: N 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6779 (mm-30) REVERT: N 91 ARG cc_start: 0.8247 (mtp85) cc_final: 0.7936 (mtp85) REVERT: N 93 ASP cc_start: 0.7892 (t0) cc_final: 0.7654 (t70) REVERT: N 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8408 (tp40) REVERT: N 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8593 (mmtm) REVERT: N 135 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7283 (mt-10) REVERT: N 148 GLU cc_start: 0.8361 (tt0) cc_final: 0.8123 (tt0) REVERT: N 173 LYS cc_start: 0.8707 (mptp) cc_final: 0.8385 (mptp) REVERT: O 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8035 (tt0) REVERT: O 63 GLU cc_start: 0.7581 (mm-30) cc_final: 0.6770 (mm-30) REVERT: O 64 ARG cc_start: 0.8090 (tpp80) cc_final: 0.7228 (ttp-170) REVERT: O 91 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7927 (mtp85) REVERT: O 93 ASP cc_start: 0.7882 (t0) cc_final: 0.7640 (t70) REVERT: O 113 GLN cc_start: 0.8720 (tp40) cc_final: 0.8434 (tp40) REVERT: O 120 LYS cc_start: 0.8496 (tttm) cc_final: 0.8118 (ttmt) REVERT: O 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8640 (mmtm) REVERT: O 135 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7281 (mt-10) REVERT: O 148 GLU cc_start: 0.8299 (tt0) cc_final: 0.8070 (tt0) REVERT: P 18 GLU cc_start: 0.8313 (tt0) cc_final: 0.8035 (tt0) REVERT: P 63 GLU cc_start: 0.7586 (mm-30) cc_final: 0.6779 (mm-30) REVERT: P 91 ARG cc_start: 0.8245 (mtp85) cc_final: 0.7931 (mtp85) REVERT: P 93 ASP cc_start: 0.7875 (t0) cc_final: 0.7648 (t70) REVERT: P 113 GLN cc_start: 0.8709 (tp40) cc_final: 0.8433 (tp40) REVERT: P 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8598 (mmtm) REVERT: P 135 GLU cc_start: 0.7572 (mt-10) cc_final: 0.7277 (mt-10) REVERT: P 141 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7509 (tm-30) REVERT: P 148 GLU cc_start: 0.8314 (tt0) cc_final: 0.8016 (tt0) REVERT: Q 16 ASP cc_start: 0.8856 (m-30) cc_final: 0.8549 (m-30) REVERT: Q 18 GLU cc_start: 0.8311 (tt0) cc_final: 0.8034 (tt0) REVERT: Q 63 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6784 (mm-30) REVERT: Q 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7935 (mtp85) REVERT: Q 93 ASP cc_start: 0.7883 (t0) cc_final: 0.7639 (t70) REVERT: Q 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8410 (tp40) REVERT: Q 125 LYS cc_start: 0.8863 (mmtt) cc_final: 0.8599 (mmtm) REVERT: Q 135 GLU cc_start: 0.7573 (mt-10) cc_final: 0.7281 (mt-10) REVERT: Q 141 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7530 (tm-30) REVERT: Q 148 GLU cc_start: 0.8340 (tt0) cc_final: 0.7918 (tt0) REVERT: R 16 ASP cc_start: 0.8848 (m-30) cc_final: 0.8525 (m-30) REVERT: R 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8040 (tt0) REVERT: R 63 GLU cc_start: 0.7588 (mm-30) cc_final: 0.6786 (mm-30) REVERT: R 68 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8153 (mt-10) REVERT: R 91 ARG cc_start: 0.8228 (mtp85) cc_final: 0.7917 (mtp85) REVERT: R 93 ASP cc_start: 0.7894 (t0) cc_final: 0.7670 (t70) REVERT: R 113 GLN cc_start: 0.8710 (tp40) cc_final: 0.8423 (tp40) REVERT: R 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8593 (mmtm) REVERT: R 135 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7274 (mt-10) REVERT: R 141 GLU cc_start: 0.7746 (mm-30) cc_final: 0.7505 (tm-30) REVERT: R 148 GLU cc_start: 0.8319 (tt0) cc_final: 0.8095 (tt0) REVERT: R 173 LYS cc_start: 0.8695 (mptp) cc_final: 0.8369 (mptp) REVERT: S 16 ASP cc_start: 0.8844 (m-30) cc_final: 0.8525 (m-30) REVERT: S 18 GLU cc_start: 0.8321 (tt0) cc_final: 0.8046 (tt0) REVERT: S 63 GLU cc_start: 0.7592 (mm-30) cc_final: 0.6783 (mm-30) REVERT: S 64 ARG cc_start: 0.8086 (tpp80) cc_final: 0.7316 (ttp-170) REVERT: S 68 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8144 (mt-10) REVERT: S 91 ARG cc_start: 0.8225 (mtp85) cc_final: 0.7920 (mtp85) REVERT: S 93 ASP cc_start: 0.7897 (t0) cc_final: 0.7669 (t70) REVERT: S 113 GLN cc_start: 0.8707 (tp40) cc_final: 0.8428 (tp40) REVERT: S 125 LYS cc_start: 0.8853 (mmtt) cc_final: 0.8593 (mmtm) REVERT: S 135 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7272 (mt-10) REVERT: S 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7497 (tm-30) REVERT: S 148 GLU cc_start: 0.8314 (tt0) cc_final: 0.8086 (tt0) REVERT: S 173 LYS cc_start: 0.8697 (mptp) cc_final: 0.8377 (mptp) REVERT: T 16 ASP cc_start: 0.8829 (m-30) cc_final: 0.8510 (m-30) REVERT: T 18 GLU cc_start: 0.8324 (tt0) cc_final: 0.8042 (tt0) REVERT: T 63 GLU cc_start: 0.7589 (mm-30) cc_final: 0.6783 (mm-30) REVERT: T 91 ARG cc_start: 0.8240 (mtp85) cc_final: 0.7905 (mtp85) REVERT: T 93 ASP cc_start: 0.7879 (t0) cc_final: 0.7637 (t70) REVERT: T 95 GLU cc_start: 0.7797 (mm-30) cc_final: 0.7591 (mm-30) REVERT: T 113 GLN cc_start: 0.8719 (tp40) cc_final: 0.8432 (tp40) REVERT: T 117 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7857 (mm-30) REVERT: T 125 LYS cc_start: 0.8879 (mmtt) cc_final: 0.8614 (mmtm) REVERT: T 135 GLU cc_start: 0.7566 (mt-10) cc_final: 0.7283 (mt-10) REVERT: T 141 GLU cc_start: 0.7697 (mm-30) cc_final: 0.7261 (mp0) REVERT: T 148 GLU cc_start: 0.8348 (tt0) cc_final: 0.7927 (tt0) REVERT: U 18 GLU cc_start: 0.8312 (tt0) cc_final: 0.8033 (tt0) REVERT: U 63 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6768 (mm-30) REVERT: U 64 ARG cc_start: 0.8078 (tpp80) cc_final: 0.7237 (ttp-170) REVERT: U 91 ARG cc_start: 0.8242 (mtp85) cc_final: 0.7932 (mtp85) REVERT: U 93 ASP cc_start: 0.7874 (t0) cc_final: 0.7643 (t70) REVERT: U 113 GLN cc_start: 0.8707 (tp40) cc_final: 0.8426 (tp40) REVERT: U 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8595 (mmtm) REVERT: U 135 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7274 (mt-10) REVERT: U 141 GLU cc_start: 0.7715 (mm-30) cc_final: 0.7507 (tm-30) REVERT: U 148 GLU cc_start: 0.8311 (tt0) cc_final: 0.8013 (tt0) REVERT: V 18 GLU cc_start: 0.8307 (tt0) cc_final: 0.8031 (tt0) REVERT: V 63 GLU cc_start: 0.7583 (mm-30) cc_final: 0.6778 (mm-30) REVERT: V 91 ARG cc_start: 0.8244 (mtp85) cc_final: 0.7934 (mtp85) REVERT: V 93 ASP cc_start: 0.7885 (t0) cc_final: 0.7648 (t70) REVERT: V 113 GLN cc_start: 0.8722 (tp40) cc_final: 0.8439 (tp40) REVERT: V 120 LYS cc_start: 0.8505 (tttm) cc_final: 0.8128 (ttmt) REVERT: V 125 LYS cc_start: 0.8856 (mmtt) cc_final: 0.8643 (mmtm) REVERT: V 135 GLU cc_start: 0.7571 (mt-10) cc_final: 0.7281 (mt-10) REVERT: V 148 GLU cc_start: 0.8305 (tt0) cc_final: 0.8081 (tt0) REVERT: W 16 ASP cc_start: 0.8853 (m-30) cc_final: 0.8533 (m-30) REVERT: W 18 GLU cc_start: 0.8328 (tt0) cc_final: 0.8050 (tt0) REVERT: W 63 GLU cc_start: 0.7595 (mm-30) cc_final: 0.6792 (mm-30) REVERT: W 91 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7955 (mtp85) REVERT: W 93 ASP cc_start: 0.7866 (t0) cc_final: 0.7645 (t70) REVERT: W 113 GLN cc_start: 0.8712 (tp40) cc_final: 0.8436 (tp40) REVERT: W 125 LYS cc_start: 0.8859 (mmtt) cc_final: 0.8597 (mmtm) REVERT: W 135 GLU cc_start: 0.7574 (mt-10) cc_final: 0.7280 (mt-10) REVERT: W 148 GLU cc_start: 0.8381 (tt0) cc_final: 0.8156 (tt0) REVERT: W 173 LYS cc_start: 0.8705 (mptp) cc_final: 0.8386 (mptp) REVERT: X 16 ASP cc_start: 0.8847 (m-30) cc_final: 0.8518 (m-30) REVERT: X 18 GLU cc_start: 0.8310 (tt0) cc_final: 0.8041 (tt0) REVERT: X 63 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6775 (mm-30) REVERT: X 68 GLU cc_start: 0.8395 (mt-10) cc_final: 0.8151 (mt-10) REVERT: X 91 ARG cc_start: 0.8233 (mtp85) cc_final: 0.7915 (mtp85) REVERT: X 93 ASP cc_start: 0.7894 (t0) cc_final: 0.7660 (t70) REVERT: X 113 GLN cc_start: 0.8708 (tp40) cc_final: 0.8421 (tp40) REVERT: X 120 LYS cc_start: 0.8514 (tttm) cc_final: 0.8230 (tttp) REVERT: X 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8610 (mmtm) REVERT: X 135 GLU cc_start: 0.7569 (mt-10) cc_final: 0.7282 (mt-10) REVERT: X 141 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7507 (tm-30) REVERT: X 148 GLU cc_start: 0.8316 (tt0) cc_final: 0.8081 (tt0) outliers start: 0 outliers final: 12 residues processed: 1425 average time/residue: 1.8048 time to fit residues: 2972.6680 Evaluate side-chains 1122 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1110 time to evaluate : 3.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain X residue 46 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 5.9990 chunk 309 optimal weight: 4.9990 chunk 171 optimal weight: 3.9990 chunk 105 optimal weight: 0.6980 chunk 208 optimal weight: 5.9990 chunk 165 optimal weight: 1.9990 chunk 319 optimal weight: 0.0270 chunk 123 optimal weight: 4.9990 chunk 194 optimal weight: 0.9980 chunk 238 optimal weight: 7.9990 chunk 370 optimal weight: 1.9990 overall best weight: 1.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 84 GLN A 137 HIS B 12 ASN B 61 HIS B 84 GLN B 137 HIS C 12 ASN C 84 GLN C 112 ASN C 137 HIS D 12 ASN D 84 GLN D 137 HIS E 12 ASN E 61 HIS E 84 GLN E 137 HIS F 12 ASN F 84 GLN F 137 HIS G 12 ASN G 84 GLN G 112 ASN G 137 HIS H 12 ASN H 61 HIS H 84 GLN H 137 HIS I 12 ASN I 84 GLN I 137 HIS J 12 ASN J 84 GLN J 137 HIS K 12 ASN K 61 HIS K 84 GLN K 137 HIS L 12 ASN L 84 GLN L 137 HIS M 12 ASN M 84 GLN M 137 HIS N 12 ASN N 61 HIS N 84 GLN N 137 HIS O 12 ASN O 84 GLN O 137 HIS P 12 ASN P 84 GLN P 137 HIS Q 12 ASN Q 84 GLN Q 137 HIS R 12 ASN R 84 GLN R 137 HIS S 12 ASN S 84 GLN S 137 HIS T 12 ASN T 61 HIS T 84 GLN T 137 HIS U 12 ASN U 84 GLN U 137 HIS V 12 ASN V 84 GLN V 112 ASN V 137 HIS W 12 ASN W 61 HIS W 84 GLN W 137 HIS X 12 ASN X 84 GLN X 137 HIS Total number of N/Q/H flips: 82 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1321 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 34776 Z= 0.152 Angle : 0.445 5.107 46824 Z= 0.235 Chirality : 0.034 0.124 4872 Planarity : 0.003 0.025 6216 Dihedral : 3.789 15.998 4608 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.36 % Allowed : 11.47 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.21 (0.13), residues: 4104 helix: 4.03 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.77 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP R 94 HIS 0.002 0.000 HIS K 119 PHE 0.011 0.002 PHE C 133 TYR 0.010 0.001 TYR F 138 ARG 0.003 0.001 ARG C 157 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1163 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 1113 time to evaluate : 3.862 Fit side-chains REVERT: A 64 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7072 (ttp-170) REVERT: A 91 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7995 (mtp85) REVERT: A 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8362 (tp40) REVERT: A 124 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7760 (tm-30) REVERT: A 125 LYS cc_start: 0.8804 (mmtt) cc_final: 0.8563 (mmtm) REVERT: A 148 GLU cc_start: 0.8345 (tt0) cc_final: 0.8084 (tt0) REVERT: B 16 ASP cc_start: 0.8894 (m-30) cc_final: 0.8591 (m-30) REVERT: B 18 GLU cc_start: 0.8447 (tt0) cc_final: 0.8163 (tt0) REVERT: B 63 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7066 (mm-30) REVERT: B 91 ARG cc_start: 0.8303 (mtp85) cc_final: 0.8028 (mtp85) REVERT: B 93 ASP cc_start: 0.8012 (t0) cc_final: 0.7693 (t70) REVERT: B 113 GLN cc_start: 0.8703 (tp40) cc_final: 0.8347 (tp40) REVERT: B 125 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8553 (mmtm) REVERT: B 141 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7332 (tm-30) REVERT: B 148 GLU cc_start: 0.8359 (tt0) cc_final: 0.7968 (tt0) REVERT: C 18 GLU cc_start: 0.8434 (tt0) cc_final: 0.8137 (tt0) REVERT: C 63 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7056 (mm-30) REVERT: C 64 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7175 (ttp-170) REVERT: C 91 ARG cc_start: 0.8268 (mtp85) cc_final: 0.8018 (mtp85) REVERT: C 93 ASP cc_start: 0.8045 (t0) cc_final: 0.7715 (t70) REVERT: C 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8354 (tp40) REVERT: C 125 LYS cc_start: 0.8810 (mmtt) cc_final: 0.8582 (mmtm) REVERT: C 141 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7395 (tm-30) REVERT: C 148 GLU cc_start: 0.8288 (tt0) cc_final: 0.8062 (tt0) REVERT: D 18 GLU cc_start: 0.8432 (tt0) cc_final: 0.8084 (tt0) REVERT: D 91 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7995 (mtp85) REVERT: D 93 ASP cc_start: 0.8042 (t0) cc_final: 0.7701 (t70) REVERT: D 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8356 (tp40) REVERT: D 125 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8600 (mmtm) REVERT: D 141 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7216 (mp0) REVERT: D 148 GLU cc_start: 0.8296 (tt0) cc_final: 0.8039 (tt0) REVERT: E 16 ASP cc_start: 0.8903 (m-30) cc_final: 0.8548 (m-30) REVERT: E 62 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7180 (mm-30) REVERT: E 64 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7105 (ttp-170) REVERT: E 91 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7996 (mtp85) REVERT: E 93 ASP cc_start: 0.8042 (t0) cc_final: 0.7712 (t70) REVERT: E 113 GLN cc_start: 0.8699 (tp40) cc_final: 0.8342 (tp40) REVERT: E 124 GLU cc_start: 0.7969 (tm-30) cc_final: 0.7712 (tm-30) REVERT: E 125 LYS cc_start: 0.8837 (mmtt) cc_final: 0.8488 (mmtm) REVERT: E 148 GLU cc_start: 0.8370 (tt0) cc_final: 0.8108 (tt0) REVERT: E 173 LYS cc_start: 0.8664 (mptp) cc_final: 0.8334 (mptp) REVERT: F 59 GLN cc_start: 0.8260 (mm110) cc_final: 0.8034 (mm110) REVERT: F 64 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7077 (ttp-170) REVERT: F 91 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7998 (mtp85) REVERT: F 113 GLN cc_start: 0.8709 (tp40) cc_final: 0.8364 (tp40) REVERT: F 120 LYS cc_start: 0.8597 (tttm) cc_final: 0.8321 (tttp) REVERT: F 124 GLU cc_start: 0.7985 (tm-30) cc_final: 0.7754 (tm-30) REVERT: F 125 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8545 (mmtm) REVERT: F 141 GLU cc_start: 0.7740 (mm-30) cc_final: 0.7215 (mp0) REVERT: F 148 GLU cc_start: 0.8357 (tt0) cc_final: 0.8102 (tt0) REVERT: G 16 ASP cc_start: 0.8895 (m-30) cc_final: 0.8546 (m-30) REVERT: G 59 GLN cc_start: 0.8249 (mm110) cc_final: 0.8017 (mm110) REVERT: G 64 ARG cc_start: 0.8174 (tpp80) cc_final: 0.7068 (ttp-170) REVERT: G 91 ARG cc_start: 0.8263 (mtp85) cc_final: 0.8002 (mtp85) REVERT: G 93 ASP cc_start: 0.8038 (t0) cc_final: 0.7713 (t70) REVERT: G 120 LYS cc_start: 0.8572 (tttm) cc_final: 0.8304 (tttp) REVERT: G 124 GLU cc_start: 0.8002 (tm-30) cc_final: 0.7771 (tm-30) REVERT: G 125 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8523 (mmtm) REVERT: G 141 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7221 (mp0) REVERT: G 148 GLU cc_start: 0.8298 (tt0) cc_final: 0.8057 (tt0) REVERT: H 16 ASP cc_start: 0.8892 (m-30) cc_final: 0.8540 (m-30) REVERT: H 59 GLN cc_start: 0.8249 (mm110) cc_final: 0.8031 (mm110) REVERT: H 62 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7217 (mm-30) REVERT: H 91 ARG cc_start: 0.8313 (mtp85) cc_final: 0.8038 (mtp85) REVERT: H 93 ASP cc_start: 0.8000 (t0) cc_final: 0.7682 (t70) REVERT: H 113 GLN cc_start: 0.8715 (tp40) cc_final: 0.8373 (tp40) REVERT: H 124 GLU cc_start: 0.7971 (tm-30) cc_final: 0.7724 (tm-30) REVERT: H 125 LYS cc_start: 0.8811 (mmtt) cc_final: 0.8490 (mmtm) REVERT: H 148 GLU cc_start: 0.8391 (tt0) cc_final: 0.8124 (tt0) REVERT: I 62 GLU cc_start: 0.7393 (mm-30) cc_final: 0.7145 (mm-30) REVERT: I 64 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7083 (ttp-170) REVERT: I 91 ARG cc_start: 0.8286 (mtp85) cc_final: 0.8015 (mtp85) REVERT: I 93 ASP cc_start: 0.8034 (t0) cc_final: 0.7682 (t70) REVERT: I 113 GLN cc_start: 0.8711 (tp40) cc_final: 0.8368 (tp40) REVERT: I 124 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7770 (tm-30) REVERT: I 125 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8565 (mmtm) REVERT: I 148 GLU cc_start: 0.8286 (tt0) cc_final: 0.8018 (tt0) REVERT: J 59 GLN cc_start: 0.8229 (mm110) cc_final: 0.8010 (mm110) REVERT: J 62 GLU cc_start: 0.7403 (mm-30) cc_final: 0.7156 (mm-30) REVERT: J 91 ARG cc_start: 0.8289 (mtp85) cc_final: 0.8020 (mtp85) REVERT: J 93 ASP cc_start: 0.8034 (t0) cc_final: 0.7681 (t70) REVERT: J 113 GLN cc_start: 0.8715 (tp40) cc_final: 0.8374 (tp40) REVERT: J 124 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7775 (tm-30) REVERT: J 125 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8565 (mmtm) REVERT: J 148 GLU cc_start: 0.8289 (tt0) cc_final: 0.8025 (tt0) REVERT: K 16 ASP cc_start: 0.8870 (m-30) cc_final: 0.8522 (m-30) REVERT: K 18 GLU cc_start: 0.8457 (tt0) cc_final: 0.8110 (tt0) REVERT: K 59 GLN cc_start: 0.8245 (mm110) cc_final: 0.8001 (mm110) REVERT: K 64 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7056 (ttp-170) REVERT: K 91 ARG cc_start: 0.8284 (mtp85) cc_final: 0.8006 (mtp85) REVERT: K 93 ASP cc_start: 0.8009 (t0) cc_final: 0.7693 (t70) REVERT: K 113 GLN cc_start: 0.8720 (tp40) cc_final: 0.8365 (tp40) REVERT: K 124 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7754 (tm-30) REVERT: K 125 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8521 (mmtm) REVERT: K 141 GLU cc_start: 0.7704 (mm-30) cc_final: 0.7248 (mp0) REVERT: K 148 GLU cc_start: 0.8364 (tt0) cc_final: 0.7974 (tt0) REVERT: L 16 ASP cc_start: 0.8892 (m-30) cc_final: 0.8591 (m-30) REVERT: L 64 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7067 (ttp-170) REVERT: L 91 ARG cc_start: 0.8263 (mtp85) cc_final: 0.8002 (mtp85) REVERT: L 93 ASP cc_start: 0.8032 (t0) cc_final: 0.7708 (t70) REVERT: L 120 LYS cc_start: 0.8573 (tttm) cc_final: 0.8305 (tttp) REVERT: L 124 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7758 (tm-30) REVERT: L 125 LYS cc_start: 0.8803 (mmtt) cc_final: 0.8583 (mmtm) REVERT: L 141 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7238 (mp0) REVERT: L 148 GLU cc_start: 0.8295 (tt0) cc_final: 0.8049 (tt0) REVERT: M 16 ASP cc_start: 0.8878 (m-30) cc_final: 0.8524 (m-30) REVERT: M 18 GLU cc_start: 0.8453 (tt0) cc_final: 0.8114 (tt0) REVERT: M 64 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7071 (ttp-170) REVERT: M 91 ARG cc_start: 0.8273 (mtp85) cc_final: 0.7996 (mtp85) REVERT: M 93 ASP cc_start: 0.8022 (t0) cc_final: 0.7722 (t70) REVERT: M 113 GLN cc_start: 0.8699 (tp40) cc_final: 0.8355 (tp40) REVERT: M 120 LYS cc_start: 0.8562 (tttm) cc_final: 0.8292 (tttp) REVERT: M 124 GLU cc_start: 0.7992 (tm-30) cc_final: 0.7760 (tm-30) REVERT: M 125 LYS cc_start: 0.8795 (mmtt) cc_final: 0.8516 (mmtm) REVERT: M 141 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7223 (mp0) REVERT: M 148 GLU cc_start: 0.8340 (tt0) cc_final: 0.8067 (tt0) REVERT: N 16 ASP cc_start: 0.8903 (m-30) cc_final: 0.8548 (m-30) REVERT: N 62 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7203 (mm-30) REVERT: N 91 ARG cc_start: 0.8272 (mtp85) cc_final: 0.7998 (mtp85) REVERT: N 93 ASP cc_start: 0.8042 (t0) cc_final: 0.7708 (t70) REVERT: N 113 GLN cc_start: 0.8699 (tp40) cc_final: 0.8344 (tp40) REVERT: N 124 GLU cc_start: 0.7962 (tm-30) cc_final: 0.7710 (tm-30) REVERT: N 125 LYS cc_start: 0.8836 (mmtt) cc_final: 0.8488 (mmtm) REVERT: N 148 GLU cc_start: 0.8372 (tt0) cc_final: 0.8109 (tt0) REVERT: N 173 LYS cc_start: 0.8669 (mptp) cc_final: 0.8328 (mptp) REVERT: O 59 GLN cc_start: 0.8216 (mm110) cc_final: 0.7988 (mm110) REVERT: O 64 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7075 (ttp-170) REVERT: O 91 ARG cc_start: 0.8284 (mtp85) cc_final: 0.8003 (mtp85) REVERT: O 93 ASP cc_start: 0.8027 (t0) cc_final: 0.7704 (t70) REVERT: O 113 GLN cc_start: 0.8709 (tp40) cc_final: 0.8357 (tp40) REVERT: O 120 LYS cc_start: 0.8542 (tttm) cc_final: 0.8172 (ttmt) REVERT: O 124 GLU cc_start: 0.7972 (tm-30) cc_final: 0.7746 (tm-30) REVERT: O 125 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8564 (mmtm) REVERT: O 148 GLU cc_start: 0.8301 (tt0) cc_final: 0.8042 (tt0) REVERT: P 91 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7992 (mtp85) REVERT: P 93 ASP cc_start: 0.8027 (t0) cc_final: 0.7707 (t70) REVERT: P 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8364 (tp40) REVERT: P 124 GLU cc_start: 0.7999 (tm-30) cc_final: 0.7768 (tm-30) REVERT: P 125 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8600 (mmtm) REVERT: P 141 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7248 (mp0) REVERT: P 148 GLU cc_start: 0.8326 (tt0) cc_final: 0.8034 (tt0) REVERT: Q 16 ASP cc_start: 0.8892 (m-30) cc_final: 0.8591 (m-30) REVERT: Q 18 GLU cc_start: 0.8448 (tt0) cc_final: 0.8166 (tt0) REVERT: Q 63 GLU cc_start: 0.7837 (mm-30) cc_final: 0.7045 (mm-30) REVERT: Q 91 ARG cc_start: 0.8299 (mtp85) cc_final: 0.8022 (mtp85) REVERT: Q 93 ASP cc_start: 0.8032 (t0) cc_final: 0.7700 (t70) REVERT: Q 113 GLN cc_start: 0.8705 (tp40) cc_final: 0.8348 (tp40) REVERT: Q 125 LYS cc_start: 0.8813 (mmtt) cc_final: 0.8556 (mmtm) REVERT: Q 141 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7328 (tm-30) REVERT: Q 148 GLU cc_start: 0.8359 (tt0) cc_final: 0.7969 (tt0) REVERT: R 16 ASP cc_start: 0.8874 (m-30) cc_final: 0.8524 (m-30) REVERT: R 91 ARG cc_start: 0.8252 (mtp85) cc_final: 0.7984 (mtp85) REVERT: R 93 ASP cc_start: 0.8037 (t0) cc_final: 0.7721 (t70) REVERT: R 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8358 (tp40) REVERT: R 124 GLU cc_start: 0.8001 (tm-30) cc_final: 0.7769 (tm-30) REVERT: R 125 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8522 (mmtm) REVERT: R 141 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7221 (mp0) REVERT: R 148 GLU cc_start: 0.8335 (tt0) cc_final: 0.8087 (tt0) REVERT: S 16 ASP cc_start: 0.8872 (m-30) cc_final: 0.8525 (m-30) REVERT: S 64 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7061 (ttp-170) REVERT: S 91 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7985 (mtp85) REVERT: S 93 ASP cc_start: 0.8041 (t0) cc_final: 0.7725 (t70) REVERT: S 113 GLN cc_start: 0.8698 (tp40) cc_final: 0.8362 (tp40) REVERT: S 124 GLU cc_start: 0.7997 (tm-30) cc_final: 0.7769 (tm-30) REVERT: S 125 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8517 (mmtm) REVERT: S 141 GLU cc_start: 0.7762 (mm-30) cc_final: 0.7223 (mp0) REVERT: S 148 GLU cc_start: 0.8324 (tt0) cc_final: 0.8074 (tt0) REVERT: T 16 ASP cc_start: 0.8876 (m-30) cc_final: 0.8524 (m-30) REVERT: T 18 GLU cc_start: 0.8460 (tt0) cc_final: 0.8115 (tt0) REVERT: T 59 GLN cc_start: 0.8246 (mm110) cc_final: 0.8003 (mm110) REVERT: T 91 ARG cc_start: 0.8285 (mtp85) cc_final: 0.8006 (mtp85) REVERT: T 93 ASP cc_start: 0.8005 (t0) cc_final: 0.7688 (t70) REVERT: T 113 GLN cc_start: 0.8717 (tp40) cc_final: 0.8363 (tp40) REVERT: T 124 GLU cc_start: 0.7991 (tm-30) cc_final: 0.7750 (tm-30) REVERT: T 125 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8522 (mmtm) REVERT: T 141 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7255 (mp0) REVERT: T 148 GLU cc_start: 0.8366 (tt0) cc_final: 0.7972 (tt0) REVERT: U 18 GLU cc_start: 0.8445 (tt0) cc_final: 0.8098 (tt0) REVERT: U 64 ARG cc_start: 0.8147 (tpp80) cc_final: 0.7077 (ttp-170) REVERT: U 91 ARG cc_start: 0.8276 (mtp85) cc_final: 0.7995 (mtp85) REVERT: U 93 ASP cc_start: 0.8006 (t0) cc_final: 0.7700 (t70) REVERT: U 113 GLN cc_start: 0.8705 (tp40) cc_final: 0.8364 (tp40) REVERT: U 120 LYS cc_start: 0.8507 (ttpp) cc_final: 0.8075 (ttmm) REVERT: U 124 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7770 (tm-30) REVERT: U 125 LYS cc_start: 0.8819 (mmtt) cc_final: 0.8592 (mmtm) REVERT: U 141 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7243 (mp0) REVERT: U 148 GLU cc_start: 0.8326 (tt0) cc_final: 0.8030 (tt0) REVERT: V 59 GLN cc_start: 0.8222 (mm110) cc_final: 0.8006 (mm110) REVERT: V 91 ARG cc_start: 0.8275 (mtp85) cc_final: 0.7988 (mtp85) REVERT: V 93 ASP cc_start: 0.8030 (t0) cc_final: 0.7703 (t70) REVERT: V 113 GLN cc_start: 0.8711 (tp40) cc_final: 0.8363 (tp40) REVERT: V 120 LYS cc_start: 0.8551 (tttm) cc_final: 0.8180 (ttmt) REVERT: V 124 GLU cc_start: 0.7974 (tm-30) cc_final: 0.7753 (tm-30) REVERT: V 125 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8566 (mmtm) REVERT: V 148 GLU cc_start: 0.8306 (tt0) cc_final: 0.8051 (tt0) REVERT: W 18 GLU cc_start: 0.8464 (tt0) cc_final: 0.8122 (tt0) REVERT: W 59 GLN cc_start: 0.8246 (mm110) cc_final: 0.8015 (mm110) REVERT: W 91 ARG cc_start: 0.8314 (mtp85) cc_final: 0.8041 (mtp85) REVERT: W 93 ASP cc_start: 0.8015 (t0) cc_final: 0.7701 (t70) REVERT: W 113 GLN cc_start: 0.8718 (tp40) cc_final: 0.8378 (tp40) REVERT: W 124 GLU cc_start: 0.7978 (tm-30) cc_final: 0.7757 (tm-30) REVERT: W 125 LYS cc_start: 0.8809 (mmtt) cc_final: 0.8519 (mmtm) REVERT: W 148 GLU cc_start: 0.8389 (tt0) cc_final: 0.8126 (tt0) REVERT: X 16 ASP cc_start: 0.8881 (m-30) cc_final: 0.8526 (m-30) REVERT: X 18 GLU cc_start: 0.8449 (tt0) cc_final: 0.8116 (tt0) REVERT: X 91 ARG cc_start: 0.8270 (mtp85) cc_final: 0.7993 (mtp85) REVERT: X 93 ASP cc_start: 0.8038 (t0) cc_final: 0.7724 (t70) REVERT: X 113 GLN cc_start: 0.8700 (tp40) cc_final: 0.8349 (tp40) REVERT: X 120 LYS cc_start: 0.8558 (tttm) cc_final: 0.8291 (tttp) REVERT: X 124 GLU cc_start: 0.7988 (tm-30) cc_final: 0.7754 (tm-30) REVERT: X 125 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8518 (mmtm) REVERT: X 141 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7222 (mp0) REVERT: X 148 GLU cc_start: 0.8339 (tt0) cc_final: 0.8070 (tt0) outliers start: 50 outliers final: 54 residues processed: 1137 average time/residue: 1.7063 time to fit residues: 2260.5436 Evaluate side-chains 1118 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 1064 time to evaluate : 3.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 4.9990 chunk 114 optimal weight: 2.9990 chunk 308 optimal weight: 7.9990 chunk 252 optimal weight: 5.9990 chunk 102 optimal weight: 8.9990 chunk 371 optimal weight: 0.9980 chunk 400 optimal weight: 4.9990 chunk 330 optimal weight: 7.9990 chunk 368 optimal weight: 4.9990 chunk 126 optimal weight: 2.9990 chunk 297 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 112 ASN B 8 GLN B 112 ASN C 8 GLN D 8 GLN D 112 ASN E 8 GLN E 112 ASN F 8 GLN F 112 ASN G 8 GLN H 8 GLN H 112 ASN I 8 GLN I 112 ASN J 8 GLN J 112 ASN K 8 GLN K 112 ASN L 8 GLN L 112 ASN M 8 GLN M 112 ASN N 8 GLN N 112 ASN O 8 GLN O 112 ASN P 8 GLN P 112 ASN Q 8 GLN Q 112 ASN R 8 GLN R 112 ASN S 8 GLN S 112 ASN T 8 GLN T 112 ASN U 8 GLN U 112 ASN V 8 GLN W 8 GLN W 112 ASN X 8 GLN X 112 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.033 34776 Z= 0.356 Angle : 0.571 6.171 46824 Z= 0.293 Chirality : 0.041 0.136 4872 Planarity : 0.004 0.032 6216 Dihedral : 4.094 14.310 4584 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.93 % Allowed : 10.89 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.66 (0.13), residues: 4104 helix: 3.66 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.53 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.002 TRP D 94 HIS 0.003 0.001 HIS N 137 PHE 0.014 0.003 PHE C 133 TYR 0.014 0.002 TYR C 40 ARG 0.004 0.001 ARG D 91 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1128 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 1057 time to evaluate : 3.940 Fit side-chains REVERT: A 64 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7096 (ttp-170) REVERT: A 113 GLN cc_start: 0.8790 (tp40) cc_final: 0.8438 (tp40) REVERT: A 124 GLU cc_start: 0.7976 (tm-30) cc_final: 0.7772 (tm-30) REVERT: A 125 LYS cc_start: 0.8855 (mmtt) cc_final: 0.8619 (mmtm) REVERT: A 148 GLU cc_start: 0.8345 (tt0) cc_final: 0.8117 (tt0) REVERT: B 16 ASP cc_start: 0.8941 (m-30) cc_final: 0.8726 (m-30) REVERT: B 125 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8640 (mmtm) REVERT: B 141 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7300 (mp0) REVERT: B 148 GLU cc_start: 0.8406 (tt0) cc_final: 0.7995 (tt0) REVERT: C 64 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7070 (ttp-170) REVERT: C 125 LYS cc_start: 0.8866 (mmtt) cc_final: 0.8469 (mmtm) REVERT: C 141 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7297 (mp0) REVERT: D 62 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7127 (mm-30) REVERT: D 125 LYS cc_start: 0.8900 (mmtt) cc_final: 0.8643 (mmtm) REVERT: D 141 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7295 (mp0) REVERT: E 64 ARG cc_start: 0.8162 (tpp80) cc_final: 0.7096 (ttp-170) REVERT: E 113 GLN cc_start: 0.8788 (tp40) cc_final: 0.8441 (tp40) REVERT: E 148 GLU cc_start: 0.8394 (tt0) cc_final: 0.8169 (tt0) REVERT: F 16 ASP cc_start: 0.8931 (m-30) cc_final: 0.8672 (m-30) REVERT: F 64 ARG cc_start: 0.8148 (tpp80) cc_final: 0.7085 (ttp-170) REVERT: F 124 GLU cc_start: 0.7975 (tm-30) cc_final: 0.7768 (tm-30) REVERT: F 125 LYS cc_start: 0.8851 (mmtt) cc_final: 0.8603 (mmtm) REVERT: F 141 GLU cc_start: 0.7756 (mm-30) cc_final: 0.7302 (mp0) REVERT: F 148 GLU cc_start: 0.8352 (tt0) cc_final: 0.8125 (tt0) REVERT: G 16 ASP cc_start: 0.8927 (m-30) cc_final: 0.8676 (m-30) REVERT: G 59 GLN cc_start: 0.8296 (mm110) cc_final: 0.8057 (mm110) REVERT: G 64 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7102 (ttp-170) REVERT: G 91 ARG cc_start: 0.8293 (mtp85) cc_final: 0.8092 (mtp85) REVERT: G 120 LYS cc_start: 0.8600 (tttm) cc_final: 0.8202 (ttmp) REVERT: G 125 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8644 (mmtm) REVERT: G 141 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7308 (mp0) REVERT: G 148 GLU cc_start: 0.8321 (tt0) cc_final: 0.8119 (tt0) REVERT: H 59 GLN cc_start: 0.8301 (mm110) cc_final: 0.8063 (mm110) REVERT: H 113 GLN cc_start: 0.8779 (tp40) cc_final: 0.8437 (tp40) REVERT: H 125 LYS cc_start: 0.8861 (mmtt) cc_final: 0.8625 (mmtm) REVERT: H 148 GLU cc_start: 0.8447 (tt0) cc_final: 0.8036 (tt0) REVERT: H 158 LYS cc_start: 0.8340 (mttt) cc_final: 0.8125 (mtmt) REVERT: I 64 ARG cc_start: 0.8122 (tpp80) cc_final: 0.7084 (ttp-170) REVERT: I 125 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8634 (mmtm) REVERT: I 148 GLU cc_start: 0.8311 (tt0) cc_final: 0.8110 (tt0) REVERT: J 59 GLN cc_start: 0.8275 (mm110) cc_final: 0.8048 (mm110) REVERT: J 125 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8632 (mmtm) REVERT: K 62 GLU cc_start: 0.7429 (mm-30) cc_final: 0.7108 (mm-30) REVERT: K 64 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7092 (ttp-170) REVERT: K 125 LYS cc_start: 0.8882 (mmtt) cc_final: 0.8634 (mmtm) REVERT: K 141 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7316 (mp0) REVERT: K 148 GLU cc_start: 0.8413 (tt0) cc_final: 0.8011 (tt0) REVERT: L 16 ASP cc_start: 0.8924 (m-30) cc_final: 0.8671 (m-30) REVERT: L 64 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7103 (ttp-170) REVERT: L 91 ARG cc_start: 0.8291 (mtp85) cc_final: 0.8090 (mtp85) REVERT: L 120 LYS cc_start: 0.8601 (tttm) cc_final: 0.8279 (tttp) REVERT: L 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8645 (mmtm) REVERT: L 141 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7305 (mp0) REVERT: M 16 ASP cc_start: 0.8917 (m-30) cc_final: 0.8656 (m-30) REVERT: M 64 ARG cc_start: 0.8141 (tpp80) cc_final: 0.7104 (ttp-170) REVERT: M 113 GLN cc_start: 0.8798 (tp40) cc_final: 0.8595 (tp40) REVERT: M 120 LYS cc_start: 0.8573 (tttm) cc_final: 0.8171 (ttmp) REVERT: M 125 LYS cc_start: 0.8869 (mmtt) cc_final: 0.8659 (mmtm) REVERT: M 141 GLU cc_start: 0.7780 (mm-30) cc_final: 0.7319 (mp0) REVERT: M 148 GLU cc_start: 0.8355 (tt0) cc_final: 0.8097 (tt0) REVERT: N 113 GLN cc_start: 0.8790 (tp40) cc_final: 0.8442 (tp40) REVERT: N 148 GLU cc_start: 0.8395 (tt0) cc_final: 0.8170 (tt0) REVERT: O 59 GLN cc_start: 0.8271 (mm110) cc_final: 0.8046 (mm110) REVERT: O 64 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7079 (ttp-170) REVERT: O 125 LYS cc_start: 0.8857 (mmtt) cc_final: 0.8621 (mmtm) REVERT: O 158 LYS cc_start: 0.8334 (mttt) cc_final: 0.8116 (mtmt) REVERT: P 124 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7766 (tm-30) REVERT: P 125 LYS cc_start: 0.8802 (mmtt) cc_final: 0.8539 (mmtm) REVERT: P 141 GLU cc_start: 0.7739 (mm-30) cc_final: 0.7308 (mp0) REVERT: P 148 GLU cc_start: 0.8353 (tt0) cc_final: 0.8127 (tt0) REVERT: Q 16 ASP cc_start: 0.8939 (m-30) cc_final: 0.8727 (m-30) REVERT: Q 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8641 (mmtm) REVERT: Q 141 GLU cc_start: 0.7764 (mm-30) cc_final: 0.7294 (mp0) REVERT: Q 148 GLU cc_start: 0.8405 (tt0) cc_final: 0.8000 (tt0) REVERT: R 113 GLN cc_start: 0.8792 (tp40) cc_final: 0.8591 (tp40) REVERT: R 141 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7305 (mp0) REVERT: R 148 GLU cc_start: 0.8344 (tt0) cc_final: 0.8131 (tt0) REVERT: S 16 ASP cc_start: 0.8909 (m-30) cc_final: 0.8659 (m-30) REVERT: S 64 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7100 (ttp-170) REVERT: S 125 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8640 (mmtm) REVERT: S 141 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7307 (mp0) REVERT: S 148 GLU cc_start: 0.8337 (tt0) cc_final: 0.8122 (tt0) REVERT: T 62 GLU cc_start: 0.7424 (mm-30) cc_final: 0.7112 (mm-30) REVERT: T 125 LYS cc_start: 0.8883 (mmtt) cc_final: 0.8637 (mmtm) REVERT: T 141 GLU cc_start: 0.7734 (mm-30) cc_final: 0.7323 (mp0) REVERT: T 148 GLU cc_start: 0.8412 (tt0) cc_final: 0.8009 (tt0) REVERT: U 64 ARG cc_start: 0.8136 (tpp80) cc_final: 0.7105 (ttp-170) REVERT: U 124 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7779 (tm-30) REVERT: U 125 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8549 (mmtm) REVERT: U 141 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7309 (mp0) REVERT: U 148 GLU cc_start: 0.8353 (tt0) cc_final: 0.8127 (tt0) REVERT: V 59 GLN cc_start: 0.8272 (mm110) cc_final: 0.8055 (mm110) REVERT: V 125 LYS cc_start: 0.8858 (mmtt) cc_final: 0.8625 (mmtm) REVERT: V 158 LYS cc_start: 0.8339 (mttt) cc_final: 0.8117 (mtmt) REVERT: W 59 GLN cc_start: 0.8298 (mm110) cc_final: 0.8056 (mm110) REVERT: W 62 GLU cc_start: 0.7475 (mm-30) cc_final: 0.7167 (mm-30) REVERT: W 125 LYS cc_start: 0.8814 (mmtt) cc_final: 0.8584 (mmtm) REVERT: W 148 GLU cc_start: 0.8448 (tt0) cc_final: 0.8037 (tt0) REVERT: W 158 LYS cc_start: 0.8342 (mttt) cc_final: 0.8129 (mtmt) REVERT: X 16 ASP cc_start: 0.8919 (m-30) cc_final: 0.8655 (m-30) REVERT: X 113 GLN cc_start: 0.8800 (tp40) cc_final: 0.8595 (tp40) REVERT: X 120 LYS cc_start: 0.8565 (tttm) cc_final: 0.8164 (ttmp) REVERT: X 125 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8658 (mmtm) REVERT: X 141 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7316 (mp0) REVERT: X 148 GLU cc_start: 0.8354 (tt0) cc_final: 0.8100 (tt0) outliers start: 71 outliers final: 69 residues processed: 1081 average time/residue: 1.8098 time to fit residues: 2261.6463 Evaluate side-chains 1050 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 981 time to evaluate : 3.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 3.9990 chunk 279 optimal weight: 1.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 177 optimal weight: 1.9990 chunk 249 optimal weight: 0.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 0.7980 chunk 194 optimal weight: 3.9990 chunk 353 optimal weight: 0.7980 chunk 106 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN A 26 ASN B 8 GLN B 26 ASN C 8 GLN C 26 ASN D 8 GLN E 8 GLN E 26 ASN F 8 GLN F 26 ASN G 8 GLN G 26 ASN H 26 ASN I 8 GLN I 26 ASN J 8 GLN J 26 ASN K 26 ASN L 8 GLN L 26 ASN M 26 ASN N 8 GLN N 26 ASN O 8 GLN P 8 GLN Q 8 GLN Q 26 ASN R 8 GLN R 26 ASN S 8 GLN S 26 ASN T 8 GLN T 26 ASN U 8 GLN V 8 GLN V 26 ASN W 8 GLN W 26 ASN X 8 GLN X 26 ASN Total number of N/Q/H flips: 41 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 34776 Z= 0.170 Angle : 0.460 5.073 46824 Z= 0.241 Chirality : 0.034 0.120 4872 Planarity : 0.003 0.024 6216 Dihedral : 3.841 15.884 4584 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.12 % Allowed : 11.52 % Favored : 86.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.27 (0.13), residues: 4104 helix: 4.11 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.64 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP G 94 HIS 0.002 0.001 HIS S 119 PHE 0.013 0.002 PHE C 133 TYR 0.012 0.001 TYR D 40 ARG 0.003 0.000 ARG U 157 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1125 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1047 time to evaluate : 4.510 Fit side-chains REVERT: A 59 GLN cc_start: 0.8287 (mm110) cc_final: 0.8032 (mm110) REVERT: A 64 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7042 (ttp-170) REVERT: A 93 ASP cc_start: 0.7958 (t0) cc_final: 0.7724 (t70) REVERT: A 113 GLN cc_start: 0.8772 (tp40) cc_final: 0.8413 (tp40) REVERT: A 124 GLU cc_start: 0.8005 (tm-30) cc_final: 0.7792 (tm-30) REVERT: A 125 LYS cc_start: 0.8808 (mmtt) cc_final: 0.8568 (mmtm) REVERT: A 148 GLU cc_start: 0.8336 (tt0) cc_final: 0.8079 (tt0) REVERT: A 158 LYS cc_start: 0.7938 (mtmt) cc_final: 0.7627 (mttt) REVERT: B 16 ASP cc_start: 0.8914 (m-30) cc_final: 0.8679 (m-30) REVERT: B 59 GLN cc_start: 0.8245 (mm110) cc_final: 0.8005 (mm110) REVERT: B 93 ASP cc_start: 0.7877 (t0) cc_final: 0.7676 (t70) REVERT: B 124 GLU cc_start: 0.7996 (tm-30) cc_final: 0.7794 (tm-30) REVERT: B 125 LYS cc_start: 0.8830 (mmtt) cc_final: 0.8544 (mmtm) REVERT: B 141 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7293 (mp0) REVERT: B 148 GLU cc_start: 0.8354 (tt0) cc_final: 0.7924 (tt0) REVERT: C 59 GLN cc_start: 0.8189 (mm110) cc_final: 0.7961 (mm110) REVERT: C 64 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7151 (ttp-170) REVERT: C 93 ASP cc_start: 0.7913 (t0) cc_final: 0.7687 (t70) REVERT: C 124 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7644 (tm-30) REVERT: C 141 GLU cc_start: 0.7779 (mm-30) cc_final: 0.7296 (mp0) REVERT: D 59 GLN cc_start: 0.8223 (mm110) cc_final: 0.7991 (mm110) REVERT: D 62 GLU cc_start: 0.7410 (mm-30) cc_final: 0.7127 (mm-30) REVERT: D 93 ASP cc_start: 0.7884 (t0) cc_final: 0.7676 (t70) REVERT: D 125 LYS cc_start: 0.8825 (mmtt) cc_final: 0.8592 (mmtm) REVERT: D 141 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7293 (mp0) REVERT: E 59 GLN cc_start: 0.8256 (mm110) cc_final: 0.8017 (mm110) REVERT: E 62 GLU cc_start: 0.7477 (mm-30) cc_final: 0.7237 (mm-30) REVERT: E 64 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7027 (ttp-170) REVERT: E 93 ASP cc_start: 0.7927 (t0) cc_final: 0.7688 (t70) REVERT: E 113 GLN cc_start: 0.8775 (tp40) cc_final: 0.8414 (tp40) REVERT: E 148 GLU cc_start: 0.8365 (tt0) cc_final: 0.8104 (tt0) REVERT: F 59 GLN cc_start: 0.8287 (mm110) cc_final: 0.8044 (mm110) REVERT: F 64 ARG cc_start: 0.8153 (tpp80) cc_final: 0.7045 (ttp-170) REVERT: F 124 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7795 (tm-30) REVERT: F 125 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8563 (mmtm) REVERT: F 141 GLU cc_start: 0.7785 (mm-30) cc_final: 0.7290 (mp0) REVERT: F 148 GLU cc_start: 0.8344 (tt0) cc_final: 0.8088 (tt0) REVERT: F 158 LYS cc_start: 0.7944 (mtmt) cc_final: 0.7633 (mttt) REVERT: G 16 ASP cc_start: 0.8904 (m-30) cc_final: 0.8629 (m-30) REVERT: G 59 GLN cc_start: 0.8257 (mm110) cc_final: 0.8012 (mm110) REVERT: G 64 ARG cc_start: 0.8126 (tpp80) cc_final: 0.7031 (ttp-170) REVERT: G 93 ASP cc_start: 0.7926 (t0) cc_final: 0.7699 (t70) REVERT: G 120 LYS cc_start: 0.8559 (tttm) cc_final: 0.8178 (ttmp) REVERT: G 125 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8579 (mmtm) REVERT: G 141 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7300 (mp0) REVERT: G 148 GLU cc_start: 0.8297 (tt0) cc_final: 0.8069 (tt0) REVERT: H 18 GLU cc_start: 0.8524 (tt0) cc_final: 0.8164 (tt0) REVERT: H 59 GLN cc_start: 0.8274 (mm110) cc_final: 0.8021 (mm110) REVERT: H 93 ASP cc_start: 0.7904 (t0) cc_final: 0.7689 (t70) REVERT: H 113 GLN cc_start: 0.8767 (tp40) cc_final: 0.8416 (tp40) REVERT: H 125 LYS cc_start: 0.8817 (mmtt) cc_final: 0.8561 (mmtm) REVERT: H 148 GLU cc_start: 0.8382 (tt0) cc_final: 0.8125 (tt0) REVERT: I 59 GLN cc_start: 0.8233 (mm110) cc_final: 0.7994 (mm110) REVERT: I 62 GLU cc_start: 0.7347 (mm-30) cc_final: 0.7119 (mm-30) REVERT: I 64 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7080 (ttp-170) REVERT: I 93 ASP cc_start: 0.7905 (t0) cc_final: 0.7664 (t70) REVERT: I 125 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8587 (mmtm) REVERT: I 148 GLU cc_start: 0.8290 (tt0) cc_final: 0.8039 (tt0) REVERT: J 59 GLN cc_start: 0.8247 (mm110) cc_final: 0.8011 (mm110) REVERT: J 62 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7111 (mm-30) REVERT: J 93 ASP cc_start: 0.7905 (t0) cc_final: 0.7665 (t70) REVERT: J 125 LYS cc_start: 0.8835 (mmtt) cc_final: 0.8585 (mmtm) REVERT: K 18 GLU cc_start: 0.8502 (tt0) cc_final: 0.8136 (tt0) REVERT: K 59 GLN cc_start: 0.8288 (mm110) cc_final: 0.8037 (mm110) REVERT: K 64 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7060 (ttp-170) REVERT: K 93 ASP cc_start: 0.7920 (t0) cc_final: 0.7685 (t70) REVERT: K 125 LYS cc_start: 0.8899 (mmtt) cc_final: 0.8623 (mmtm) REVERT: K 141 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7309 (mp0) REVERT: K 148 GLU cc_start: 0.8369 (tt0) cc_final: 0.7947 (tt0) REVERT: L 16 ASP cc_start: 0.8903 (m-30) cc_final: 0.8623 (m-30) REVERT: L 59 GLN cc_start: 0.8250 (mm110) cc_final: 0.8006 (mm110) REVERT: L 64 ARG cc_start: 0.8125 (tpp80) cc_final: 0.7031 (ttp-170) REVERT: L 93 ASP cc_start: 0.7924 (t0) cc_final: 0.7699 (t70) REVERT: L 120 LYS cc_start: 0.8590 (tttm) cc_final: 0.8220 (ttmp) REVERT: L 125 LYS cc_start: 0.8860 (mmtt) cc_final: 0.8579 (mmtm) REVERT: L 141 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7302 (mp0) REVERT: M 59 GLN cc_start: 0.8256 (mm110) cc_final: 0.8020 (mm110) REVERT: M 64 ARG cc_start: 0.8143 (tpp80) cc_final: 0.7030 (ttp-170) REVERT: M 120 LYS cc_start: 0.8533 (tttm) cc_final: 0.8161 (ttmp) REVERT: M 125 LYS cc_start: 0.8862 (mmtt) cc_final: 0.8627 (mmtm) REVERT: M 141 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7282 (mp0) REVERT: M 148 GLU cc_start: 0.8337 (tt0) cc_final: 0.8069 (tt0) REVERT: N 59 GLN cc_start: 0.8254 (mm110) cc_final: 0.8017 (mm110) REVERT: N 62 GLU cc_start: 0.7469 (mm-30) cc_final: 0.7245 (mm-30) REVERT: N 93 ASP cc_start: 0.7927 (t0) cc_final: 0.7684 (t70) REVERT: N 113 GLN cc_start: 0.8775 (tp40) cc_final: 0.8416 (tp40) REVERT: N 148 GLU cc_start: 0.8365 (tt0) cc_final: 0.8103 (tt0) REVERT: O 59 GLN cc_start: 0.8224 (mm110) cc_final: 0.7993 (mm110) REVERT: O 64 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7028 (ttp-170) REVERT: O 93 ASP cc_start: 0.7920 (t0) cc_final: 0.7707 (t70) REVERT: O 125 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8594 (mmtm) REVERT: P 93 ASP cc_start: 0.7899 (t0) cc_final: 0.7680 (t70) REVERT: P 125 LYS cc_start: 0.8772 (mmtt) cc_final: 0.8563 (mmtm) REVERT: P 141 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7392 (tm-30) REVERT: P 148 GLU cc_start: 0.8313 (tt0) cc_final: 0.8074 (tt0) REVERT: Q 16 ASP cc_start: 0.8913 (m-30) cc_final: 0.8646 (m-30) REVERT: Q 59 GLN cc_start: 0.8251 (mm110) cc_final: 0.8012 (mm110) REVERT: Q 125 LYS cc_start: 0.8832 (mmtt) cc_final: 0.8566 (mmtm) REVERT: Q 141 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7287 (mp0) REVERT: Q 148 GLU cc_start: 0.8359 (tt0) cc_final: 0.7934 (tt0) REVERT: R 59 GLN cc_start: 0.8254 (mm110) cc_final: 0.8021 (mm110) REVERT: R 93 ASP cc_start: 0.7936 (t0) cc_final: 0.7710 (t70) REVERT: R 113 GLN cc_start: 0.8769 (tp40) cc_final: 0.8408 (tp40) REVERT: R 141 GLU cc_start: 0.7806 (mm-30) cc_final: 0.7300 (mp0) REVERT: R 148 GLU cc_start: 0.8335 (tt0) cc_final: 0.8095 (tt0) REVERT: S 59 GLN cc_start: 0.8252 (mm110) cc_final: 0.8017 (mm110) REVERT: S 64 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7033 (ttp-170) REVERT: S 93 ASP cc_start: 0.7937 (t0) cc_final: 0.7714 (t70) REVERT: S 125 LYS cc_start: 0.8829 (mmtt) cc_final: 0.8584 (mmtm) REVERT: S 141 GLU cc_start: 0.7804 (mm-30) cc_final: 0.7300 (mp0) REVERT: S 148 GLU cc_start: 0.8329 (tt0) cc_final: 0.8087 (tt0) REVERT: T 18 GLU cc_start: 0.8505 (tt0) cc_final: 0.8141 (tt0) REVERT: T 59 GLN cc_start: 0.8283 (mm110) cc_final: 0.8037 (mm110) REVERT: T 93 ASP cc_start: 0.7921 (t0) cc_final: 0.7682 (t70) REVERT: T 125 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8605 (mmtm) REVERT: T 141 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7316 (mp0) REVERT: T 148 GLU cc_start: 0.8368 (tt0) cc_final: 0.7945 (tt0) REVERT: U 64 ARG cc_start: 0.8159 (tpp80) cc_final: 0.7080 (ttp-170) REVERT: U 124 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7803 (tm-30) REVERT: U 125 LYS cc_start: 0.8779 (mmtt) cc_final: 0.8530 (mmtm) REVERT: U 141 GLU cc_start: 0.7776 (mm-30) cc_final: 0.7301 (mp0) REVERT: U 148 GLU cc_start: 0.8312 (tt0) cc_final: 0.8074 (tt0) REVERT: V 59 GLN cc_start: 0.8229 (mm110) cc_final: 0.8002 (mm110) REVERT: V 93 ASP cc_start: 0.7919 (t0) cc_final: 0.7703 (t70) REVERT: V 125 LYS cc_start: 0.8843 (mmtt) cc_final: 0.8597 (mmtm) REVERT: W 59 GLN cc_start: 0.8274 (mm110) cc_final: 0.8026 (mm110) REVERT: W 62 GLU cc_start: 0.7458 (mm-30) cc_final: 0.7225 (mm-30) REVERT: W 93 ASP cc_start: 0.7904 (t0) cc_final: 0.7696 (t70) REVERT: W 125 LYS cc_start: 0.8777 (mmtt) cc_final: 0.8488 (mmtm) REVERT: W 148 GLU cc_start: 0.8380 (tt0) cc_final: 0.8120 (tt0) REVERT: X 59 GLN cc_start: 0.8261 (mm110) cc_final: 0.8028 (mm110) REVERT: X 93 ASP cc_start: 0.7924 (t0) cc_final: 0.7724 (t70) REVERT: X 120 LYS cc_start: 0.8531 (tttm) cc_final: 0.8163 (ttmp) REVERT: X 125 LYS cc_start: 0.8865 (mmtt) cc_final: 0.8589 (mmtm) REVERT: X 141 GLU cc_start: 0.7770 (mm-30) cc_final: 0.7287 (mp0) REVERT: X 148 GLU cc_start: 0.8338 (tt0) cc_final: 0.8069 (tt0) outliers start: 78 outliers final: 59 residues processed: 1071 average time/residue: 1.8132 time to fit residues: 2246.8548 Evaluate side-chains 1057 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 998 time to evaluate : 3.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 110 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 3.9990 chunk 223 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 293 optimal weight: 0.9980 chunk 162 optimal weight: 0.8980 chunk 336 optimal weight: 8.9990 chunk 272 optimal weight: 0.0470 chunk 0 optimal weight: 8.9990 chunk 201 optimal weight: 0.5980 chunk 353 optimal weight: 10.0000 chunk 99 optimal weight: 0.7980 overall best weight: 0.6678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN D 8 GLN D 26 ASN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN L 8 GLN M 8 GLN N 8 GLN O 8 GLN O 26 ASN P 8 GLN P 26 ASN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 8 GLN U 26 ASN V 8 GLN W 8 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 34776 Z= 0.120 Angle : 0.422 5.056 46824 Z= 0.223 Chirality : 0.032 0.114 4872 Planarity : 0.002 0.022 6216 Dihedral : 3.631 15.767 4584 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 1.25 % Allowed : 12.64 % Favored : 86.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.78 (0.13), residues: 4104 helix: 4.48 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.77 (0.27), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP C 94 HIS 0.001 0.000 HIS C 66 PHE 0.011 0.002 PHE C 133 TYR 0.009 0.001 TYR O 138 ARG 0.002 0.000 ARG O 157 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1120 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 1074 time to evaluate : 3.962 Fit side-chains REVERT: A 18 GLU cc_start: 0.8448 (tt0) cc_final: 0.8159 (tt0) REVERT: A 59 GLN cc_start: 0.8272 (mm110) cc_final: 0.8005 (mm110) REVERT: A 64 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7169 (ttp-170) REVERT: A 93 ASP cc_start: 0.7807 (t0) cc_final: 0.7592 (t70) REVERT: A 113 GLN cc_start: 0.8745 (tp40) cc_final: 0.8389 (tp40) REVERT: A 124 GLU cc_start: 0.8008 (tm-30) cc_final: 0.7774 (tm-30) REVERT: A 125 LYS cc_start: 0.8769 (mmtt) cc_final: 0.8502 (mmtm) REVERT: A 148 GLU cc_start: 0.8344 (tt0) cc_final: 0.8081 (tt0) REVERT: B 16 ASP cc_start: 0.8822 (m-30) cc_final: 0.8587 (m-30) REVERT: B 18 GLU cc_start: 0.8423 (tt0) cc_final: 0.8150 (tt0) REVERT: B 63 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7163 (mm-30) REVERT: B 124 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7771 (tm-30) REVERT: B 125 LYS cc_start: 0.8805 (mmtt) cc_final: 0.8339 (mmtm) REVERT: B 141 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7178 (mp0) REVERT: B 148 GLU cc_start: 0.8361 (tt0) cc_final: 0.7942 (tt0) REVERT: C 59 GLN cc_start: 0.8152 (mm110) cc_final: 0.7905 (mm110) REVERT: C 64 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7167 (ttp-170) REVERT: C 93 ASP cc_start: 0.7771 (t0) cc_final: 0.7570 (t70) REVERT: C 113 GLN cc_start: 0.8701 (tp40) cc_final: 0.8268 (tp40) REVERT: C 141 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7179 (mp0) REVERT: D 59 GLN cc_start: 0.8140 (mm110) cc_final: 0.7925 (mm110) REVERT: D 62 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7174 (mm-30) REVERT: D 93 ASP cc_start: 0.7771 (t0) cc_final: 0.7570 (t70) REVERT: D 125 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8427 (mmtm) REVERT: D 141 GLU cc_start: 0.7663 (mm-30) cc_final: 0.7174 (mp0) REVERT: E 18 GLU cc_start: 0.8449 (tt0) cc_final: 0.8144 (tt0) REVERT: E 59 GLN cc_start: 0.8171 (mm110) cc_final: 0.7952 (mm110) REVERT: E 64 ARG cc_start: 0.8164 (tpp80) cc_final: 0.7141 (ttp-170) REVERT: E 113 GLN cc_start: 0.8718 (tp40) cc_final: 0.8347 (tp40) REVERT: E 148 GLU cc_start: 0.8367 (tt0) cc_final: 0.8105 (tt0) REVERT: F 59 GLN cc_start: 0.8271 (mm110) cc_final: 0.8011 (mm110) REVERT: F 64 ARG cc_start: 0.8151 (tpp80) cc_final: 0.7169 (ttp-170) REVERT: F 93 ASP cc_start: 0.7794 (t0) cc_final: 0.7590 (t70) REVERT: F 124 GLU cc_start: 0.8026 (tm-30) cc_final: 0.7790 (tm-30) REVERT: F 125 LYS cc_start: 0.8789 (mmtt) cc_final: 0.8477 (mmtm) REVERT: F 141 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7254 (mp0) REVERT: F 148 GLU cc_start: 0.8353 (tt0) cc_final: 0.8087 (tt0) REVERT: G 16 ASP cc_start: 0.8844 (m-30) cc_final: 0.8603 (m-30) REVERT: G 59 GLN cc_start: 0.8231 (mm110) cc_final: 0.7986 (mm110) REVERT: G 64 ARG cc_start: 0.8156 (tpp80) cc_final: 0.7150 (ttp-170) REVERT: G 120 LYS cc_start: 0.8546 (tttm) cc_final: 0.8219 (ttmp) REVERT: G 125 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8528 (mmtm) REVERT: G 141 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7257 (mp0) REVERT: G 148 GLU cc_start: 0.8294 (tt0) cc_final: 0.8055 (tt0) REVERT: H 16 ASP cc_start: 0.8844 (m-30) cc_final: 0.8544 (m-30) REVERT: H 59 GLN cc_start: 0.8246 (mm110) cc_final: 0.8012 (mm110) REVERT: H 62 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7223 (mm-30) REVERT: H 113 GLN cc_start: 0.8715 (tp40) cc_final: 0.8358 (tp40) REVERT: H 125 LYS cc_start: 0.8765 (mmtt) cc_final: 0.8490 (mmtm) REVERT: H 148 GLU cc_start: 0.8380 (tt0) cc_final: 0.8122 (tt0) REVERT: I 18 GLU cc_start: 0.8441 (tt0) cc_final: 0.8149 (tt0) REVERT: I 59 GLN cc_start: 0.8174 (mm110) cc_final: 0.7928 (mm110) REVERT: I 64 ARG cc_start: 0.8142 (tpp80) cc_final: 0.7165 (ttp-170) REVERT: I 93 ASP cc_start: 0.7764 (t0) cc_final: 0.7561 (t70) REVERT: I 125 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8468 (mmtm) REVERT: I 148 GLU cc_start: 0.8297 (tt0) cc_final: 0.8068 (tt0) REVERT: J 59 GLN cc_start: 0.8227 (mm110) cc_final: 0.7987 (mm110) REVERT: J 62 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7118 (mm-30) REVERT: J 93 ASP cc_start: 0.7766 (t0) cc_final: 0.7560 (t70) REVERT: J 125 LYS cc_start: 0.8704 (mmtt) cc_final: 0.8468 (mmtm) REVERT: K 59 GLN cc_start: 0.8269 (mm110) cc_final: 0.7997 (mm110) REVERT: K 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7185 (mm-30) REVERT: K 64 ARG cc_start: 0.8137 (tpp80) cc_final: 0.7074 (ttp-170) REVERT: K 93 ASP cc_start: 0.7788 (t0) cc_final: 0.7586 (t70) REVERT: K 125 LYS cc_start: 0.8827 (mmtt) cc_final: 0.8554 (mmtm) REVERT: K 141 GLU cc_start: 0.7646 (mm-30) cc_final: 0.7193 (mp0) REVERT: K 148 GLU cc_start: 0.8368 (tt0) cc_final: 0.7958 (tt0) REVERT: L 16 ASP cc_start: 0.8821 (m-30) cc_final: 0.8576 (m-30) REVERT: L 18 GLU cc_start: 0.8451 (tt0) cc_final: 0.8178 (tt0) REVERT: L 59 GLN cc_start: 0.8197 (mm110) cc_final: 0.7943 (mm110) REVERT: L 64 ARG cc_start: 0.8155 (tpp80) cc_final: 0.7152 (ttp-170) REVERT: L 120 LYS cc_start: 0.8546 (tttm) cc_final: 0.8215 (ttmp) REVERT: L 125 LYS cc_start: 0.8750 (mmtt) cc_final: 0.8529 (mmtm) REVERT: L 141 GLU cc_start: 0.7753 (mm-30) cc_final: 0.7250 (mp0) REVERT: M 59 GLN cc_start: 0.8205 (mm110) cc_final: 0.7961 (mm110) REVERT: M 64 ARG cc_start: 0.8138 (tpp80) cc_final: 0.7174 (ttp-170) REVERT: M 120 LYS cc_start: 0.8531 (tttm) cc_final: 0.8253 (ttmp) REVERT: M 125 LYS cc_start: 0.8732 (mmtt) cc_final: 0.8519 (mmtm) REVERT: M 141 GLU cc_start: 0.7732 (mm-30) cc_final: 0.7241 (mp0) REVERT: M 148 GLU cc_start: 0.8344 (tt0) cc_final: 0.8077 (tt0) REVERT: N 18 GLU cc_start: 0.8449 (tt0) cc_final: 0.8145 (tt0) REVERT: N 59 GLN cc_start: 0.8201 (mm110) cc_final: 0.7952 (mm110) REVERT: N 62 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7193 (mm-30) REVERT: N 93 ASP cc_start: 0.7793 (t0) cc_final: 0.7588 (t70) REVERT: N 113 GLN cc_start: 0.8717 (tp40) cc_final: 0.8349 (tp40) REVERT: N 148 GLU cc_start: 0.8367 (tt0) cc_final: 0.8102 (tt0) REVERT: O 59 GLN cc_start: 0.8206 (mm110) cc_final: 0.7955 (mm110) REVERT: O 64 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7165 (ttp-170) REVERT: O 120 LYS cc_start: 0.8505 (tttm) cc_final: 0.8124 (ttmt) REVERT: O 125 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8436 (mmtm) REVERT: P 63 GLU cc_start: 0.7979 (mm-30) cc_final: 0.7235 (mm-30) REVERT: P 124 GLU cc_start: 0.8031 (tm-30) cc_final: 0.7807 (tm-30) REVERT: P 125 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8489 (mmtm) REVERT: P 141 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7249 (mp0) REVERT: P 148 GLU cc_start: 0.8318 (tt0) cc_final: 0.8069 (tt0) REVERT: Q 16 ASP cc_start: 0.8835 (m-30) cc_final: 0.8607 (m-30) REVERT: Q 59 GLN cc_start: 0.8192 (mm110) cc_final: 0.7937 (mm110) REVERT: Q 125 LYS cc_start: 0.8696 (mmtt) cc_final: 0.8453 (mmtm) REVERT: Q 141 GLU cc_start: 0.7683 (mm-30) cc_final: 0.7171 (mp0) REVERT: Q 148 GLU cc_start: 0.8359 (tt0) cc_final: 0.7945 (tt0) REVERT: R 18 GLU cc_start: 0.8441 (tt0) cc_final: 0.8145 (tt0) REVERT: R 59 GLN cc_start: 0.8198 (mm110) cc_final: 0.7959 (mm110) REVERT: R 93 ASP cc_start: 0.7801 (t0) cc_final: 0.7600 (t70) REVERT: R 113 GLN cc_start: 0.8729 (tp40) cc_final: 0.8366 (tp40) REVERT: R 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7243 (mp0) REVERT: R 148 GLU cc_start: 0.8324 (tt0) cc_final: 0.8078 (tt0) REVERT: S 18 GLU cc_start: 0.8446 (tt0) cc_final: 0.8144 (tt0) REVERT: S 59 GLN cc_start: 0.8197 (mm110) cc_final: 0.7956 (mm110) REVERT: S 64 ARG cc_start: 0.8154 (tpp80) cc_final: 0.7164 (ttp-170) REVERT: S 93 ASP cc_start: 0.7803 (t0) cc_final: 0.7602 (t70) REVERT: S 125 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8460 (mmtm) REVERT: S 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7244 (mp0) REVERT: S 148 GLU cc_start: 0.8319 (tt0) cc_final: 0.8072 (tt0) REVERT: T 59 GLN cc_start: 0.8269 (mm110) cc_final: 0.7999 (mm110) REVERT: T 62 GLU cc_start: 0.7435 (mm-30) cc_final: 0.7184 (mm-30) REVERT: T 93 ASP cc_start: 0.7787 (t0) cc_final: 0.7581 (t70) REVERT: T 125 LYS cc_start: 0.8770 (mmtt) cc_final: 0.8528 (mmtm) REVERT: T 141 GLU cc_start: 0.7657 (mm-30) cc_final: 0.7198 (mp0) REVERT: T 148 GLU cc_start: 0.8368 (tt0) cc_final: 0.7957 (tt0) REVERT: U 59 GLN cc_start: 0.8254 (mm110) cc_final: 0.7984 (mm110) REVERT: U 62 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7144 (mm-30) REVERT: U 64 ARG cc_start: 0.8116 (tpp80) cc_final: 0.7148 (ttp-170) REVERT: U 124 GLU cc_start: 0.8029 (tm-30) cc_final: 0.7805 (tm-30) REVERT: U 125 LYS cc_start: 0.8768 (mmtt) cc_final: 0.8490 (mmtm) REVERT: U 141 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7253 (mp0) REVERT: U 148 GLU cc_start: 0.8315 (tt0) cc_final: 0.8064 (tt0) REVERT: V 59 GLN cc_start: 0.8214 (mm110) cc_final: 0.7968 (mm110) REVERT: V 120 LYS cc_start: 0.8548 (tttm) cc_final: 0.8164 (ttmt) REVERT: V 125 LYS cc_start: 0.8689 (mmtt) cc_final: 0.8444 (mmtm) REVERT: W 59 GLN cc_start: 0.8248 (mm110) cc_final: 0.8009 (mm110) REVERT: W 62 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7224 (mm-30) REVERT: W 125 LYS cc_start: 0.8698 (mmtt) cc_final: 0.8496 (mmtm) REVERT: W 148 GLU cc_start: 0.8384 (tt0) cc_final: 0.8125 (tt0) REVERT: X 59 GLN cc_start: 0.8206 (mm110) cc_final: 0.7965 (mm110) REVERT: X 120 LYS cc_start: 0.8528 (tttm) cc_final: 0.8281 (tttp) REVERT: X 125 LYS cc_start: 0.8735 (mmtt) cc_final: 0.8509 (mmtm) REVERT: X 141 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7245 (mp0) REVERT: X 148 GLU cc_start: 0.8341 (tt0) cc_final: 0.8078 (tt0) outliers start: 46 outliers final: 34 residues processed: 1085 average time/residue: 1.7970 time to fit residues: 2257.3045 Evaluate side-chains 1048 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 1014 time to evaluate : 4.