Starting phenix.real_space_refine on Mon Jun 23 23:24:36 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7svu_25453/06_2025/7svu_25453.cif Found real_map, /net/cci-nas-00/data/ceres_data/7svu_25453/06_2025/7svu_25453.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7svu_25453/06_2025/7svu_25453.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7svu_25453/06_2025/7svu_25453.map" model { file = "/net/cci-nas-00/data/ceres_data/7svu_25453/06_2025/7svu_25453.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7svu_25453/06_2025/7svu_25453.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.176 sd= 0.689 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 89 5.49 5 Mg 11 5.21 5 S 116 5.16 5 C 17459 2.51 5 N 5051 2.21 5 O 5289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 84 residue(s): 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28015 Number of models: 1 Model: "" Number of chains: 35 Chain: "1" Number of atoms: 560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 560 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain: "2" Number of atoms: 588 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 588 Classifications: {'DNA': 28} Link IDs: {'rna3p': 27} Chain breaks: 1 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "a" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "b" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "c" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "d" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "e" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "f" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "h" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "j" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "k" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "X" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain: "Y" Number of atoms: 1314 Number of conformers: 1 Conformer: "" Number of residues, atoms: 165, 1314 Classifications: {'peptide': 165} Link IDs: {'PTRANS': 13, 'TRANS': 151} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.99, per 1000 atoms: 0.61 Number of scatterers: 28015 At special positions: 0 Unit cell: (136.99, 142.31, 168.91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 116 16.00 P 89 15.00 Mg 11 11.99 O 5289 8.00 N 5051 7.00 C 17459 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 Atom "ATOM 484 O5' DT 1 25 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=8, symmetry=0 Number of additional bonds: simple=8, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.61 Conformation dependent library (CDL) restraints added in 3.3 seconds 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6156 Finding SS restraints... Secondary structure from input PDB file: 181 helices and 22 sheets defined 59.9% alpha, 6.0% beta 22 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 9.48 Creating SS restraints... Processing helix chain 'A' and resid 19 through 29 Processing helix chain 'A' and resid 36 through 53 Processing helix chain 'A' and resid 65 through 75 Processing helix chain 'A' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE A 106 " --> pdb=" O PRO A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 134 Processing helix chain 'A' and resid 145 through 149 Processing helix chain 'A' and resid 150 through 152 No H-bonds generated for 'chain 'A' and resid 150 through 152' Processing helix chain 'A' and resid 153 through 164 Processing helix chain 'A' and resid 173 through 181 removed outlier: 4.012A pdb=" N ASP A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 215 Processing helix chain 'A' and resid 226 through 238 removed outlier: 4.355A pdb=" N ILE A 232 " --> pdb=" O GLU A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG A 258 " --> pdb=" O ARG A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 273 Processing helix chain 'a' and resid 575 through 581 removed outlier: 3.931A pdb=" N ARG a 579 " --> pdb=" O TYR a 575 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 29 Processing helix chain 'B' and resid 36 through 53 Processing helix chain 'B' and resid 65 through 75 Processing helix chain 'B' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 134 Processing helix chain 'B' and resid 145 through 149 Processing helix chain 'B' and resid 150 through 152 No H-bonds generated for 'chain 'B' and resid 150 through 152' Processing helix chain 'B' and resid 153 through 164 Processing helix chain 'B' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP B 177 " --> pdb=" O THR B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 183 through 190 removed outlier: 3.955A pdb=" N ARG B 189 " --> pdb=" O GLN B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 200 through 215 Processing helix chain 'B' and resid 226 through 238 removed outlier: 4.356A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 264 through 273 Processing helix chain 'b' and resid 575 through 581 removed outlier: 3.930A pdb=" N ARG b 579 " --> pdb=" O TYR b 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 29 Processing helix chain 'C' and resid 36 through 53 Processing helix chain 'C' and resid 65 through 75 Processing helix chain 'C' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 121 through 134 Processing helix chain 'C' and resid 145 through 149 Processing helix chain 'C' and resid 150 through 152 No H-bonds generated for 'chain 'C' and resid 150 through 152' Processing helix chain 'C' and resid 153 through 164 Processing helix chain 'C' and resid 173 through 181 removed outlier: 4.011A pdb=" N ASP C 177 " --> pdb=" O THR C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 215 Processing helix chain 'C' and resid 226 through 238 removed outlier: 4.355A pdb=" N ILE C 232 " --> pdb=" O GLU C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 240 through 258 removed outlier: 3.656A pdb=" N ARG C 258 " --> pdb=" O ARG C 254 " (cutoff:3.500A) Processing helix chain 'C' and resid 264 through 273 Processing helix chain 'c' and resid 575 through 581 removed outlier: 3.930A pdb=" N ARG c 579 " --> pdb=" O TYR c 575 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 29 Processing helix chain 'D' and resid 36 through 53 Processing helix chain 'D' and resid 65 through 75 Processing helix chain 'D' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE D 106 " --> pdb=" O PRO D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 121 through 134 Processing helix chain 'D' and resid 145 through 149 Processing helix chain 'D' and resid 150 through 152 No H-bonds generated for 'chain 'D' and resid 150 through 152' Processing helix chain 'D' and resid 153 through 164 Processing helix chain 'D' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP D 177 " --> pdb=" O THR D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 183 through 190 removed outlier: 3.955A pdb=" N ARG D 189 " --> pdb=" O GLN D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 200 through 215 Processing helix chain 'D' and resid 226 through 238 removed outlier: 4.356A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG D 258 " --> pdb=" O ARG D 254 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 273 Processing helix chain 'd' and resid 575 through 581 removed outlier: 3.931A pdb=" N ARG d 579 " --> pdb=" O TYR d 575 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 29 Processing helix chain 'E' and resid 36 through 53 Processing helix chain 'E' and resid 65 through 75 Processing helix chain 'E' and resid 101 through 113 removed outlier: 3.873A pdb=" N PHE E 106 " --> pdb=" O PRO E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 134 Processing helix chain 'E' and resid 145 through 149 Processing helix chain 'E' and resid 150 through 152 No H-bonds generated for 'chain 'E' and resid 150 through 152' Processing helix chain 'E' and resid 153 through 164 Processing helix chain 'E' and resid 173 through 181 removed outlier: 4.011A pdb=" N ASP E 