Starting phenix.real_space_refine on Sat Jul 4 19:00:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ygl_39255/07_2026/8ygl_39255.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ygl_39255/07_2026/8ygl_39255.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ygl_39255/07_2026/8ygl_39255.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ygl_39255/07_2026/8ygl_39255.map" model { file = "/net/cci-nas-00/data/ceres_data/8ygl_39255/07_2026/8ygl_39255.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ygl_39255/07_2026/8ygl_39255.cif" } resolution = 2.6 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= 0.001 sd= 0.051 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: 7 Type Number sf(0) Gaussians Fe 1 7.16 5 P 17 5.49 5 Mg 34 5.21 5 S 66 5.16 5 C 16441 2.51 5 N 3181 2.21 5 O 3482 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 23222 Number of models: 1 Model: "" Number of chains: 68 Chain: "0" Number of atoms: 360 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 360 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "1" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "2" Number of atoms: 319 Number of conformers: 1 Conformer: "" Number of residues, atoms: 39, 319 Classifications: {'peptide': 39} Link IDs: {'PTRANS': 1, 'TRANS': 37} Chain: "3" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "7" Number of atoms: 387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 387 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 2, 'TRANS': 42} Chain: "8" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "9" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "B" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "C" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "E" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "G" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "H" Number of atoms: 1980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 254, 1980 Classifications: {'peptide': 254} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 235} Chain: "I" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 446 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "J" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "K" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "L" Number of atoms: 2231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 281, 2231 Classifications: {'peptide': 281} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 267} Chain: "M" Number of atoms: 2432 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2432 Classifications: {'peptide': 304} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 294} Chain: "N" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "O" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "P" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "Q" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "R" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "S" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "T" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "U" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "V" Number of atoms: 352 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 352 Classifications: {'peptide': 43} Link IDs: {'PTRANS': 1, 'TRANS': 41} Chain: "W" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 438 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 2, 'TRANS': 49} Chain: "X" Number of atoms: 379 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 379 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "Z" Number of atoms: 344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 42, 344 Classifications: {'peptide': 42} Link IDs: {'PTRANS': 1, 'TRANS': 40} Chain: "a" Number of atoms: 412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 412 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 308 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 1, 'TRANS': 35} Chain: "0" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 145 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "1" Number of atoms: 98 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 98 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "2" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "3" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "7" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 61 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Chain: "8" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "9" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 175 Unusual residues: {'BCL': 1, 'PC1': 3} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 53 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 53 Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 187 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 187 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 17 Chain: "E" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 78 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 78 Unusual residues: {'CDL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "I" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 497 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 497 Unusual residues: {'BCL': 2, 'BPH': 2, 'PC1': 3, 'U10': 4} Classifications: {'undetermined': 11} Link IDs: {None: 10} Unresolved non-hydrogen bonds: 179 Unresolved non-hydrogen angles: 204 Unresolved non-hydrogen dihedrals: 198 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'U10:plan-6': 3, 'U10:plan-7': 4, 'U10:plan-8': 4, 'U10:plan-9': 4, 'U10:plan-2': 1, 'U10:plan-3': 1, 'U10:plan-4': 1, 'U10:plan-5': 2, 'U10:plan-11': 1} Unresolved non-hydrogen planarities: 104 Chain: "M" Number of atoms: 576 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 575 Ad-hoc single atom residues: {'FE2': 1} Unusual residues: {'BCL': 2, 'CDL': 2, 'PC1': 3, 'SPO': 1, 'U10': 2} Classifications: {'undetermined': 10} Link IDs: {None: 8} Chain breaks: 1 Unresolved non-hydrogen bonds: 87 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 94 Planarities with less than four sites: {'U10:plan-6': 1, 'U10:plan-7': 2, 'U10:plan-8': 2, 'U10:plan-9': 2} Unresolved non-hydrogen planarities: 35 Chain: "N" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 182 Unusual residues: {'BCL': 1, 'PC1': 1, 'SPO': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 22 Chain: "P" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "T" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'BCL': 1, 'SPO': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "V" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 87 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 87 Unusual residues: {'SPO': 1, 'U10': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 20 Planarities with less than four sites: {'SPO:plan-4': 1, 'U10:plan-7': 1, 'U10:plan-8': 1, 'U10:plan-9': 1} Unresolved non-hydrogen planarities: 18 Chain: "Z" Number of atoms: 108 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 108 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "a" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 56 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 103 Unusual residues: {'BCL': 1, 'SPO': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.16, per 1000 atoms: 0.22 Number of scatterers: 23222 At special positions: 0 Unit cell: (92.9, 132.847, 136.563, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 1 26.01 S 66 16.00 P 17 15.00 Mg 34 11.99 O 3482 8.00 N 3181 7.00 C 16441 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=14, symmetry=0 Number of additional bonds: simple=14, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.24 Conformation dependent library (CDL) restraints added in 709.2 milliseconds 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4258 Finding SS restraints... Secondary structure from input PDB file: 103 helices and 8 sheets defined 73.9% alpha, 3.