Starting phenix.real_space_refine on Sun Feb 8 04:00:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pf1_13364/02_2026/7pf1_13364.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pf1_13364/02_2026/7pf1_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 { model { file = "/net/cci-nas-00/data/ceres_data/7pf1_13364/02_2026/7pf1_13364.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pf1_13364/02_2026/7pf1_13364.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7pf1_13364/02_2026/7pf1_13364.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pf1_13364/02_2026/7pf1_13364.map" } 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 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. Time to flip 24 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/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: 10.29, per 1000 atoms: 0.25 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 - 3.00 Amino acid : True - 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: 3.87 Conformation dependent library (CDL) restraints added in 1.5 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: 1.02 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: 7.97 Time building geometry restraints manager: 4.79 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: 0.00 - 1.52: 32223 1.52 - 3.04: 11681 3.04 - 4.55: 2266 4.55 - 6.07: 463 6.07 - 7.59: 335 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 Time spend for trying shortcut: 0.01 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: 3.280 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.740 Check model and map are aligned: 0.120 Set scattering table: 0.120 Process input model: 37.970 Find NCS groups from input model: 1.390 Set up NCS constraints: 0.090 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:8.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.880 ------------------------------------------------------------------------------- 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= 1.256 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.018 0.005 ARG A 79 TYR 0.097 0.022 TYR B 140 PHE 0.053 0.017 PHE E 44 TRP 0.035 0.012 TRP C 96 HIS 0.028 0.009 HIS K 121 Details of bonding type rmsd covalent geometry : bond 0.01962 (34872) covalent geometry : angle 1.65981 (46968) hydrogen bonds : bond 0.13342 ( 2712) hydrogen bonds : angle 4.90353 ( 8136) *********************** 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 to be fit. rotamer outliers: 24 poor density : 1032 time to evaluate : 1.773 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: 1.1520 time to fit residues: 1368.7008 Evaluate side-chains 508 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 508 time to evaluate : 1.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 197 optimal weight: 1.9990 chunk 388 optimal weight: 5.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 2.9990 chunk 401 optimal weight: 0.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 68 HIS 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: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.173825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.155058 restraints weight = 30088.295| |-----------------------------------------------------------------------------| r_work (start): 0.3676 rms_B_bonded: 0.54 r_work: 0.3555 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3400 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work (final): 0.3400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.4605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 34872 Z= 0.119 Angle : 0.512 5.383 46968 Z= 0.284 Chirality : 0.036 0.159 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.426 22.685 4536 Min Nonbonded Distance : 1.879 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 1.95 % Allowed : 8.44 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.77 (0.13), residues: 4128 helix: 3.72 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.59 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 12 TYR 0.019 0.002 TYR P 42 PHE 0.011 0.002 PHE V 135 TRP 0.004 0.001 TRP P 96 HIS 0.006 0.001 HIS J 108 Details of bonding type rmsd covalent geometry : bond 0.00227 (34872) covalent geometry : angle 0.51236 (46968) hydrogen bonds : bond 0.04455 ( 2712) hydrogen bonds : angle 3.54789 ( 