Starting phenix.real_space_refine on Sun Mar 24 12:27:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/03_2024/7pf1_13364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/03_2024/7pf1_13364.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/03_2024/7pf1_13364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/03_2024/7pf1_13364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/03_2024/7pf1_13364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/03_2024/7pf1_13364.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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: 6 Type Number sf(0) Gaussians Mg 167 5.21 5 S 168 5.16 5 Cl 96 4.86 5 C 21408 2.51 5 N 6000 2.21 5 O 13807 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "T PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 41646 Number of models: 1 Model: "" Number of chains: 72 Chain: "A" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "B" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "C" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "D" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "E" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "F" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "G" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "H" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "I" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "J" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "K" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "L" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "M" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "N" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "O" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "P" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "Q" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "R" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "S" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "T" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "U" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "V" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "W" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "X" Number of atoms: 1424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 174, 1424 Classifications: {'peptide': 174} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 170} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "C" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "D" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "E" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' CL': 4, ' MG': 8} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Unusual residues: {' CL': 5, ' MG': 8} Classifications: {'undetermined': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "I" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 3, ' MG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "J" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "K" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "L" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "M" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Unusual residues: {' CL': 5, ' MG': 7} Classifications: {'undetermined': 12} Link IDs: {None: 11} Chain: "N" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 4, ' MG': 7} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "O" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 4, ' MG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "P" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "Q" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 3, ' MG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "R" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 3, ' MG': 7} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "S" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "T" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' CL': 5, ' MG': 6} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "U" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "V" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "W" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Unusual residues: {' CL': 4, ' MG': 6} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "X" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Unusual residues: {' CL': 3, ' MG': 6} Classifications: {'undetermined': 9} Link IDs: {None: 8} Chain: "A" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "B" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "C" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "D" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "E" Number of atoms: 296 Number of conformers: 1 Conformer: "" Number of residues, atoms: 296, 296 Classifications: {'water': 296} Link IDs: {None: 295} Chain: "F" Number of atoms: 292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 292, 292 Classifications: {'water': 292} Link IDs: {None: 291} Chain: "G" Number of atoms: 300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 300 Classifications: {'water': 300} Link IDs: {None: 299} Chain: "H" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 297 Classifications: {'water': 297} Link IDs: {None: 296} Chain: "I" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "J" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "K" Number of atoms: 297 Number of conformers: 1 Conformer: "" Number of residues, atoms: 297, 297 Classifications: {'water': 297} Link IDs: {None: 296} Chain: "L" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "M" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "N" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "O" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "P" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "Q" Number of atoms: 303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 303, 303 Classifications: {'water': 303} Link IDs: {None: 302} Chain: "R" Number of atoms: 295 Number of conformers: 1 Conformer: "" Number of residues, atoms: 295, 295 Classifications: {'water': 295} Link IDs: {None: 294} Chain: "S" Number of atoms: 293 Number of conformers: 1 Conformer: "" Number of residues, atoms: 293, 293 Classifications: {'water': 293} Link IDs: {None: 292} Chain: "T" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "U" Number