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 110 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 6.9990 chunk 355 optimal weight: 5.9990 chunk 77 optimal weight: 0.9980 chunk 231 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 394 optimal weight: 0.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 1.9990 chunk 207 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN D 8 GLN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN L 8 GLN N 8 GLN O 8 GLN P 8 GLN P 59 GLN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 8 GLN V 8 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34776 Z= 0.229 Angle : 0.496 5.375 46824 Z= 0.258 Chirality : 0.036 0.127 4872 Planarity : 0.003 0.025 6216 Dihedral : 3.824 14.517 4584 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.37 % Allowed : 12.96 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.29 (0.13), residues: 4104 helix: 4.13 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.61 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP U 94 HIS 0.002 0.001 HIS G 137 PHE 0.013 0.002 PHE B 133 TYR 0.011 0.002 TYR K 138 ARG 0.003 0.000 ARG U 157 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1111 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 1024 time to evaluate : 4.029 Fit side-chains REVERT: A 59 GLN cc_start: 0.8299 (mm110) cc_final: 0.8045 (mm110) REVERT: A 64 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7120 (ttp-170) REVERT: A 113 GLN cc_start: 0.8780 (tp40) cc_final: 0.8467 (tp40) REVERT: A 124 GLU cc_start: 0.7995 (tm-30) cc_final: 0.7789 (tm-30) REVERT: A 125 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8548 (mmtm) REVERT: A 148 GLU cc_start: 0.8342 (tt0) cc_final: 0.8090 (tt0) REVERT: B 16 ASP cc_start: 0.8912 (m-30) cc_final: 0.8698 (m-30) REVERT: B 125 LYS cc_start: 0.8839 (mmtt) cc_final: 0.8572 (mmtm) REVERT: B 141 GLU cc_start: 0.7767 (mm-30) cc_final: 0.7274 (mp0) REVERT: B 148 GLU cc_start: 0.8364 (tt0) cc_final: 0.7951 (tt0) REVERT: C 59 GLN cc_start: 0.8202 (mm110) cc_final: 0.7975 (mm110) REVERT: C 64 ARG cc_start: 0.8158 (tpp80) cc_final: 0.7125 (ttp-170) REVERT: C 141 GLU cc_start: 0.7737 (mm-30) cc_final: 0.7270 (mp0) REVERT: D 59 GLN cc_start: 0.8237 (mm110) cc_final: 0.8000 (mm110) REVERT: D 62 GLU cc_start: 0.7392 (mm-30) cc_final: 0.7113 (mm-30) REVERT: D 93 ASP cc_start: 0.7985 (t0) cc_final: 0.7784 (t70) REVERT: D 125 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8488 (mmtm) REVERT: D 141 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7264 (mp0) REVERT: E 59 GLN cc_start: 0.8268 (mm110) cc_final: 0.8017 (mm110) REVERT: E 64 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7123 (ttp-170) REVERT: E 148 GLU cc_start: 0.8369 (tt0) cc_final: 0.8114 (tt0) REVERT: F 59 GLN cc_start: 0.8298 (mm110) cc_final: 0.8047 (mm110) REVERT: F 64 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7121 (ttp-170) REVERT: F 125 LYS cc_start: 0.8790 (mmtt) cc_final: 0.8583 (mmtm) REVERT: F 141 GLU cc_start: 0.7783 (mm-30) cc_final: 0.7289 (mp0) REVERT: F 148 GLU cc_start: 0.8355 (tt0) cc_final: 0.8105 (tt0) REVERT: G 16 ASP cc_start: 0.8906 (m-30) cc_final: 0.8654 (m-30) REVERT: G 59 GLN cc_start: 0.8278 (mm110) cc_final: 0.8026 (mm110) REVERT: G 64 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7122 (ttp-170) REVERT: G 120 LYS cc_start: 0.8602 (tttm) cc_final: 0.8223 (ttmp) REVERT: G 125 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8516 (mmtm) REVERT: G 141 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7298 (mp0) REVERT: G 148 GLU cc_start: 0.8303 (tt0) cc_final: 0.8072 (tt0) REVERT: H 59 GLN cc_start: 0.8281 (mm110) cc_final: 0.8046 (mm110) REVERT: H 62 GLU cc_start: 0.7451 (mm-30) cc_final: 0.7221 (mm-30) REVERT: H 125 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8453 (mmtm) REVERT: H 148 GLU cc_start: 0.8383 (tt0) cc_final: 0.7980 (tt0) REVERT: I 59 GLN cc_start: 0.8243 (mm110) cc_final: 0.7997 (mm110) REVERT: I 64 ARG cc_start: 0.8182 (tpp80) cc_final: 0.7127 (ttp-170) REVERT: I 125 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8486 (mmtm) REVERT: I 148 GLU cc_start: 0.8293 (tt0) cc_final: 0.8072 (tt0) REVERT: J 59 GLN cc_start: 0.8261 (mm110) cc_final: 0.8060 (mm110) REVERT: J 62 GLU cc_start: 0.7354 (mm-30) cc_final: 0.7082 (mm-30) REVERT: J 125 LYS cc_start: 0.8731 (mmtt) cc_final: 0.8486 (mmtm) REVERT: K 18 GLU cc_start: 0.8546 (tt0) cc_final: 0.8173 (tt0) REVERT: K 59 GLN cc_start: 0.8299 (mm110) cc_final: 0.8034 (mm110) REVERT: K 64 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7068 (ttp-170) REVERT: K 125 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8480 (mmtm) REVERT: K 141 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7284 (mp0) REVERT: K 148 GLU cc_start: 0.8376 (tt0) cc_final: 0.7969 (tt0) REVERT: L 16 ASP cc_start: 0.8903 (m-30) cc_final: 0.8699 (m-30) REVERT: L 59 GLN cc_start: 0.8266 (mm110) cc_final: 0.8028 (mm110) REVERT: L 64 ARG cc_start: 0.8183 (tpp80) cc_final: 0.7124 (ttp-170) REVERT: L 120 LYS cc_start: 0.8601 (tttm) cc_final: 0.8224 (ttmp) REVERT: L 125 LYS cc_start: 0.8719 (mmtt) cc_final: 0.8504 (mmtm) REVERT: L 141 GLU cc_start: 0.7793 (mm-30) cc_final: 0.7295 (mp0) REVERT: M 59 GLN cc_start: 0.8273 (mm110) cc_final: 0.8036 (mm110) REVERT: M 64 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7123 (ttp-170) REVERT: M 91 ARG cc_start: 0.8278 (mtp85) cc_final: 0.8074 (mtp85) REVERT: M 120 LYS cc_start: 0.8582 (tttm) cc_final: 0.8223 (tttp) REVERT: M 125 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8528 (mmtm) REVERT: M 141 GLU cc_start: 0.7742 (mm-30) cc_final: 0.7258 (mp0) REVERT: M 148 GLU cc_start: 0.8349 (tt0) cc_final: 0.8082 (tt0) REVERT: N 59 GLN cc_start: 0.8267 (mm110) cc_final: 0.8019 (mm110) REVERT: N 148 GLU cc_start: 0.8369 (tt0) cc_final: 0.8112 (tt0) REVERT: O 59 GLN cc_start: 0.8247 (mm110) cc_final: 0.7999 (mm110) REVERT: O 64 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7113 (ttp-170) REVERT: O 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8464 (mmtm) REVERT: P 124 GLU cc_start: 0.8006 (tm-30) cc_final: 0.7805 (tm-30) REVERT: P 125 LYS cc_start: 0.8785 (mmtt) cc_final: 0.8521 (mmtm) REVERT: P 141 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7291 (mp0) REVERT: P 148 GLU cc_start: 0.8333 (tt0) cc_final: 0.8095 (tt0) REVERT: Q 16 ASP cc_start: 0.8909 (m-30) cc_final: 0.8707 (m-30) REVERT: Q 18 GLU cc_start: 0.8532 (tt0) cc_final: 0.8164 (tt0) REVERT: Q 59 GLN cc_start: 0.8266 (mm110) cc_final: 0.8022 (mm110) REVERT: Q 125 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8466 (mmtm) REVERT: Q 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7269 (mp0) REVERT: Q 148 GLU cc_start: 0.8365 (tt0) cc_final: 0.7951 (tt0) REVERT: R 59 GLN cc_start: 0.8268 (mm110) cc_final: 0.8033 (mm110) REVERT: R 91 ARG cc_start: 0.8247 (mtp85) cc_final: 0.8037 (mtp85) REVERT: R 141 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7293 (mp0) REVERT: R 148 GLU cc_start: 0.8337 (tt0) cc_final: 0.8108 (tt0) REVERT: S 59 GLN cc_start: 0.8267 (mm110) cc_final: 0.8033 (mm110) REVERT: S 64 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7115 (ttp-170) REVERT: S 91 ARG cc_start: 0.8245 (mtp85) cc_final: 0.8032 (mtp85) REVERT: S 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8484 (mmtm) REVERT: S 141 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7295 (mp0) REVERT: S 148 GLU cc_start: 0.8333 (tt0) cc_final: 0.8095 (tt0) REVERT: T 59 GLN cc_start: 0.8298 (mm110) cc_final: 0.8039 (mm110) REVERT: T 62 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7183 (mm-30) REVERT: T 125 LYS cc_start: 0.8759 (mmtt) cc_final: 0.8483 (mmtm) REVERT: T 141 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7288 (mp0) REVERT: T 148 GLU cc_start: 0.8374 (tt0) cc_final: 0.7961 (tt0) REVERT: U 62 GLU cc_start: 0.7415 (mm-30) cc_final: 0.7102 (mm-30) REVERT: U 64 ARG cc_start: 0.8178 (tpp80) cc_final: 0.7134 (ttp-170) REVERT: U 91 ARG cc_start: 0.8265 (mtp85) cc_final: 0.8053 (mtp85) REVERT: U 124 GLU cc_start: 0.8004 (tm-30) cc_final: 0.7803 (tm-30) REVERT: U 125 LYS cc_start: 0.8782 (mmtt) cc_final: 0.8516 (mmtm) REVERT: U 141 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7284 (mp0) REVERT: U 148 GLU cc_start: 0.8334 (tt0) cc_final: 0.8088 (tt0) REVERT: V 59 GLN cc_start: 0.8251 (mm110) cc_final: 0.8010 (mm110) REVERT: V 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8468 (mmtm) REVERT: W 59 GLN cc_start: 0.8284 (mm110) cc_final: 0.8043 (mm110) REVERT: W 62 GLU cc_start: 0.7487 (mm-30) cc_final: 0.7260 (mm-30) REVERT: W 125 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8457 (mmtm) REVERT: W 148 GLU cc_start: 0.8386 (tt0) cc_final: 0.7982 (tt0) REVERT: X 59 GLN cc_start: 0.8277 (mm110) cc_final: 0.8041 (mm110) REVERT: X 62 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7131 (mm-30) REVERT: X 120 LYS cc_start: 0.8580 (tttm) cc_final: 0.8222 (tttp) REVERT: X 125 LYS cc_start: 0.8776 (mmtt) cc_final: 0.8540 (mmtm) REVERT: X 141 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7261 (mp0) REVERT: X 148 GLU cc_start: 0.8351 (tt0) cc_final: 0.8081 (tt0) outliers start: 87 outliers final: 84 residues processed: 1048 average time/residue: 1.8130 time to fit residues: 2197.5097 Evaluate side-chains 1077 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 993 time to evaluate : 3.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 110 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 7.9990 chunk 44 optimal weight: 0.9980 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 0.9980 chunk 332 optimal weight: 0.8980 chunk 220 optimal weight: 0.8980 chunk 393 optimal weight: 5.9990 chunk 246 optimal weight: 0.7980 chunk 239 optimal weight: 4.9990 chunk 181 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN E 8 GLN I 8 GLN J 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN T 8 GLN U 8 GLN V 8 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 34776 Z= 0.137 Angle : 0.439 5.083 46824 Z= 0.231 Chirality : 0.033 0.118 4872 Planarity : 0.002 0.023 6216 Dihedral : 3.674 15.882 4584 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 2.12 % Allowed : 13.48 % Favored : 84.