8136) *********************** 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 702 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 630 time to evaluate : 1.711 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 119 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7442 (tt0) REVERT: A 159 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7843 (mtt180) REVERT: B 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: C 119 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7447 (tt0) REVERT: C 159 ARG cc_start: 0.8036 (mtt180) cc_final: 0.7832 (mtt180) REVERT: D 119 GLU cc_start: 0.7747 (OUTLIER) cc_final: 0.7486 (tt0) REVERT: D 159 ARG cc_start: 0.8038 (mtt180) cc_final: 0.7834 (mtt180) REVERT: E 119 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.7440 (tt0) REVERT: F 119 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7492 (tt0) REVERT: G 119 GLU cc_start: 0.7711 (OUTLIER) cc_final: 0.7445 (tt0) REVERT: H 119 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: H 159 ARG cc_start: 0.8042 (mtt180) cc_final: 0.7835 (mtt180) REVERT: I 119 GLU cc_start: 0.7721 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: I 159 ARG cc_start: 0.8041 (mtt180) cc_final: 0.7837 (mtt180) REVERT: J 119 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: J 159 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7849 (mtt180) REVERT: K 119 GLU cc_start: 0.7724 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: K 159 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7824 (mtt180) REVERT: L 119 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: L 159 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7833 (mtt180) REVERT: M 119 GLU cc_start: 0.7742 (OUTLIER) cc_final: 0.7470 (tt0) REVERT: N 119 GLU cc_start: 0.7713 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: O 119 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7481 (tt0) REVERT: O 159 ARG cc_start: 0.8052 (mtt180) cc_final: 0.7849 (mtt180) REVERT: P 119 GLU cc_start: 0.7712 (OUTLIER) cc_final: 0.7448 (tt0) REVERT: P 159 ARG cc_start: 0.8040 (mtt180) cc_final: 0.7830 (mtt180) REVERT: Q 119 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7489 (tt0) REVERT: Q 159 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7839 (mtt180) REVERT: R 119 GLU cc_start: 0.7710 (OUTLIER) cc_final: 0.7453 (tt0) REVERT: R 159 ARG cc_start: 0.8027 (mtt180) cc_final: 0.7824 (mtt180) REVERT: S 119 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7450 (tt0) REVERT: T 119 GLU cc_start: 0.7705 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: U 119 GLU cc_start: 0.7707 (OUTLIER) cc_final: 0.7460 (tt0) REVERT: V 119 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7456 (tt0) REVERT: V 159 ARG cc_start: 0.8046 (mtt180) cc_final: 0.7842 (mtt180) REVERT: W 119 GLU cc_start: 0.7723 (OUTLIER) cc_final: 0.7457 (tt0) REVERT: X 119 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.7455 (tt0) REVERT: X 159 ARG cc_start: 0.8045 (mtt180) cc_final: 0.7836 (mtt180) outliers start: 72 outliers final: 0 residues processed: 654 average time/residue: 1.1724 time to fit residues: 882.5906 Evaluate side-chains 545 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 521 time to evaluate : 1.766 ------------------------------------------------------------------------------- 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 2 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 100 optimal weight: 10.0000 chunk 128 optimal weight: 9.9990 chunk 331 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 282 optimal weight: 1.9990 chunk 153 optimal weight: 3.9990 chunk 374 optimal weight: 9.9990 chunk 281 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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 115 GLN G 115 GLN H 115 GLN I 115 GLN J 115 GLN K 115 GLN L 115 GLN M 115 GLN N 115 GLN O 115 GLN P 115 GLN Q 115 GLN R 115 GLN S 115 GLN T 115 GLN U 115 GLN V 115 GLN W 115 GLN X 115 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.146054 restraints weight = 29276.543| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 0.56 r_work: 0.3454 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 1.94 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7944 moved from start: 0.5200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 34872 Z= 0.158 Angle : 0.558 5.502 46968 Z= 