of atoms: 304 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 304 Classifications: {'water': 304} Link IDs: {None: 303} Chain: "V" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} Chain: "W" Number of atoms: 302 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 302 Classifications: {'water': 302} Link IDs: {None: 301} Chain: "X" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 301 Classifications: {'water': 301} Link IDs: {None: 300} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 833 SG CYS A 105 117.711 91.607 71.393 1.00 16.28 S ATOM 2257 SG CYS B 105 61.120 40.905 14.802 1.00 16.28 S ATOM 3681 SG CYS C 105 61.119 14.800 91.606 1.00 16.28 S ATOM 5105 SG CYS D 105 117.711 40.906 61.121 1.00 16.28 S ATOM 6529 SG CYS E 105 61.119 91.607 117.712 1.00 16.28 S ATOM 7953 SG CYS F 105 14.799 40.905 71.392 1.00 16.28 S ATOM 9377 SG CYS G 105 61.120 117.712 40.907 1.00 16.28 S ATOM 10801 SG CYS H 105 14.799 71.391 91.607 1.00 16.28 S ATOM 12225 SG CYS I 105 40.904 61.120 117.712 1.00 16.28 S ATOM 13649 SG CYS J 105 71.391 117.711 91.608 1.00 16.28 S ATOM 15073 SG CYS K 105 14.799 61.120 40.905 1.00 16.28 S ATOM 16497 SG CYS L 105 91.607 61.121 14.802 1.00 16.28 S ATOM 17921 SG CYS M 105 91.607 14.800 71.392 1.00 16.28 S ATOM 19345 SG CYS N 105 40.905 71.393 14.802 1.00 16.28 S ATOM 20769 SG CYS O 105 117.711 61.120 91.608 1.00 16.28 S ATOM 22193 SG CYS P 105 14.799 91.607 61.121 1.00 16.28 S ATOM 23617 SG CYS Q 105 91.606 71.392 117.713 1.00 16.28 S ATOM 25041 SG CYS R 105 40.905 14.800 61.120 1.00 16.28 S ATOM 26465 SG CYS S 105 40.904 117.711 71.393 1.00 16.28 S ATOM 27889 SG CYS T 105 117.712 71.393 40.906 1.00 16.28 S ATOM 29313 SG CYS U 105 71.391 40.905 117.712 1.00 16.28 S ATOM 30737 SG CYS V 105 71.391 14.800 40.906 1.00 16.28 S ATOM 32161 SG CYS W 105 91.606 117.712 61.121 1.00 16.28 S ATOM 33585 SG CYS X 105 71.392 91.607 14.802 1.00 16.28 S Time building chain proxies: 22.58, per 1000 atoms: 0.54 Number of scatterers: 41646 At special positions: 0 Unit cell: (133.168, 133.168, 133.168, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 96 17.00 S 168 16.00 Mg 167 11.99 O 13807 8.00 N 6000 7.00 C 21408 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: 20.45 Conformation dependent library (CDL) restraints added in 6.0 seconds 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8016 Finding SS restraints... Secondary structure from input PDB file: 144 helices and 0 sheets defined 78.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.34 Creating SS restraints... Processing helix chain 'A' and resid 16 through 45 Processing helix chain 'A' and resid 51 through 80 Processing helix chain 'A' and resid 98 through 127 Processing helix chain 'A' and resid 129 through 140 Processing helix chain 'A' and resid 140 through 162 Processing helix chain 'A' and resid 166 through 177 Processing helix chain 'B' and resid 16 through 45 Processing helix chain 'B' and resid 51 through 80 Processing helix chain 'B' and resid 98 through 127 Processing helix chain 'B' and resid 129 through 140 Processing helix chain 'B' and resid 140 through 162 Processing helix chain 'B' and resid 166 through 177 Processing helix chain 'C' and resid 16 through 45 Processing helix chain 'C' and resid 51 through 80 Processing helix chain 'C' and resid 98 through 127 Processing helix chain 'C' and resid 129 through 140 Processing helix chain 'C' and resid 140 through 162 Processing helix chain 'C' and resid 166 through 177 Processing helix chain 'D' and resid 16 through 45 Processing helix chain 'D' and resid 51 through 80 Processing helix chain 'D' and resid 98 through 127 Processing helix chain 'D' and resid 129 through 140 Processing helix chain 'D' and resid 140 through 162 Processing helix chain 'D' and resid 166 through 177 Processing helix chain 'E' and resid 16 through 45 Processing helix chain 'E' and resid 51 through 80 Processing helix chain 'E' and resid 98 through 127 Processing helix chain 'E' and resid 129 through 140 Processing helix chain 'E' and resid 140 through 162 Processing helix chain 'E' and resid 166 through 177 Processing helix chain 'F' and resid 16 through 45 Processing helix chain 'F' and resid 51 through 80 Processing helix chain 'F' and resid 98 through 127 Processing helix chain 'F' and resid 129 through 140 Processing helix chain 'F' and resid 140 through 162 Processing helix chain 'F' and resid 166 through 177 Processing helix chain 'G' and resid 16 through 45 Processing helix chain 'G' and resid 51 through 80 Processing helix chain 'G' and resid 98 through 127 Processing helix chain 'G' and resid 129 through 140 Processing helix chain 'G' and resid 140 through 162 Processing helix chain 'G' and resid 166 through 177 Processing helix chain 'H' and resid 16 through 45 Processing helix chain 'H' and resid 51 through 80 Processing helix chain 'H' and resid 98 through 127 Processing helix chain 'H' and resid 129 through 140 Processing helix chain 'H' and resid 140 through 162 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'I' and resid 16 through 45 Processing helix chain 'I' and resid 51 through 80 Processing helix chain 'I' and resid 98 through 127 Processing helix chain 'I' and resid 129 through 140 Processing helix chain 'I' and resid 140 through 162 Processing helix chain 'I' and resid 166 through 177 Processing helix chain 'J' and resid 16 through 45 Processing helix chain 'J' and resid 51 through 80 Processing helix chain 'J' and resid 98 through 127 Processing helix chain 'J' and resid 129 through 140 Processing helix chain 'J' and resid 140 through 162 Processing helix chain 'J' and resid 166 through 177 Processing helix chain 'K' and resid 16 through 45 Processing helix chain 'K' and resid 51 through 80 Processing helix chain 'K' and resid 98 through 127 Processing helix chain 'K' and resid 129 through 140 Processing helix chain 'K' and resid 140 through 162 Processing helix chain 'K' and resid 166 through 177 Processing helix chain 'L' and resid 16 through 45 Processing helix chain 'L' and resid 51 through 80 Processing helix chain 'L' and resid 98 through 127 Processing helix chain 'L' and resid 129 through 140 Processing helix chain 