177 " --> pdb=" O THR E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 200 through 215 Processing helix chain 'E' and resid 226 through 238 removed outlier: 4.355A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG E 258 " --> pdb=" O ARG E 254 " (cutoff:3.500A) Processing helix chain 'E' and resid 264 through 273 Processing helix chain 'e' and resid 575 through 581 removed outlier: 3.931A pdb=" N ARG e 579 " --> pdb=" O TYR e 575 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 29 Processing helix chain 'F' and resid 36 through 53 Processing helix chain 'F' and resid 65 through 75 Processing helix chain 'F' and resid 101 through 113 removed outlier: 3.874A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 145 through 149 Processing helix chain 'F' and resid 150 through 152 No H-bonds generated for 'chain 'F' and resid 150 through 152' Processing helix chain 'F' and resid 153 through 164 Processing helix chain 'F' and resid 173 through 181 removed outlier: 4.013A pdb=" N ASP F 177 " --> pdb=" O THR F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 183 through 190 removed outlier: 3.954A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 200 through 215 Processing helix chain 'F' and resid 226 through 238 removed outlier: 4.356A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 240 through 258 removed outlier: 3.657A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 264 through 273 Processing helix chain 'f' and resid 575 through 581 removed outlier: 3.930A pdb=" N ARG f 579 " --> pdb=" O TYR f 575 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 36 through 53 Processing helix chain 'G' and resid 65 through 75 Processing helix chain 'G' and resid 101 through 112 removed outlier: 4.070A pdb=" N PHE G 106 " --> pdb=" O PRO G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 121 through 134 Processing helix chain 'G' and resid 145 through 149 Processing helix chain 'G' and resid 150 through 152 No H-bonds generated for 'chain 'G' and resid 150 through 152' Processing helix chain 'G' and resid 153 through 164 Processing helix chain 'G' and resid 173 through 181 removed outlier: 4.085A pdb=" N ASP G 177 " --> pdb=" O THR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 183 through 190 removed outlier: 3.555A pdb=" N GLU G 188 " --> pdb=" O GLU G 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG G 189 " --> pdb=" O GLN G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 200 through 215 Processing helix chain 'G' and resid 226 through 238 removed outlier: 3.979A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 240 through 258 Processing helix chain 'G' and resid 264 through 273 Processing helix chain 'H' and resid 20 through 29 Processing helix chain 'H' and resid 36 through 53 removed outlier: 3.725A pdb=" N THR H 41 " --> pdb=" O GLN H 37 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N LEU H 42 " --> pdb=" O GLN H 38 " (cutoff:3.500A) Processing helix chain 'H' and resid 65 through 75 Processing helix chain 'H' and resid 101 through 113 removed outlier: 4.025A pdb=" N PHE H 106 " --> pdb=" O PRO H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 121 through 134 Processing helix chain 'H' and resid 145 through 149 Processing helix chain 'H' and resid 150 through 152 No H-bonds generated for 'chain 'H' and resid 150 through 152' Processing helix chain 'H' and resid 153 through 164 Processing helix chain 'H' and resid 173 through 181 removed outlier: 4.067A pdb=" N ASP H 177 " --> pdb=" O THR H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 183 through 190 removed outlier: 3.572A pdb=" N GLU H 188 " --> pdb=" O GLU H 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 215 Processing helix chain 'H' and resid 226 through 238 removed outlier: 4.260A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 258 removed outlier: 3.591A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 264 through 273 Processing helix chain 'h' and resid 576 through 581 Processing helix chain 'I' and resid 20 through 29 Processing helix chain 'I' and resid 36 through 53 Processing helix chain 'I' and resid 65 through 75 Processing helix chain 'I' and resid 101 through 112 removed outlier: 4.069A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 121 through 134 Processing helix chain 'I' and resid 145 through 149 Processing helix chain 'I' and resid 150 through 152 No H-bonds generated for 'chain 'I' and resid 150 through 152' Processing helix chain 'I' and resid 153 through 164 Processing helix chain 'I' and resid 173 through 181 removed outlier: 4.085A pdb=" N ASP I 177 " --> pdb=" O THR I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 183 through 190 removed outlier: 3.554A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 200 through 215 Processing helix chain 'I' and resid 226 through 238 removed outlier: 3.980A pdb=" N ILE I 232 " --> pdb=" O GLU I 228 " (cutoff:3.500A) Processing helix chain 'I' and resid 240 through 258 Processing helix chain 'I' and resid 264 through 273 Processing helix chain 'J' and resid 20 through 29 Processing helix chain 'J' and resid 36 through 53 removed outlier: 3.726A pdb=" N THR J 41 " --> pdb=" O GLN J 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU J 42 " --> pdb=" O GLN J 38 " (cutoff:3.500A) Processing helix chain 'J' and resid 65 through 75 Processing helix chain 'J' and resid 101 through 113 removed outlier: 4.025A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 121 through 134 Processing helix chain 'J' and resid 145 through 149 Processing helix chain 'J' and resid 150 through 152 No H-bonds generated for 'chain 'J' and resid 150 through 152' Processing helix chain 'J' and resid 153 through 164 Processing helix chain 'J' and resid 173 through 181 removed outlier: 4.066A pdb=" N ASP J 177 " --> pdb=" O THR J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 183 through 190 removed outlier: 3.573A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 200 through 215 Processing helix chain 'J' and resid 226 through 238 removed outlier: 4.259A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 240 through 258 removed outlier: 3.590A pdb=" N ARG J 258 " --> pdb=" O ARG J 254 " (cutoff:3.500A) Processing helix chain 'J' and resid 264 through 273 Processing helix chain 'j' and resid 576 through 581 Processing helix chain 'K' and resid 20 through 29 Processing helix chain 'K' and resid 36 through 53 removed outlier: 3.726A pdb=" N THR K 41 " --> pdb=" O GLN K 37 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LEU K 42 " --> pdb=" O GLN K 38 " (cutoff:3.500A) Processing helix chain 'K' and resid 65 through 75 Processing helix chain 'K' and resid 101 through 113 removed outlier: 4.025A pdb=" N PHE K 106 " --> pdb=" O PRO K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 121 through 134 Processing helix chain 'K' and resid 145 through 149 Processing helix chain 'K' and resid 150 through 152 No H-bonds generated for 'chain 'K' and resid 150 through 152' Processing helix chain 'K' and resid 153 through 164 Processing helix chain 'K' and resid 173 through 181 removed outlier: 4.067A pdb=" N ASP K 177 " --> pdb=" O THR K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 183 through 190 removed outlier: 3.573A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 215 Processing helix chain 'K' and resid 226 through 238 removed outlier: 4.259A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 240 through 258 removed outlier: 3.591A pdb=" N ARG K 258 " --> pdb=" O ARG K 254 " (cutoff:3.500A) Processing helix chain 'K' and resid 264 through 273 Processing helix chain 'k' and resid 576 through 581 Processing helix chain 'X' and resid 21 through 33 Processing helix chain 'X' and resid 36 through 45 Processing helix chain 'X' and resid 47 through 53 removed outlier: 4.403A pdb=" N VAL X 50 " --> pdb=" O GLY X 47 " (cutoff:3.500A) Processing helix chain 