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain '0' and resid 13 through 46 Processing helix chain '1' and resid 6 through 11 Processing helix chain '1' and resid 12 through 38 removed outlier: 3.529A pdb=" N LYS 1 38 " --> pdb=" O ILE 1 34 " (cutoff:3.500A) Processing helix chain '1' and resid 42 through 52 Processing helix chain '2' and resid 13 through 46 removed outlier: 3.842A pdb=" N VAL 2 23 " --> pdb=" O GLU 2 19 " (cutoff:3.500A) Processing helix chain '3' and resid 3 through 5 No H-bonds generated for 'chain '3' and resid 3 through 5' Processing helix chain '3' and resid 6 through 11 removed outlier: 4.078A pdb=" N VAL 3 10 " --> pdb=" O LYS 3 6 " (cutoff:3.500A) Processing helix chain '3' and resid 12 through 38 Processing helix chain '3' and resid 42 through 51 Processing helix chain '7' and resid 3 through 10 Processing helix chain '7' and resid 12 through 37 Processing helix chain '8' and resid 13 through 46 Processing helix chain '9' and resid 3 through 9 Processing helix chain '9' and resid 12 through 37 Processing helix chain '9' and resid 42 through 51 Processing helix chain 'A' and resid 3 through 9 Processing helix chain 'A' and resid 12 through 38 Processing helix chain 'A' and resid 42 through 51 removed outlier: 3.549A pdb=" N TYR A 51 " --> pdb=" O GLY A 47 " (cutoff:3.500A) Processing helix chain 'B' and resid 13 through 46 Processing helix chain 'C' and resid 18 through 51 Processing helix chain 'D' and resid 3 through 5 No H-bonds generated for 'chain 'D' and resid 3 through 5' Processing helix chain 'D' and resid 6 through 11 Processing helix chain 'D' and resid 12 through 38 Processing helix chain 'D' and resid 42 through 52 Processing helix chain 'E' and resid 13 through 46 Processing helix chain 'F' and resid 3 through 10 removed outlier: 3.579A pdb=" N ILE F 7 " --> pdb=" O PHE F 4 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TRP F 8 " --> pdb=" O TYR F 5 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 38 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'G' and resid 13 through 46 Processing helix chain 'H' and resid 11 through 35 Processing helix chain 'H' and resid 77 through 84 Processing helix chain 'H' and resid 107 through 112 Processing helix chain 'H' and resid 113 through 117 Processing helix chain 'H' and resid 198 through 200 No H-bonds generated for 'chain 'H' and resid 198 through 200' Processing helix chain 'H' and resid 230 through 248 removed outlier: 3.773A pdb=" N GLY H 244 " --> pdb=" O TYR H 240 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TRP H 245 " --> pdb=" O VAL H 241 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N LEU H 246 " --> pdb=" O ALA H 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 5 No H-bonds generated for 'chain 'I' and resid 3 through 5' Processing helix chain 'I' and resid 6 through 11 Processing helix chain 'I' and resid 12 through 38 removed outlier: 3.563A pdb=" N LYS I 38 " --> pdb=" O ILE I 34 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 52 Processing helix chain 'J' and resid 13 through 46 Processing helix chain 'K' and resid 3 through 5 No H-bonds generated for 'chain 'K' and resid 3 through 5' Processing helix chain 'K' and resid 6 through 11 Processing helix chain 'K' and resid 12 through 37 Processing helix chain 'K' and resid 42 through 52 Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 58 Processing helix chain 'L' and resid 84 through 113 Processing helix chain 'L' and resid 116 through 134 removed outlier: 3.641A pdb=" N PHE L 124 " --> pdb=" O PHE L 120 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N ALA L 125 " --> pdb=" O ALA L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 134 through 141 Processing helix chain 'L' and resid 142 through 146 removed outlier: 3.797A pdb=" N TYR L 145 " --> pdb=" O SER L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 152 through 164 removed outlier: 3.741A pdb=" N ASP L 156 " --> pdb=" O TRP L 152 " (cutoff:3.500A) Processing helix chain 'L' and resid 165 through 166 No H-bonds generated for 'chain 'L' and resid 165 through 166' Processing helix chain 'L' and resid 167 through 170 Processing helix chain 'L' and resid 171 through 200 Processing helix chain 'L' and resid 209 through 222 removed outlier: 3.600A pdb=" N GLU L 213 " --> pdb=" O THR L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 226 through 251 removed outlier: 3.885A pdb=" N HIS L 231 " --> pdb=" O THR L 227 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 263 Processing helix chain 'L' and resid 264 through 269 removed outlier: 3.883A pdb=" N VAL L 268 " --> pdb=" O TRP L 264 " (cutoff:3.500A) Processing helix chain 'M' and resid 37 through 42 removed outlier: 3.555A pdb=" N GLY M 41 " --> pdb=" O TRP M 37 " (cutoff:3.500A) Processing helix chain 'M' and resid 54 through 79 Processing helix chain 'M' and resid 82 through 89 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 140 removed outlier: 3.753A pdb=" N LEU M 140 " --> pdb=" O ARG M 136 " (cutoff:3.500A) Processing helix chain 'M' and resid 144 through 162 removed outlier: 3.807A pdb=" N SER M 152 " --> pdb=" O TRP M 148 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ALA M 153 " --> pdb=" O ALA M 149 " (cutoff:3.500A) Processing helix chain 'M' and resid 162 through 169 removed outlier: 3.536A pdb=" N ILE M 166 " --> pdb=" O PHE M 162 " (cutoff:3.500A) Processing helix chain 'M' and resid 170 through 174 Processing helix chain 'M' and resid 178 through 193 removed outlier: 3.831A pdb=" N LEU M 183 " --> pdb=" O ILE M 179 " (cutoff:3.500A) Processing helix chain 'M' and resid 195 through 198 Processing helix chain 'M' and resid 199 through 226 Processing helix chain 'M' and resid 227 through 230 Processing helix chain 'M' and resid 233 through 240 removed outlier: 3.862A pdb=" N VAL M 239 " --> pdb=" O LEU M 235 " (cutoff:3.500A) Processing helix chain 'M' and resid 242 through 257 Processing helix chain 'M' and resid 264 through 290 removed outlier: 3.512A pdb=" N TRP M 268 " --> pdb=" O GLY M 264 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N VAL M 276 " --> pdb=" O PHE M 272 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N THR M 277 " --> pdb=" O GLY M 273 " (cutoff:3.500A) removed outlier: 5.489A pdb=" N GLY M 288 " --> pdb=" O ILE M 284 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N THR M 289 " --> pdb=" O LEU M 285 " (cutoff:3.500A) Processing helix chain 'M' and resid 293 through 301 removed outlier: 3.516A pdb=" N TRP M 297 " --> pdb=" O ASN M 293 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 46 Processing helix chain 'O' and resid 3 through 10 Processing helix chain 'O' and resid 12 through 37 removed outlier: 3.779A pdb=" N VAL O 18 " --> pdb=" O ARG O 14 " (cutoff:3.500A) Processing helix chain 'O' and resid 42 through 52 Processing helix chain 'P' and resid 13 through 46 Processing helix chain 'Q' and resid 3 through 10 removed outlier: 3.734A pdb=" N TRP Q 8 " --> pdb=" O TYR Q 5 