0.314 Chirality : 0.039 0.162 4944 Planarity : 0.003 0.022 6192 Dihedral : 4.488 19.906 4536 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.35 % Allowed : 9.20 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.89 (0.13), residues: 4128 helix: 3.83 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.51 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG H 159 TYR 0.026 0.003 TYR M 42 PHE 0.010 0.002 PHE W 84 TRP 0.006 0.002 TRP T 96 HIS 0.006 0.002 HIS I 139 Details of bonding type rmsd covalent geometry : bond 0.00314 (34872) covalent geometry : angle 0.55808 (46968) hydrogen bonds : bond 0.05893 ( 2712) hydrogen bonds : angle 3.69572 ( 8136) *********************** 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 648 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 598 time to evaluate : 1.570 Fit side-chains REVERT: A 48 ASP cc_start: 0.8544 (p0) cc_final: 0.8335 (p0) REVERT: B 48 ASP cc_start: 0.8557 (p0) cc_final: 0.8356 (p0) REVERT: C 48 ASP cc_start: 0.8557 (p0) cc_final: 0.8347 (p0) REVERT: F 48 ASP cc_start: 0.8564 (p0) cc_final: 0.8363 (p0) REVERT: G 48 ASP cc_start: 0.8554 (p0) cc_final: 0.8348 (p0) REVERT: H 48 ASP cc_start: 0.8552 (p0) cc_final: 0.8348 (p0) REVERT: I 48 ASP cc_start: 0.8559 (p0) cc_final: 0.8352 (p0) REVERT: L 48 ASP cc_start: 0.8557 (p0) cc_final: 0.8345 (p0) REVERT: N 48 ASP cc_start: 0.8559 (p0) cc_final: 0.8354 (p0) REVERT: O 48 ASP cc_start: 0.8552 (p0) cc_final: 0.8346 (p0) REVERT: Q 48 ASP cc_start: 0.8553 (p0) cc_final: 0.8348 (p0) REVERT: T 48 ASP cc_start: 0.8561 (p0) cc_final: 0.8356 (p0) REVERT: U 48 ASP cc_start: 0.8558 (p0) cc_final: 0.8356 (p0) REVERT: V 48 ASP cc_start: 0.8557 (p0) cc_final: 0.8351 (p0) REVERT: W 48 ASP cc_start: 0.8562 (p0) cc_final: 0.8356 (p0) REVERT: X 48 ASP cc_start: 0.8560 (p0) cc_final: 0.8345 (p0) outliers start: 50 outliers final: 0 residues processed: 600 average time/residue: 0.9963 time to fit residues: 697.9187 Evaluate side-chains 558 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 558 time to evaluate : 1.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 106 optimal weight: 6.9990 chunk 174 optimal weight: 6.9990 chunk 391 optimal weight: 4.9990 chunk 250 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 319 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 353 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 359 optimal weight: 7.9990 chunk 184 optimal weight: 5.9990 overall best weight: 2.6584 ------------------------------------------------------------------------------- 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 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.164126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.145364 restraints weight = 29510.600| |-----------------------------------------------------------------------------| r_work (start): 0.3568 rms_B_bonded: 0.56 r_work: 0.3445 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3291 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3291 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7956 moved from start: 0.5352 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 34872 Z= 0.161 Angle : 0.548 5.607 46968 Z= 0.310 Chirality : 0.039 0.158 4944 Planarity : 0.003 0.019 6192 Dihedral : 4.559 19.609 4536 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 1.03 % Allowed : 10.25 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.83 (0.13), residues: 4128 helix: 3.81 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.39 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG H 12 TYR 0.023 0.003 TYR V 42 PHE 0.010 0.002 PHE E 44 TRP 0.006 0.002 TRP N 96 HIS 0.005 0.002 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00324 (34872) covalent geometry : angle 0.54809 (46968) hydrogen bonds : bond 0.05978 ( 2712) hydrogen bonds : angle 3.65528 ( 8136) *********************** 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 658 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 620 time to evaluate : 1.568 Fit side-chains outliers start: 38 outliers final: 0 residues processed: 644 average time/residue: 1.0894 time to fit residues: 813.7123 Evaluate side-chains 562 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 562 time to evaluate : 1.