'X' and resid 65 through 75 removed outlier: 3.983A pdb=" N ALA X 71 " --> pdb=" O LEU X 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER X 72 " --> pdb=" O GLU X 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL X 73 " --> pdb=" O ALA X 69 " (cutoff:3.500A) Processing helix chain 'X' and resid 77 through 83 Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'X' and resid 111 through 116 Processing helix chain 'X' and resid 142 through 146 Processing helix chain 'X' and resid 158 through 164 removed outlier: 4.017A pdb=" N LYS X 163 " --> pdb=" O GLU X 160 " (cutoff:3.500A) Processing helix chain 'Y' and resid 21 through 33 Processing helix chain 'Y' and resid 36 through 45 Processing helix chain 'Y' and resid 47 through 53 removed outlier: 4.404A pdb=" N VAL Y 50 " --> pdb=" O GLY Y 47 " (cutoff:3.500A) Processing helix chain 'Y' and resid 65 through 75 removed outlier: 3.982A pdb=" N ALA Y 71 " --> pdb=" O LEU Y 67 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N SER Y 72 " --> pdb=" O GLU Y 68 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL Y 73 " --> pdb=" O ALA Y 69 " (cutoff:3.500A) Processing helix chain 'Y' and resid 77 through 83 Processing helix chain 'Y' and resid 100 through 104 Processing helix chain 'Y' and resid 111 through 116 Processing helix chain 'Y' and resid 142 through 146 Processing helix chain 'Y' and resid 158 through 164 removed outlier: 4.018A pdb=" N LYS Y 163 " --> pdb=" O GLU Y 160 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 33 Processing sheet with id=AA2, first strand: chain 'A' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU A 141 " --> pdb=" O VAL A 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL A 171 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE A 143 " --> pdb=" O VAL A 171 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AA4, first strand: chain 'B' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU B 141 " --> pdb=" O VAL B 169 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL B 171 " --> pdb=" O LEU B 141 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE B 143 " --> pdb=" O VAL B 171 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 33 Processing sheet with id=AA6, first strand: chain 'C' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU C 141 " --> pdb=" O VAL C 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL C 171 " --> pdb=" O LEU C 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE C 143 " --> pdb=" O VAL C 171 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 33 Processing sheet with id=AA8, first strand: chain 'D' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU D 141 " --> pdb=" O VAL D 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL D 171 " --> pdb=" O LEU D 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE D 143 " --> pdb=" O VAL D 171 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 33 Processing sheet with id=AB1, first strand: chain 'E' and resid 91 through 94 removed outlier: 6.597A pdb=" N LEU E 141 " --> pdb=" O VAL E 169 " (cutoff:3.500A) removed outlier: 7.656A pdb=" N VAL E 171 " --> pdb=" O LEU E 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE E 143 " --> pdb=" O VAL E 171 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 33 Processing sheet with id=AB3, first strand: chain 'F' and resid 91 through 94 removed outlier: 6.598A pdb=" N LEU F 141 " --> pdb=" O VAL F 169 " (cutoff:3.500A) removed outlier: 7.655A pdb=" N VAL F 171 " --> pdb=" O LEU F 141 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ILE F 143 " --> pdb=" O VAL F 171 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 91 through 94 removed outlier: 6.750A pdb=" N VAL G 92 " --> pdb=" O ILE G 142 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N LEU G 141 " --> pdb=" O VAL G 169 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL G 171 " --> pdb=" O LEU G 141 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE G 143 " --> pdb=" O VAL G 171 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 32 through 33 Processing sheet with id=AB6, first strand: chain 'H' and resid 91 through 94 removed outlier: 6.765A pdb=" N VAL H 92 " --> pdb=" O ILE H 142 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU H 141 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL H 171 " --> pdb=" O LEU H 141 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE H 143 " --> pdb=" O VAL H 171 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 91 through 94 removed outlier: 6.751A pdb=" N VAL I 92 " --> pdb=" O ILE I 142 " (cutoff:3.500A) removed outlier: 6.597A pdb=" N LEU I 141 " --> pdb=" O VAL I 169 " (cutoff:3.500A) removed outlier: 7.622A pdb=" N VAL I 171 " --> pdb=" O LEU I 141 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N ILE I 143 " --> pdb=" O VAL I 171 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'J' and resid 32 through 33 Processing sheet with id=AB9, first strand: chain 'J' and resid 91 through 94 removed outlier: 6.765A pdb=" N VAL J 92 " --> pdb=" O ILE J 142 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU J 141 " --> pdb=" O VAL J 169 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL J 171 " --> pdb=" O LEU J 141 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE J 143 " --> pdb=" O VAL J 171 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'K' and resid 32 through 33 Processing sheet with id=AC2, first strand: chain 'K' and resid 91 through 94 removed outlier: 6.765A pdb=" N VAL K 92 " --> pdb=" O ILE K 142 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N LEU K 141 " --> pdb=" O VAL K 169 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL K 171 " --> pdb=" O LEU K 141 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ILE K 143 " --> pdb=" O VAL K 171 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'X' and resid 121 through 122 Processing sheet with id=AC4, first strand: chain 'Y' and resid 121 through 122 1301 hydrogen bonds defined for protein. 3693 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 44 hydrogen bonds 88 hydrogen bond angles 0 basepair planarities 22 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 8.83 Time building geometry restraints manager: 8.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 4484 1.29 - 1.42: 7161 1.42 - 1.55: 16626 1.55 - 1.69: 168 1.69 - 1.82: 170 Bond restraints: 28609 Sorted by residual: bond pdb=" C5 ATP J 302 " pdb=" N7 ATP J 302 " ideal model delta sigma weight residual 1.387 1.286 0.101 1.00e-02 1.00e+04 1.02e+02 bond pdb=" C4 ATP J 302 " pdb=" N9 ATP J 302 " ideal model delta sigma weight residual 1.374 1.278 0.096 1.00e-02 1.00e+04 9.19e+01 bond pdb=" C4 ATP A 302 " pdb=" C5 ATP A 302 " ideal model delta sigma weight residual 1.388 1.472 -0.084 1.00e-02 1.00e+04 7.04e+01 bond pdb=" C4 ATP D 302 " pdb=" C5 ATP D 302 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.95e+01 bond pdb=" C4 ATP G 302 " pdb=" C5 ATP G 302 " ideal model delta sigma weight residual 1.388 1.471 -0.083 1.00e-02 1.00e+04 6.93e+01 ... (remaining 28604 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.40: 37852 5.40 - 10.79: 875 10.79 - 16.19: 44 16.19 - 21.58: 24 21.58 - 26.98: 2 Bond angle restraints: 38797 Sorted by residual: angle pdb=" PA ATP J 302 " pdb=" O3A ATP J 302 " pdb=" PB ATP J 302 " ideal model delta sigma weight residual 136.83 109.85 26.98 1.00e+00 1.00e+00 7.28e+02 angle pdb=" PB ATP J 302 " pdb=" O3B ATP J 302 " pdb=" PG ATP J 302 " ideal model delta sigma weight residual 139.87 113.39 26.48 1.00e+00 1.00e+00 7.01e+02 angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 120.44 19.43 1.00e+00 1.00e+00 3.78e+02 angle pdb=" PB ATP C 302 " pdb=" O3B ATP C 302 " pdb=" PG ATP C 302 " ideal model delta sigma weight residual 139.87 120.46 19.41 1.00e+00 1.00e+00 3.77e+02 angle pdb=" PB ATP A 302 " pdb=" O3B ATP A 302 " pdb=" PG ATP A 302 " ideal model delta sigma weight residual 139.87 