Starting phenix.real_space_refine (version: dev) on Wed Dec 21 08:01:00 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/12_2022/7pf1_13364.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/12_2022/7pf1_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_13364/12_2022/7pf1_13364.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/12_2022/7pf1_13364.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/12_2022/7pf1_13364.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf1_13364/12_2022/7pf1_13364.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 Convert atoms to be neutral 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: 0.13s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4807/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: 23.76, per 1000 atoms: 0.57 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: 21.26 Conformation dependent library (CDL) restraints added in 4.8 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: 0.90 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: 12.73 Time building geometry restraints manager: 21.51 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 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. 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: 6.120 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: 12.730 Check model and map are aligned: 0.560 Convert atoms to be neutral: 0.330 Process input model: 104.980 Find NCS groups from input model: 3.500 Set up NCS constraints: 0.480 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:13.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 142.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 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 : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.65 % 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 *********************** 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 : 5.144 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: 2.1185 time to fit residues: 2547.8881 Evaluate side-chains 508 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 508 time to evaluate : 4.957 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6246 ------------------------------------------------------------------------------- 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: 0.8034 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 : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer Outliers : 1.30 % 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 *********************** 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 : 5.503 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: 48 outliers final: 0 residues processed: 723 average time/residue: 2.0317 time to fit residues: 1720.3223 Evaluate side-chains 634 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 634 time to evaluate : 5.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 205 optimal weight: 10.0000 chunk 114 optimal weight: 0.5980 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: 6.9990 chunk 330 optimal weight: 3.9990 chunk 368 optimal weight: 8.9990 chunk 126 optimal weight: 0.9980 chunk 297 optimal weight: 2.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- 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 60 HIS E 68 HIS E 115 GLN F 60 HIS F 68 HIS F 115 GLN G 60 HIS G 68 HIS G 115 GLN H 68 HIS H 115 GLN I 60 HIS 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 60 HIS O 68 HIS O 115 GLN P 60 HIS 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 60 HIS T 68 HIS T 115 GLN U 60 HIS U 68 HIS U 115 GLN V 60 HIS V 68 HIS V 115 GLN W 60 HIS W 68 HIS W 115 GLN X 68 HIS X 115 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.5185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 34872 Z= 0.222 Angle : 0.580 5.670 46968 Z= 0.326 Chirality : 0.040 0.164 4944 Planarity : 0.003 0.020 6192 Dihedral : 4.567 19.381 4536 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 1.30 % 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: 4.79 (0.13), residues: 4128 helix: 3.79 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.35 (0.25), residues: 840 *********************** 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 658 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 610 time to evaluate : 5.221 Fit side-chains outliers start: 48 outliers final: 24 residues processed: 634 average time/residue: 1.8057 time to fit residues: 1370.2513 Evaluate side-chains 569 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 545 time to evaluate : 4.983 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 6.6576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 7.9990 chunk 192 optimal weight: 4.9990 chunk 41 optimal weight: 5.9990 chunk 177 optimal weight: 0.2980 chunk 249 optimal weight: 7.9990 chunk 372 optimal weight: 1.9990 chunk 394 optimal weight: 5.9990 chunk 194 optimal weight: 0.0870 chunk 353 optimal weight: 6.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.2764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN A 144 GLN B 108 HIS B 115 GLN B 144 GLN C 108 HIS C 115 GLN C 144 GLN D 108 HIS D 115 GLN D 144 GLN E 108 HIS E 115 GLN E 144 GLN F 108 HIS F 115 GLN F 144 GLN G 108 HIS G 115 GLN G 144 GLN H 108 HIS H 115 GLN I 115 GLN I 144 GLN J 115 GLN J 144 GLN K 108 HIS K 115 GLN K 144 GLN L 108 HIS L 115 GLN L 144 GLN M 108 HIS M 115 GLN M 144 GLN N 108 HIS N 115 GLN N 144 GLN O 108 HIS O 115 GLN O 144 GLN P 108 HIS P 115 GLN P 144 GLN Q 108 HIS Q 115 GLN Q 144 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN S 144 GLN T 108 HIS T 115 GLN T 144 GLN U 108 HIS U 115 GLN U 144 GLN V 108 HIS V 115 GLN V 144 GLN W 115 GLN W 144 GLN X 108 HIS X 115 GLN X 144 GLN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.5308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.017 34872 Z= 0.179 Angle : 0.520 5.474 46968 Z= 0.295 Chirality : 0.037 0.154 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.471 20.048 4536 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.65 % 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: 5.04 (0.13), residues: 4128 helix: 3.99 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.29 (0.24), residues: 840 *********************** 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 561 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 537 time to evaluate : 5.131 Fit side-chains outliers start: 24 outliers final: 24 residues processed: 561 average time/residue: 1.8916 time to fit residues: 1263.2796 Evaluate side-chains 551 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 527 time to evaluate : 4.877 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 24 residues processed: 0 time to fit residues: 6.6676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 4.9990 chunk 293 optimal weight: 5.9990 chunk 162 optimal weight: 6.9990 chunk 336 optimal weight: 1.9990 chunk 272 optimal weight: 0.3980 chunk 0 optimal weight: 20.0000 chunk 201 optimal weight: 7.9990 chunk 353 optimal weight: 5.9990 chunk 99 optimal weight: 9.9990 overall best weight: 3.