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL Q 10 " --> pdb=" O ILE Q 7 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 38 Processing helix chain 'Q' and resid 42 through 51 Processing helix chain 'R' and resid 13 through 46 Processing helix chain 'S' and resid 3 through 5 No H-bonds generated for 'chain 'S' and resid 3 through 5' Processing helix chain 'S' and resid 6 through 11 Processing helix chain 'S' and resid 12 through 38 removed outlier: 3.561A pdb=" N VAL S 16 " --> pdb=" O ASP S 12 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LYS S 38 " --> pdb=" O ILE S 34 " (cutoff:3.500A) Processing helix chain 'S' and resid 42 through 51 Processing helix chain 'T' and resid 13 through 46 Processing helix chain 'U' and resid 3 through 10 Processing helix chain 'U' and resid 12 through 38 removed outlier: 3.505A pdb=" N LYS U 38 " --> pdb=" O ILE U 34 " (cutoff:3.500A) Processing helix chain 'U' and resid 42 through 51 Processing helix chain 'V' and resid 13 through 46 Processing helix chain 'W' and resid 3 through 5 No H-bonds generated for 'chain 'W' and resid 3 through 5' Processing helix chain 'W' and resid 6 through 11 Processing helix chain 'W' and resid 12 through 38 Processing helix chain 'W' and resid 42 through 52 Processing helix chain 'X' and resid 15 through 51 Processing helix chain 'X' and resid 52 through 58 removed outlier: 6.028A pdb=" N GLN X 55 " --> pdb=" O LEU X 52 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 46 removed outlier: 4.407A pdb=" N GLN Z 16 " --> pdb=" O LEU Z 12 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N GLN Z 18 " --> pdb=" O ASP Z 14 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLU Z 19 " --> pdb=" O GLU Z 15 " (cutoff:3.500A) Processing helix chain 'a' and resid 12 through 38 removed outlier: 3.718A pdb=" N VAL a 16 " --> pdb=" O ASP a 12 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N VAL a 18 " --> pdb=" O ARG a 14 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLY a 21 " --> pdb=" O PHE a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 42 through 51 removed outlier: 3.749A pdb=" N VAL a 46 " --> pdb=" O ASN a 42 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N GLY a 47 " --> pdb=" O TRP a 43 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 15 No H-bonds generated for 'chain 'b' and resid 13 through 15' Processing helix chain 'b' and resid 16 through 46 removed outlier: 4.318A pdb=" N ILE b 44 " --> pdb=" O ILE b 40 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TRP b 45 " --> pdb=" O ALA b 41 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 62 through 66 removed outlier: 4.296A pdb=" N GLY H 71 " --> pdb=" O LEU H 66 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 91 through 93 Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.766A pdb=" N GLU H 184 " --> pdb=" O SER H 169 " (cutoff:3.500A) removed outlier: 4.967A pdb=" N LEU H 171 " --> pdb=" O TYR H 182 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N TYR H 182 " --> pdb=" O LEU H 171 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N VAL H 173 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL H 180 " --> pdb=" O VAL H 173 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 137 removed outlier: 6.489A pdb=" N VAL H 164 " --> pdb=" O ALA H 159 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ALA H 159 " --> pdb=" O VAL H 164 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLY H 166 " --> pdb=" O VAL H 157 " (cutoff:3.500A) removed outlier: 7.500A pdb=" N VAL H 209 " --> pdb=" O PRO H 156 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N GLN H 158 " --> pdb=" O VAL H 209 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 145 through 149 removed outlier: 6.906A pdb=" N GLN M 12 " --> pdb=" O THR H 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.982A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 66 through 67 Processing sheet with id=AA8, first strand: chain 'M' and resid 35 through 36 1296 hydrogen bonds defined for protein. 3732 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.91 Time building geometry restraints manager: 2.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.38: 8734 1.38 - 1.56: 15019 1.56 - 1.74: 68 1.74 - 1.92: 128 1.92 - 2.10: 136 Bond restraints: 24085 Sorted by residual: bond pdb=" NA BCL 8 101 " pdb="MG BCL 8 101 " ideal model delta sigma weight residual 2.170 2.009 0.161 2.40e-02 1.74e+03 4.51e+01 bond pdb=" NA BCL N 102 " pdb="MG BCL N 102 " ideal model delta sigma weight residual 2.170 2.010 0.160 2.40e-02 1.74e+03 4.46e+01 bond pdb=" NA BCL E 101 " pdb="MG BCL E 101 " ideal model delta sigma weight residual 2.170 2.010 0.160 2.40e-02 1.74e+03 4.43e+01 bond pdb=" NA BCL b 102 " pdb="MG BCL b 102 " ideal model delta sigma weight residual 2.170 2.011 0.159 2.40e-02 1.74e+03 4.39e+01 bond pdb=" NA BCL M 404 " pdb="MG BCL M 404 " ideal model delta sigma weight residual 2.170 2.014 0.156 2.40e-02 1.74e+03 4.23e+01 ... (remaining 24080 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 30832 2.32 - 4.63: 1760 4.63 - 6.95: 356 6.95 - 9.27: 43 9.27 - 11.58: 34 Bond angle restraints: 33025 Sorted by residual: angle pdb=" ND BCL V 102 " pdb="MG BCL V 102 " pdb=" NC BCL V 102 " ideal model delta sigma weight residual 85.24 80.08 5.15 9.98e-01 1.00e+00 2.67e+01 angle pdb=" ND BCL T 101 " pdb="MG BCL T 101 " pdb=" NC BCL T 101 " ideal model delta sigma weight residual 85.24 80.12 5.12 9.98e-01 1.00e+00 2.63e+01 angle pdb=" ND BCL E 101 " pdb="MG BCL E 101 " pdb=" NC BCL E 101 " ideal model delta sigma weight residual 85.24 80.19 5.05 9.98e-01 1.00e+00 2.56e+01 angle pdb=" ND BCL M 405 " pdb="MG BCL M 405 " pdb=" NC BCL M 405 " ideal model delta sigma weight residual 85.24 80.19 5.04 9.98e-01 1.00e+00 2.56e+01 angle pdb=" ND BCL 8 101 " pdb="MG BCL 8 101 " pdb=" NC BCL 8 101 " ideal model delta sigma weight residual 85.24 80.21 5.03 9.98e-01 1.00e+00 2.54e+01 ... (remaining 33020 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.06: 12268 35.06 - 70.12: 678 70.12 - 105.18: 41 105.18 - 140.24: 5 140.24 - 175.30: 5 Dihedral angle restraints: 12997 sinusoidal: 6371 harmonic: 6626 Sorted by residual: dihedral pdb=" CBD BCL 1 101 " pdb=" CGD BCL 1 101 " pdb=" O2D BCL 1 101 " pdb=" CED BCL 1 101 " ideal model delta sinusoidal sigma weight residual -180.00 -14.79 -165.21 1 5.00e+00 4.00e-02 7.55e+02 dihedral pdb=" C1 BCL N 102 " pdb=" CGA BCL N 102 " pdb=" O2A BCL N 102 " pdb=" CBA BCL N 102 " ideal model delta sinusoidal sigma weight residual -180.00 -4.70 -175.30 1 6.00e+00 2.78e-02 5.32e+02 dihedral pdb=" CBD BCL U 101 " pdb=" CGD BCL U 101 " pdb=" O2D BCL U 101 " pdb=" CED BCL U 101 " ideal model delta sinusoidal sigma weight residual -180.00 -70.60 -109.40 1 5.00e+00 4.00e-02 5.12e+02 ... (remaining 12994 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.042: 3162 1.042 - 2.085: 0 2.085 - 3.127: 0 3.127 - 4.169: 0 4.169 - 5.212: 6 Chirality restraints: 3168 Sorted by residual: chirality pdb=" C18 BCL E 101 " pdb=" C17 BCL E 101 " pdb=" C19 BCL E 101 " pdb=" C20 BCL E 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.79e+02 chirality pdb=" C18 BCL J 101 " pdb=" C17 BCL J 101 " pdb=" C19 BCL J 101 " pdb=" C20 BCL J 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.50 5.21 2.00e-01 2.50e+01 6.78e+02 chirality pdb=" C18 BCL C 101 " pdb=" C17 BCL C 101 " pdb=" C19 BCL C 101 " pdb=" C20 BCL C 101 " both_signs ideal