'L' and resid 140 through 162 Processing helix chain 'L' and resid 166 through 177 Processing helix chain 'M' and resid 16 through 45 Processing helix chain 'M' and resid 51 through 80 Processing helix chain 'M' and resid 98 through 127 Processing helix chain 'M' and resid 129 through 140 Processing helix chain 'M' and resid 140 through 162 Processing helix chain 'M' and resid 166 through 177 Processing helix chain 'N' and resid 16 through 45 Processing helix chain 'N' and resid 51 through 80 Processing helix chain 'N' and resid 98 through 127 Processing helix chain 'N' and resid 129 through 140 Processing helix chain 'N' and resid 140 through 162 Processing helix chain 'N' and resid 166 through 177 Processing helix chain 'O' and resid 16 through 45 Processing helix chain 'O' and resid 51 through 80 Processing helix chain 'O' and resid 98 through 127 Processing helix chain 'O' and resid 129 through 140 Processing helix chain 'O' and resid 140 through 162 Processing helix chain 'O' and resid 166 through 177 Processing helix chain 'P' and resid 16 through 45 Processing helix chain 'P' and resid 51 through 80 Processing helix chain 'P' and resid 98 through 127 Processing helix chain 'P' and resid 129 through 140 Processing helix chain 'P' and resid 140 through 162 Processing helix chain 'P' and resid 166 through 177 Processing helix chain 'Q' and resid 16 through 45 Processing helix chain 'Q' and resid 51 through 80 Processing helix chain 'Q' and resid 98 through 127 Processing helix chain 'Q' and resid 129 through 140 Processing helix chain 'Q' and resid 140 through 162 Processing helix chain 'Q' and resid 166 through 177 Processing helix chain 'R' and resid 16 through 45 Processing helix chain 'R' and resid 51 through 80 Processing helix chain 'R' and resid 98 through 127 Processing helix chain 'R' and resid 129 through 140 Processing helix chain 'R' and resid 140 through 162 Processing helix chain 'R' and resid 166 through 177 Processing helix chain 'S' and resid 16 through 45 Processing helix chain 'S' and resid 51 through 80 Processing helix chain 'S' and resid 98 through 127 Processing helix chain 'S' and resid 129 through 140 Processing helix chain 'S' and resid 140 through 162 Processing helix chain 'S' and resid 166 through 177 Processing helix chain 'T' and resid 16 through 45 Processing helix chain 'T' and resid 51 through 80 Processing helix chain 'T' and resid 98 through 127 Processing helix chain 'T' and resid 129 through 140 Processing helix chain 'T' and resid 140 through 162 Processing helix chain 'T' and resid 166 through 177 Processing helix chain 'U' and resid 16 through 45 Processing helix chain 'U' and resid 51 through 80 Processing helix chain 'U' and resid 98 through 127 Processing helix chain 'U' and resid 129 through 140 Processing helix chain 'U' and resid 140 through 162 Processing helix chain 'U' and resid 166 through 177 Processing helix chain 'V' and resid 16 through 45 Processing helix chain 'V' and resid 51 through 80 Processing helix chain 'V' and resid 98 through 127 Processing helix chain 'V' and resid 129 through 140 Processing helix chain 'V' and resid 140 through 162 Processing helix chain 'V' and resid 166 through 177 Processing helix chain 'W' and resid 16 through 45 Processing helix chain 'W' and resid 51 through 80 Processing helix chain 'W' and resid 98 through 127 Processing helix chain 'W' and resid 129 through 140 Processing helix chain 'W' and resid 140 through 162 Processing helix chain 'W' and resid 166 through 177 Processing helix chain 'X' and resid 16 through 45 Processing helix chain 'X' and resid 51 through 80 Processing helix chain 'X' and resid 98 through 127 Processing helix chain 'X' and resid 129 through 140 Processing helix chain 'X' and resid 140 through 162 Processing helix chain 'X' and resid 166 through 177 2712 hydrogen bonds defined for protein. 8136 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: 12.41 Time building geometry restraints manager: 21.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 8124 1.33 - 1.47: 9939 1.47 - 1.61: 16545 1.61 - 1.75: 0 1.75 - 1.89: 264 Bond restraints: 34872 Sorted by residual: bond pdb=" C SER D 166 " pdb=" O SER D 166 " ideal model delta sigma weight residual 1.233 1.341 -0.108 1.21e-02 6.83e+03 8.01e+01 bond pdb=" C SER I 166 " pdb=" O SER I 166 " ideal model delta sigma weight residual 1.233 1.341 -0.108 1.21e-02 6.83e+03 7.98e+01 bond pdb=" C SER J 166 " pdb=" O SER J 166 " ideal model delta sigma weight residual 1.233 1.340 -0.108 1.21e-02 6.83e+03 7.92e+01 bond pdb=" C SER V 166 " pdb=" O SER V 166 " ideal model delta sigma weight residual 1.233 1.340 -0.108 1.21e-02 6.83e+03 7.92e+01 bond pdb=" C SER H 166 " pdb=" O SER H 166 " ideal model delta sigma weight residual 1.233 1.340 -0.108 1.21e-02 6.83e+03 7.92e+01 ... (remaining 34867 not shown) Histogram of bond angle deviations from ideal: 98.06 - 105.25: 408 105.25 - 112.45: 15645 112.45 - 119.64: 14505 119.64 - 126.84: 16028 126.84 - 134.04: 382 Bond angle restraints: 46968 Sorted by residual: angle pdb=" CA SER K 166 " pdb=" C SER K 166 " pdb=" O SER K 166 " ideal model delta sigma weight residual 121.02 126.52 -5.50 1.15e+00 7.56e-01 2.29e+01 angle pdb=" CA SER L 166 " pdb=" C SER L 166 " pdb=" O SER L 166 " ideal model delta sigma weight residual 121.02 126.52 -5.50 1.15e+00 7.56e-01 2.29e+01 angle pdb=" CA SER T 166 " pdb=" C SER T 166 " pdb=" O SER T 166 " ideal model delta sigma weight residual 121.02 126.52 -5.50 1.15e+00 7.56e-01 2.28e+01 angle pdb=" CA SER D 166 " pdb=" C SER D 166 " pdb=" O SER D 166 " ideal model delta sigma weight residual 121.02 126.50 -5.48 1.15e+00 7.56e-01 2.27e+01 angle pdb=" CA SER W 166 " pdb=" C SER W 166 " pdb=" O SER W 166 " ideal model delta sigma weight residual 121.02 126.49 -5.47 1.15e+00 7.56e-01 2.26e+01 ... (remaining 46963 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.78: 19353 16.78 - 33.57: 1257 33.57 - 50.35: 294 50.35 - 67.13: 72 67.13 - 83.91: 120 Dihedral angle restraints: 21096 sinusoidal: 8712 harmonic: 12384 Sorted by residual: dihedral pdb=" C TYR U 42 " pdb=" N TYR U 42 " pdb=" CA TYR U 42 " pdb=" CB TYR U 42 " ideal model delta harmonic sigma weight residual -122.60 -132.43 9.83 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR D 42 " pdb=" N TYR D 42 " pdb=" CA TYR D 42 " pdb=" CB TYR D 42 " ideal model delta harmonic sigma weight residual -122.60 -132.43 9.83 0 2.50e+00 1.60e-01 1.55e+01 dihedral pdb=" C TYR S 42 " pdb=" N TYR S 42 " pdb=" CA TYR S 42 " pdb=" CB TYR S 42 " ideal model delta harmonic sigma weight residual -122.60 -132.42 9.82 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 21093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 2215 0.076 - 0.152: 1524 0.152 - 0.228: 965 0.228 - 0.303: 192 0.303 - 0.379: 48 Chirality restraints: 4944 Sorted by residual: chirality pdb=" CA TYR S 42 " pdb=" N TYR S 42 " pdb=" C TYR S 42 " pdb=" CB TYR S 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CA TYR V 42 " pdb=" N TYR V 42 " pdb=" C TYR V 42 " pdb=" CB TYR V 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 chirality pdb=" CA TYR U 42 " pdb=" N TYR U 42 " pdb=" C TYR U 42 " pdb=" CB TYR U 42 " both_signs ideal model delta sigma weight residual False 2.51 2.13 0.38 2.00e-01 2.50e+01 3.56e+00 ... (remaining 4941 not shown) Planarity restraints: 6192 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 140 " 0.097 2.00e-02 2.50e+03 5.00e-02 5.00e+01 pdb=" CG TYR B 140 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR B 140 " -0.050 2.00e-02 2.50e+03 pdb=" CD2 TYR B 140 " -0.028 2.00e-02 2.50e+03 pdb=" CE1 TYR B 140 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR B 140 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR B 140 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 140 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 140 " 0.097 2.00e-02 2.50e+03 4.99e-02 4.99e+01 pdb=" CG TYR G 140 " -0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR G 140 " -0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR G 140 " -0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR G 140 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G 140 " -0.016 2.00e-02 2.50e+03 pdb=" CZ TYR G 140 " -0.004 2.00e-02 2.50e+03 pdb=" OH TYR G 140 " 0.057 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 140 " -0.097 2.00e-02 2.50e+03 4.99e-02 4.98e+01 pdb=" CG TYR L 140 " 0.060 2.00e-02 2.50e+03 pdb=" CD1 TYR L 140 " 0.051 2.00e-02 2.50e+03 pdb=" CD2 TYR L 140 " 0.029 2.00e-02 2.50e+03 pdb=" CE1 TYR L 140 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR L 140 " 0.016 2.00e-02 2.50e+03 pdb=" CZ TYR L 140 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR L 140 " -0.056 2.00e-02 2.50e+03 ... (remaining 6189 not shown) Histogram of nonbonded interaction distances: 1.77 - 2.39: 765 2.39 - 3.02: 30960 3.02 - 3.65: 72760 3.65 - 4.27: 125428 4.27 - 4.90: 185366 Nonbonded interactions: 415279 Sorted by model distance: nonbonded pdb="MG MG R 207 " pdb=" O HOH R 341 " model vdw 1.766 2.170 nonbonded pdb="MG MG F 208 " pdb=" O HOH F 339 " model vdw 1.766 2.170 nonbonded pdb="MG MG P 206 " pdb=" O HOH P 341 " model vdw 1.766 2.170 nonbonded pdb="MG MG L 208 " pdb=" O HOH L 341 " model vdw 1.766 2.170 nonbonded pdb="MG MG E 208 " pdb=" O HOH E 341 " model vdw 1.766 2.170 ... (remaining 415274 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' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'B' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'C' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'D' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'E' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'F' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'G' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'H' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'I' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'J' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'K' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'L' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'M' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'N' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'O' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'P' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'Q' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'R' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'S' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'T' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'U' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'V' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'W' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) selection = (chain 'X' and (resid 6 through 179 or resid 202 through 203 or resid 206 throug \ h 209)) } 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: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 11.070 Check model and map are aligned: 0.590 Set scattering table: 0.330 Process input model: 104.110 Find NCS groups from input model: 3.790 Set up NCS constraints: 0.500 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:10.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 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 : 0.020 0.143 34872 Z= 1.281 Angle : 1.660 7.589 46968 Z= 1.058 Chirality : 0.122 0.379 4944 Planarity : 0.013 0.051 6192 Dihedral : 14.319 83.915 13080 Min Nonbonded Distance : 1.766 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.65 % Allowed : 1.95 % Favored : 97.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.11), residues: 4128 helix: 1.02 (0.08), residues: 3216 sheet: None (None), residues: 0 loop : 0.16 (0.21), residues: 912 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.012 TRP C 96 HIS 0.028 0.009 HIS K 121 PHE 0.053 0.017 PHE E 44 TYR 0.097 0.022 TYR B 140 ARG 0.018 0.005 ARG A 79 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1056 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 1032 time to evaluate : 5.214 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 24 outliers final: 0 residues processed: 1032 average time/residue: 2.2153 time to fit residues: 2636.5652 Evaluate side-chains 508 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 4.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 344 optimal weight: 0.6980 chunk 309 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 208 optimal weight: 3.9990 chunk 165 optimal weight: 30.0000 chunk 319 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 194 optimal weight: 7.9990 chunk 238 optimal weight: 5.9990 chunk 370 optimal weight: 0.