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 60 HIS A 115 GLN A 142 ASN B 115 GLN C 115 GLN C 142 ASN D 115 GLN D 142 ASN E 60 HIS E 115 GLN F 60 HIS F 115 GLN F 142 ASN G 60 HIS G 115 GLN G 142 ASN H 115 GLN I 60 HIS I 115 GLN I 142 ASN J 115 GLN J 142 ASN K 115 GLN K 142 ASN L 115 GLN L 142 ASN M 115 GLN N 115 GLN O 60 HIS O 115 GLN P 60 HIS P 115 GLN P 142 ASN Q 115 GLN R 115 GLN R 142 ASN 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 W 142 ASN X 60 HIS X 115 GLN X 142 ASN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8111 moved from start: 0.5446 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= 0.260 Angle : 0.602 6.154 46968 Z= 0.339 Chirality : 0.041 0.160 4944 Planarity : 0.004 0.020 6192 Dihedral : 4.653 19.161 4536 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.27 % 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: 4.60 (0.13), residues: 4128 helix: 3.66 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.24 (0.24), residues: 840 *********************** 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 644 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 597 time to evaluate : 5.136 Fit side-chains outliers start: 47 outliers final: 24 residues processed: 619 average time/residue: 1.8944 time to fit residues: 1394.8634 Evaluate side-chains 593 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 569 time to evaluate : 4.970 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 0 residues processed: 24 average time/residue: 0.3673 time to fit residues: 23.4952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 132 optimal weight: 0.9990 chunk 355 optimal weight: 6.9990 chunk 77 optimal weight: 8.9990 chunk 231 optimal weight: 0.9990 chunk 97 optimal weight: 7.9990 chunk 394 optimal weight: 5.9990 chunk 327 optimal weight: 4.9990 chunk 182 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 130 optimal weight: 7.9990 chunk 207 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 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 I 142 ASN J 60 HIS J 115 GLN J 142 ASN K 115 GLN K 142 ASN L 115 GLN L 142 ASN M 115 GLN M 142 ASN N 115 GLN N 142 ASN O 115 GLN O 142 ASN P 60 HIS P 115 GLN P 142 ASN 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 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: 52 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.5471 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= 0.255 Angle : 0.589 6.059 46968 Z= 0.333 Chirality : 0.040 0.158 4944 Planarity : 0.003 0.019 6192 Dihedral : 4.633 19.328 4536 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % 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: 4.55 (0.13), residues: 4128 helix: 3.63 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.21 (0.25), residues: 840 *********************** 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 584 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 584 time to evaluate : 4.982 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 584 average time/residue: 1.9706 time to fit residues: 1366.5751 Evaluate side-chains 550 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 550 time to evaluate : 4.792 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 380 optimal weight: 0.7980 chunk 44 optimal weight: 6.9990 chunk 224 optimal weight: 4.9990 chunk 288 optimal weight: 10.0000 chunk 223 optimal weight: 2.9990 chunk 332 optimal weight: 9.9990 chunk 220 optimal weight: 9.9990 chunk 393 optimal weight: 7.9990 chunk 246 optimal weight: 0.9980 chunk 239 optimal weight: 10.0000 chunk 181 optimal weight: 8.9990 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 115 GLN C 115 GLN D 115 GLN E 60 HIS E 115 GLN F 60 HIS F 115 GLN G 115 GLN H 115 GLN H 142 ASN I 115 GLN J 60 HIS J 115 GLN K 115 GLN L 115 GLN M 115 GLN N 115 GLN O 60 HIS O 115 GLN P 60 HIS P 115 GLN Q 115 GLN R 115 GLN S 115 GLN T 60 HIS T 115 GLN U 60 HIS U 115 GLN V 60 HIS V 115 GLN W 115 GLN X 60 HIS X 115 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.5545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.023 34872 Z= 0.234 Angle : 0.572 5.915 46968 Z= 0.323 Chirality : 0.039 0.158 4944 Planarity : 0.003 0.017 6192 Dihedral : 4.597 19.674 4536 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.00 % 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: 4.68 (0.13), residues: 4128 helix: 3.73 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.24 (0.25), residues: 840 *********************** 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 582 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 582 time to evaluate : 4.741 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 582 average time/residue: 1.8730 time to fit residues: 1304.8413 Evaluate side-chains 566 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 566 time to evaluate : 4.769 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 243 optimal weight: 2.9990 chunk 157 optimal weight: 3.9990 chunk 234 optimal weight: 5.9990 chunk 118 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 chunk 250 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 194 optimal weight: 0.9990 chunk 36 optimal weight: 7.9990 chunk 309 optimal weight: 5.