120.47 19.40 1.00e+00 1.00e+00 3.76e+02 ... (remaining 38792 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.98: 16977 29.98 - 59.95: 665 59.95 - 89.93: 93 89.93 - 119.90: 1 119.90 - 149.88: 4 Dihedral angle restraints: 17740 sinusoidal: 8222 harmonic: 9518 Sorted by residual: dihedral pdb=" N ARG J 116 " pdb=" C ARG J 116 " pdb=" CA ARG J 116 " pdb=" CB ARG J 116 " ideal model delta harmonic sigma weight residual 122.80 138.90 -16.10 0 2.50e+00 1.60e-01 4.15e+01 dihedral pdb=" C TYR j 582 " pdb=" N TYR j 582 " pdb=" CA TYR j 582 " pdb=" CB TYR j 582 " ideal model delta harmonic sigma weight residual -122.60 -137.36 14.76 0 2.50e+00 1.60e-01 3.48e+01 dihedral pdb=" C TYR k 582 " pdb=" N TYR k 582 " pdb=" CA TYR k 582 " pdb=" CB TYR k 582 " ideal model delta harmonic sigma weight residual -122.60 -137.33 14.73 0 2.50e+00 1.60e-01 3.47e+01 ... (remaining 17737 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.134: 3637 0.134 - 0.267: 536 0.267 - 0.401: 83 0.401 - 0.534: 14 0.534 - 0.668: 12 Chirality restraints: 4282 Sorted by residual: chirality pdb=" CA TYR j 582 " pdb=" N TYR j 582 " pdb=" C TYR j 582 " pdb=" CB TYR j 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA TYR k 582 " pdb=" N TYR k 582 " pdb=" C TYR k 582 " pdb=" CB TYR k 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 chirality pdb=" CA TYR e 582 " pdb=" N TYR e 582 " pdb=" C TYR e 582 " pdb=" CB TYR e 582 " both_signs ideal model delta sigma weight residual False 2.51 1.84 0.67 2.00e-01 2.50e+01 1.11e+01 ... (remaining 4279 not shown) Planarity restraints: 4690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER A 255 " -0.030 2.00e-02 2.50e+03 5.94e-02 3.52e+01 pdb=" C SER A 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER A 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU A 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER F 255 " -0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C SER F 255 " 0.103 2.00e-02 2.50e+03 pdb=" O SER F 255 " -0.037 2.00e-02 2.50e+03 pdb=" N LEU F 256 " -0.036 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 255 " 0.030 2.00e-02 2.50e+03 5.93e-02 3.52e+01 pdb=" C SER D 255 " -0.103 2.00e-02 2.50e+03 pdb=" O SER D 255 " 0.037 2.00e-02 2.50e+03 pdb=" N LEU D 256 " 0.036 2.00e-02 2.50e+03 ... (remaining 4687 not shown) Histogram of nonbonded interaction distances: 0.87 - 1.68: 30 1.68 - 2.48: 279 2.48 - 3.29: 32569 3.29 - 4.09: 66214 4.09 - 4.90: 117354 Warning: very small nonbonded interaction distances. Nonbonded interactions: 216446 Sorted by model distance: nonbonded pdb=" CZ ARG F 116 " pdb=" OE2 GLU K 184 " model vdw 0.871 3.270 nonbonded pdb=" NH2 ARG B 85 " pdb=" C LYS I 273 " model vdw 0.897 3.350 nonbonded pdb=" NH2 ARG F 116 " pdb=" OE2 GLU K 184 " model vdw 0.949 3.120 nonbonded pdb=" NH2 ARG A 85 " pdb=" C LYS H 273 " model vdw 0.964 3.350 nonbonded pdb=" CG1 VAL I 220 " pdb=" O LYS I 261 " model vdw 0.974 3.460 ... (remaining 216441 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 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'X' selection = chain 'Y' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'h' selection = chain 'j' selection = chain 'k' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.920 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: 1.120 Check model and map are aligned: 0.220 Set scattering table: 0.280 Process input model: 67.730 Find NCS groups from input model: 1.230 Set up NCS constraints: 0.170 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:2.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7287 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 : 0.023 0.993 28617 Z= 1.867 Angle : 1.915 26.975 38797 Z= 1.453 Chirality : 0.108 0.668 4282 Planarity : 0.011 0.076 4690 Dihedral : 15.097 149.877 11584 Min Nonbonded Distance : 0.871 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.15 % Allowed : 2.28 % Favored : 97.56 % Rotamer: Outliers : 0.42 % Allowed : 2.80 % Favored : 96.78 % Cbeta Deviations : 0.39 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.14), residues: 3239 helix: -0.71 (0.11), residues: 1810 sheet: 2.49 (0.30), residues: 253 loop : 0.13 (0.18), residues: 1176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP Y 10 HIS 0.004 0.000 HIS Y 152 PHE 0.027 0.001 PHE F 125 TYR 0.026 0.002 TYR G 112 ARG 0.004 0.000 ARG Y 155 Details of bonding type rmsd hydrogen bonds : bond 0.26080 ( 1345) hydrogen bonds : angle 7.78225 ( 3781) covalent geometry : bond 0.01954 (28609) covalent geometry : angle 1.91536 (38797) Misc. bond : bond 0.71833 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1515 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 1503 time to evaluate : 2.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 78 LYS cc_start: 0.7247 (mttt) cc_final: 0.6638 (mtpp) REVERT: A 183 ASP cc_start: 0.7583 (t0) cc_final: 0.7348 (t70) REVERT: B 42 LEU cc_start: 0.8379 (tp) cc_final: 0.8072 (tt) REVERT: B 53 ARG cc_start: 0.8234 (mmt-90) cc_final: 0.6921 (mmt90) REVERT: B 104 ASP cc_start: 0.8384 (m-30) cc_final: 0.8058 (m-30) REVERT: B 132 VAL cc_start: 0.8763 (m) cc_final: 0.8378 (t) REVERT: C 36 LEU cc_start: 0.8563 (mt) cc_final: 0.8339 (mp) REVERT: C 78 LYS cc_start: 0.7228 (mttt) cc_final: 0.6364 (mtpp) REVERT: C 125 PHE cc_start: 0.8777 (m-10) cc_final: 0.8520 (m-80) REVERT: C 130 ILE cc_start: 0.9291 (mm) cc_final: 0.9071 (mt) REVERT: C 136 CYS cc_start: 0.6789 (t) cc_final: 0.6476 (t) REVERT: C 145 GLU cc_start: 0.7343 (mt-10) cc_final: 0.7118 (mt-10) REVERT: D 25 ILE cc_start: 0.6918 (mm) cc_final: 0.6690 (mm) REVERT: D 73 TYR cc_start: 0.8844 (t80) cc_final: 0.8555 (t80) REVERT: D 78 LYS cc_start: 0.8027 (mttt) cc_final: 0.7531 (mmmm) REVERT: D 132 VAL cc_start: 0.8744 (m) cc_final: 0.8376 (p) REVERT: E 33 ILE cc_start: 0.8898 (mt) cc_final: 0.8503 (mt) REVERT: E 47 ASP cc_start: 0.5398 (t70) cc_final: 0.5099 (t70) REVERT: E 53 ARG cc_start: 0.8154 (mmt-90) cc_final: 0.7895 (mpt180) REVERT: E 78 LYS cc_start: 0.7479 (mttt) cc_final: 0.6746 (mtpp) REVERT: E 89 VAL cc_start: 0.7578 (t) cc_final: 0.7289 (m) REVERT: E 93 TYR cc_start: 0.8633 (t80) cc_final: 0.8023 (t80) REVERT: E 144 ASP cc_start: 0.8459 (t0) cc_final: 0.8087 (t0) REVERT: E 159 ASP cc_start: 0.7352 (t70) cc_final: 0.6982 (t0) REVERT: E 163 ASP cc_start: 0.6178 (t70) cc_final: 0.5825 (t0) REVERT: F 34 VAL cc_start: 0.8419 (t) cc_final: 0.7988 (m) REVERT: F 41 THR cc_start: 0.8352 (m) cc_final: 0.8139 (m) REVERT: F 42 LEU cc_start: 0.8462 (tp) cc_final: 0.8215 (tt) REVERT: F 49 LYS cc_start: 0.8693 (mmtt) cc_final: 0.8442 (mmmm) REVERT: G 115 TYR cc_start: 0.7959 (t80) cc_final: 0.6409 (t80) REVERT: G 153 THR cc_start: 0.8722 (p) cc_final: 0.8503 (t) REVERT: G 180 ILE cc_start: 0.9060 (mt) cc_final: 0.8859 (mm) REVERT: G 268 LEU cc_start: 0.8967 (tp) cc_final: 0.8525 (tt) REVERT: G 269 GLN cc_start: 0.7805 (mt0) cc_final: 0.7566 (mt0) REVERT: G 275 TYR cc_start: 0.6406 (m-80) cc_final: 0.6003 (m-80) REVERT: H 64 THR cc_start: 0.8349 (p) cc_final: 0.8146 (p) REVERT: H 89 VAL cc_start: 0.8633 (t) cc_final: 0.8330 (m) REVERT: H 132 VAL cc_start: 0.8755 (m) cc_final: 0.8471 (t) REVERT: H 184 GLU cc_start: 0.6849 (mt-10) cc_final: 0.6374 (mt-10) REVERT: H 232 ILE cc_start: 0.8302 (mt) cc_final: 0.8091 (mt) REVERT: h 573 TRP cc_start: 0.7670 (m-90) cc_final: 0.7466 (m-90) REVERT: I 25 ILE cc_start: 0.7916 (mm) cc_final: 0.7687 (mm) REVERT: I 33 ILE cc_start: 0.8870 (mt) cc_final: 0.8649 (mm) REVERT: I 44 ASP cc_start: 0.7698 (m-30) cc_final: 0.7492 (m-30) REVERT: I 64 THR cc_start: 0.8336 (p) cc_final: 0.8135 (p) REVERT: I 240 TYR cc_start: 0.8569 (m-80) cc_final: 0.8331 (m-80) REVERT: I 268 LEU cc_start: 0.8837 (tp) cc_final: 0.8578 (tp) REVERT: I 269 GLN cc_start: 0.7871 (mt0) cc_final: 0.7670 (mt0) REVERT: J 29 LYS cc_start: 0.8469 (ttpt) cc_final: 0.8225 (ttpp) REVERT: J 47 ASP cc_start: 0.7743 (t70) cc_final: 0.7482 (t0) REVERT: J 91 VAL cc_start: 