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 ASN A 115 GLN B 112 ASN B 115 GLN C 112 ASN C 115 GLN D 112 ASN D 115 GLN E 112 ASN E 115 GLN F 112 ASN F 115 GLN G 112 ASN G 115 GLN H 112 ASN H 115 GLN I 112 ASN I 115 GLN J 112 ASN J 115 GLN K 112 ASN K 115 GLN L 112 ASN L 115 GLN M 112 ASN M 115 GLN N 112 ASN N 115 GLN O 112 ASN O 115 GLN P 112 ASN P 115 GLN Q 112 ASN Q 115 GLN R 112 ASN R 115 GLN S 112 ASN S 115 GLN T 112 ASN T 115 GLN U 112 ASN U 115 GLN V 112 ASN V 115 GLN W 112 ASN W 115 GLN X 112 ASN X 115 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7762 moved from start: 0.4545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 34872 Z= 0.151 Angle : 0.517 5.461 46968 Z= 0.287 Chirality : 0.036 0.157 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.408 21.452 4536 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.30 % Allowed : 8.04 % Favored : 90.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.77 (0.13), residues: 4128 helix: 3.74 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.53 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP T 96 HIS 0.004 0.001 HIS O 108 PHE 0.011 0.002 PHE R 135 TYR 0.021 0.002 TYR E 42 ARG 0.001 0.000 ARG E 46 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 723 time to evaluate : 4.883 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 HIS cc_start: 0.8061 (t-170) cc_final: 0.7859 (t70) REVERT: A 119 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: A 159 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7560 (mtt180) REVERT: B 119 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: B 159 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7572 (mtt180) REVERT: C 119 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7234 (tt0) REVERT: C 159 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7559 (mtt180) REVERT: D 119 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: D 159 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7559 (mtt180) REVERT: E 108 HIS cc_start: 0.8069 (t-170) cc_final: 0.7867 (t70) REVERT: E 119 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7260 (tt0) REVERT: E 159 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7572 (mtt180) REVERT: F 119 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7239 (tt0) REVERT: F 159 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7568 (mtt180) REVERT: G 119 GLU cc_start: 0.7520 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: G 159 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7570 (mtt180) REVERT: H 119 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7264 (tt0) REVERT: H 159 ARG cc_start: 0.7789 (mtt180) cc_final: 0.7568 (mtt180) REVERT: I 119 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: I 159 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7559 (mtt180) REVERT: J 108 HIS cc_start: 0.8066 (t-170) cc_final: 0.7866 (t70) REVERT: J 119 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: J 159 ARG cc_start: 0.7780 (mtt180) cc_final: 0.7563 (mtt180) REVERT: K 108 HIS cc_start: 0.8067 (t-170) cc_final: 0.7864 (t70) REVERT: K 119 GLU cc_start: 0.7521 (OUTLIER) cc_final: 0.7238 (tt0) REVERT: K 159 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7563 (mtt180) REVERT: L 108 HIS cc_start: 0.8066 (t-170) cc_final: 0.7864 (t70) REVERT: L 119 GLU cc_start: 0.7522 (OUTLIER) cc_final: 0.7240 (tt0) REVERT: L 159 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7564 (mtt180) REVERT: M 108 HIS cc_start: 0.8053 (t-170) cc_final: 0.7850 (t70) REVERT: M 119 GLU cc_start: 0.7529 (OUTLIER) cc_final: 0.7242 (tt0) REVERT: M 159 ARG cc_start: 0.7784 (mtt180) cc_final: 0.7570 (mtt180) REVERT: N 119 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: N 159 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7572 (mtt180) REVERT: O 119 GLU cc_start: 0.7517 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: O 159 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7559 (mtt180) REVERT: P 119 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7237 (tt0) REVERT: P 159 ARG cc_start: 0.7785 (mtt180) cc_final: 0.7559 (mtt180) REVERT: Q 108 HIS cc_start: 0.8060 (t-170) cc_final: 0.7858 (t70) REVERT: Q 119 GLU cc_start: 0.7512 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: Q 159 ARG cc_start: 0.7787 (mtt180) cc_final: 0.7565 (mtt180) REVERT: R 119 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7231 (tt0) REVERT: R 159 ARG cc_start: 0.7778 (mtt180) cc_final: 0.7558 (mtt180) REVERT: S 119 GLU cc_start: 0.7513 (OUTLIER) cc_final: 0.7227 (tt0) REVERT: S 159 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7566 (mtt180) REVERT: T 119 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: T 159 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7570 (mtt180) REVERT: U 119 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7261 (tt0) REVERT: U 159 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7571 (mtt180) REVERT: V 119 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7233 (tt0) REVERT: V 159 ARG cc_start: 0.7779 (mtt180) cc_final: 0.7560 (mtt180) REVERT: W 119 GLU cc_start: 0.7514 (OUTLIER) cc_final: 0.7254 (tt0) REVERT: W 159 ARG cc_start: 0.7782 (mtt180) cc_final: 0.7572 (mtt180) REVERT: X 119 GLU cc_start: 0.7511 (OUTLIER) cc_final: 0.7230 (tt0) REVERT: X 159 ARG cc_start: 0.7783 (mtt180) cc_final: 0.7561 (mtt180) outliers start: 48 outliers final: 0 residues processed: 723 average time/residue: 2.1633 time to fit residues: 1814.7076 Evaluate side-chains 658 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 634 time to evaluate : 3.