model delta sigma weight residual False 2.71 -2.49 5.20 2.00e-01 2.50e+01 6.75e+02 ... (remaining 3165 not shown) Planarity restraints: 4033 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL 1 101 " -0.361 1.50e-02 4.44e+03 3.04e-01 2.05e+03 pdb=" C2 BCL 1 101 " 0.524 1.50e-02 4.44e+03 pdb=" C3 BCL 1 101 " 0.114 1.50e-02 4.44e+03 pdb=" C4 BCL 1 101 " -0.093 1.50e-02 4.44e+03 pdb=" C5 BCL 1 101 " -0.185 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL 2 101 " 0.359 1.50e-02 4.44e+03 3.02e-01 2.03e+03 pdb=" C2 BCL 2 101 " -0.525 1.50e-02 4.44e+03 pdb=" C3 BCL 2 101 " -0.111 1.50e-02 4.44e+03 pdb=" C4 BCL 2 101 " 0.104 1.50e-02 4.44e+03 pdb=" C5 BCL 2 101 " 0.173 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.355 1.50e-02 4.44e+03 2.98e-01 1.97e+03 pdb=" C2 BCL E 101 " -0.514 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " -0.109 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " 0.187 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " 0.081 1.50e-02 4.44e+03 ... (remaining 4030 not shown) Histogram of nonbonded interaction distances: 1.90 - 2.50: 111 2.50 - 3.10: 15754 3.10 - 3.70: 35340 3.70 - 4.30: 56331 4.30 - 4.90: 91740 Nonbonded interactions: 199276 Sorted by model distance: nonbonded pdb=" OE1 GLN O 20 " pdb=" OH TYR P 24 " model vdw 1.900 3.040 nonbonded pdb=" OG SER M 152 " pdb=" OG1 THR M 277 " model vdw 1.965 3.040 nonbonded pdb=" O CYS L 248 " pdb=" OG1 THR L 252 " model vdw 2.005 3.040 nonbonded pdb=" OH TYR 0 24 " pdb=" OE1 GLN 9 20 " model vdw 2.008 3.040 nonbonded pdb=" OE1 GLN K 20 " pdb=" OH TYR N 24 " model vdw 2.011 3.040 ... (remaining 199271 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: 0.00 Found NCS groups: ncs_group { reference = (chain '0' and resid 10 through 48) selection = (chain '2' and resid 10 through 48) selection = (chain '8' and resid 10 through 48) selection = (chain 'B' and resid 10 through 48) selection = (chain 'C' and resid 15 through 53) selection = (chain 'E' and resid 10 through 48) selection = (chain 'G' and resid 10 through 48) selection = (chain 'J' and resid 10 through 48) selection = (chain 'N' and resid 10 through 48) selection = (chain 'P' and resid 10 through 48) selection = (chain 'R' and resid 10 through 48) selection = (chain 'T' and resid 10 through 48) selection = (chain 'V' and resid 10 through 48) selection = (chain 'Z' and resid 10 through 48) } ncs_group { reference = (chain '1' and resid 4 through 52) selection = (chain '3' and resid 4 through 52) selection = (chain '9' and resid 4 through 52) selection = (chain 'A' and resid 4 through 52) selection = (chain 'D' and resid 4 through 52) selection = (chain 'F' and resid 4 through 52) selection = (chain 'I' and resid 4 through 52) selection = (chain 'K' and resid 4 through 52) selection = (chain 'O' and resid 4 through 52) selection = (chain 'Q' and resid 4 through 52) selection = (chain 'S' and resid 4 through 52) selection = (chain 'U' and resid 4 through 52) selection = (chain 'W' and resid 4 through 52) selection = (chain 'a' and resid 4 through 52) } 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: 2.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.400 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 20.720 Find NCS groups from input model: 0.540 Set up NCS constraints: 0.040 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:7.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 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 0.881 24099 Z= 1.679 Angle : 1.226 11.583 33025 Z= 0.583 Chirality : 0.241 5.212 3168 Planarity : 0.028 0.330 4033 Dihedral : 19.079 175.295 8739 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: -1.59 (0.16), residues: 2229 helix: -0.76 (0.11), residues: 1533 sheet: 0.78 (1.05), residues: 30 loop : -1.51 (0.22), residues: 666 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 14 TYR 0.021 0.001 TYR b 43 PHE 0.057 0.002 PHE M 216 TRP 0.043 0.002 TRP L 273 HIS 0.010 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.01242 / 0.54 (24085) covalent geometry : angle 1.22580 / 0.58 (33025) hydrogen bonds : bond 0.12738 / 8.30 ( 1294) hydrogen bonds : angle 5.06783 / 3.67 ( 3732) Misc. bond : bond 0.65991 / 40.45 ( 14) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 232 time to evaluate : 0.900 Fit side-chains REVERT: 1 30 MET cc_start: 0.5672 (tmm) cc_final: 0.5434 (tmm) REVERT: F 41 TYR cc_start: 0.8542 (m-80) cc_final: 0.8187 (m-80) REVERT: L 8 ARG cc_start: 0.8446 (ttp80) cc_final: 0.8049 (ttp-170) REVERT: M 27 LEU cc_start: 0.8486 (mm) cc_final: 0.8274 (mt) outliers start: 0 outliers final: 0 residues processed: 232 average time/residue: 0.6327 time to fit residues: 168.5173 Evaluate side-chains 186 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.766 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 216 optimal weight: 9.9990 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 66 optimal weight: 6.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 6.9990 chunk 212 optimal weight: 3.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 20 GLN 2 16 GLN 3 20 GLN 7 20 GLN 9 42 ASN C 23 GLN D 9 GLN ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 42 ASN ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 195 ASN ** O 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 GLN T 21 HIS Z 16 GLN b 21 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.152587 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3338 r_free = 0.3338 target = 0.114199 restraints weight = 26069.697| |-----------------------------------------------------------------------------| r_work (start): 0.3314 rms_B_bonded: 1.29 r_work: 0.3196 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3086 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3086 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 24099 Z= 0.162 Angle : 0.822 16.156 33025 Z= 0.318 Chirality : 0.040 0.329 3168 Planarity : 0.004 0.048 4033 Dihedral : 18.442 179.915 4665 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.17 % Favored : 98.83 % Rotamer: Outliers : 1.03 % Allowed : 7.23 % Favored : 91.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.03 (0.17), residues: 2229 helix: 1.27 (0.12), residues: 1554 sheet: 2.17 (1.22), residues: 20 loop : -0.68 (0.24), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D 53 TYR 0.014 0.001 TYR M 193 PHE 0.019 0.001 PHE S 11 TRP 0.019 0.002 TRP L 267 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00390 / 0.16 (24085) covalent geometry : angle 0.82198 / 0.32 (33025) hydrogen bonds : bond 0.05238 / 3.41 ( 1294) hydrogen bonds : angle 3.82991 / 2.78 ( 3732) Misc. bond : bond 0.00241 / 0.14 ( 14) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 213 time to evaluate : 0.713 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5697 (tmm) cc_final: 0.5314 (tmm) REVERT: 7 3 LYS cc_start: 0.8115 (mtpt) cc_final: 0.7901 (mtpp) REVERT: 7 15 ARG cc_start: 0.7561 (mmt180) cc_final: 0.7354 (mmt180) REVERT: C 30 MET cc_start: 0.7549 (mmm) cc_final: 0.7282 (mmm) REVERT: F 3 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7907 (mmtp) REVERT: F 41 TYR cc_start: 0.8993 (m-80) cc_final: 0.8556 (m-80) REVERT: H 46 ASP cc_start: 0.7990 (p0) cc_final: 0.7707 (p0) REVERT: H 68 ASN cc_start: 0.8588 (m110) cc_final: 0.8342 (m-40) REVERT: H 178 GLN cc_start: 0.8695 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: H 184 GLU cc_start: 0.8545 (tt0) cc_final: 