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 GLN E 115 GLN G 115 GLN H 115 GLN I 115 GLN J 115 GLN K 115 GLN N 115 GLN P 60 HIS P 115 GLN Q 115 GLN R 115 GLN R 144 GLN U 60 HIS U 115 GLN V 60 HIS V 115 GLN X 115 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8081 moved from start: 0.5562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 34872 Z= 0.148 Angle : 0.482 5.152 46968 Z= 0.272 Chirality : 0.035 0.140 4944 Planarity : 0.002 0.013 6192 Dihedral : 4.361 19.585 4536 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.19 % 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: 5.29 (0.13), residues: 4128 helix: 4.15 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.48 (0.25), residues: 840 *********************** 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 538 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 531 time to evaluate : 5.151 Fit side-chains outliers start: 7 outliers final: 0 residues processed: 531 average time/residue: 1.9620 time to fit residues: 1234.8750 Evaluate side-chains 528 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 4.869 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.4026 ------------------------------------------------------------------------------- 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: 0.5980 chunk 376 optimal weight: 7.9990 chunk 343 optimal weight: 5.9990 chunk 366 optimal weight: 4.9990 chunk 220 optimal weight: 8.9990 chunk 159 optimal weight: 0.6980 chunk 287 optimal weight: 10.0000 chunk 112 optimal weight: 9.9990 chunk 331 optimal weight: 9.9990 chunk 346 optimal weight: 0.7980 chunk 365 optimal weight: 10.0000 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS J 60 HIS P 60 HIS Q 115 GLN S 115 GLN T 60 HIS T 115 GLN U 60 HIS V 60 HIS X 60 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.5554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 34872 Z= 0.199 Angle : 0.538 5.637 46968 Z= 0.303 Chirality : 0.038 0.152 4944 Planarity : 0.003 0.013 6192 Dihedral : 4.474 19.941 4536 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.27 % 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: 4.99 (0.13), residues: 4128 helix: 3.92 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.44 (0.25), residues: 840 *********************** 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 545 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 535 time to evaluate : 4.761 Fit side-chains outliers start: 10 outliers final: 0 residues processed: 535 average time/residue: 1.9501 time to fit residues: 1239.9566 Evaluate side-chains 528 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 528 time to evaluate : 5.474 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 7.0188 ------------------------------------------------------------------------------- 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: 8.9990 chunk 387 optimal weight: 3.9990 chunk 236 optimal weight: 4.9990 chunk 183 optimal weight: 4.9990 chunk 269 optimal weight: 6.9990 chunk 406 optimal weight: 5.9990 chunk 374 optimal weight: 10.0000 chunk 323 optimal weight: 0.4980 chunk 33 optimal weight: 10.0000 chunk 250 optimal weight: 10.0000 chunk 198 optimal weight: 0.9990 overall best weight: 3.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 GLN B 115 GLN C 115 GLN D 115 GLN E 115 GLN F 60 HIS F 115 GLN G 115 GLN H 115 GLN I 60 HIS I 115 GLN J 60 HIS J 115 GLN K 115 GLN L 115 GLN M 115 GLN N 115 GLN O 115 GLN P 60 HIS P 115 GLN Q 115 GLN R 115 GLN S 115 GLN T 60 HIS T 115 GLN U 60 HIS U 115 GLN V 60 HIS V 115 GLN W 115 GLN X 60 HIS X 115 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.5589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 34872 Z= 0.224 Angle : 0.567 5.996 46968 Z= 0.320 Chirality : 0.039 0.154 4944 Planarity : 0.003 0.016 6192 Dihedral : 4.504 19.677 4536 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer Outliers : 0.08 % 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: 4.83 (0.13), residues: 4128 helix: 3.81 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.41 (0.25), residues: 840 ********************** 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 563 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 560 time to evaluate : 4.980 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 560 average time/residue: 1.8881 time to fit residues: 1260.0184 Evaluate side-chains 552 residues out of total 3696 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 552 time to evaluate : 4.945 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5462 ------------------------------------------------------------------------------- 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: 2.9990 chunk 99 optimal weight: 9.9990 chunk 298 optimal weight: 0.8980 chunk 47 optimal weight: 5.9990 chunk 89 optimal weight: 7.9990 chunk 324 optimal weight: 9.9990 chunk 135 optimal weight: 9.9990 chunk 332 optimal weight: 0.9980 chunk 41 optimal weight: 7.9990 chunk 59 optimal weight: 0.9980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 60 HIS J 60 HIS O 60 HIS P 60 HIS Q 115 GLN T 60 HIS T 115 GLN U 60 HIS U 115 GLN V 60 HIS X 60 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.163096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3571 r_free = 0.3571 target = 0.145416 restraints weight = 29799.637| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 0.54 r_work: 0.3447 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3295 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3295 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.5578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 34872 Z= 0.188 Angle : 0.529 5.580 46968 Z= 0.298 Chirality : 0.037 0.152 4944 Planarity : 0.003 0.013 6192 Dihedral : 4.441 19.788 4536 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer Outliers : 0.05 % 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: 5.04 (0.13), residues: 4128 helix: 3.97 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.42 (0.25), residues: 840 =============================================================================== Job complete usr+sys time: 19122.10 seconds wall clock time: 339 minutes 29.83 seconds (20369.83 seconds total)