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 47 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 389 optimal weight: 0.7980 chunk 268 optimal weight: 9.9990 chunk 391 optimal weight: 7.9990 chunk 366 optimal weight: 10.0000 chunk 80 optimal weight: 0.3980 chunk 169 optimal weight: 7.9990 chunk 351 optimal weight: 2.9990 chunk 370 optimal weight: 9.9990 chunk 218 optimal weight: 0.9990 overall best weight: 1.4386 ------------------------------------------------------------------------------- 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 108 HIS B 115 GLN C 108 HIS C 115 GLN C 142 ASN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN K 142 ASN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 51 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.166498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.147672 restraints weight = 29927.941| |-----------------------------------------------------------------------------| r_work (start): 0.3593 rms_B_bonded: 0.56 r_work: 0.3469 rms_B_bonded: 1.16 restraints_weight: 0.5000 r_work: 0.3313 rms_B_bonded: 2.00 restraints_weight: 0.2500 r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.5507 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= 0.125 Angle : 0.486 5.070 46968 Z= 0.275 Chirality : 0.036 0.142 4944 Planarity : 0.003 0.016 6192 Dihedral : 4.366 19.038 4536 Min Nonbonded Distance : 1.954 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.08 % Allowed : 11.55 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.09 (0.13), residues: 4128 helix: 4.03 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.33 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG X 159 TYR 0.019 0.002 TYR N 42 PHE 0.010 0.002 PHE A 44 TRP 0.006 0.002 TRP F 96 HIS 0.003 0.001 HIS E 154 Details of bonding type rmsd covalent geometry : bond 0.00233 (34872) covalent geometry : angle 0.48589 (46968) hydrogen bonds : bond 0.05162 ( 2712) hydrogen bonds : angle 3.46820 ( 8136) *********************** 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 534 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 531 time to evaluate : 1.753 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 532 average time/residue: 1.1739 time to fit residues: 720.3821 Evaluate side-chains 497 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 497 time to evaluate : 1.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 230 optimal weight: 0.5980 chunk 324 optimal weight: 9.9990 chunk 146 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 77 optimal weight: 5.9990 chunk 92 optimal weight: 5.9990 chunk 325 optimal weight: 2.9990 chunk 403 optimal weight: 7.9990 chunk 345 optimal weight: 10.0000 chunk 226 optimal weight: 7.9990 chunk 119 optimal weight: 6.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- 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 68 HIS B 108 HIS B 115 GLN C 108 HIS C 115 GLN D 68 HIS D 108 HIS D 115 GLN E 68 HIS E 108 HIS E 115 GLN F 68 HIS F 108 HIS F 115 GLN G 68 HIS G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 60 HIS I 68 HIS I 108 HIS I 115 GLN J 68 HIS J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 60 HIS L 68 HIS L 108 HIS L 115 GLN M 68 HIS M 108 HIS M 115 GLN N 68 HIS N 108 HIS N 115 GLN O 68 HIS O 108 HIS O 115 GLN P 68 HIS P 108 HIS P 115 GLN Q 68 HIS Q 108 HIS Q 115 GLN R 68 HIS R 108 HIS R 115 GLN S 68 HIS S 108 HIS S 115 GLN T 68 HIS T 108 HIS T 115 GLN U 60 HIS U 68 HIS U 108 HIS U 115 GLN V 68 HIS V 108 HIS V 115 GLN W 68 HIS W 108 HIS W 115 GLN X 60 HIS X 68 HIS X 108 HIS X 115 GLN Total number of N/Q/H flips: 72 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.163096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.144461 restraints weight = 29825.899| |-----------------------------------------------------------------------------| r_work (start): 0.3550 rms_B_bonded: 0.56 r_work: 0.3437 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3287 rms_B_bonded: 1.92 restraints_weight: 0.2500 r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.5532 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= 0.216 Angle : 0.635 6.528 46968 Z= 0.358 Chirality : 0.042 0.163 4944 Planarity : 0.004 0.020 6192 Dihedral : 4.704 18.432 4536 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 12.12 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.62 (0.13), residues: 4128 helix: 3.64 