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 GLU Chi-restraints excluded: chain B residue 119 GLU Chi-restraints excluded: chain C residue 119 GLU Chi-restraints excluded: chain D residue 119 GLU Chi-restraints excluded: chain E residue 119 GLU Chi-restraints excluded: chain F residue 119 GLU Chi-restraints excluded: chain G residue 119 GLU Chi-restraints excluded: chain H residue 119 GLU Chi-restraints excluded: chain I residue 119 GLU Chi-restraints excluded: chain J residue 119 GLU Chi-restraints excluded: chain K residue 119 GLU Chi-restraints excluded: chain L residue 119 GLU Chi-restraints excluded: chain M residue 119 GLU Chi-restraints excluded: chain N residue 119 GLU Chi-restraints excluded: chain O residue 119 GLU Chi-restraints excluded: chain P residue 119 GLU Chi-restraints excluded: chain Q residue 119 GLU Chi-restraints excluded: chain R residue 119 GLU Chi-restraints excluded: chain S residue 119 GLU Chi-restraints excluded: chain T residue 119 GLU Chi-restraints excluded: chain U residue 119 GLU Chi-restraints excluded: chain V residue 119 GLU Chi-restraints excluded: chain W residue 119 GLU Chi-restraints excluded: chain X residue 119 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 9.9990 chunk 114 optimal weight: 0.7980 chunk 308 optimal weight: 10.0000 chunk 252 optimal weight: 10.0000 chunk 102 optimal weight: 20.0000 chunk 371 optimal weight: 10.0000 chunk 400 optimal weight: 5.9990 chunk 330 optimal weight: 0.9980 chunk 368 optimal weight: 5.9990 chunk 126 optimal weight: 0.5980 chunk 297 optimal weight: 2.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 HIS A 115 GLN B 68 HIS B 115 GLN C 68 HIS C 115 GLN D 68 HIS D 115 GLN E 68 HIS E 115 GLN F 68 HIS F 115 GLN G 68 HIS G 115 GLN H 68 HIS H 115 GLN I 68 HIS I 115 GLN J 68 HIS J 115 GLN K 68 HIS K 115 GLN L 68 HIS L 115 GLN M 68 HIS M 115 GLN N 68 HIS N 115 GLN O 68 HIS O 115 GLN P 68 HIS P 115 GLN Q 68 HIS Q 115 GLN R 68 HIS R 115 GLN S 68 HIS S 115 GLN T 68 HIS T 115 GLN U 68 HIS U 115 GLN V 68 HIS V 115 GLN W 68 HIS W 115 GLN X 68 HIS X 115 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 34872 Z= 0.188 Angle : 0.539 5.386 46968 Z= 0.302 Chirality : 0.038 0.153 4944 Planarity : 0.003 0.016 6192 Dihedral : 4.461 19.423 4536 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 1.54 % Allowed : 7.28 % Favored : 91.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 5.01 (0.13), residues: 4128 helix: 3.94 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.47 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP F 96 HIS 0.006 0.002 HIS Q 108 PHE 0.010 0.002 PHE K 54 TYR 0.026 0.003 TYR F 42 ARG 0.002 0.001 ARG X 159 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 633 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 576 time to evaluate : 4.719 Fit side-chains REVERT: J 108 HIS cc_start: 0.8105 (t70) cc_final: 0.7905 (t70) REVERT: K 108 HIS cc_start: 0.8101 (t70) cc_final: 0.7901 (t70) outliers start: 57 outliers final: 9 residues processed: 585 average time/residue: 2.0330 time to fit residues: 1392.6747 Evaluate side-chains 544 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 535 time to evaluate : 4.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 9 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 366 optimal weight: 0.9990 chunk 279 optimal weight: 3.9990 chunk 192 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 177 optimal weight: 2.9990 chunk 249 optimal weight: 6.9990 chunk 372 optimal weight: 5.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 2.9990 chunk 353 optimal weight: 5.9990 chunk 106 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN A 144 GLN B 115 GLN C 115 GLN C 144 GLN D 115 GLN D 144 GLN E 108 HIS E 115 GLN F 115 GLN F 144 GLN G 115 GLN G 144 GLN H 115 GLN I 115 GLN J 115 GLN K 115 GLN L 108 HIS L 115 GLN L 144 GLN M 108 HIS M 115 GLN M 144 GLN N 115 GLN O 115 GLN P 115 GLN P 144 GLN Q 108 HIS Q 115 GLN Q 144 GLN R 115 GLN S 115 GLN T 115 GLN U 115 GLN U 144 GLN V 115 GLN V 144 GLN W 115 GLN W 144 GLN X 115 GLN X 144 GLN Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 34872 Z= 0.215 Angle : 0.560 5.726 46968 Z= 0.316 Chirality : 0.039 0.160 4944 Planarity : 0.003 0.018 6192 Dihedral : 4.566 19.645 4536 Min Nonbonded Distance : 1.906 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.30 % Allowed : 9.42 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.87 (0.13), residues: 4128 helix: 3.86 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.31 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP W 96 HIS 0.006 0.002 HIS H 139 PHE 0.010 0.002 PHE I 44 TYR 0.026 0.003 TYR G 42 ARG 0.004 0.000 ARG P 12 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 623 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 575 time to evaluate : 4.874 Fit side-chains REVERT: J 108 HIS cc_start: 0.8130 (t70) cc_final: 0.7859 (t70) REVERT: K 108 HIS cc_start: 0.8131 (t70) cc_final: 0.7860 (t70) outliers start: 48 outliers final: 24 residues processed: 576 average time/residue: 1.9610 time to fit residues: 1329.9417 Evaluate side-chains 564 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 540 time to evaluate : 4.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 9 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 328 optimal weight: 10.0000 chunk 223 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 293 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 336 optimal weight: 3.9990 chunk 272 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 6.9990 chunk 353 optimal weight: 3.9990 chunk 99 optimal weight: 10.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN A 142 ASN B 115 GLN B 142 ASN C 115 GLN C 142 ASN D 60 HIS D 115 GLN D 142 ASN E 108 HIS E 115 GLN E 142 ASN F 60 HIS F 115 GLN F 142 ASN G 115 GLN G 142 ASN H 115 GLN I 115 GLN J 108 HIS J 115 GLN J 142 ASN K 108 HIS K 115 GLN K 142 ASN L 108 HIS L 115 GLN L 142 ASN M 108 HIS M 115 GLN M 142 ASN N 115 GLN O 115 GLN P 60 HIS P 115 GLN P 142 ASN Q 108 HIS Q 115 GLN Q 142 ASN R 115 GLN R 142 ASN S 115 GLN S 142 ASN T 115 GLN U 60 HIS U 115 GLN U 142 ASN V 60 HIS V 115 GLN V 142 ASN W 115 GLN W 142 ASN X 60 HIS X 115 GLN X 142 ASN Total number of N/Q/H flips: 56 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.5477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 34872 Z= 0.264 Angle : 0.600 6.111 46968 Z= 0.339 Chirality : 0.041 0.161 4944 Planarity : 0.004 0.019 6192 Dihedral : 4.653 19.179 4536 Min Nonbonded Distance : 1.890 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.27 % Allowed : 10.09 % Favored : 88.