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.64 (0.13), residues: 4104 helix: 4.37 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.73 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP W 94 HIS 0.001 0.000 HIS I 66 PHE 0.012 0.002 PHE D 133 TYR 0.010 0.001 TYR W 138 ARG 0.002 0.000 ARG V 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1082 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 1004 time to evaluate : 3.723 Fit side-chains REVERT: A 59 GLN cc_start: 0.8279 (mm110) cc_final: 0.8027 (mm110) REVERT: A 64 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7102 (ttp-170) REVERT: A 113 GLN cc_start: 0.8757 (tp40) cc_final: 0.8451 (tp40) REVERT: A 125 LYS cc_start: 0.8788 (mmtt) cc_final: 0.8571 (mmtm) REVERT: A 148 GLU cc_start: 0.8343 (tt0) cc_final: 0.8083 (tt0) REVERT: B 59 GLN cc_start: 0.8204 (mm110) cc_final: 0.7957 (mm110) REVERT: B 93 ASP cc_start: 0.7835 (t0) cc_final: 0.7631 (t70) REVERT: B 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8454 (mmtm) REVERT: B 141 GLU cc_start: 0.7755 (mm-30) cc_final: 0.7248 (mp0) REVERT: B 148 GLU cc_start: 0.8361 (tt0) cc_final: 0.7942 (tt0) REVERT: C 18 GLU cc_start: 0.8462 (tt0) cc_final: 0.8153 (tt0) REVERT: C 59 GLN cc_start: 0.8176 (mm110) cc_final: 0.7929 (mm110) REVERT: C 64 ARG cc_start: 0.8157 (tpp80) cc_final: 0.7106 (ttp-170) REVERT: C 141 GLU cc_start: 0.7675 (mm-30) cc_final: 0.7185 (mp0) REVERT: D 18 GLU cc_start: 0.8457 (tt0) cc_final: 0.8129 (tt0) REVERT: D 63 GLU cc_start: 0.7953 (mm-30) cc_final: 0.7181 (mm-30) REVERT: D 125 LYS cc_start: 0.8706 (mmtt) cc_final: 0.8470 (mmtm) REVERT: D 141 GLU cc_start: 0.7665 (mm-30) cc_final: 0.7184 (mp0) REVERT: E 18 GLU cc_start: 0.8483 (tt0) cc_final: 0.8180 (tt0) REVERT: E 59 GLN cc_start: 0.8212 (mm110) cc_final: 0.7953 (mm110) REVERT: E 64 ARG cc_start: 0.8152 (tpp80) cc_final: 0.7087 (ttp-170) REVERT: E 113 GLN cc_start: 0.8694 (tp40) cc_final: 0.8285 (tp40) REVERT: E 148 GLU cc_start: 0.8365 (tt0) cc_final: 0.8105 (tt0) REVERT: F 18 GLU cc_start: 0.8474 (tt0) cc_final: 0.8156 (tt0) REVERT: F 59 GLN cc_start: 0.8277 (mm110) cc_final: 0.8034 (mm110) REVERT: F 64 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7102 (ttp-170) REVERT: F 125 LYS cc_start: 0.8806 (mmtt) cc_final: 0.8589 (mmtm) REVERT: F 141 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7247 (mp0) REVERT: F 148 GLU cc_start: 0.8350 (tt0) cc_final: 0.8091 (tt0) REVERT: G 16 ASP cc_start: 0.8874 (m-30) cc_final: 0.8571 (m-30) REVERT: G 59 GLN cc_start: 0.8241 (mm110) cc_final: 0.8009 (mm110) REVERT: G 62 GLU cc_start: 0.7433 (mm-30) cc_final: 0.7127 (mm-30) REVERT: G 64 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7109 (ttp-170) REVERT: G 93 ASP cc_start: 0.7830 (t0) cc_final: 0.7622 (t70) REVERT: G 120 LYS cc_start: 0.8568 (tttm) cc_final: 0.8213 (ttmp) REVERT: G 125 LYS cc_start: 0.8688 (mmtt) cc_final: 0.8451 (mmtm) REVERT: G 141 GLU cc_start: 0.7752 (mm-30) cc_final: 0.7257 (mp0) REVERT: G 148 GLU cc_start: 0.8303 (tt0) cc_final: 0.8074 (tt0) REVERT: H 59 GLN cc_start: 0.8259 (mm110) cc_final: 0.8031 (mm110) REVERT: H 62 GLU cc_start: 0.7455 (mm-30) cc_final: 0.7229 (mm-30) REVERT: H 125 LYS cc_start: 0.8692 (mmtt) cc_final: 0.8433 (mmtm) REVERT: H 148 GLU cc_start: 0.8379 (tt0) cc_final: 0.7981 (tt0) REVERT: I 18 GLU cc_start: 0.8472 (tt0) cc_final: 0.8171 (tt0) REVERT: I 59 GLN cc_start: 0.8184 (mm110) cc_final: 0.7931 (mm110) REVERT: I 64 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7094 (ttp-170) REVERT: I 93 ASP cc_start: 0.7822 (t0) cc_final: 0.7609 (t70) REVERT: I 125 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8443 (mmtm) REVERT: I 148 GLU cc_start: 0.8292 (tt0) cc_final: 0.8067 (tt0) REVERT: J 59 GLN cc_start: 0.8231 (mm110) cc_final: 0.8007 (mm110) REVERT: J 62 GLU cc_start: 0.7358 (mm-30) cc_final: 0.7092 (mm-30) REVERT: J 93 ASP cc_start: 0.7820 (t0) cc_final: 0.7602 (t70) REVERT: J 125 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8485 (mmtm) REVERT: K 59 GLN cc_start: 0.8278 (mm110) cc_final: 0.8016 (mm110) REVERT: K 62 GLU cc_start: 0.7442 (mm-30) cc_final: 0.7184 (mm-30) REVERT: K 64 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7051 (ttp-170) REVERT: K 93 ASP cc_start: 0.7845 (t0) cc_final: 0.7630 (t70) REVERT: K 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8478 (mmtm) REVERT: K 141 GLU cc_start: 0.7648 (mm-30) cc_final: 0.7203 (mp0) REVERT: K 148 GLU cc_start: 0.8370 (tt0) cc_final: 0.7963 (tt0) REVERT: L 16 ASP cc_start: 0.8887 (m-30) cc_final: 0.8665 (m-30) REVERT: L 59 GLN cc_start: 0.8231 (mm110) cc_final: 0.7984 (mm110) REVERT: L 64 ARG cc_start: 0.8139 (tpp80) cc_final: 0.7094 (ttp-170) REVERT: L 93 ASP cc_start: 0.7826 (t0) cc_final: 0.7617 (t70) REVERT: L 120 LYS cc_start: 0.8568 (tttm) cc_final: 0.8215 (ttmp) REVERT: L 141 GLU cc_start: 0.7733 (mm-30) cc_final: 0.7251 (mp0) REVERT: M 59 GLN cc_start: 0.8211 (mm110) cc_final: 0.7971 (mm110) REVERT: M 64 ARG cc_start: 0.8179 (tpp80) cc_final: 0.7103 (ttp-170) REVERT: M 93 ASP cc_start: 0.7850 (t0) cc_final: 0.7644 (t70) REVERT: M 120 LYS cc_start: 0.8548 (tttm) cc_final: 0.8279 (tttp) REVERT: M 125 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8499 (mmtm) REVERT: M 141 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7245 (mp0) REVERT: M 148 GLU cc_start: 0.8343 (tt0) cc_final: 0.8079 (tt0) REVERT: N 18 GLU cc_start: 0.8485 (tt0) cc_final: 0.8181 (tt0) REVERT: N 59 GLN cc_start: 0.8208 (mm110) cc_final: 0.7954 (mm110) REVERT: N 93 ASP cc_start: 0.7845 (t0) cc_final: 0.7632 (t70) REVERT: N 113 GLN cc_start: 0.8702 (tp40) cc_final: 0.8286 (tp40) REVERT: N 148 GLU cc_start: 0.8366 (tt0) cc_final: 0.8106 (tt0) REVERT: O 18 GLU cc_start: 0.8470 (tt0) cc_final: 0.8152 (tt0) REVERT: O 59 GLN cc_start: 0.8209 (mm110) cc_final: 0.7983 (mm110) REVERT: O 64 ARG cc_start: 0.8167 (tpp80) cc_final: 0.7111 (ttp-170) REVERT: O 93 ASP cc_start: 0.7842 (t0) cc_final: 0.7628 (t70) REVERT: O 125 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8444 (mmtm) REVERT: P 59 GLN cc_start: 0.8205 (mm110) cc_final: 0.7964 (mm110) REVERT: P 93 ASP cc_start: 0.7824 (t0) cc_final: 0.7617 (t70) REVERT: P 124 GLU cc_start: 0.8025 (tm-30) cc_final: 0.7808 (tm-30) REVERT: P 125 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8477 (mmtm) REVERT: P 141 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7248 (mp0) REVERT: P 148 GLU cc_start: 0.8318 (tt0) cc_final: 0.8070 (tt0) REVERT: Q 59 GLN cc_start: 0.8239 (mm110) cc_final: 0.7993 (mm110) REVERT: Q 93 ASP cc_start: 0.7830 (t0) cc_final: 0.7622 (t70) REVERT: Q 125 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8443 (mmtm) REVERT: Q 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7246 (mp0) REVERT: Q 148 GLU cc_start: 0.8357 (tt0) cc_final: 0.7946 (tt0) REVERT: R 18 GLU cc_start: 0.8470 (tt0) cc_final: 0.8167 (tt0) REVERT: R 59 GLN cc_start: 0.8208 (mm110) cc_final: 0.7970 (mm110) REVERT: R 141 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7246 (mp0) REVERT: R 148 GLU cc_start: 0.8340 (tt0) cc_final: 0.8098 (tt0) REVERT: S 18 GLU cc_start: 0.8485 (tt0) cc_final: 0.8192 (tt0) REVERT: S 59 GLN cc_start: 0.8209 (mm110) cc_final: 0.7971 (mm110) REVERT: S 64 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7097 (ttp-170) REVERT: S 125 LYS cc_start: 0.8702 (mmtt) cc_final: 0.8467 (mmtm) REVERT: S 141 GLU cc_start: 0.7749 (mm-30) cc_final: 0.7249 (mp0) REVERT: S 148 GLU cc_start: 0.8333 (tt0) cc_final: 0.8089 (tt0) REVERT: T 59 GLN cc_start: 0.8277 (mm110) cc_final: 0.8018 (mm110) REVERT: T 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7191 (mm-30) REVERT: T 93 ASP cc_start: 0.7843 (t0) cc_final: 0.7628 (t70) REVERT: T 125 LYS cc_start: 0.8722 (mmtt) cc_final: 0.8473 (mmtm) REVERT: T 141 GLU cc_start: 0.7658 (mm-30) cc_final: 0.7204 (mp0) REVERT: T 148 GLU cc_start: 0.8371 (tt0) cc_final: 0.7963 (tt0) REVERT: U 62 GLU cc_start: 0.7368 (mm-30) cc_final: 0.7133 (mm-30) REVERT: U 64 ARG cc_start: 0.8160 (tpp80) cc_final: 0.7129 (ttp-170) REVERT: U 93 ASP cc_start: 0.7820 (t0) cc_final: 0.7605 (t70) REVERT: U 124 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7805 (tm-30) REVERT: U 125 LYS cc_start: 0.8771 (mmtt) cc_final: 0.8472 (mmtm) REVERT: U 141 GLU cc_start: 0.7721 (mm-30) cc_final: 0.7247 (mp0) REVERT: U 148 GLU cc_start: 0.8314 (tt0) cc_final: 0.8065 (tt0) REVERT: V 18 GLU cc_start: 0.8467 (tt0) cc_final: 0.8152 (tt0) REVERT: V 59 GLN cc_start: 0.8211 (mm110) cc_final: 0.7991 (mm110) REVERT: V 93 ASP cc_start: 0.7842 (t0) cc_final: 0.7628 (t70) REVERT: V 125 LYS cc_start: 0.8687 (mmtt) cc_final: 0.8447 (mmtm) REVERT: W 59 GLN cc_start: 0.8260 (mm110) cc_final: 0.8031 (mm110) REVERT: W 62 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7227 (mm-30) REVERT: W 93 ASP cc_start: 0.7813 (t0) cc_final: 0.7613 (t70) REVERT: W 125 LYS cc_start: 0.8701 (mmtt) cc_final: 0.8453 (mmtm) REVERT: W 148 GLU cc_start: 0.8382 (tt0) cc_final: 0.8129 (tt0) REVERT: X 59 GLN cc_start: 0.8216 (mm110) cc_final: 0.7979 (mm110) REVERT: X 62 GLU cc_start: 0.7440 (mm-30) cc_final: 0.7161 (mm-30) REVERT: X 120 LYS cc_start: 0.8548 (tttm) cc_final: 0.8277 (tttp) REVERT: X 125 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8492 (mmtm) REVERT: X 141 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7247 (mp0) REVERT: X 148 GLU cc_start: 0.8345 (tt0) cc_final: 0.8081 (tt0) outliers start: 78 outliers final: 71 residues processed: 1039 average time/residue: 1.7823 time to fit residues: 2141.9230 Evaluate side-chains 1069 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 998 time to evaluate : 3.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 46 ASP Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 46 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 46 ASP Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 46 ASP Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 46 ASP Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 46 ASP Chi-restraints excluded: chain N residue 173 LYS Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 46 ASP Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 46 ASP Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 46 ASP Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 46 ASP Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 46 ASP Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 46 ASP Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 158 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 4.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 0.8980 chunk 118 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 250 optimal weight: 4.9990 chunk 267 optimal weight: 2.9990 chunk 194 optimal weight: 4.9990 chunk 36 optimal weight: 6.9990 chunk 309 optimal weight: 3.9990 overall best weight: 2.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN D 8 GLN D 59 GLN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN L 8 GLN M 137 HIS N 8 GLN O 8 GLN P 8 GLN P 137 HIS Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 8 GLN U 137 HIS V 8 GLN W 8 GLN X 8 GLN X 137 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.1814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 34776 Z= 0.283 Angle : 0.530 5.478 46824 Z= 0.275 Chirality : 0.038 0.128 4872 Planarity : 0.003 0.026 6216 Dihedral : 3.905 13.953 4584 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.48 % Allowed : 13.53 % Favored : 83.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.02 (0.13), residues: 4104 helix: 3.95 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.45 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP P 94 HIS 0.003 0.001 HIS R 119 PHE 0.014 0.002 PHE B 133 TYR 0.012 0.002 TYR C 138 ARG 0.003 0.001 ARG I 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1075 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 91 poor density : 984 time to evaluate : 3.651 Fit side-chains REVERT: A 59 GLN cc_start: 0.8311 (mm110) cc_final: 0.8056 (mm110) REVERT: A 64 ARG cc_start: 0.8205 (tpp80) cc_final: 0.7152 (ttp-170) REVERT: A 113 GLN cc_start: 0.8786 (tp40) cc_final: 0.8489 (tp40) REVERT: A 125 LYS cc_start: 0.8784 (mmtt) cc_final: 0.8514 (mmtm) REVERT: A 148 GLU cc_start: 0.8341 (tt0) cc_final: 0.8088 (tt0) REVERT: A 158 LYS cc_start: 0.8705 (OUTLIER) cc_final: 0.8469 (tppp) REVERT: B 59 GLN cc_start: 0.8276 (mm110) cc_final: 0.8044 (mm110) REVERT: B 62 GLU cc_start: 0.7461 (mm-30) cc_final: 0.7138 (mm-30) REVERT: B 125 LYS cc_start: 0.8734 (mmtt) cc_final: 0.8500 (mmtm) REVERT: B 141 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7303 (mp0) REVERT: B 148 GLU cc_start: 0.8390 (tt0) cc_final: 0.7992 (tt0) REVERT: C 59 GLN cc_start: 0.8246 (mm110) cc_final: 0.8027 (mm110) REVERT: C 64 ARG cc_start: 0.8170 (tpp80) cc_final: 0.7145 (ttp-170) REVERT: C 141 GLU cc_start: 0.7736 (mm-30) cc_final: 0.7269 (mp0) REVERT: D 125 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8490 (mmtm) REVERT: D 141 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7288 (mp0) REVERT: E 59 GLN cc_start: 0.8281 (mm110) cc_final: 0.8046 (mm110) REVERT: E 64 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7147 (ttp-170) REVERT: E 148 GLU cc_start: 0.8369 (tt0) cc_final: 0.8112 (tt0) REVERT: F 59 GLN cc_start: 0.8308 (mm110) cc_final: 0.8048 (mm110) REVERT: F 64 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7149 (ttp-170) REVERT: F 125 LYS cc_start: 0.8745 (mmtt) cc_final: 0.8485 (mmtm) REVERT: F 141 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7301 (mp0) REVERT: F 148 GLU cc_start: 0.8348 (tt0) cc_final: 0.8099 (tt0) REVERT: F 158 LYS cc_start: 0.8710 (OUTLIER) cc_final: 0.8476 (tppp) REVERT: G 16 ASP cc_start: 0.8930 (m-30) cc_final: 0.8688 (m-30) REVERT: G 59 GLN cc_start: 0.8288 (mm110) cc_final: 0.8058 (mm110) REVERT: G 64 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7151 (ttp-170) REVERT: G 120 LYS cc_start: 0.8587 (tttm) cc_final: 0.8202 (tttp) REVERT: G 125 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8464 (mmtm) REVERT: G 141 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7306 (mp0) REVERT: G 148 GLU cc_start: 0.8297 (tt0) cc_final: 0.8079 (tt0) REVERT: H 59 GLN cc_start: 0.8303 (mm110) cc_final: 0.8068 (mm110) REVERT: H 62 GLU cc_start: 0.7484 (mm-30) cc_final: 0.7240 (mm-30) REVERT: H 125 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8462 (mmtm) REVERT: H 148 GLU cc_start: 0.8402 (tt0) cc_final: 0.7996 (tt0) REVERT: H 158 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8461 (tppp) REVERT: I 59 GLN cc_start: 0.8255 (mm110) cc_final: 0.8024 (mm110) REVERT: I 64 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7147 (ttp-170) REVERT: I 125 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8482 (mmtm) REVERT: I 148 GLU cc_start: 0.8286 (tt0) cc_final: 0.8083 (tt0) REVERT: J 59 GLN cc_start: 0.8269 (mm110) cc_final: 0.8047 (mm110) REVERT: J 62 GLU cc_start: 0.7360 (mm-30) cc_final: 0.7083 (mm-30) REVERT: J 125 LYS cc_start: 0.8726 (mmtt) cc_final: 0.8488 (mmtm) REVERT: K 59 GLN cc_start: 0.8310 (mm110) cc_final: 0.8052 (mm110) REVERT: K 62 GLU cc_start: 0.7470 (mm-30) cc_final: 0.7211 (mm-30) REVERT: K 64 ARG cc_start: 0.8145 (tpp80) cc_final: 0.7081 (ttp-170) REVERT: K 125 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8499 (mmtm) REVERT: K 141 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7292 (mp0) REVERT: K 148 GLU cc_start: 0.8403 (tt0) cc_final: 0.8014 (tt0) REVERT: L 59 GLN cc_start: 0.8281 (mm110) cc_final: 0.8054 (mm110) REVERT: L 64 ARG cc_start: 0.8187 (tpp80) cc_final: 0.7144 (ttp-170) REVERT: L 120 LYS cc_start: 0.8589 (tttm) cc_final: 0.8206 (tttp) REVERT: L 141 GLU cc_start: 0.7795 (mm-30) cc_final: 0.7306 (mp0) REVERT: M 59 GLN cc_start: 0.8287 (mm110) cc_final: 0.8062 (mm110) REVERT: M 62 GLU cc_start: 0.7459 (mm-30) cc_final: 0.7125 (mm-30) REVERT: M 64 ARG cc_start: 0.8184 (tpp80) cc_final: 0.7159 (ttp-170) REVERT: M 120 LYS cc_start: 0.8602 (tttm) cc_final: 0.8229 (tttp) REVERT: M 125 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8497 (mmtm) REVERT: M 141 GLU cc_start: 0.7745 (mm-30) cc_final: 0.7274 (mp0) REVERT: M 148 GLU cc_start: 0.8345 (tt0) cc_final: 0.8066 (tt0) REVERT: N 59 GLN cc_start: 0.8278 (mm110) cc_final: 0.8046 (mm110) REVERT: N 62 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7268 (mm-30) REVERT: N 134 ILE cc_start: 0.9005 (mt) cc_final: 0.8802 (mm) REVERT: N 148 GLU cc_start: 0.8385 (tt0) cc_final: 0.8125 (tt0) REVERT: O 59 GLN cc_start: 0.8256 (mm110) cc_final: 0.8020 (mm110) REVERT: O 64 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7143 (ttp-170) REVERT: O 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8461 (mmtm) REVERT: P 59 GLN cc_start: 0.8278 (mm110) cc_final: 0.8051 (mm110) REVERT: P 125 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8557 (mmtm) REVERT: P 141 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7308 (mp0) REVERT: P 148 GLU cc_start: 0.8334 (tt0) cc_final: 0.8102 (tt0) REVERT: Q 59 GLN cc_start: 0.8282 (mm110) cc_final: 0.8053 (mm110) REVERT: Q 125 LYS cc_start: 0.8730 (mmtt) cc_final: 0.8503 (mmtm) REVERT: Q 141 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7292 (mp0) REVERT: Q 148 GLU cc_start: 0.8390 (tt0) cc_final: 0.7999 (tt0) REVERT: R 59 GLN cc_start: 0.8282 (mm110) cc_final: 0.8059 (mm110) REVERT: R 141 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7297 (mp0) REVERT: R 148 GLU cc_start: 0.8335 (tt0) cc_final: 0.8115 (tt0) REVERT: S 59 GLN cc_start: 0.8280 (mm110) cc_final: 0.8056 (mm110) REVERT: S 64 ARG cc_start: 0.8207 (tpp80) cc_final: 0.7146 (ttp-170) REVERT: S 125 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8484 (mmtm) REVERT: S 134 ILE cc_start: 0.9003 (mt) cc_final: 0.8796 (mm) REVERT: S 141 GLU cc_start: 0.7799 (mm-30) cc_final: 0.7306 (mp0) REVERT: S 148 GLU cc_start: 0.8327 (tt0) cc_final: 0.8105 (tt0) REVERT: T 59 GLN cc_start: 0.8310 (mm110) cc_final: 0.8056 (mm110) REVERT: T 62 GLU cc_start: 0.7464 (mm-30) cc_final: 0.7167 (mm-30) REVERT: T 125 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8499 (mmtm) REVERT: T 141 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7299 (mp0) REVERT: T 148 GLU cc_start: 0.8402 (tt0) cc_final: 0.8010 (tt0) REVERT: U 62 GLU cc_start: 0.7394 (mm-30) cc_final: 0.7094 (mm-30) REVERT: U 64 ARG cc_start: 0.8177 (tpp80) cc_final: 0.7135 (ttp-170) REVERT: U 125 LYS cc_start: 0.8798 (mmtt) cc_final: 0.8558 (mmtm) REVERT: U 134 ILE cc_start: 0.9007 (mt) cc_final: 0.8798 (mm) REVERT: U 141 GLU cc_start: 0.7765 (mm-30) cc_final: 0.7300 (mp0) REVERT: U 148 GLU cc_start: 0.8333 (tt0) cc_final: 0.8097 (tt0) REVERT: V 59 GLN cc_start: 0.8261 (mm110) cc_final: 0.8034 (mm110) REVERT: V 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8458 (mmtm) REVERT: W 59 GLN cc_start: 0.8304 (mm110) cc_final: 0.8064 (mm110) REVERT: W 62 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7241 (mm-30) REVERT: W 125 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8464 (mmtm) REVERT: W 148 GLU cc_start: 0.8384 (tt0) cc_final: 0.7992 (tt0) REVERT: X 59 GLN cc_start: 0.8291 (mm110) cc_final: 0.8066 (mm110) REVERT: X 120 LYS cc_start: 0.8599 (tttm) cc_final: 0.8227 (tttp) REVERT: X 125 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8521 (mmtm) REVERT: X 141 GLU cc_start: 0.7743 (mm-30) cc_final: 0.7272 (mp0) REVERT: X 148 GLU cc_start: 0.8345 (tt0) cc_final: 0.8075 (tt0) outliers start: 91 outliers final: 81 residues processed: 1008 average time/residue: 1.7974 time to fit residues: 2092.3545 Evaluate side-chains 1026 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 942 time to evaluate : 4.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain C residue 123 THR Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain H residue 158 LYS Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 60 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 158 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.0970 chunk 376 optimal weight: 4.9990 chunk 343 optimal weight: 2.9990 chunk 366 optimal weight: 0.9990 chunk 220 optimal weight: 5.9990 chunk 159 optimal weight: 6.9990 chunk 287 optimal weight: 3.9990 chunk 112 optimal weight: 4.9990 chunk 331 optimal weight: 0.0670 chunk 346 optimal weight: 3.9990 chunk 365 optimal weight: 5.9990 overall best weight: 1.6322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 8 GLN E 8 GLN H 8 GLN I 8 GLN J 8 GLN N 8 GLN O 8 GLN P 8 GLN R 8 GLN T 8 GLN U 8 GLN V 8 GLN W 8 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 34776 Z= 0.194 Angle : 0.478 5.085 46824 Z= 0.251 Chirality : 0.035 0.123 4872 Planarity : 0.003 0.025 6216 Dihedral : 3.805 15.368 4584 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 2.23 % Allowed : 14.00 % Favored : 83.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 5.28 (0.13), residues: 4104 helix: 4.14 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.50 (0.26), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP V 94 HIS 0.002 0.001 HIS P 119 PHE 0.013 0.002 PHE N 133 TYR 0.011 0.001 TYR C 138 ARG 0.002 0.000 ARG D 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1050 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 82 poor density : 968 time to evaluate : 3.923 Fit side-chains REVERT: A 59 GLN cc_start: 0.8295 (mm110) cc_final: 0.8065 (mm110) REVERT: A 64 ARG cc_start: 0.8198 (tpp80) cc_final: 0.7122 (ttp-170) REVERT: A 113 GLN cc_start: 0.8791 (tp40) cc_final: 0.8498 (tp40) REVERT: A 125 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8490 (mmtm) REVERT: A 148 GLU cc_start: 0.8337 (tt0) cc_final: 0.8079 (tt0) REVERT: A 158 LYS cc_start: 0.8582 (OUTLIER) cc_final: 0.8343 (tppp) REVERT: B 59 GLN cc_start: 0.8254 (mm110) cc_final: 0.8014 (mm110) REVERT: B 62 GLU cc_start: 0.7436 (mm-30) cc_final: 0.7122 (mm-30) REVERT: B 125 LYS cc_start: 0.8742 (mmtt) cc_final: 0.8468 (mmtm) REVERT: B 141 GLU cc_start: 0.7731 (mm-30) cc_final: 0.7268 (mp0) REVERT: B 148 GLU cc_start: 0.8357 (tt0) cc_final: 0.7942 (tt0) REVERT: C 59 GLN cc_start: 0.8213 (mm110) cc_final: 0.7986 (mm110) REVERT: C 64 ARG cc_start: 0.8166 (tpp80) cc_final: 0.7131 (ttp-170) REVERT: C 141 GLU cc_start: 0.7703 (mm-30) cc_final: 0.7263 (mp0) REVERT: D 59 GLN cc_start: 0.8234 (mm110) cc_final: 0.8003 (mm110) REVERT: D 125 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8502 (mmtm) REVERT: D 141 GLU cc_start: 0.7696 (mm-30) cc_final: 0.7247 (mp0) REVERT: E 59 GLN cc_start: 0.8258 (mm110) cc_final: 0.8010 (mm110) REVERT: E 64 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7115 (ttp-170) REVERT: E 148 GLU cc_start: 0.8362 (tt0) cc_final: 0.8100 (tt0) REVERT: F 59 GLN cc_start: 0.8292 (mm110) cc_final: 0.8026 (mm110) REVERT: F 64 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7121 (ttp-170) REVERT: F 125 LYS cc_start: 0.8725 (mmtt) cc_final: 0.8481 (mmtm) REVERT: F 141 GLU cc_start: 0.7708 (mm-30) cc_final: 0.7262 (mp0) REVERT: F 148 GLU cc_start: 0.8349 (tt0) cc_final: 0.8096 (tt0) REVERT: F 158 LYS cc_start: 0.8586 (OUTLIER) cc_final: 0.8352 (tppp) REVERT: G 16 ASP cc_start: 0.8906 (m-30) cc_final: 0.8643 (m-30) REVERT: G 59 GLN cc_start: 0.8259 (mm110) cc_final: 0.8036 (mm110) REVERT: G 64 ARG cc_start: 0.8191 (tpp80) cc_final: 0.7135 (ttp-170) REVERT: G 120 LYS cc_start: 0.8606 (tttm) cc_final: 0.8226 (ttmp) REVERT: G 125 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8471 (mmtm) REVERT: G 141 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7284 (mp0) REVERT: G 148 GLU cc_start: 0.8293 (tt0) cc_final: 0.8068 (tt0) REVERT: H 59 GLN cc_start: 0.8270 (mm110) cc_final: 0.8048 (mm110) REVERT: H 62 GLU cc_start: 0.7452 (mm-30) cc_final: 0.7226 (mm-30) REVERT: H 125 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8474 (mmtm) REVERT: H 148 GLU cc_start: 0.8379 (tt0) cc_final: 0.7991 (tt0) REVERT: I 59 GLN cc_start: 0.8253 (mm110) cc_final: 0.8010 (mm110) REVERT: I 64 ARG cc_start: 0.8186 (tpp80) cc_final: 0.7136 (ttp-170) REVERT: I 125 LYS cc_start: 0.8737 (mmtt) cc_final: 0.8468 (mmtm) REVERT: I 148 GLU cc_start: 0.8278 (tt0) cc_final: 0.8070 (tt0) REVERT: J 59 GLN cc_start: 0.8244 (mm110) cc_final: 0.8035 (mm110) REVERT: J 62 GLU cc_start: 0.7373 (mm-30) cc_final: 0.7051 (mm-30) REVERT: J 125 LYS cc_start: 0.8711 (mmtt) cc_final: 0.8489 (mmtm) REVERT: K 59 GLN cc_start: 0.8293 (mm110) cc_final: 0.8054 (mm110) REVERT: K 62 GLU cc_start: 0.7437 (mm-30) cc_final: 0.7163 (mm-30) REVERT: K 64 ARG cc_start: 0.8149 (tpp80) cc_final: 0.7077 (ttp-170) REVERT: K 125 LYS cc_start: 0.8749 (mmtt) cc_final: 0.8516 (mmtm) REVERT: K 141 GLU cc_start: 0.7681 (mm-30) cc_final: 0.7279 (mp0) REVERT: K 148 GLU cc_start: 0.8367 (tt0) cc_final: 0.7961 (tt0) REVERT: L 59 GLN cc_start: 0.8255 (mm110) cc_final: 0.8017 (mm110) REVERT: L 64 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7126 (ttp-170) REVERT: L 120 LYS cc_start: 0.8612 (tttm) cc_final: 0.8228 (ttmp) REVERT: L 141 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7287 (mp0) REVERT: M 59 GLN cc_start: 0.8264 (mm110) cc_final: 0.8024 (mm110) REVERT: M 62 GLU cc_start: 0.7444 (mm-30) cc_final: 0.7122 (mm-30) REVERT: M 64 ARG cc_start: 0.8185 (tpp80) cc_final: 0.7146 (ttp-170) REVERT: M 120 LYS cc_start: 0.8584 (tttm) cc_final: 0.8212 (ttmp) REVERT: M 125 LYS cc_start: 0.8727 (mmtt) cc_final: 0.8512 (mmtm) REVERT: M 141 GLU cc_start: 0.7709 (mm-30) cc_final: 0.7254 (mp0) REVERT: M 148 GLU cc_start: 0.8341 (tt0) cc_final: 0.8075 (tt0) REVERT: N 59 GLN cc_start: 0.8250 (mm110) cc_final: 0.8003 (mm110) REVERT: N 148 GLU cc_start: 0.8363 (tt0) cc_final: 0.8097 (tt0) REVERT: O 59 GLN cc_start: 0.8238 (mm110) cc_final: 0.7995 (mm110) REVERT: O 64 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7121 (ttp-170) REVERT: O 125 LYS cc_start: 0.8717 (mmtt) cc_final: 0.8455 (mmtm) REVERT: P 125 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8518 (mmtm) REVERT: P 141 GLU cc_start: 0.7690 (mm-30) cc_final: 0.7256 (mp0) REVERT: P 148 GLU cc_start: 0.8334 (tt0) cc_final: 0.8096 (tt0) REVERT: Q 59 GLN cc_start: 0.8261 (mm110) cc_final: 0.8020 (mm110) REVERT: Q 125 LYS cc_start: 0.8736 (mmtt) cc_final: 0.8480 (mmtm) REVERT: Q 141 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7251 (mp0) REVERT: Q 148 GLU cc_start: 0.8356 (tt0) cc_final: 0.7948 (tt0) REVERT: R 59 GLN cc_start: 0.8259 (mm110) cc_final: 0.8023 (mm110) REVERT: R 141 GLU cc_start: 0.7725 (mm-30) cc_final: 0.7262 (mp0) REVERT: R 148 GLU cc_start: 0.8328 (tt0) cc_final: 0.8103 (tt0) REVERT: S 59 GLN cc_start: 0.8259 (mm110) cc_final: 0.8022 (mm110) REVERT: S 64 ARG cc_start: 0.8196 (tpp80) cc_final: 0.7113 (ttp-170) REVERT: S 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8486 (mmtm) REVERT: S 141 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7261 (mp0) REVERT: S 148 GLU cc_start: 0.8322 (tt0) cc_final: 0.8094 (tt0) REVERT: T 59 GLN cc_start: 0.8293 (mm110) cc_final: 0.8055 (mm110) REVERT: T 62 GLU cc_start: 0.7467 (mm-30) cc_final: 0.7197 (mm-30) REVERT: T 125 LYS cc_start: 0.8748 (mmtt) cc_final: 0.8516 (mmtm) REVERT: T 141 GLU cc_start: 0.7693 (mm-30) cc_final: 0.7282 (mp0) REVERT: T 148 GLU cc_start: 0.8366 (tt0) cc_final: 0.7959 (tt0) REVERT: U 18 GLU cc_start: 0.8538 (tt0) cc_final: 0.8161 (tt0) REVERT: U 64 ARG cc_start: 0.8169 (tpp80) cc_final: 0.7118 (ttp-170) REVERT: U 125 LYS cc_start: 0.8794 (mmtt) cc_final: 0.8275 (mmtm) REVERT: U 141 GLU cc_start: 0.7689 (mm-30) cc_final: 0.7251 (mp0) REVERT: U 148 GLU cc_start: 0.8328 (tt0) cc_final: 0.8090 (tt0) REVERT: V 59 GLN cc_start: 0.8242 (mm110) cc_final: 0.8006 (mm110) REVERT: V 125 LYS cc_start: 0.8713 (mmtt) cc_final: 0.8467 (mmtm) REVERT: W 59 GLN cc_start: 0.8270 (mm110) cc_final: 0.8045 (mm110) REVERT: W 62 GLU cc_start: 0.7453 (mm-30) cc_final: 0.7231 (mm-30) REVERT: W 125 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8468 (mmtm) REVERT: W 148 GLU cc_start: 0.8382 (tt0) cc_final: 0.7997 (tt0) REVERT: X 59 GLN cc_start: 0.8268 (mm110) cc_final: 0.8028 (mm110) REVERT: X 120 LYS cc_start: 0.8584 (tttm) cc_final: 0.8210 (ttmp) REVERT: X 125 LYS cc_start: 0.8740 (mmtt) cc_final: 0.8519 (mmtm) REVERT: X 141 GLU cc_start: 0.7706 (mm-30) cc_final: 0.7253 (mp0) REVERT: X 148 GLU cc_start: 0.8344 (tt0) cc_final: 0.8073 (tt0) outliers start: 82 outliers final: 78 residues processed: 992 average time/residue: 1.8353 time to fit residues: 2110.1606 Evaluate side-chains 1048 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 80 poor density : 968 time to evaluate : 4.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 46 ASP Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 158 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 46 ASP Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 46 ASP Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 158 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 5.9990 chunk 387 optimal weight: 7.9990 chunk 236 optimal weight: 5.9990 chunk 183 optimal weight: 1.9990 chunk 269 optimal weight: 0.8980 chunk 406 optimal weight: 4.9990 chunk 374 optimal weight: 5.9990 chunk 323 optimal weight: 4.9990 chunk 33 optimal weight: 7.9990 chunk 250 optimal weight: 3.9990 chunk 198 optimal weight: 2.9990 overall best weight: 2.