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.46 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG S 12 TYR 0.023 0.003 TYR N 42 PHE 0.012 0.003 PHE H 44 TRP 0.008 0.003 TRP T 96 HIS 0.007 0.002 HIS B 139 Details of bonding type rmsd covalent geometry : bond 0.00462 (34872) covalent geometry : angle 0.63524 (46968) hydrogen bonds : bond 0.06692 ( 2712) hydrogen bonds : angle 3.75950 ( 8136) *********************** 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 563 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 563 time to evaluate : 1.603 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 563 average time/residue: 1.0425 time to fit residues: 684.0968 Evaluate side-chains 516 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 516 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 187 optimal weight: 5.9990 chunk 216 optimal weight: 0.6980 chunk 25 optimal weight: 8.9990 chunk 100 optimal weight: 10.0000 chunk 213 optimal weight: 1.9990 chunk 296 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 50 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 355 optimal weight: 6.9990 chunk 250 optimal weight: 0.5980 overall best weight: 1.6584 ------------------------------------------------------------------------------- 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 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN K 142 ASN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.165693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.147261 restraints weight = 29946.584| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 0.56 r_work: 0.3465 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3310 rms_B_bonded: 1.98 restraints_weight: 0.2500 r_work (final): 0.3310 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.5633 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= 0.133 Angle : 0.509 5.336 46968 Z= 0.289 Chirality : 0.036 0.143 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.475 19.031 4536 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 0.38 % Allowed : 11.50 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.07 (0.13), residues: 4128 helix: 3.97 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.53 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 159 TYR 0.020 0.002 TYR P 42 PHE 0.011 0.002 PHE H 44 TRP 0.008 0.002 TRP W 96 HIS 0.003 0.001 HIS S 131 Details of bonding type rmsd covalent geometry : bond 0.00254 (34872) covalent geometry : angle 0.50931 (46968) hydrogen bonds : bond 0.05383 ( 2712) hydrogen bonds : angle 3.51581 ( 8136) *********************** 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 532 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 518 time to evaluate : 1.712 Fit side-chains outliers start: 14 outliers final: 0 residues processed: 518 average time/residue: 1.1335 time to fit residues: 680.7793 Evaluate side-chains 513 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 513 time to evaluate : 1.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 208 optimal weight: 4.9990 chunk 153 optimal weight: 0.0870 chunk 131 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 107 optimal weight: 1.9990 chunk 338 optimal weight: 10.0000 chunk 261 optimal weight: 0.9990 chunk 307 optimal weight: 10.0000 chunk 217 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 226 optimal weight: 7.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- 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 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 48 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.166582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.148197 restraints weight = 30047.088| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 0.56 r_work: 0.3477 rms_B_bonded: 1.14 restraints_weight: 0.5000 r_work: 0.3323 rms_B_bonded: 1.99 restraints_weight: 0.2500 r_work (final): 0.3323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.5629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 34872 Z= 0.126 Angle : 0.493 5.110 46968 Z= 0.279 Chirality : 0.036 0.143 4944 Planarity : 0.003 0.017 6192 Dihedral : 4.391 18.967 4536 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.70 % Allowed : 11.39 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.23 (0.13), residues: 4128 helix: 4.09 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.53 