0.8841 (t) cc_final: 0.8631 (p) REVERT: J 104 ASP cc_start: 0.7781 (m-30) cc_final: 0.7559 (m-30) REVERT: J 124 ASP cc_start: 0.7962 (m-30) cc_final: 0.7404 (m-30) REVERT: J 129 THR cc_start: 0.8665 (m) cc_final: 0.8405 (t) REVERT: J 211 TRP cc_start: 0.8211 (t-100) cc_final: 0.7843 (t-100) REVERT: J 220 VAL cc_start: 0.8367 (OUTLIER) cc_final: 0.8042 (t) REVERT: J 235 SER cc_start: 0.8846 (t) cc_final: 0.8582 (p) REVERT: J 246 GLU cc_start: 0.6675 (tt0) cc_final: 0.6372 (tt0) REVERT: J 268 LEU cc_start: 0.8813 (tp) cc_final: 0.8550 (tt) REVERT: K 91 VAL cc_start: 0.8304 (t) cc_final: 0.7994 (m) REVERT: K 121 THR cc_start: 0.7298 (t) cc_final: 0.6825 (t) REVERT: K 145 GLU cc_start: 0.7354 (mt-10) cc_final: 0.7122 (mt-10) REVERT: K 164 LEU cc_start: 0.7717 (mt) cc_final: 0.7424 (mt) REVERT: K 220 VAL cc_start: 0.5870 (OUTLIER) cc_final: 0.5624 (t) REVERT: X 35 LEU cc_start: 0.8484 (pt) cc_final: 0.8070 (pp) REVERT: Y 13 LEU cc_start: 0.8212 (mm) cc_final: 0.7921 (mm) REVERT: Y 25 PHE cc_start: 0.7999 (t80) cc_final: 0.7507 (t80) outliers start: 12 outliers final: 7 residues processed: 1513 average time/residue: 0.4628 time to fit residues: 1031.5804 Evaluate side-chains 1135 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 1126 time to evaluate : 3.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 116 ARG Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain I residue 220 VAL Chi-restraints excluded: chain J residue 117 VAL Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain K residue 220 VAL Chi-restraints excluded: chain K residue 224 LEU Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 270 optimal weight: 1.9990 chunk 242 optimal weight: 1.9990 chunk 134 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 163 optimal weight: 1.9990 chunk 129 optimal weight: 0.7980 chunk 250 optimal weight: 0.9990 chunk 97 optimal weight: 0.9980 chunk 152 optimal weight: 2.9990 chunk 186 optimal weight: 1.9990 chunk 290 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 98 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 43 HIS f 577 GLN G 38 GLN G 98 GLN I 206 ASN J 38 GLN J 80 GLN J 185 GLN K 38 GLN X 34 HIS X 57 HIS X 94 HIS Y 137 GLN Y 165 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.122682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.103505 restraints weight = 56311.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.106565 restraints weight = 25307.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.108444 restraints weight = 14015.392| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.4010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 28617 Z= 0.165 Angle : 0.713 11.124 38797 Z= 0.386 Chirality : 0.046 0.238 4282 Planarity : 0.006 0.099 4690 Dihedral : 16.046 154.746 4713 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.75 % Allowed : 16.60 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.22 (0.15), residues: 3239 helix: 1.11 (0.12), residues: 1826 sheet: 2.54 (0.32), residues: 253 loop : 0.06 (0.18), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP X 114 HIS 0.007 0.001 HIS X 57 PHE 0.025 0.002 PHE F 125 TYR 0.017 0.001 TYR B 112 ARG 0.009 0.001 ARG B 85 Details of bonding type rmsd hydrogen bonds : bond 0.05274 ( 1345) hydrogen bonds : angle 4.82138 ( 3781) covalent geometry : bond 0.00348 (28609) covalent geometry : angle 0.71316 (38797) Misc. bond : bond 0.00182 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1310 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1203 time to evaluate : 3.154 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8124 (m-30) cc_final: 0.7880 (m-30) REVERT: A 144 ASP cc_start: 0.7641 (m-30) cc_final: 0.7396 (m-30) REVERT: A 188 GLU cc_start: 0.8092 (mm-30) cc_final: 0.7831 (mm-30) REVERT: A 229 MET cc_start: 0.8895 (mtt) cc_final: 0.8672 (mtm) REVERT: A 247 ILE cc_start: 0.7550 (mm) cc_final: 0.7107 (mm) REVERT: a 573 TRP cc_start: 0.8020 (m-90) cc_final: 0.7504 (m-10) REVERT: B 62 SER cc_start: 0.7442 (p) cc_final: 0.6590 (p) REVERT: B 73 TYR cc_start: 0.8880 (t80) cc_final: 0.8427 (t80) REVERT: B 110 THR cc_start: 0.8717 (m) cc_final: 0.8473 (m) REVERT: B 139 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7366 (mm-30) REVERT: B 183 ASP cc_start: 0.7407 (t0) cc_final: 0.7082 (t0) REVERT: B 270 GLU cc_start: 0.7994 (tm-30) cc_final: 0.7693 (tm-30) REVERT: B 275 TYR cc_start: 0.6240 (m-80) cc_final: 0.5701 (m-80) REVERT: C 24 GLU cc_start: 0.8503 (mm-30) cc_final: 0.7988 (mm-30) REVERT: C 40 LYS cc_start: 0.8496 (tttt) cc_final: 0.7977 (ttpt) REVERT: C 111 GLU cc_start: 0.7481 (tm-30) cc_final: 0.6883 (tm-30) REVERT: C 112 TYR cc_start: 0.8822 (t80) cc_final: 0.8492 (t80) REVERT: C 136 CYS cc_start: 0.7221 (t) cc_final: 0.6720 (t) REVERT: C 183 ASP cc_start: 0.7496 (t0) cc_final: 0.7208 (t0) REVERT: C 204 PHE cc_start: 0.7680 (t80) cc_final: 0.7335 (t80) REVERT: C 206 ASN cc_start: 0.8701 (m-40) cc_final: 0.8463 (m110) REVERT: C 230 LEU cc_start: 0.8547 (mt) cc_final: 0.8319 (mp) REVERT: C 260 LEU cc_start: 0.7640 (mm) cc_final: 0.7369 (mp) REVERT: c 575 TYR cc_start: 0.8500 (t80) cc_final: 0.7869 (t80) REVERT: D 25 ILE cc_start: 0.7666 (mm) cc_final: 0.7333 (mm) REVERT: D 61 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7432 (mt-10) REVERT: D 66 LYS cc_start: 0.8631 (mtmm) cc_final: 0.8420 (mtmt) REVERT: D 73 TYR cc_start: 0.8908 (t80) cc_final: 0.8700 (t80) REVERT: D 89 VAL cc_start: 0.8725 (t) cc_final: 0.8384 (m) REVERT: D 111 GLU cc_start: 0.7739 (mt-10) cc_final: 0.7462 (mt-10) REVERT: D 144 ASP cc_start: 0.8580 (t0) cc_final: 0.7944 (m-30) REVERT: D 177 ASP cc_start: 0.8428 (m-30) cc_final: 0.8189 (m-30) REVERT: D 182 ARG cc_start: 0.8095 (OUTLIER) cc_final: 0.7463 (mpp80) REVERT: D 264 ASP cc_start: 0.6915 (OUTLIER) cc_final: 0.6690 (p0) REVERT: E 89 VAL cc_start: 0.7977 (t) cc_final: 0.7602 (m) REVERT: E 92 VAL cc_start: 0.9030 (m) cc_final: 0.8766 (p) REVERT: E 159 ASP cc_start: 0.7669 (t70) cc_final: 0.7192 (t0) REVERT: E 163 ASP cc_start: 0.7139 (t70) cc_final: 0.6684 (t0) REVERT: E 186 VAL cc_start: 0.8312 (m) cc_final: 0.8052 (p) REVERT: F 34 VAL cc_start: 0.8929 (t) cc_final: 0.8641 (m) REVERT: F 49 LYS cc_start: 0.8902 (mmtt) cc_final: 0.8454 (mmmm) REVERT: F 88 THR cc_start: 0.8363 (m) cc_final: 0.7696 (t) REVERT: F 140 MET cc_start: 0.7396 (OUTLIER) cc_final: 0.7072 (ttp) REVERT: F 144 ASP cc_start: 0.8566 (t70) cc_final: 0.7719 (t70) REVERT: F 145 GLU cc_start: 0.7662 (mt-10) cc_final: 0.7294 (mt-10) REVERT: F 164 LEU cc_start: 0.8497 (mt) cc_final: 0.8145 (mp) REVERT: F 173 THR cc_start: 0.8889 (t) cc_final: 0.8646 (p) REVERT: F 187 LEU cc_start: 0.8593 (tt) cc_final: 0.8314 (tp) REVERT: F 240 TYR cc_start: 0.8031 (m-80) cc_final: 0.7807 (m-80) REVERT: G 73 TYR cc_start: 0.8851 (t80) cc_final: 0.8565 (t80) REVERT: G 108 LYS cc_start: 0.8382 (tttm) cc_final: 0.8045 (tttm) REVERT: G 116 ARG cc_start: 0.7912 (mtm180) cc_final: 0.7687 (mtp180) REVERT: G 127 ASP cc_start: 0.8081 (t70) cc_final: 0.7698 (t0) REVERT: G 238 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7717 (mt-10) REVERT: G 264 ASP cc_start: 0.7848 (p0) cc_final: 0.7571 (p0) REVERT: G 268 LEU cc_start: 0.8895 (tp) cc_final: 0.8382 (tt) REVERT: H 89 VAL cc_start: 0.8719 (t) cc_final: 0.8301 (m) REVERT: H 105 LEU cc_start: 0.8870 (tp) cc_final: 0.8663 (tp) REVERT: H 110 THR cc_start: 0.8669 (m) cc_final: 0.8281 (p) REVERT: H 188 GLU cc_start: 0.8207 (mp0) cc_final: 0.7510 (mp0) REVERT: H 225 LYS cc_start: 0.7379 (ptmm) cc_final: 0.7121 (tttm) REVERT: H 245 ASP cc_start: 0.8324 (t0) cc_final: 0.7936 (t0) REVERT: H 247 ILE cc_start: 0.8688 (mm) cc_final: 0.8483 (mm) REVERT: H 269 GLN cc_start: 0.8345 (mt0) cc_final: 0.7995 (mt0) REVERT: I 25 ILE cc_start: 0.8302 (mm) cc_final: 0.7901 (mm) REVERT: I 33 ILE cc_start: 0.9105 (mt) cc_final: 0.8877 (mm) REVERT: I 55 SER cc_start: 0.8874 (p) cc_final: 0.8490 (p) REVERT: I 64 THR cc_start: 0.8144 (p) cc_final: 0.7878 (p) REVERT: I 115 TYR cc_start: 0.8688 (t80) cc_final: 0.8337 (t80) REVERT: I 144 ASP cc_start: 0.8590 (t0) cc_final: 0.8307 (t70) REVERT: I 231 ARG cc_start: 0.8072 (ttm170) cc_final: 0.7813 (ttm-80) REVERT: I 245 ASP cc_start: 0.8167 (t70) cc_final: 0.7785 (t0) REVERT: I 271 VAL cc_start: 0.8752 (t) cc_final: 0.8515 (p) REVERT: J 28 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.7815 (mm) REVERT: J 29 LYS cc_start: 0.8675 (ttpt) cc_final: 0.8264 (ttpp) REVERT: J 111 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7077 (mt-10) REVERT: J 162 GLU cc_start: 0.6453 (mt-10) cc_final: 0.6230 (mt-10) REVERT: J 229 MET cc_start: 0.6502 (mmt) cc_final: 0.6273 (mmt) REVERT: J 246 GLU cc_start: 0.7580 (tt0) cc_final: 0.7305 (tt0) REVERT: J 271 VAL cc_start: 0.7987 (t) cc_final: 0.7711 (p) REVERT: K 73 TYR cc_start: 0.8774 (t80) cc_final: 0.8537 (t80) REVERT: K 164 LEU cc_start: 0.8049 (mt) cc_final: 0.7798 (mt) REVERT: K 181 LYS cc_start: 0.8373 (OUTLIER) cc_final: 0.8133 (mptt) REVERT: K 215 VAL cc_start: 0.8705 (t) cc_final: 0.8300 (m) REVERT: K 269 GLN cc_start: 0.8906 (tp40) cc_final: 0.8132 (tp40) REVERT: X 11 LEU cc_start: 0.8574 (pp) cc_final: 0.8368 (pp) REVERT: X 35 LEU cc_start: 0.8342 (pt) cc_final: 0.8042 (pp) REVERT: X 80 ARG cc_start: 0.7908 (tpt170) cc_final: 0.7506 (tpm170) REVERT: X 142 MET cc_start: 0.7447 (mmt) cc_final: 0.6961 (mmt) REVERT: Y 10 TRP cc_start: 0.8986 (p-90) cc_final: 0.8718 (p-90) REVERT: Y 22 LEU cc_start: 0.8084 (tt) cc_final: 0.7685 (tp) REVERT: Y 29 PHE cc_start: 0.8865 (t80) cc_final: 0.8611 (t80) REVERT: Y 40 LEU cc_start: 0.8535 (tp) cc_final: 0.8261 (tp) REVERT: Y 84 MET cc_start: 0.7850 (mtt) cc_final: 0.7504 (mtt) REVERT: Y 95 GLU cc_start: 0.7911 (OUTLIER) cc_final: 0.7697 (tp30) REVERT: Y 104 TYR cc_start: 0.6767 (m-10) cc_final: 0.6523 (m-10) REVERT: Y 137 GLN cc_start: 0.7482 (mm-40) cc_final: 0.7042 (mp10) REVERT: Y 156 MET cc_start: 0.6710 (mtm) cc_final: 0.6330 (mtm) REVERT: Y 164 LEU cc_start: 0.9102 (mm) cc_final: 0.8812 (mm) outliers start: 107 outliers final: 62 residues processed: 1237 average time/residue: 0.4425 time to fit residues: 844.7434 Evaluate side-chains 1138 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 1070 time to evaluate : 3.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 227 LYS Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain B residue 68 VAL Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain D residue 49 LYS Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 264 ASP Chi-restraints excluded: chain d residue 581 GLU Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 100 CYS Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 136 CYS Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 143 ILE Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 573 TRP Chi-restraints excluded: chain G residue 55 SER Chi-restraints excluded: chain G residue 163 ASP Chi-restraints excluded: chain G residue 199 LEU Chi-restraints excluded: chain G residue 211 TRP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 235 SER Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 28 LEU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 117 VAL Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 81 GLN Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 100 CYS Chi-restraints excluded: chain J residue 163 ASP Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 173 THR Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 95 GLU Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 151 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 142 optimal weight: 5.9990 chunk 316 optimal weight: 4.9990 chunk 119 optimal weight: 3.9990 chunk 319 optimal weight: 3.9990 chunk 311 optimal weight: 5.9990 chunk 284 optimal weight: 5.9990 chunk 304 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 42 optimal weight: 0.4980 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 185 GLN ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN D 80 GLN ** E 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 77 HIS f 577 GLN G 38 GLN H 185 GLN I 80 GLN I 213 GLN J 38 GLN J 185 GLN K 38 GLN K 98 GLN X 125 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.113167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.094640 restraints weight = 56061.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.097608 restraints weight = 24557.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.099448 restraints weight = 13435.435| |-----------------------------------------------------------------------------| r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.5192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.120 28617 Z= 0.266 Angle : 0.725 9.907 38797 Z= 0.394 Chirality : 0.048 0.326 4282 Planarity : 0.006 0.094 4690 Dihedral : 16.190 153.727 4703 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.53 % Allowed : 19.23 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.15), residues: 3239 helix: 1.04 (0.12), residues: 1861 sheet: 2.28 (0.30), residues: 253 loop : -0.27 (0.19), residues: 1125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP Y 114 HIS 0.011 0.002 HIS E 77 PHE 0.021 0.002 PHE I 204 TYR 0.020 0.002 TYR I 275 ARG 0.010 0.001 ARG H 53 Details of bonding type rmsd hydrogen bonds : bond 0.06698 ( 1345) hydrogen bonds : angle 4.83330 ( 3781) covalent geometry : bond 0.00595 (28609) covalent geometry : angle 0.72473 (38797) Misc. bond : bond 0.00348 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1307 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 158 poor density : 1149 time to evaluate : 3.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8066 (m-30) cc_final: 0.7747 (m-30) REVERT: A 144 ASP cc_start: 0.7863 (m-30) cc_final: 0.7482 (m-30) REVERT: A 159 ASP cc_start: 0.8003 (t0) cc_final: 0.7786 (t0) REVERT: A 163 ASP cc_start: 0.7645 (m-30) cc_final: 0.7417 (m-30) REVERT: A 246 GLU cc_start: 0.6882 (tp30) cc_final: 0.5256 (tm-30) REVERT: A 250 GLU cc_start: 0.8267 (tp30) cc_final: 0.7502 (pt0) REVERT: A 254 ARG cc_start: 0.6588 (mmm-85) cc_final: 0.6231 (mmm-85) REVERT: a 573 TRP cc_start: 0.8177 (m-90) cc_final: 0.7335 (m-10) REVERT: B 62 SER cc_start: 0.7490 (p) cc_final: 0.7151 (p) REVERT: B 73 TYR cc_start: 0.9034 (t80) cc_final: 0.8828 (t80) REVERT: B 183 ASP cc_start: 0.7666 (t0) cc_final: 0.7431 (t0) REVERT: B 269 GLN cc_start: 0.7853 (mt0) cc_final: 0.7574 (mt0) REVERT: B 270 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7608 (tm-30) REVERT: C 24 GLU cc_start: 0.8508 (mm-30) cc_final: 0.7965 (mm-30) REVERT: C 40 LYS cc_start: 0.8745 (tttt) cc_final: 0.8222 (ttpt) REVERT: C 111 GLU cc_start: 0.7646 (tm-30) cc_final: 0.7426 (tm-30) REVERT: C 129 THR cc_start: 0.8687 (t) cc_final: 0.8446 (m) REVERT: C 136 CYS cc_start: 0.7336 (t) cc_final: 0.6975 (t) REVERT: C 183 ASP cc_start: 0.7626 (t0) cc_final: 0.7316 (t0) REVERT: C 225 LYS cc_start: 0.8852 (pttt) cc_final: 0.8316 (ptmm) REVERT: C 230 LEU cc_start: 0.8706 (mt) cc_final: 0.8452 (mp) REVERT: C 238 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7926 (mt-10) REVERT: C 260 LEU cc_start: 0.8071 (mm) cc_final: 0.7834 (mp) REVERT: c 575 TYR cc_start: 0.8602 (t80) cc_final: 0.8372 (t80) REVERT: D 25 ILE cc_start: 0.7847 (mm) cc_final: 0.7541 (mm) REVERT: D 53 ARG cc_start: 0.8485 (mmt-90) cc_final: 0.8199 (mmt-90) REVERT: D 73 TYR cc_start: 0.9010 (t80) cc_final: 0.8801 (t80) REVERT: D 89 VAL cc_start: 0.8916 (t) cc_final: 0.8585 (m) REVERT: D 115 TYR cc_start: 0.8749 (m-10) cc_final: 0.8454 (m-80) REVERT: D 144 ASP cc_start: 0.8608 (t0) cc_final: 0.8020 (m-30) REVERT: D 182 ARG cc_start: 0.8481 (OUTLIER) cc_final: 0.7986 (mpp80) REVERT: D 229 MET cc_start: 0.8146 (mmm) cc_final: 0.7829 (mmm) REVERT: D 230 LEU cc_start: 0.8394 (tp) cc_final: 0.8131 (tp) REVERT: E 39 VAL cc_start: 0.8941 (t) cc_final: 0.8728 (p) REVERT: E 46 LEU cc_start: 0.8600 (mt) cc_final: 0.8128 (mp) REVERT: E 85 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7440 (mpp80) REVERT: E 89 VAL cc_start: 0.8664 (t) cc_final: 0.8236 (m) REVERT: E 107 LYS cc_start: 0.8979 (tttt) cc_final: 0.8474 (ttmt) REVERT: E 159 ASP cc_start: 0.7806 (t70) cc_final: 0.7475 (t0) REVERT: E 163 ASP cc_start: 0.7758 (t70) cc_final: 0.7547 (t70) REVERT: E 164 LEU cc_start: 0.8559 (mt) cc_final: 0.8154 (mm) REVERT: E 177 ASP cc_start: 0.8294 (m-30) cc_final: 0.7916 (m-30) REVERT: E 186 VAL cc_start: 0.9009 (m) cc_final: 0.8750 (p) REVERT: E 203 ASP cc_start: 0.7460 (m-30) cc_final: 0.7237 (m-30) REVERT: E 204 PHE cc_start: 0.8518 (t80) cc_final: 0.8153 (t80) REVERT: E 255 SER cc_start: 0.7796 (m) cc_final: 0.7538 (p) REVERT: F 34 VAL cc_start: 0.9025 (t) cc_final: 0.8729 (m) REVERT: F 41 THR cc_start: 0.8899 (m) cc_final: 0.8533 (p) REVERT: F 49 LYS cc_start: 0.8992 (mmtt) cc_final: 0.8790 (mmmt) REVERT: F 88 THR cc_start: 0.8549 (m) cc_final: 0.8024 (t) REVERT: F 92 VAL cc_start: 0.8261 (t) cc_final: 0.8050 (p) REVERT: F 140 MET cc_start: 0.8060 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: F 145 GLU cc_start: 0.7898 (mt-10) cc_final: 0.7405 (mt-10) REVERT: F 164 LEU cc_start: 0.8482 (mt) cc_final: 0.8231 (mp) REVERT: F 187 LEU cc_start: 0.9032 (tt) cc_final: 0.8832 (tp) REVERT: F 188 GLU cc_start: 0.8081 (mm-30) cc_final: 0.7831 (mm-30) REVERT: F 275 TYR cc_start: 0.5370 (m-80) cc_final: 0.4160 (m-80) REVERT: f 578 LEU cc_start: 0.7587 (mt) cc_final: 0.6595 (mt) REVERT: G 49 LYS cc_start: 0.9106 (mmtt) cc_final: 0.8581 (mmmm) REVERT: G 54 LYS cc_start: 0.8931 (mtmt) cc_final: 0.8682 (mtmt) REVERT: G 92 VAL cc_start: 0.9192 (t) cc_final: 0.8950 (p) REVERT: G 93 TYR cc_start: 0.9269 (t80) cc_final: 0.9059 (t80) REVERT: G 108 LYS cc_start: 0.8512 (tttm) cc_final: 0.8234 (tttm) REVERT: G 129 THR cc_start: 0.8845 (m) cc_final: 0.8592 (p) REVERT: G 183 ASP cc_start: 0.7779 (t0) cc_final: 0.7551 (t0) REVERT: G 265 LYS cc_start: 0.7760 (OUTLIER) cc_final: 0.7464 (tttp) REVERT: G 268 LEU cc_start: 0.8828 (tp) cc_final: 0.8420 (tt) REVERT: G 274 GLU cc_start: 0.8182 (mt-10) cc_final: 0.7842 (mt-10) REVERT: H 89 VAL cc_start: 0.8992 (t) cc_final: 0.8629 (m) REVERT: H 215 VAL cc_start: 0.8539 (t) cc_final: 0.8329 (m) REVERT: H 269 GLN cc_start: 0.8084 (mt0) cc_final: 0.7691 (mt0) REVERT: I 33 ILE cc_start: 0.9204 (mt) cc_final: 0.8956 (mm) REVERT: I 42 LEU cc_start: 0.8985 (tp) cc_final: 0.8775 (tp) REVERT: I 46 LEU cc_start: 0.8977 (OUTLIER) cc_final: 0.8585 (mp) REVERT: I 54 LYS cc_start: 0.8721 (OUTLIER) cc_final: 0.8284 (mtpp) REVERT: I 55 SER cc_start: 0.9031 (p) cc_final: 0.8729 (p) REVERT: I 114 LYS cc_start: 0.8825 (mtpp) cc_final: 0.8478 (mtpp) REVERT: I 128 ARG cc_start: 0.8695 (ttm170) cc_final: 0.8208 (mtp180) REVERT: I 139 GLU cc_start: 0.7729 (mt-10) cc_final: 0.7404 (mt-10) REVERT: I 159 ASP cc_start: 0.7959 (OUTLIER) cc_final: 0.7754 (m-30) REVERT: I 204 PHE cc_start: 0.8645 (t80) cc_final: 0.8417 (t80) REVERT: I 230 LEU cc_start: 0.8644 (OUTLIER) cc_final: 0.8329 (mm) REVERT: I 268 LEU cc_start: 0.9063 (tp) cc_final: 0.8836 (tp) REVERT: J 28 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8175 (mm) REVERT: J 29 LYS cc_start: 0.8716 (ttpt) cc_final: 0.8370 (ttmm) REVERT: J 111 GLU cc_start: 0.7493 (mt-10) cc_final: 0.7112 (mt-10) REVERT: J 116 ARG cc_start: 0.6404 (ptp-170) cc_final: 0.6165 (ptp-170) REVERT: J 180 ILE cc_start: 0.8653 (mt) cc_final: 0.8405 (mm) REVERT: J 183 ASP cc_start: 0.7897 (t0) cc_final: 0.7649 (t0) REVERT: J 204 PHE cc_start: 0.8510 (t80) cc_final: 0.8303 (t80) REVERT: J 234 THR cc_start: 0.8391 (t) cc_final: 0.7978 (p) REVERT: J 240 TYR cc_start: 0.8898 (m-80) cc_final: 0.8684 (m-80) REVERT: J 246 GLU cc_start: 0.7472 (tt0) cc_final: 0.7163 (tt0) REVERT: j 581 GLU cc_start: 0.7964 (tp30) cc_final: 0.7764 (tp30) REVERT: K 91 VAL cc_start: 0.8852 (t) cc_final: 0.8576 (m) REVERT: K 123 SER cc_start: 0.7487 (p) cc_final: 0.7242 (t) REVERT: K 124 ASP cc_start: 0.7665 (m-30) cc_final: 0.7417 (m-30) REVERT: K 145 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7592 (mt-10) REVERT: K 164 LEU cc_start: 0.8485 (mt) cc_final: 0.8179 (mt) REVERT: K 181 LYS cc_start: 0.8388 (OUTLIER) cc_final: 0.8170 (mptt) REVERT: K 215 VAL cc_start: 0.8801 (t) cc_final: 0.8375 (m) REVERT: K 245 ASP cc_start: 0.8717 (t70) cc_final: 0.8480 (t70) REVERT: K 269 GLN cc_start: 0.9012 (tp40) cc_final: 0.8424 (tp40) REVERT: K 270 GLU cc_start: 0.7756 (tm-30) cc_final: 0.7454 (tm-30) REVERT: K 271 VAL cc_start: 0.8940 (t) cc_final: 0.8485 (p) REVERT: X 10 TRP cc_start: 0.8176 (p-90) cc_final: 0.7475 (p-90) REVERT: X 11 LEU cc_start: 0.8663 (pp) cc_final: 0.8450 (pp) REVERT: X 79 GLN cc_start: 0.8216 (mp10) cc_final: 0.7982 (pm20) REVERT: X 80 ARG cc_start: 0.7823 (tpt170) cc_final: 0.7398 (tpm170) REVERT: X 153 ARG cc_start: 0.6607 (mmm160) cc_final: 0.6366 (mmm160) REVERT: Y 22 LEU cc_start: 0.8357 (tt) cc_final: 0.8023 (tp) REVERT: Y 64 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7996 (mm-40) REVERT: Y 84 MET cc_start: 0.7875 (mtt) cc_final: 0.7592 (mtt) REVERT: Y 137 GLN cc_start: 0.7669 (mm-40) cc_final: 0.7061 (mp10) REVERT: Y 142 MET cc_start: 0.6868 (tpp) cc_final: 0.6334 (tpp) REVERT: Y 146 TRP cc_start: 0.8438 (m-10) cc_final: 0.8183 (m-10) outliers start: 158 outliers final: 100 residues processed: 1216 average time/residue: 0.4378 time to fit residues: 819.6215 Evaluate side-chains 1180 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 1069 time to evaluate : 2.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 142 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 257 SER Chi-restraints excluded: chain A residue 262 LYS Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 34 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 160 ILE Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 136 CYS Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 85 ARG Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 173 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain E residue 256 LEU Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 163 ASP Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain f residue 573 TRP Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 166 ILE Chi-restraints excluded: chain G residue 212 GLU Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 265 LYS Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 226 SER Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 51 LYS Chi-restraints excluded: chain I residue 54 LYS Chi-restraints excluded: chain I residue 68 VAL Chi-restraints excluded: chain I residue 124 ASP Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 166 ILE Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 215 VAL Chi-restraints excluded: chain I residue 222 SER Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 20 TRP Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 153 THR Chi-restraints excluded: chain K residue 163 ASP Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 181 LYS Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 213 GLN Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain k residue 572 VAL Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 36 SER Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 64 GLN Chi-restraints excluded: chain Y residue 154 CYS Chi-restraints excluded: chain Y residue 158 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 302 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 194 optimal weight: 0.4980 chunk 299 optimal weight: 7.9990 chunk 136 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 269 GLN B 81 GLN C 38 GLN C 206 ASN D 81 GLN D 98 GLN E 213 GLN ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN J 185 GLN K 38 GLN Y 34 HIS ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.113391 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.095046 restraints weight = 56430.231| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.098020 restraints weight = 24396.035| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.099855 restraints weight = 13294.256| |-----------------------------------------------------------------------------| r_work (final): 0.3362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.5678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 28617 Z= 0.194 Angle : 0.661 15.955 38797 Z= 0.355 Chirality : 0.044 0.261 4282 Planarity : 0.007 0.281 4690 Dihedral : 15.939 151.348 4702 Min Nonbonded Distance : 1.838 Molprobity Statistics. All-atom Clashscore : 7.