0.8281 (tt0) REVERT: H 228 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8174 (pt0) REVERT: L 8 ARG cc_start: 0.8847 (ttp80) cc_final: 0.8641 (ttp-170) REVERT: L 258 ASP cc_start: 0.7988 (t0) cc_final: 0.7775 (t0) REVERT: M 26 ASP cc_start: 0.7999 (t0) cc_final: 0.7636 (t70) REVERT: M 36 ASN cc_start: 0.8097 (m-40) cc_final: 0.7756 (t0) REVERT: M 69 MET cc_start: 0.9253 (mmp) cc_final: 0.9021 (mmp) REVERT: Q 6 LYS cc_start: 0.8089 (mttt) cc_final: 0.7820 (mttp) REVERT: Q 9 GLN cc_start: 0.8256 (mt0) cc_final: 0.7881 (mm110) REVERT: S 51 TYR cc_start: 0.8523 (m-80) cc_final: 0.7913 (m-80) REVERT: W 11 PHE cc_start: 0.7377 (OUTLIER) cc_final: 0.6209 (m-10) outliers start: 20 outliers final: 8 residues processed: 221 average time/residue: 0.5495 time to fit residues: 141.7144 Evaluate side-chains 198 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 3 LYS Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain J residue 8 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 171 ASN Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 147 optimal weight: 0.7980 chunk 143 optimal weight: 0.9980 chunk 20 optimal weight: 5.9990 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 10.0000 chunk 122 optimal weight: 0.7980 chunk 116 optimal weight: 4.9990 chunk 191 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 144 optimal weight: 0.9990 chunk 154 optimal weight: 3.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 16 GLN ** L 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 200 ASN M 5 GLN W 42 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.151566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.113109 restraints weight = 26266.229| |-----------------------------------------------------------------------------| r_work (start): 0.3308 rms_B_bonded: 1.29 r_work: 0.3189 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.2264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24099 Z= 0.125 Angle : 0.714 15.452 33025 Z= 0.277 Chirality : 0.037 0.138 3168 Planarity : 0.003 0.042 4033 Dihedral : 17.545 179.982 4665 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.19 % Allowed : 9.14 % Favored : 89.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.92 (0.17), residues: 2229 helix: 1.98 (0.13), residues: 1556 sheet: 2.46 (1.16), residues: 20 loop : -0.49 (0.24), residues: 653 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 46 TYR 0.013 0.001 TYR M 303 PHE 0.017 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.006 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.13 (24085) covalent geometry : angle 0.71361 / 0.28 (33025) hydrogen bonds : bond 0.04761 / 3.11 ( 1294) hydrogen bonds : angle 3.56536 / 2.58 ( 3732) Misc. bond : bond 0.00220 / 0.14 ( 14) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 212 time to evaluate : 0.777 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6081 (tmm) cc_final: 0.5632 (tmm) REVERT: 1 41 TYR cc_start: 0.7429 (m-80) cc_final: 0.6728 (m-80) REVERT: A 1 MET cc_start: 0.7971 (tpp) cc_final: 0.7739 (tpt) REVERT: H 46 ASP cc_start: 0.8052 (p0) cc_final: 0.7700 (p0) REVERT: H 178 GLN cc_start: 0.8656 (OUTLIER) cc_final: 0.8237 (mt0) REVERT: H 184 GLU cc_start: 0.8477 (tt0) cc_final: 0.8241 (tt0) REVERT: H 228 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8165 (pt0) REVERT: H 235 ASP cc_start: 0.7932 (OUTLIER) cc_final: 0.7481 (t70) REVERT: I 7 ILE cc_start: 0.8889 (tt) cc_final: 0.8671 (tp) REVERT: L 8 ARG cc_start: 0.8846 (ttp80) cc_final: 0.8639 (ttp-170) REVERT: L 56 MET cc_start: 0.8692 (mtp) cc_final: 0.8490 (mtp) REVERT: L 202 GLU cc_start: 0.7966 (mt-10) cc_final: 0.7708 (mt-10) REVERT: M 26 ASP cc_start: 0.7933 (t0) cc_final: 0.7570 (t70) REVERT: M 36 ASN cc_start: 0.7975 (m-40) cc_final: 0.7685 (t0) REVERT: M 69 MET cc_start: 0.9238 (mmp) cc_final: 0.9020 (mmp) REVERT: M 158 MET cc_start: 0.8837 (mmm) cc_final: 0.8580 (mmm) REVERT: O 5 TYR cc_start: 0.8372 (p90) cc_final: 0.7987 (p90) REVERT: Q 9 GLN cc_start: 0.8138 (mt0) cc_final: 0.7774 (mm110) REVERT: S 51 TYR cc_start: 0.8490 (m-80) cc_final: 0.7967 (m-80) REVERT: V 37 ILE cc_start: 0.8559 (mt) cc_final: 0.8354 (mm) REVERT: W 11 PHE cc_start: 0.7405 (OUTLIER) cc_final: 0.6350 (m-10) REVERT: X 40 CYS cc_start: 0.8283 (m) cc_final: 0.8049 (m) outliers start: 23 outliers final: 6 residues processed: 222 average time/residue: 0.5275 time to fit residues: 137.3105 Evaluate side-chains 205 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 195 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain R residue 44 ILE Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain b residue 40 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 105 optimal weight: 5.9990 chunk 200 optimal weight: 8.9990 chunk 18 optimal weight: 0.7980 chunk 53 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 197 optimal weight: 0.2980 chunk 170 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 134 optimal weight: 1.9990 chunk 79 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 2.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 9 GLN 7 42 ASN D 20 GLN F 32 HIS L 171 ASN L 200 ASN L 205 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.145812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.107347 restraints weight = 26627.194| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 1.27 r_work: 0.3104 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 24099 Z= 0.194 Angle : 0.801 20.243 33025 Z= 0.318 Chirality : 0.041 0.162 3168 Planarity : 0.004 0.045 4033 Dihedral : 18.088 179.850 4665 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.91 % Allowed : 9.76 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 1.78 (0.17), residues: 2229 helix: 1.84 (0.12), residues: 1544 sheet: 1.25 (1.01), residues: 27 loop : -0.38 (0.24), residues: 658 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 46 TYR 0.019 0.002 TYR M 193 PHE 0.023 0.002 PHE S 11 TRP 0.017 0.002 TRP M 74 HIS 0.009 0.001 HIS M 266 Details of bonding type rmsd/Z covalent geometry : bond 0.00475 / 0.19 (24085) covalent geometry : angle 0.80138 / 0.32 (33025) hydrogen bonds : bond 0.05487 / 3.60 ( 1294) hydrogen bonds : angle 3.70756 / 2.69 ( 3732) Misc. bond : bond 0.00301 / 0.19 ( 14) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 209 time to evaluate : 0.591 Fit side-chains REVERT: 1 30 MET cc_start: 0.6080 (tmm) cc_final: 0.5654 (tmm) REVERT: 1 41 TYR cc_start: 0.7376 (m-80) cc_final: 0.6586 (m-80) REVERT: H 46 ASP cc_start: 0.8269 (p0) cc_final: 0.7875 (p0) REVERT: H 184 GLU cc_start: 0.8555 (tt0) cc_final: 0.8292 (tt0) REVERT: H 228 GLU cc_start: 0.8474 (OUTLIER) cc_final: 0.8193 (pt0) REVERT: M 26 ASP cc_start: 0.7982 (t0) cc_final: 0.7557 (t70) REVERT: M 36 ASN cc_start: 0.8086 (m-40) cc_final: 0.7732 (t0) REVERT: M 69 MET cc_start: 0.9258 (mmp) cc_final: 0.9008 (mmp) REVERT: O 5 TYR cc_start: 0.8406 (p90) cc_final: 0.7961 (p90) REVERT: O 26 LEU cc_start: 0.8537 (OUTLIER) cc_final: 0.8246 (mp) REVERT: Q 9 GLN cc_start: 0.8271 (mt0) cc_final: 0.8005 (mm-40) REVERT: S 51 TYR cc_start: 0.8527 (m-80) cc_final: 0.7999 (m-80) REVERT: U 15 ARG cc_start: 0.5672 (ttp80) cc_final: 0.5163 (mtp180) REVERT: U 53 ARG cc_start: 0.8506 (OUTLIER) cc_final: 0.7629 (ptt-90) REVERT: W 11 PHE cc_start: 0.7408 (OUTLIER) cc_final: 0.6291 (m-10) REVERT: X 39 ILE cc_start: 0.7838 (OUTLIER) cc_final: 0.7509 (mp) outliers start: 37 outliers final: 10 residues processed: 228 