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 159 TYR 0.018 0.002 TYR E 42 PHE 0.011 0.002 PHE A 84 TRP 0.008 0.002 TRP E 96 HIS 0.003 0.001 HIS S 131 Details of bonding type rmsd covalent geometry : bond 0.00237 (34872) covalent geometry : angle 0.49292 (46968) hydrogen bonds : bond 0.05120 ( 2712) hydrogen bonds : angle 3.45902 ( 8136) *********************** 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 530 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 504 time to evaluate : 1.634 Fit side-chains REVERT: K 48 ASP cc_start: 0.8505 (p0) cc_final: 0.8300 (p0) outliers start: 26 outliers final: 0 residues processed: 505 average time/residue: 1.0451 time to fit residues: 614.8335 Evaluate side-chains 502 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 502 time to evaluate : 1.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 53 optimal weight: 5.9990 chunk 340 optimal weight: 10.0000 chunk 228 optimal weight: 3.9990 chunk 386 optimal weight: 7.9990 chunk 235 optimal weight: 5.9990 chunk 229 optimal weight: 1.9990 chunk 266 optimal weight: 6.9990 chunk 139 optimal weight: 5.9990 chunk 153 optimal weight: 0.9990 chunk 253 optimal weight: 7.9990 chunk 397 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 108 HIS B 115 GLN C 60 HIS C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 60 HIS E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 60 HIS G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 60 HIS I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 60 HIS K 108 HIS K 115 GLN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 60 HIS N 108 HIS N 115 GLN O 60 HIS O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 60 HIS Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 60 HIS U 108 HIS V 108 HIS V 115 GLN W 60 HIS W 108 HIS W 115 GLN X 60 HIS X 108 HIS X 115 GLN Total number of N/Q/H flips: 58 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.163703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.145171 restraints weight = 29975.583| |-----------------------------------------------------------------------------| r_work (start): 0.3562 rms_B_bonded: 0.56 r_work: 0.3442 rms_B_bonded: 1.13 restraints_weight: 0.5000 r_work: 0.3288 rms_B_bonded: 1.95 restraints_weight: 0.2500 r_work (final): 0.3288 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 34872 Z= 0.187 Angle : 0.596 6.150 46968 Z= 0.337 Chirality : 0.040 0.154 4944 Planarity : 0.003 0.015 6192 Dihedral : 4.658 19.084 4536 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.70 % Allowed : 12.31 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.91 (0.13), residues: 4128 helix: 3.83 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.63 (0.24), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG P 159 TYR 0.020 0.003 TYR U 42 PHE 0.011 0.003 PHE H 44 TRP 0.008 0.002 TRP J 96 HIS 0.005 0.002 HIS S 139 Details of bonding type rmsd covalent geometry : bond 0.00393 (34872) covalent geometry : angle 0.59640 (46968) hydrogen bonds : bond 0.06308 ( 2712) hydrogen bonds : angle 3.68923 ( 8136) *********************** 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 to be fit. rotamer outliers: 26 poor density : 551 time to evaluate : 1.726 Fit side-chains outliers start: 26 outliers final: 0 residues processed: 551 average time/residue: 1.1363 time to fit residues: 724.8840 Evaluate side-chains 532 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 532 time to evaluate : 1.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 408 random chunks: chunk 64 optimal weight: 0.9990 chunk 190 optimal weight: 10.0000 chunk 185 optimal weight: 0.1980 chunk 32 optimal weight: 7.9990 chunk 269 optimal weight: 7.9990 chunk 104 optimal weight: 4.9990 chunk 384 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 34 optimal weight: 20.0000 chunk 188 optimal weight: 10.0000 chunk 285 optimal weight: 0.6980 overall best weight: 1.1786 ------------------------------------------------------------------------------- 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 108 HIS B 115 GLN C 108 HIS C 115 GLN D 108 HIS D 115 GLN E 108 HIS E 115 GLN F 108 HIS F 115 GLN G 108 HIS G 115 GLN H 108 HIS H 115 GLN I 108 HIS I 115 GLN J 108 HIS J 115 GLN K 108 HIS K 115 GLN K 142 ASN L 108 HIS L 115 GLN M 108 HIS M 115 GLN