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN C 8 GLN D 8 GLN E 8 GLN F 8 GLN G 8 GLN H 8 GLN I 8 GLN J 8 GLN K 8 GLN L 8 GLN M 8 GLN N 8 GLN O 8 GLN P 8 GLN Q 8 GLN R 8 GLN S 8 GLN T 8 GLN U 8 GLN V 8 GLN W 8 GLN X 8 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8236 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 34776 Z= 0.319 Angle : 0.563 6.066 46824 Z= 0.291 Chirality : 0.039 0.128 4872 Planarity : 0.004 0.027 6216 Dihedral : 3.975 13.482 4584 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.37 % Allowed : 13.75 % Favored : 83.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.83 (0.13), residues: 4104 helix: 3.89 (0.08), residues: 3240 sheet: None (None), residues: 0 loop : 0.18 (0.24), residues: 864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP V 94 HIS 0.003 0.001 HIS L 119 PHE 0.014 0.003 PHE C 133 TYR 0.012 0.002 TYR R 40 ARG 0.003 0.001 ARG O 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8208 Ramachandran restraints generated. 4104 Oldfield, 0 Emsley, 4104 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1061 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 974 time to evaluate : 4.008 Fit side-chains REVERT: A 64 ARG cc_start: 0.8204 (tpp80) cc_final: 0.7165 (ttp-170) REVERT: A 113 GLN cc_start: 0.8796 (tp40) cc_final: 0.8498 (tp40) REVERT: A 125 LYS cc_start: 0.8723 (mmtt) cc_final: 0.8491 (mmtm) REVERT: A 148 GLU cc_start: 0.8344 (tt0) cc_final: 0.8093 (tt0) REVERT: A 158 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8474 (tppp) REVERT: B 59 GLN cc_start: 0.8282 (mm110) cc_final: 0.8052 (mm110) REVERT: B 62 GLU cc_start: 0.7472 (mm-30) cc_final: 0.7146 (mm-30) REVERT: B 125 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8481 (mmtm) REVERT: B 141 GLU cc_start: 0.7803 (mm-30) cc_final: 0.7306 (mp0) REVERT: B 148 GLU cc_start: 0.8403 (tt0) cc_final: 0.8007 (tt0) REVERT: C 59 GLN cc_start: 0.8255 (mm110) cc_final: 0.8034 (mm110) REVERT: C 64 ARG cc_start: 0.8201 (tpp80) cc_final: 0.7173 (ttp-170) REVERT: C 141 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7302 (mp0) REVERT: D 59 GLN cc_start: 0.8257 (mm110) cc_final: 0.8028 (mm110) REVERT: D 125 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8472 (mmtm) REVERT: D 141 GLU cc_start: 0.7771 (mm-30) cc_final: 0.7297 (mp0) REVERT: E 59 GLN cc_start: 0.8288 (mm110) cc_final: 0.8054 (mm110) REVERT: E 64 ARG cc_start: 0.8195 (tpp80) cc_final: 0.7151 (ttp-170) REVERT: E 148 GLU cc_start: 0.8387 (tt0) cc_final: 0.8144 (tt0) REVERT: F 16 ASP cc_start: 0.8933 (m-30) cc_final: 0.8648 (m-30) REVERT: F 59 GLN cc_start: 0.8316 (mm110) cc_final: 0.8061 (mm110) REVERT: F 64 ARG cc_start: 0.8202 (tpp80) cc_final: 0.7159 (ttp-170) REVERT: F 125 LYS cc_start: 0.8724 (mmtt) cc_final: 0.8468 (mmtm) REVERT: F 141 GLU cc_start: 0.7807 (mm-30) cc_final: 0.7323 (mp0) REVERT: F 148 GLU cc_start: 0.8347 (tt0) cc_final: 0.8108 (tt0) REVERT: F 158 LYS cc_start: 0.8722 (OUTLIER) cc_final: 0.8482 (tppp) REVERT: G 16 ASP cc_start: 0.8925 (m-30) cc_final: 0.8688 (m-30) REVERT: G 59 GLN cc_start: 0.8304 (mm110) cc_final: 0.8070 (mm110) REVERT: G 62 GLU cc_start: 0.7460 (mm-30) cc_final: 0.7135 (mm-30) REVERT: G 64 ARG cc_start: 0.8193 (tpp80) cc_final: 0.7164 (ttp-170) REVERT: G 120 LYS cc_start: 0.8622 (tttm) cc_final: 0.8228 (ttmp) REVERT: G 125 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8469 (mmtm) REVERT: G 141 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7327 (mp0) REVERT: G 148 GLU cc_start: 0.8296 (tt0) cc_final: 0.8082 (tt0) REVERT: H 59 GLN cc_start: 0.8326 (mm110) cc_final: 0.8097 (mm110) REVERT: H 62 GLU cc_start: 0.7498 (mm-30) cc_final: 0.7242 (mm-30) REVERT: H 125 LYS cc_start: 0.8716 (mmtt) cc_final: 0.8469 (mmtm) REVERT: H 148 GLU cc_start: 0.8426 (tt0) cc_final: 0.8028 (tt0) REVERT: I 59 GLN cc_start: 0.8262 (mm110) cc_final: 0.8032 (mm110) REVERT: I 64 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7155 (ttp-170) REVERT: I 125 LYS cc_start: 0.8728 (mmtt) cc_final: 0.8507 (mmtm) REVERT: I 148 GLU cc_start: 0.8312 (tt0) cc_final: 0.8094 (tt0) REVERT: J 59 GLN cc_start: 0.8275 (mm110) cc_final: 0.8058 (mm110) REVERT: J 62 GLU cc_start: 0.7366 (mm-30) cc_final: 0.7076 (mm-30) REVERT: J 125 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8494 (mmtm) REVERT: K 59 GLN cc_start: 0.8318 (mm110) cc_final: 0.8058 (mm110) REVERT: K 64 ARG cc_start: 0.8146 (tpp80) cc_final: 0.7092 (ttp-170) REVERT: K 125 LYS cc_start: 0.8760 (mmtt) cc_final: 0.8522 (mmtm) REVERT: K 141 GLU cc_start: 0.7748 (mm-30) cc_final: 0.7321 (mp0) REVERT: K 148 GLU cc_start: 0.8413 (tt0) cc_final: 0.8024 (tt0) REVERT: L 59 GLN cc_start: 0.8288 (mm110) cc_final: 0.8064 (mm110) REVERT: L 64 ARG cc_start: 0.8180 (tpp80) cc_final: 0.7149 (ttp-170) REVERT: L 120 LYS cc_start: 0.8625 (tttm) cc_final: 0.8291 (tttp) REVERT: L 124 GLU cc_start: 0.8012 (tm-30) cc_final: 0.7777 (pp20) REVERT: L 141 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7326 (mp0) REVERT: M 59 GLN cc_start: 0.8296 (mm110) cc_final: 0.8071 (mm110) REVERT: M 62 GLU cc_start: 0.7457 (mm-30) cc_final: 0.7131 (mm-30) REVERT: M 64 ARG cc_start: 0.8168 (tpp80) cc_final: 0.7143 (ttp-170) REVERT: M 120 LYS cc_start: 0.8599 (tttm) cc_final: 0.8213 (ttmp) REVERT: M 125 LYS cc_start: 0.8729 (mmtt) cc_final: 0.8500 (mmtm) REVERT: M 141 GLU cc_start: 0.7801 (mm-30) cc_final: 0.7314 (mp0) REVERT: M 148 GLU cc_start: 0.8358 (tt0) cc_final: 0.8084 (tt0) REVERT: N 59 GLN cc_start: 0.8285 (mm110) cc_final: 0.8052 (mm110) REVERT: N 148 GLU cc_start: 0.8383 (tt0) cc_final: 0.8138 (tt0) REVERT: O 59 GLN cc_start: 0.8264 (mm110) cc_final: 0.8024 (mm110) REVERT: O 64 ARG cc_start: 0.8200 (tpp80) cc_final: 0.7147 (ttp-170) REVERT: O 125 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8463 (mmtm) REVERT: P 125 LYS cc_start: 0.8796 (mmtt) cc_final: 0.8512 (mmtm) REVERT: P 141 GLU cc_start: 0.7788 (mm-30) cc_final: 0.7320 (mp0) REVERT: P 148 GLU cc_start: 0.8334 (tt0) cc_final: 0.8111 (tt0) REVERT: Q 125 LYS cc_start: 0.8720 (mmtt) cc_final: 0.8483 (mmtm) REVERT: Q 141 GLU cc_start: 0.7791 (mm-30) cc_final: 0.7302 (mp0) REVERT: Q 148 GLU cc_start: 0.8403 (tt0) cc_final: 0.8015 (tt0) REVERT: R 59 GLN cc_start: 0.8290 (mm110) cc_final: 0.8064 (mm110) REVERT: R 124 GLU cc_start: 0.8086 (tm-30) cc_final: 0.7698 (pp20) REVERT: R 141 GLU cc_start: 0.7819 (mm-30) cc_final: 0.7322 (mp0) REVERT: R 148 GLU cc_start: 0.8332 (tt0) cc_final: 0.8109 (tt0) REVERT: S 59 GLN cc_start: 0.8288 (mm110) cc_final: 0.8064 (mm110) REVERT: S 64 ARG cc_start: 0.8203 (tpp80) cc_final: 0.7151 (ttp-170) REVERT: S 125 LYS cc_start: 0.8715 (mmtt) cc_final: 0.8486 (mmtm) REVERT: S 141 GLU cc_start: 0.7821 (mm-30) cc_final: 0.7323 (mp0) REVERT: S 148 GLU cc_start: 0.8327 (tt0) cc_final: 0.8101 (tt0) REVERT: T 59 GLN cc_start: 0.8301 (mm110) cc_final: 0.8048 (mm110) REVERT: T 62 GLU cc_start: 0.7463 (mm-30) cc_final: 0.7212 (mm-30) REVERT: T 125 LYS cc_start: 0.8761 (mmtt) cc_final: 0.8522 (mmtm) REVERT: T 141 GLU cc_start: 0.7760 (mm-30) cc_final: 0.7327 (mp0) REVERT: T 148 GLU cc_start: 0.8412 (tt0) cc_final: 0.8019 (tt0) REVERT: U 64 ARG cc_start: 0.8176 (tpp80) cc_final: 0.7134 (ttp-170) REVERT: U 141 GLU cc_start: 0.7789 (mm-30) cc_final: 0.7318 (mp0) REVERT: U 148 GLU cc_start: 0.8332 (tt0) cc_final: 0.8107 (tt0) REVERT: V 59 GLN cc_start: 0.8265 (mm110) cc_final: 0.8037 (mm110) REVERT: V 125 LYS cc_start: 0.8718 (mmtt) cc_final: 0.8472 (mmtm) REVERT: W 59 GLN cc_start: 0.8327 (mm110) cc_final: 0.8089 (mm110) REVERT: W 62 GLU cc_start: 0.7499 (mm-30) cc_final: 0.7243 (mm-30) REVERT: W 125 LYS cc_start: 0.8721 (mmtt) cc_final: 0.8471 (mmtm) REVERT: W 148 GLU cc_start: 0.8431 (tt0) cc_final: 0.8035 (tt0) REVERT: X 59 GLN cc_start: 0.8298 (mm110) cc_final: 0.8075 (mm110) REVERT: X 120 LYS cc_start: 0.8599 (tttm) cc_final: 0.8213 (ttmp) REVERT: X 125 LYS cc_start: 0.8738 (mmtt) cc_final: 0.8514 (mmtm) REVERT: X 141 GLU cc_start: 0.7800 (mm-30) cc_final: 0.7311 (mp0) REVERT: X 148 GLU cc_start: 0.8359 (tt0) cc_final: 0.8093 (tt0) outliers start: 87 outliers final: 84 residues processed: 998 average time/residue: 1.7789 time to fit residues: 2054.2784 Evaluate side-chains 1036 residues out of total 3672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 950 time to evaluate : 3.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 SER Chi-restraints excluded: chain A residue 60 SER Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 158 LYS Chi-restraints excluded: chain B residue 7 SER Chi-restraints excluded: chain B residue 60 SER Chi-restraints excluded: chain B residue 95 GLU Chi-restraints excluded: chain B residue 110 SER Chi-restraints excluded: chain C residue 7 SER Chi-restraints excluded: chain C residue 60 SER Chi-restraints excluded: chain C residue 95 GLU Chi-restraints excluded: chain D residue 7 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 95 GLU Chi-restraints excluded: chain E residue 7 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 95 GLU Chi-restraints excluded: chain E residue 123 THR Chi-restraints excluded: chain F residue 7 SER Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 158 LYS Chi-restraints excluded: chain G residue 7 SER Chi-restraints excluded: chain G residue 60 SER Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 95 GLU Chi-restraints excluded: chain I residue 7 SER Chi-restraints excluded: chain I residue 60 SER Chi-restraints excluded: chain I residue 95 GLU Chi-restraints excluded: chain J residue 7 SER Chi-restraints excluded: chain J residue 60 SER Chi-restraints excluded: chain J residue 95 GLU Chi-restraints excluded: chain J residue 110 SER Chi-restraints excluded: chain K residue 7 SER Chi-restraints excluded: chain K residue 60 SER Chi-restraints excluded: chain K residue 95 GLU Chi-restraints excluded: chain K residue 110 SER Chi-restraints excluded: chain L residue 7 SER Chi-restraints excluded: chain L residue 60 SER Chi-restraints excluded: chain L residue 95 GLU Chi-restraints excluded: chain M residue 7 SER Chi-restraints excluded: chain M residue 60 SER Chi-restraints excluded: chain M residue 95 GLU Chi-restraints excluded: chain M residue 110 SER Chi-restraints excluded: chain M residue 158 LYS Chi-restraints excluded: chain N residue 7 SER Chi-restraints excluded: chain N residue 60 SER Chi-restraints excluded: chain N residue 95 GLU Chi-restraints excluded: chain N residue 123 THR Chi-restraints excluded: chain O residue 7 SER Chi-restraints excluded: chain O residue 60 SER Chi-restraints excluded: chain O residue 95 GLU Chi-restraints excluded: chain O residue 110 SER Chi-restraints excluded: chain P residue 7 SER Chi-restraints excluded: chain P residue 60 SER Chi-restraints excluded: chain P residue 95 GLU Chi-restraints excluded: chain Q residue 7 SER Chi-restraints excluded: chain Q residue 60 SER Chi-restraints excluded: chain Q residue 95 GLU Chi-restraints excluded: chain Q residue 110 SER Chi-restraints excluded: chain Q residue 158 LYS Chi-restraints excluded: chain R residue 7 SER Chi-restraints excluded: chain R residue 60 SER Chi-restraints excluded: chain R residue 95 GLU Chi-restraints excluded: chain S residue 7 SER Chi-restraints excluded: chain S residue 60 SER Chi-restraints excluded: chain S residue 95 GLU Chi-restraints excluded: chain T residue 7 SER Chi-restraints excluded: chain T residue 60 SER Chi-restraints excluded: chain T residue 95 GLU Chi-restraints excluded: chain T residue 110 SER Chi-restraints excluded: chain U residue 7 SER Chi-restraints excluded: chain U residue 60 SER Chi-restraints excluded: chain U residue 95 GLU Chi-restraints excluded: chain V residue 7 SER Chi-restraints excluded: chain V residue 60 SER Chi-restraints excluded: chain V residue 95 GLU Chi-restraints excluded: chain V residue 110 SER Chi-restraints excluded: chain W residue 7 SER Chi-restraints excluded: chain W residue 95 GLU Chi-restraints excluded: chain X residue 7 SER Chi-restraints excluded: chain X residue 60 SER Chi-restraints excluded: chain X residue 95 GLU Chi-restraints excluded: chain X residue 110 SER Chi-restraints excluded: chain X residue 158 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 3.9990 chunk 344 optimal weight: 3.9990 chunk 99 optimal weight: 0.9980 chunk 298 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 3.9990 chunk 324 optimal weight: 4.9990 chunk 135 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 8 GLN B 8 GLN B 137 HIS C 8 GLN E 8 GLN E 137 HIS F 8 GLN G 8 GLN H 8 GLN I 8 GLN I 137 HIS J 8 GLN J 137 HIS L 8 GLN N 8 GLN N 137 HIS O 8 GLN O 137 HIS P 8 GLN Q 8 GLN R 8 GLN R 137 HIS S 8 GLN S 137 HIS T 8 GLN U 8 GLN V 8 GLN V 137 HIS W 8 GLN X 8 GLN Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3021 r_free = 0.3021 target = 0.095943 restraints weight = 43083.607| |-----------------------------------------------------------------------------| r_work (start): 0.3024 rms_B_bonded: 1.35 r_work: 0.2912 rms_B_bonded: 1.76 restraints_weight: 0.5000 r_work: 0.2801 rms_B_bonded: 3.05 restraints_weight: 0.2500 r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 34776 Z= 0.263 Angle : 0.526 5.444 46824 Z= 0.273 Chirality : 0.037 0.127 4872 Planarity : 0.003 0.026 6216 Dihedral : 3.916 14.784 4584 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 2.34 % Allowed : 14.03 % Favored : 83.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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: 4.91 (0.13), residues: 4104 helix: 3.89 (0.08), residues: 3264 sheet: None (None), residues: 0 loop : 0.32 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP P 94 HIS 0.003 0.001 HIS P 119 PHE 0.014 0.002 PHE Q 133 TYR 0.013 0.002 TYR Q 40 ARG 0.003 0.001 ARG C 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25327.68 seconds wall clock time: 444 minutes 50.91 seconds (26690.91 seconds total)