average time/residue: 0.5164 time to fit residues: 137.3679 Evaluate side-chains 209 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 194 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain O residue 30 MET Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 10 THR Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 150 optimal weight: 0.7980 chunk 176 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 0.6980 chunk 195 optimal weight: 3.9990 chunk 199 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 33 optimal weight: 0.8980 chunk 157 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 20 GLN L 200 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.149519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.111098 restraints weight = 26430.796| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.30 r_work: 0.3157 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 24099 Z= 0.115 Angle : 0.694 19.487 33025 Z= 0.268 Chirality : 0.036 0.134 3168 Planarity : 0.003 0.039 4033 Dihedral : 17.281 179.956 4665 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.76 % Allowed : 10.48 % Favored : 87.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.30 (0.17), residues: 2229 helix: 2.24 (0.12), residues: 1551 sheet: 1.47 (1.00), residues: 27 loop : -0.20 (0.25), residues: 651 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 46 TYR 0.014 0.001 TYR M 193 PHE 0.021 0.001 PHE L 217 TRP 0.017 0.001 TRP M 74 HIS 0.005 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.12 (24085) covalent geometry : angle 0.69352 / 0.27 (33025) hydrogen bonds : bond 0.04669 / 3.06 ( 1294) hydrogen bonds : angle 3.47596 / 2.51 ( 3732) Misc. bond : bond 0.00173 / 0.11 ( 14) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 214 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5949 (tmm) cc_final: 0.5519 (tmm) REVERT: 1 41 TYR cc_start: 0.7404 (m-80) cc_final: 0.6621 (m-80) REVERT: A 40 ASP cc_start: 0.8509 (t0) cc_final: 0.8257 (t0) REVERT: D 42 ASN cc_start: 0.8957 (t0) cc_final: 0.8408 (t0) REVERT: H 46 ASP cc_start: 0.8245 (p0) cc_final: 0.7862 (p0) REVERT: H 150 ARG cc_start: 0.7788 (mtt180) cc_final: 0.6030 (pmt170) REVERT: H 184 GLU cc_start: 0.8495 (tt0) cc_final: 0.8241 (tt0) REVERT: H 228 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: I 3 LYS cc_start: 0.8546 (mtpp) cc_final: 0.8263 (mtpt) REVERT: I 7 ILE cc_start: 0.8842 (tt) cc_final: 0.8588 (tp) REVERT: M 26 ASP cc_start: 0.7956 (t0) cc_final: 0.7533 (t70) REVERT: M 36 ASN cc_start: 0.7973 (m-40) cc_final: 0.7684 (t0) REVERT: M 69 MET cc_start: 0.9208 (mmp) cc_final: 0.8896 (mmp) REVERT: N 12 LEU cc_start: 0.7218 (OUTLIER) cc_final: 0.6989 (mp) REVERT: O 5 TYR cc_start: 0.8376 (p90) cc_final: 0.7978 (p90) REVERT: O 26 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8196 (mp) REVERT: Q 9 GLN cc_start: 0.8139 (mt0) cc_final: 0.7899 (mm-40) REVERT: S 51 TYR cc_start: 0.8453 (m-80) cc_final: 0.7946 (m-80) REVERT: U 53 ARG cc_start: 0.8394 (OUTLIER) cc_final: 0.7539 (ptt180) REVERT: W 11 PHE cc_start: 0.7378 (OUTLIER) cc_final: 0.6380 (m-10) REVERT: X 39 ILE cc_start: 0.7824 (OUTLIER) cc_final: 0.7482 (mp) REVERT: X 40 CYS cc_start: 0.8360 (m) cc_final: 0.8097 (m) REVERT: X 58 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8324 (mt0) outliers start: 34 outliers final: 13 residues processed: 232 average time/residue: 0.5195 time to fit residues: 140.1849 Evaluate side-chains 218 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 54 LEU Chi-restraints excluded: chain D residue 20 GLN Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 205 GLN Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain N residue 12 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain X residue 58 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 107 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 32 optimal weight: 5.9990 chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 1.9990 chunk 180 optimal weight: 0.6980 chunk 99 optimal weight: 2.9990 chunk 133 optimal weight: 4.9990 chunk 162 optimal weight: 3.9990 chunk 169 optimal weight: 6.9990 chunk 138 optimal weight: 0.8980 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 42 ASN M 10 GLN b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.148414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.110158 restraints weight = 26607.297| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.29 r_work: 0.3142 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3034 rms_B_bonded: 3.52 restraints_weight: 0.2500 r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24099 Z= 0.139 Angle : 0.716 20.114 33025 Z= 0.279 Chirality : 0.038 0.133 3168 Planarity : 0.003 0.038 4033 Dihedral : 17.212 179.904 4665 Min Nonbonded Distance : 2.277 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.91 % Allowed : 11.10 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.29 (0.17), residues: 2229 helix: 2.25 (0.12), residues: 1538 sheet: 1.52 (0.99), residues: 27 loop : -0.22 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.016 0.001 TYR M 193 PHE 0.019 0.001 PHE L 217 TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.14 (24085) covalent geometry : angle 0.71582 / 0.28 (33025) hydrogen bonds : bond 0.04856 / 3.18 ( 1294) hydrogen bonds : angle 3.50445 / 2.54 ( 3732) Misc. bond : bond 0.00229 / 0.14 ( 14) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 203 time to evaluate : 0.707 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.5995 (tmm) cc_final: 0.5545 (tmm) REVERT: H 46 ASP cc_start: 0.8237 (p0) cc_final: 0.7883 (p0) REVERT: H 55 LEU cc_start: 0.7812 (mt) cc_final: 0.6967 (tt) REVERT: H 150 ARG cc_start: 0.7819 (OUTLIER) cc_final: 0.6048 (pmt170) REVERT: H 178 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8273 (mt0) REVERT: H 184 GLU cc_start: 0.8505 (tt0) cc_final: 0.8279 (tt0) REVERT: H 228 GLU cc_start: 0.8449 (OUTLIER) cc_final: 0.8161 (pt0) REVERT: H 235 ASP cc_start: 0.8119 (OUTLIER) cc_final: 0.7751 (t0) REVERT: I 7 ILE cc_start: 0.8864 (tt) cc_final: 0.8619 (tp) REVERT: M 26 ASP cc_start: 0.7848 (t0) cc_final: 0.7403 (t70) REVERT: M 36 ASN cc_start: 0.7997 (OUTLIER) cc_final: 0.7693 (t0) REVERT: M 69 MET cc_start: 0.9220 (mmp) cc_final: 0.8966 (mmp) REVERT: O 5 TYR cc_start: 0.8369 (p90) cc_final: 0.7969 (p90) REVERT: O 26 LEU cc_start: 0.8469 (OUTLIER) cc_final: 0.8167 (mp) REVERT: Q 9 GLN cc_start: 0.8199 (mt0) cc_final: 0.7862 (mm110) REVERT: U 53 ARG cc_start: 0.8436 (OUTLIER) cc_final: 0.7498 (ptt180) REVERT: W 11 PHE cc_start: 0.7388 (OUTLIER) cc_final: 0.6385 (m-10) REVERT: X 39 ILE cc_start: 0.7813 (OUTLIER) cc_final: 0.7450 (mp) REVERT: X 40 CYS cc_start: 0.8355 (m) cc_final: 0.8103 (m) outliers start: 37 outliers final: 14 residues processed: 223 average time/residue: 0.5045 time to fit residues: 131.4666 Evaluate side-chains 220 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 197 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain D residue 11 PHE Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 228 GLU Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 39 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 98 optimal weight: 4.9990 chunk 92 optimal weight: 0.7980 chunk 189 optimal weight: 0.8980 chunk 101 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 192 optimal weight: 0.8980 chunk 168 optimal weight: 5.9990 chunk 4 optimal weight: 10.0000 chunk 179 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 