N 108 HIS N 115 GLN O 108 HIS O 115 GLN P 108 HIS P 115 GLN Q 108 HIS Q 115 GLN R 108 HIS R 115 GLN S 108 HIS S 115 GLN T 108 HIS T 115 GLN U 108 HIS U 115 GLN V 108 HIS V 115 GLN W 108 HIS W 115 GLN X 108 HIS X 115 GLN Total number of N/Q/H flips: 49 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.166846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.148606 restraints weight = 30136.726| |-----------------------------------------------------------------------------| r_work (start): 0.3599 rms_B_bonded: 0.56 r_work: 0.3489 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 1.93 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.5743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 34872 Z= 0.119 Angle : 0.493 5.045 46968 Z= 0.278 Chirality : 0.036 0.140 4944 Planarity : 0.003 0.017 6192 Dihedral : 4.384 18.957 4536 Min Nonbonded Distance : 1.960 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.08 % Allowed : 11.55 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 33.33 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 5.26 (0.13), residues: 4128 helix: 4.11 (0.08), residues: 3288 sheet: None (None), residues: 0 loop : 0.56 (0.23), residues: 840 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 159 TYR 0.018 0.002 TYR A 42 PHE 0.010 0.002 PHE R 44 TRP 0.007 0.002 TRP Q 96 HIS 0.003 0.001 HIS T 154 Details of bonding type rmsd covalent geometry : bond 0.00220 (34872) covalent geometry : angle 0.49282 (46968) hydrogen bonds : bond 0.04897 ( 2712) hydrogen bonds : angle 3.43074 ( 8136) ********************** 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 550 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 510 time to evaluate : 1.884 Fit side-chains outliers start: 40 outliers final: 0 residues processed: 510 average time/residue: 1.1750 time to fit residues: 693.4055 Evaluate side-chains 512 residues out of total 3696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 512 time to evaluate : 2.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.7349 > 50: distance: 70 - 89: 8.282 distance: 74 - 96: 12.540 distance: 78 - 82: 3.484 distance: 79 - 104: 7.350 distance: 82 - 83: 6.543 distance: 83 - 84: 5.676 distance: 83 - 86: 6.009 distance: 84 - 85: 4.749 distance: 84 - 89: 8.277 distance: 85 - 112: 12.231 distance: 86 - 87: 9.275 distance: 86 - 88: 9.655 distance: 89 - 90: 10.127 distance: 90 - 91: 4.332 distance: 90 - 93: 8.962 distance: 91 - 92: 12.908 distance: 91 - 96: 10.693 distance: 92 - 123: 22.233 distance: 93 - 94: 10.465 distance: 93 - 95: 13.922 distance: 96 - 97: 15.136 distance: 97 - 98: 31.732 distance: 97 - 100: 39.376 distance: 98 - 99: 25.307 distance: 98 - 104: 16.687 distance: 99 - 132: 28.572 distance: 100 - 101: 21.537 distance: 101 - 102: 14.907 distance: 101 - 103: 7.109 distance: 104 - 105: 9.875 distance: 105 - 106: 22.666 distance: 105 - 108: 6.880 distance: 106 - 107: 9.161 distance: 106 - 112: 34.258 distance: 107 - 140: 21.533 distance: 108 - 109: 21.714 distance: 109 - 110: 9.153 distance: 109 - 111: 14.113 distance: 112 - 113: 14.845 distance: 113 - 114: 19.429 distance: 113 - 116: 15.525 distance: 114 - 115: 20.344 distance: 114 - 123: 23.298 distance: 116 - 117: 12.292 distance: 117 - 118: 16.643 distance: 118 - 119: 8.794 distance: 119 - 120: 14.473 distance: 120 - 121: 10.853 distance: 120 - 122: 6.761 distance: 123 - 124: 25.476 distance: 124 - 125: 25.565 distance: 124 - 127: 20.690 distance: 125 - 126: 19.662 distance: 125 - 132: 27.157 distance: 127 - 128: 20.999 distance: 128 - 129: 18.671 distance: 129 - 130: 17.963 distance: 130 - 131: 32.029 distance: 132 - 133: 14.494 distance: 133 - 134: 15.950 distance: 133 - 136: 22.702 distance: 134 - 135: 23.077 distance: 134 - 140: 17.938 distance: 136 - 137: 19.983 distance: 137 - 138: 28.063 distance: 138 - 139: 24.483 distance: 140 - 141: 13.852 distance: 141 - 142: 30.441 distance: 142 - 143: 24.208 distance: 142 - 144: 7.279 distance: 144 - 145: 28.946 distance: 145 - 146: 20.896 distance: 145 - 148: 40.292 distance: 146 - 147: 22.580 distance: 146 - 149: 32.149 distance: 149 - 150: 39.637 distance: 149 - 155: 8.157 distance: 150 - 151: 29.217 distance: 150 - 153: 24.578 distance: 151 - 152: 46.652 distance: 151 - 156: 29.032 distance: 153 - 154: 19.793 distance: 154 - 155: 22.919 distance: 168 - 176: 3.008