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.58 (0.13), residues: 4128 helix: 3.66 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.003 TRP F 96 HIS 0.007 0.002 HIS N 139 PHE 0.012 0.003 PHE I 44 TYR 0.024 0.003 TYR M 42 ARG 0.003 0.001 ARG G 12 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 582 time to evaluate : 4.680 Fit side-chains outliers start: 47 outliers final: 24 residues processed: 604 average time/residue: 1.9716 time to fit residues: 1398.2247 Evaluate side-chains 589 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 565 time to evaluate : 4.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 9 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.8980 chunk 355 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 231 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 2.9990 chunk 32 optimal weight: 4.9990 chunk 130 optimal weight: 0.9980 chunk 207 optimal weight: 5.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN A 142 ASN B 115 GLN B 142 ASN B 144 GLN C 115 GLN C 142 ASN D 115 GLN D 142 ASN E 108 HIS E 115 GLN E 142 ASN E 144 GLN F 115 GLN F 142 ASN G 115 GLN G 142 ASN H 115 GLN H 144 GLN I 115 GLN I 142 ASN I 144 GLN J 108 HIS J 115 GLN J 142 ASN J 144 GLN K 108 HIS K 115 GLN K 142 ASN K 144 GLN L 108 HIS L 115 GLN L 142 ASN M 108 HIS M 115 GLN M 142 ASN N 115 GLN N 142 ASN N 144 GLN O 115 GLN O 142 ASN O 144 GLN P 60 HIS P 115 GLN P 142 ASN Q 108 HIS Q 115 GLN Q 142 ASN R 115 GLN R 142 ASN R 144 GLN S 115 GLN S 142 ASN T 115 GLN T 142 ASN T 144 GLN U 60 HIS U 115 GLN U 142 ASN V 60 HIS V 115 GLN V 142 ASN W 115 GLN W 142 ASN X 60 HIS X 115 GLN X 142 ASN Total number of N/Q/H flips: 68 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.5498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 34872 Z= 0.205 Angle : 0.538 5.642 46968 Z= 0.305 Chirality : 0.038 0.154 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.536 19.718 4536 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 0.68 % Allowed : 10.93 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.78 (0.13), residues: 4128 helix: 3.81 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.20 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP Q 96 HIS 0.004 0.002 HIS L 139 PHE 0.012 0.002 PHE A 44 TYR 0.022 0.003 TYR F 42 ARG 0.002 0.000 ARG U 12 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 581 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 556 time to evaluate : 4.799 Fit side-chains outliers start: 25 outliers final: 24 residues processed: 557 average time/residue: 2.1275 time to fit residues: 1379.8171 Evaluate side-chains 573 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 549 time to evaluate : 5.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 9 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 288 optimal weight: 6.9990 chunk 223 optimal weight: 4.9990 chunk 332 optimal weight: 5.9990 chunk 220 optimal weight: 6.9990 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 7.9990 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 0.6980 overall best weight: 3.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS A 115 GLN B 115 GLN C 115 GLN E 108 HIS E 115 GLN E 142 ASN F 60 HIS H 115 GLN H 142 ASN I 60 HIS I 115 GLN J 60 HIS J 108 HIS K 108 HIS K 142 ASN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 115 GLN O 60 HIS P 60 HIS Q 108 HIS Q 115 GLN R 115 GLN S 115 GLN T 60 HIS T 115 GLN U 60 HIS U 115 GLN V 60 HIS W 115 GLN X 60 HIS X 115 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 34872 Z= 0.250 Angle : 0.590 6.058 46968 Z= 0.332 Chirality : 0.040 0.156 4944 Planarity : 0.003 0.016 6192 Dihedral : 4.612 19.148 4536 Min Nonbonded Distance : 1.899 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.65 % Allowed : 10.98 % Favored : 88.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.61 (0.13), residues: 4128 helix: 3.67 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.23 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.003 TRP B 96 HIS 0.005 0.002 HIS H 139 PHE 0.012 0.003 PHE A 44 TYR 0.022 0.003 TYR O 42 ARG 0.003 0.001 ARG T 12 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 582 time to evaluate : 5.115 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 582 average time/residue: 1.9979 time to fit residues: 1368.8942 Evaluate side-chains 573 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 549 time to evaluate : 4.889 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 SER Chi-restraints excluded: chain B residue 9 SER Chi-restraints excluded: chain C residue 9 SER Chi-restraints excluded: chain D residue 9 SER Chi-restraints excluded: chain E residue 9 SER Chi-restraints excluded: chain F residue 9 SER Chi-restraints excluded: chain G residue 9 SER Chi-restraints excluded: chain H residue 9 SER Chi-restraints excluded: chain I residue 9 SER Chi-restraints excluded: chain J residue 9 SER Chi-restraints excluded: chain K residue 9 SER Chi-restraints excluded: chain L residue 9 SER Chi-restraints excluded: chain M residue 9 SER Chi-restraints excluded: chain N residue 9 SER Chi-restraints excluded: chain O residue 9 SER Chi-restraints excluded: chain P residue 9 SER Chi-restraints excluded: chain Q residue 9 SER Chi-restraints excluded: chain R residue 9 SER Chi-restraints excluded: chain S residue 9 SER Chi-restraints excluded: chain T residue 9 SER Chi-restraints excluded: chain U residue 9 SER Chi-restraints excluded: chain V residue 9 SER Chi-restraints excluded: chain W residue 9 SER Chi-restraints excluded: chain X residue 9 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 1.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 0.9990 chunk 118 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 76 optimal weight: 0.9980 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 6.9990 chunk 194 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 4.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 HIS B 115 GLN D 115 GLN E 108 HIS E 115 GLN F 115 GLN G 115 GLN H 115 GLN I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 108 HIS M 108 HIS N 115 GLN O 115 GLN P 60 HIS P 115 GLN Q 108 HIS Q 115 GLN S 144 GLN U 60 HIS V 60 HIS V 115 GLN X 60 HIS X 115 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7806 moved from start: 0.5581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 34872 Z= 0.150 Angle : 0.485 5.185 46968 Z= 0.274 Chirality : 0.036 0.142 4944 Planarity : 0.002 0.013 6192 Dihedral : 4.360 19.560 4536 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.60 % Allowed : 11.01 % Favored : 88.