42 ASN L 200 ASN b 39 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.109833 restraints weight = 26538.794| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.28 r_work: 0.3140 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3032 rms_B_bonded: 3.50 restraints_weight: 0.2500 r_work (final): 0.3032 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.2938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24099 Z= 0.138 Angle : 0.713 20.512 33025 Z= 0.279 Chirality : 0.038 0.133 3168 Planarity : 0.003 0.039 4033 Dihedral : 17.070 179.907 4665 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.07 % Allowed : 11.51 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.36 (0.17), residues: 2229 helix: 2.29 (0.12), residues: 1538 sheet: 1.52 (0.98), residues: 27 loop : -0.16 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.017 0.001 TYR M 193 PHE 0.020 0.001 PHE L 217 TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 (24085) covalent geometry : angle 0.71252 / 0.28 (33025) hydrogen bonds : bond 0.04866 / 3.19 ( 1294) hydrogen bonds : angle 3.48802 / 2.52 ( 3732) Misc. bond : bond 0.00228 / 0.14 ( 14) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 212 time to evaluate : 0.710 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6020 (tmm) cc_final: 0.5501 (tmm) REVERT: H 150 ARG cc_start: 0.7811 (OUTLIER) cc_final: 0.6041 (pmt170) REVERT: H 178 GLN cc_start: 0.8664 (OUTLIER) cc_final: 0.8276 (mt0) REVERT: H 184 GLU cc_start: 0.8532 (tt0) cc_final: 0.8291 (tt0) REVERT: H 235 ASP cc_start: 0.8116 (OUTLIER) cc_final: 0.7723 (t0) REVERT: I 7 ILE cc_start: 0.8856 (tt) cc_final: 0.8611 (tp) REVERT: M 26 ASP cc_start: 0.7766 (t0) cc_final: 0.7309 (t70) REVERT: M 36 ASN cc_start: 0.7996 (OUTLIER) cc_final: 0.7696 (t0) REVERT: M 69 MET cc_start: 0.9221 (mmp) cc_final: 0.8906 (mmp) REVERT: O 5 TYR cc_start: 0.8372 (p90) cc_final: 0.7901 (p90) REVERT: O 26 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8167 (mp) REVERT: Q 9 GLN cc_start: 0.8148 (mt0) cc_final: 0.7804 (mm110) REVERT: U 53 ARG cc_start: 0.8458 (OUTLIER) cc_final: 0.7528 (ptt180) REVERT: W 11 PHE cc_start: 0.7325 (OUTLIER) cc_final: 0.6321 (m-10) REVERT: X 39 ILE cc_start: 0.7821 (OUTLIER) cc_final: 0.7453 (mp) REVERT: X 40 CYS cc_start: 0.8328 (m) cc_final: 0.8068 (m) REVERT: b 43 TYR cc_start: 0.5000 (OUTLIER) cc_final: 0.4669 (t80) outliers start: 40 outliers final: 13 residues processed: 236 average time/residue: 0.5080 time to fit residues: 140.4769 Evaluate side-chains 226 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 150 ARG Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain H residue 235 ASP Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 137 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 177 optimal weight: 5.9990 chunk 191 optimal weight: 4.9990 chunk 179 optimal weight: 5.9990 chunk 77 optimal weight: 2.9990 chunk 110 optimal weight: 2.9990 chunk 123 optimal weight: 0.7980 chunk 163 optimal weight: 0.8980 chunk 136 optimal weight: 3.9990 chunk 59 optimal weight: 5.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 42 ASN L 200 ASN S 9 GLN b 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.147318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.109009 restraints weight = 26134.696| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 1.29 r_work: 0.3120 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24099 Z= 0.161 Angle : 0.744 21.145 33025 Z= 0.293 Chirality : 0.039 0.141 3168 Planarity : 0.003 0.039 4033 Dihedral : 17.221 179.873 4665 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Rotamer: Outliers : 1.70 % Allowed : 12.39 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.24 (0.17), residues: 2229 helix: 2.19 (0.12), residues: 1539 sheet: 1.44 (0.98), residues: 27 loop : -0.17 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 46 TYR 0.018 0.001 TYR M 193 PHE 0.020 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.008 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.16 (24085) covalent geometry : angle 0.74397 / 0.29 (33025) hydrogen bonds : bond 0.05096 / 3.34 ( 1294) hydrogen bonds : angle 3.54680 / 2.57 ( 3732) Misc. bond : bond 0.00263 / 0.17 ( 14) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 208 time to evaluate : 0.731 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6076 (tmm) cc_final: 0.5543 (tmm) REVERT: F 41 TYR cc_start: 0.8920 (m-80) cc_final: 0.8615 (m-80) REVERT: H 178 GLN cc_start: 0.8714 (OUTLIER) cc_final: 0.8326 (mt0) REVERT: H 184 GLU cc_start: 0.8518 (tt0) cc_final: 0.8244 (tt0) REVERT: I 3 LYS cc_start: 0.8559 (mtpp) cc_final: 0.8189 (mtmm) REVERT: K 3 LYS cc_start: 0.7896 (mttm) cc_final: 0.7695 (tttm) REVERT: M 26 ASP cc_start: 0.7798 (t0) cc_final: 0.7323 (t70) REVERT: M 36 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7716 (t0) REVERT: M 69 MET cc_start: 0.9280 (mmp) cc_final: 0.9034 (mmp) REVERT: O 5 TYR cc_start: 0.8413 (p90) cc_final: 0.7968 (p90) REVERT: O 26 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (mp) REVERT: Q 9 GLN cc_start: 0.8222 (mt0) cc_final: 0.7842 (mm110) REVERT: U 15 ARG cc_start: 0.5617 (ttp80) cc_final: 0.5053 (mtp180) REVERT: U 45 ASP cc_start: 0.8296 (m-30) cc_final: 0.7926 (m-30) REVERT: U 53 ARG cc_start: 0.8411 (OUTLIER) cc_final: 0.7483 (ptt180) REVERT: W 11 PHE cc_start: 0.7406 (OUTLIER) cc_final: 0.6329 (m-10) REVERT: X 39 ILE cc_start: 0.7841 (OUTLIER) cc_final: 0.7466 (mp) REVERT: b 43 TYR cc_start: 0.5106 (OUTLIER) cc_final: 0.4758 (t80) outliers start: 33 outliers final: 15 residues processed: 228 average time/residue: 0.5003 time to fit residues: 132.6505 Evaluate side-chains 226 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 204 time to evaluate : 0.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain K residue 30 MET Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 3 optimal weight: 0.9980 chunk 77 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 183 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 207 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 205 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 191 optimal weight: 4.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 200 ASN b 39 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.148487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.110784 restraints weight = 26521.491| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.26 r_work: 0.3147 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.46 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 24099 Z= 0.132 Angle : 0.710 20.709 33025 Z= 0.278 Chirality : 0.037 0.133 3168 Planarity : 0.003 0.038 4033 Dihedral : 16.960 179.925 4665 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.45 % Allowed : 12.65 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.38 (0.17), residues: 2229 helix: 2.31 (0.12), residues: 1538 sheet: 1.48 (0.98), residues: 27 loop : -0.16 (0.24), residues: 664 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.016 0.001 TYR M 193 PHE 0.017 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (24085) covalent geometry : angle 0.71020 / 0.28 (33025) hydrogen bonds : bond 0.04837 / 3.17 ( 1294) hydrogen bonds : angle 3.48783 / 2.52 ( 3732) Misc. bond : bond 0.00217 / 0.14 ( 14) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 208 time to evaluate : 0.778 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6069 (tmm) cc_final: 0.5523 (tmm) REVERT: H 178 GLN cc_start: 0.8650 (OUTLIER) cc_final: 0.8289 (mt0) REVERT: H 184 GLU cc_start: 0.8502 (tt0) cc_final: 0.8250 (tt0) REVERT: I 3 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8121 (mtmm) REVERT: M 26 ASP cc_start: 0.7800 (t0) cc_final: 0.7323 (t70) REVERT: M 36 ASN cc_start: 0.7985 (OUTLIER) cc_final: 0.7707 (t0) REVERT: M 69 MET cc_start: 0.9228 (mmp) cc_final: 0.8927 (mmp) REVERT: O 5 TYR cc_start: 0.8334 (p90) cc_final: 0.7870 (p90) REVERT: O 26 LEU cc_start: 0.8392 (OUTLIER) cc_final: 0.8106 (mp) REVERT: Q 9 GLN cc_start: 0.8133 (mt0) cc_final: 0.7770 (mm110) REVERT: U 53 ARG cc_start: 0.8362 (OUTLIER) cc_final: 0.7495 (ptt180) REVERT: W 11 PHE cc_start: 0.7293 (OUTLIER) cc_final: 0.6269 (m-10) REVERT: X 39 ILE cc_start: 0.7792 (OUTLIER) cc_final: 0.7418 (mp) REVERT: X 40 CYS cc_start: 0.8310 (m) cc_final: 0.8031 (m) REVERT: b 43 TYR cc_start: 0.5156 (OUTLIER) cc_final: 0.4793 (t80) outliers start: 28 outliers final: 16 residues processed: 225 average time/residue: 0.5102 time to fit residues: 134.3628 Evaluate side-chains 225 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 202 time to evaluate : 2.379 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 55 LEU Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 120 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 90 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 197 optimal weight: 1.9990 chunk 139 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 40 optimal weight: 4.9990 chunk 186 optimal weight: 5.9990 chunk 127 optimal weight: 4.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 7 42 ASN L 200 ASN O 9 GLN b 39 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.147926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109455 restraints weight = 26332.007| |-----------------------------------------------------------------------------| r_work (start): 0.3249 rms_B_bonded: 1.31 r_work: 0.3128 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3020 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3020 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 moved from start: 0.3072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24099 Z= 0.140 Angle : 0.718 20.444 33025 Z= 0.282 Chirality : 0.038 0.132 3168 Planarity : 0.003 0.038 4033 Dihedral : 16.910 179.910 4665 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 1.29 % Allowed : 12.91 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.35 (0.17), residues: 2229 helix: 2.29 (0.12), residues: 1539 sheet: 1.42 (0.98), residues: 27 loop : -0.17 (0.24), residues: 663 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.017 0.001 TYR M 193 PHE 0.018 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (24085) covalent geometry : angle 0.71822 / 0.28 (33025) hydrogen bonds : bond 0.04888 / 3.20 ( 1294) hydrogen bonds : angle 3.50192 / 2.53 ( 3732) Misc. bond : bond 0.00230 / 0.15 ( 14) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4458 Ramachandran restraints generated. 2229 Oldfield, 0 Emsley, 2229 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 203 time to evaluate : 0.807 Fit side-chains revert: symmetry clash REVERT: 1 30 MET cc_start: 0.6098 (tmm) cc_final: 0.5533 (tmm) REVERT: H 178 GLN cc_start: 0.8670 (OUTLIER) cc_final: 0.8290 (mt0) REVERT: H 184 GLU cc_start: 0.8517 (tt0) cc_final: 0.8247 (tt0) REVERT: I 3 LYS cc_start: 0.8508 (mtpp) cc_final: 0.8146 (mtmm) REVERT: M 26 ASP cc_start: 0.7874 (t0) cc_final: 0.7301 (t0) REVERT: M 36 ASN cc_start: 0.7994 (OUTLIER) cc_final: 0.7715 (t0) REVERT: M 69 MET cc_start: 0.9222 (mmp) cc_final: 0.8911 (mmp) REVERT: O 5 TYR cc_start: 0.8404 (p90) cc_final: 0.7966 (p90) REVERT: O 26 LEU cc_start: 0.8457 (OUTLIER) cc_final: 0.8183 (mp) REVERT: Q 9 GLN cc_start: 0.8192 (mt0) cc_final: 0.7823 (mm110) REVERT: U 15 ARG cc_start: 0.5683 (ttp80) cc_final: 0.5198 (mtp180) REVERT: U 53 ARG cc_start: 0.8431 (OUTLIER) cc_final: 0.7521 (ptt180) REVERT: W 11 PHE cc_start: 0.7313 (OUTLIER) cc_final: 0.6291 (m-10) REVERT: X 39 ILE cc_start: 0.7853 (OUTLIER) cc_final: 0.7471 (mp) REVERT: X 40 CYS cc_start: 0.8363 (m) cc_final: 0.8091 (m) REVERT: b 43 TYR cc_start: 0.5158 (OUTLIER) cc_final: 0.4819 (t80) outliers start: 25 outliers final: 15 residues processed: 219 average time/residue: 0.5279 time to fit residues: 134.9409 Evaluate side-chains 222 residues out of total 1937 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 200 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain 2 residue 20 LEU Chi-restraints excluded: chain 7 residue 1 MET Chi-restraints excluded: chain G residue 13 SER Chi-restraints excluded: chain H residue 178 GLN Chi-restraints excluded: chain H residue 214 SER Chi-restraints excluded: chain I residue 2 SER Chi-restraints excluded: chain L residue 32 VAL Chi-restraints excluded: chain L residue 54 THR Chi-restraints excluded: chain L residue 248 CYS Chi-restraints excluded: chain M residue 36 ASN Chi-restraints excluded: chain M residue 99 ASP Chi-restraints excluded: chain M residue 235 LEU Chi-restraints excluded: chain O residue 26 LEU Chi-restraints excluded: chain P residue 26 SER Chi-restraints excluded: chain Q residue 10 VAL Chi-restraints excluded: chain U residue 30 MET Chi-restraints excluded: chain U residue 53 ARG Chi-restraints excluded: chain V residue 22 SER Chi-restraints excluded: chain W residue 11 PHE Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 39 ILE Chi-restraints excluded: chain b residue 43 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 218 random chunks: chunk 67 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 153 optimal weight: 3.9990 chunk 194 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 155 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 8.9990 chunk 168 optimal weight: 5.9990 chunk 148 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 1 20 GLN I 20 GLN L 200 ASN O 9 GLN b 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.148044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.109508 restraints weight = 26275.654| |-----------------------------------------------------------------------------| r_work (start): 0.3257 rms_B_bonded: 1.32 r_work: 0.3136 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3028 rms_B_bonded: 3.58 restraints_weight: 0.2500 r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.3114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 24099 Z= 0.138 Angle : 0.712 20.320 33025 Z= 0.280 Chirality : 0.038 0.133 3168 Planarity : 0.003 0.038 4033 Dihedral : 16.862 179.915 4665 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.34 % Allowed : 12.75 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.41 % 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: 2.37 (0.17), residues: 2229 helix: 2.31 (0.12), residues: 1539 sheet: 1.74 (1.16), residues: 17 loop : -0.16 (0.24), residues: 673 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 46 TYR 0.017 0.001 TYR M 193 PHE 0.019 0.001 PHE S 11 TRP 0.016 0.001 TRP M 74 HIS 0.007 0.001 HIS M 182 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.14 (24085) covalent geometry : angle 0.71226 / 0.28 (33025) hydrogen bonds : bond 0.04865 / 3.19 ( 1294) hydrogen bonds : angle 3.49515 / 2.52 ( 3732) Misc. bond : bond 0.00228 / 0.14 ( 14) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7135.00 seconds wall clock time: 122 minutes 28.29 seconds (7348.29 seconds total)