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4128 helix: 4.13 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.49 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP J 96 HIS 0.004 0.001 HIS I 131 PHE 0.011 0.002 PHE B 44 TYR 0.019 0.002 TYR B 42 ARG 0.001 0.000 ARG O 12 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 532 time to evaluate : 4.811 Fit side-chains outliers start: 22 outliers final: 0 residues processed: 532 average time/residue: 2.0950 time to fit residues: 1301.0547 Evaluate side-chains 528 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 357 optimal weight: 0.3980 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 1.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 5.9990 chunk 287 optimal weight: 6.9990 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 10.0000 chunk 346 optimal weight: 5.9990 chunk 365 optimal weight: 10.0000 overall best weight: 4.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 108 HIS C 60 HIS D 60 HIS D 115 GLN E 108 HIS F 60 HIS F 115 GLN G 60 HIS G 115 GLN H 60 HIS I 60 HIS J 60 HIS J 108 HIS J 115 GLN K 60 HIS K 108 HIS K 115 GLN L 108 HIS M 60 HIS M 108 HIS N 60 HIS O 60 HIS O 115 GLN P 60 HIS P 115 GLN Q 108 HIS R 60 HIS S 60 HIS U 60 HIS V 60 HIS V 115 GLN X 60 HIS X 115 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.5588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 34872 Z= 0.269 Angle : 0.602 6.218 46968 Z= 0.339 Chirality : 0.041 0.158 4944 Planarity : 0.004 0.017 6192 Dihedral : 4.580 19.186 4536 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.19 % Allowed : 11.20 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.65 (0.13), residues: 4128 helix: 3.68 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.34 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP F 96 HIS 0.005 0.002 HIS H 139 PHE 0.012 0.003 PHE B 44 TYR 0.020 0.003 TYR P 42 ARG 0.003 0.000 ARG V 12 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 570 time to evaluate : 4.815 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 570 average time/residue: 2.0091 time to fit residues: 1345.8221 Evaluate side-chains 552 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 5.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 240 optimal weight: 7.9990 chunk 387 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 2.9990 chunk 269 optimal weight: 5.9990 chunk 406 optimal weight: 4.9990 chunk 374 optimal weight: 4.9990 chunk 323 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 250 optimal weight: 8.9990 chunk 198 optimal weight: 6.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 108 HIS A 115 GLN B 115 GLN C 60 HIS C 115 GLN D 60 HIS D 115 GLN E 60 HIS E 108 HIS E 115 GLN F 60 HIS F 115 GLN G 60 HIS G 115 GLN H 60 HIS H 115 GLN I 60 HIS I 115 GLN J 60 HIS J 108 HIS J 115 GLN K 60 HIS K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 60 HIS M 108 HIS M 115 GLN N 60 HIS N 115 GLN O 115 GLN P 60 HIS P 115 GLN Q 108 HIS Q 115 GLN R 60 HIS R 115 GLN S 60 HIS S 115 GLN T 60 HIS T 115 GLN U 60 HIS U 115 GLN V 60 HIS V 115 GLN W 60 HIS W 115 GLN X 60 HIS X 115 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 34872 Z= 0.287 Angle : 0.618 6.461 46968 Z= 0.348 Chirality : 0.042 0.161 4944 Planarity : 0.004 0.020 6192 Dihedral : 4.631 19.048 4536 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 12.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.19 % Allowed : 11.61 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.47 (0.13), residues: 4128 helix: 3.56 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.26 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP T 96 HIS 0.006 0.002 HIS W 60 PHE 0.012 0.003 PHE B 44 TYR 0.022 0.003 TYR C 42 ARG 0.003 0.000 ARG F 12 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8256 Ramachandran restraints generated. 4128 Oldfield, 0 Emsley, 4128 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 573 time to evaluate : 5.114 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 573 average time/residue: 2.0239 time to fit residues: 1365.3826 Evaluate side-chains 550 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 5.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 257 optimal weight: 7.9990 chunk 344 optimal weight: 4.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 0.8980 chunk 41 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 108 HIS B 60 HIS C 60 HIS D 60 HIS D 115 GLN E 60 HIS E 108 HIS F 60 HIS F 115 GLN G 60 HIS G 115 GLN H 60 HIS I 60 HIS J 60 HIS J 108 HIS J 115 GLN K 60 HIS K 108 HIS K 115 GLN L 60 HIS L 108 HIS M 60 HIS M 108 HIS N 60 HIS O 60 HIS O 115 GLN P 60 HIS P 115 GLN Q 108 HIS R 60 HIS S 60 HIS T 60 HIS U 60 HIS V 60 HIS V 115 GLN W 60 HIS X 60 HIS X 115 GLN Total number of N/Q/H flips: 39 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.161866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.144063 restraints weight = 29838.319| |-----------------------------------------------------------------------------| r_work (start): 0.3549 rms_B_bonded: 0.54 r_work: 0.3436 rms_B_bonded: 1.09 restraints_weight: 0.5000 r_work: 0.3281 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.5607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 34872 Z= 0.304 Angle : 0.631 6.576 46968 Z= 0.356 Chirality : 0.042 0.163 4944 Planarity : 0.004 0.019 6192 Dihedral : 4.680 18.953 4536 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.19 % Allowed : 11.61 % Favored : 88.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % 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: 4.45 (0.13), residues: 4128 helix: 3.53 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.30 (0.25), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.003 TRP J 96 HIS 0.006 0.002 HIS D 60 PHE 0.012 0.003 PHE B 44 TYR 0.021 0.003 TYR O 42 ARG 0.003 0.000 ARG O 12 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 20030.31 seconds wall clock time: 354 minutes 36.62 seconds (21276.62 seconds total)