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 5.11 % Allowed : 22.00 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.15), residues: 3239 helix: 1.25 (0.12), residues: 1849 sheet: 2.15 (0.30), residues: 253 loop : -0.28 (0.19), residues: 1137 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP Y 114 HIS 0.007 0.001 HIS E 77 PHE 0.029 0.001 PHE B 204 TYR 0.015 0.002 TYR G 115 ARG 0.037 0.001 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.05487 ( 1345) hydrogen bonds : angle 4.67302 ( 3781) covalent geometry : bond 0.00431 (28609) covalent geometry : angle 0.66059 (38797) Misc. bond : bond 0.00499 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1268 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 146 poor density : 1122 time to evaluate : 2.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 124 ASP cc_start: 0.8044 (m-30) cc_final: 0.7740 (m-30) REVERT: A 144 ASP cc_start: 0.7954 (m-30) cc_final: 0.7624 (m-30) REVERT: A 163 ASP cc_start: 0.7614 (m-30) cc_final: 0.7352 (m-30) REVERT: A 229 MET cc_start: 0.8868 (mtt) cc_final: 0.8603 (mtm) REVERT: A 246 GLU cc_start: 0.6898 (tp30) cc_final: 0.6208 (tm-30) REVERT: a 573 TRP cc_start: 0.8219 (m-90) cc_final: 0.7242 (m-10) REVERT: B 66 LYS cc_start: 0.8117 (OUTLIER) cc_final: 0.7811 (pttp) REVERT: B 73 TYR cc_start: 0.9042 (t80) cc_final: 0.8834 (t80) REVERT: B 183 ASP cc_start: 0.7656 (t0) cc_final: 0.7378 (t0) REVERT: B 269 GLN cc_start: 0.7862 (mt0) cc_final: 0.7599 (mt0) REVERT: B 270 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7490 (tm-30) REVERT: B 273 LYS cc_start: 0.8850 (tppp) cc_final: 0.8630 (ttmm) REVERT: C 24 GLU cc_start: 0.8525 (mm-30) cc_final: 0.7921 (mm-30) REVERT: C 40 LYS cc_start: 0.8761 (tttt) cc_final: 0.8213 (ttpt) REVERT: C 78 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7954 (mmmt) REVERT: C 111 GLU cc_start: 0.7613 (tm-30) cc_final: 0.7267 (tm-30) REVERT: C 129 THR cc_start: 0.8609 (OUTLIER) cc_final: 0.8372 (m) REVERT: C 136 CYS cc_start: 0.7329 (t) cc_final: 0.7058 (t) REVERT: C 183 ASP cc_start: 0.7546 (t0) cc_final: 0.7228 (t0) REVERT: C 225 LYS cc_start: 0.8789 (pttt) cc_final: 0.8426 (pttm) REVERT: C 230 LEU cc_start: 0.8638 (mt) cc_final: 0.8356 (mp) REVERT: C 238 GLU cc_start: 0.8296 (mt-10) cc_final: 0.7932 (mt-10) REVERT: C 260 LEU cc_start: 0.8135 (mm) cc_final: 0.7919 (mp) REVERT: C 275 TYR cc_start: 0.8487 (m-80) cc_final: 0.8072 (m-10) REVERT: D 25 ILE cc_start: 0.7698 (mm) cc_final: 0.7344 (mm) REVERT: D 53 ARG cc_start: 0.8266 (mmt-90) cc_final: 0.7451 (mmt-90) REVERT: D 66 LYS cc_start: 0.8917 (mtmt) cc_final: 0.8631 (mttp) REVERT: D 89 VAL cc_start: 0.8916 (t) cc_final: 0.8631 (m) REVERT: D 139 GLU cc_start: 0.7845 (mm-30) cc_final: 0.7370 (mm-30) REVERT: D 144 ASP cc_start: 0.8575 (t0) cc_final: 0.8234 (m-30) REVERT: D 145 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7932 (mt-10) REVERT: D 182 ARG cc_start: 0.8460 (OUTLIER) cc_final: 0.7940 (mpp80) REVERT: D 229 MET cc_start: 0.8021 (mmm) cc_final: 0.7720 (mmm) REVERT: D 238 GLU cc_start: 0.7991 (mm-30) cc_final: 0.7777 (mp0) REVERT: D 250 GLU cc_start: 0.7969 (tp30) cc_final: 0.7596 (tp30) REVERT: E 49 LYS cc_start: 0.8370 (mmtt) cc_final: 0.8022 (mmtm) REVERT: E 87 PRO cc_start: 0.8738 (Cg_exo) cc_final: 0.7945 (Cg_endo) REVERT: E 89 VAL cc_start: 0.8695 (t) cc_final: 0.8321 (m) REVERT: E 152 GLU cc_start: 0.7827 (mp0) cc_final: 0.7602 (mp0) REVERT: E 163 ASP cc_start: 0.7815 (t70) cc_final: 0.7451 (t70) REVERT: E 164 LEU cc_start: 0.8598 (mt) cc_final: 0.8154 (mm) REVERT: E 177 ASP cc_start: 0.8277 (m-30) cc_final: 0.7933 (m-30) REVERT: E 186 VAL cc_start: 0.9003 (m) cc_final: 0.8740 (p) REVERT: E 189 ARG cc_start: 0.7482 (mpt-90) cc_final: 0.7188 (mtt90) REVERT: E 203 ASP cc_start: 0.7492 (m-30) cc_final: 0.7245 (m-30) REVERT: E 250 GLU cc_start: 0.8293 (mm-30) cc_final: 0.8039 (mm-30) REVERT: F 41 THR cc_start: 0.8923 (m) cc_final: 0.8542 (p) REVERT: F 66 LYS cc_start: 0.8870 (mtmm) cc_final: 0.7871 (mtmm) REVERT: F 88 THR cc_start: 0.8472 (m) cc_final: 0.7983 (t) REVERT: F 111 GLU cc_start: 0.7809 (mt-10) cc_final: 0.7330 (mt-10) REVERT: F 140 MET cc_start: 0.8049 (OUTLIER) cc_final: 0.7715 (ttp) REVERT: F 144 ASP cc_start: 0.8591 (t70) cc_final: 0.8177 (t0) REVERT: F 145 GLU cc_start: 0.7913 (mt-10) cc_final: 0.7006 (mt-10) REVERT: F 148 ARG cc_start: 0.8567 (mtt180) cc_final: 0.8282 (mtt180) REVERT: F 184 GLU cc_start: 0.6995 (tt0) cc_final: 0.6581 (tt0) REVERT: F 188 GLU cc_start: 0.7987 (mm-30) cc_final: 0.7773 (mm-30) REVERT: F 246 GLU cc_start: 0.7679 (tt0) cc_final: 0.7358 (tt0) REVERT: F 274 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7567 (mt-10) REVERT: f 579 ARG cc_start: 0.6506 (ttm170) cc_final: 0.6291 (ttm-80) REVERT: G 38 GLN cc_start: 0.8125 (mm-40) cc_final: 0.7584 (mt0) REVERT: G 49 LYS cc_start: 0.9124 (mmtt) cc_final: 0.8604 (mmmm) REVERT: G 92 VAL cc_start: 0.9150 (t) cc_final: 0.8864 (p) REVERT: G 108 LYS cc_start: 0.8481 (tttm) cc_final: 0.8207 (tttm) REVERT: G 115 TYR cc_start: 0.8480 (t80) cc_final: 0.8056 (t80) REVERT: G 129 THR cc_start: 0.8931 (m) cc_final: 0.8573 (p) REVERT: G 183 ASP cc_start: 0.7731 (t0) cc_final: 0.7436 (t0) REVERT: G 250 GLU cc_start: 0.8137 (OUTLIER) cc_final: 0.7850 (mt-10) REVERT: G 268 LEU cc_start: 0.8804 (tp) cc_final: 0.8388 (tt) REVERT: G 274 GLU cc_start: 0.8157 (mt-10) cc_final: 0.7833 (mt-10) REVERT: H 66 LYS cc_start: 0.8951 (mtmm) cc_final: 0.8714 (mttm) REVERT: H 89 VAL cc_start: 0.9049 (t) cc_final: 0.8725 (m) REVERT: H 245 ASP cc_start: 0.8374 (t0) cc_final: 0.7883 (t0) REVERT: H 269 GLN cc_start: 0.8136 (mt0) cc_final: 0.7676 (mt0) REVERT: I 24 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7795 (mm-30) REVERT: I 42 LEU cc_start: 0.8939 (tp) cc_final: 0.8712 (tp) REVERT: I 46 LEU cc_start: 0.9008 (OUTLIER) cc_final: 0.8692 (mp) REVERT: I 114 LYS cc_start: 0.8882 (mtpp) cc_final: 0.8502 (mtpp) REVERT: I 128 ARG cc_start: 0.8702 (ttm170) cc_final: 0.8180 (mtp180) REVERT: I 139 GLU cc_start: 0.7747 (mt-10) cc_final: 0.7416 (mt-10) REVERT: I 229 MET cc_start: 0.7865 (mmt) cc_final: 0.7544 (mmp) REVERT: I 230 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8373 (mm) REVERT: I 245 ASP cc_start: 0.8405 (t70) cc_final: 0.8162 (t0) REVERT: I 268 LEU cc_start: 0.8992 (tp) cc_final: 0.8672 (tp) REVERT: J 28 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8183 (mm) REVERT: J 29 LYS cc_start: 0.8653 (ttpt) cc_final: 0.8180 (ttpt) REVERT: J 91 VAL cc_start: 0.9142 (t) cc_final: 0.8816 (p) REVERT: J 162 GLU cc_start: 0.6562 (mt-10) cc_final: 0.6296 (mt-10) REVERT: J 183 ASP cc_start: 0.7824 (t0) cc_final: 0.7550 (t0) REVERT: J 230 LEU cc_start: 0.8543 (OUTLIER) cc_final: 0.7882 (tp) REVERT: J 234 THR cc_start: 0.8490 (t) cc_final: 0.8056 (p) REVERT: J 246 GLU cc_start: 0.7612 (tt0) cc_final: 0.7233 (tt0) REVERT: j 581 GLU cc_start: 0.8023 (tp30) cc_final: 0.7784 (tp30) REVERT: K 91 VAL cc_start: 0.8851 (t) cc_final: 0.8615 (m) REVERT: K 123 SER cc_start: 0.7505 (p) cc_final: 0.7205 (t) REVERT: K 124 ASP cc_start: 0.7588 (m-30) cc_final: 0.7316 (m-30) REVERT: K 145 GLU cc_start: 0.7935 (mt-10) cc_final: 0.7732 (mt-10) REVERT: K 164 LEU cc_start: 0.8555 (mt) cc_final: 0.8277 (mt) REVERT: K 215 VAL cc_start: 0.8786 (t) cc_final: 0.8361 (m) REVERT: K 245 ASP cc_start: 0.8647 (t70) cc_final: 0.8398 (t70) REVERT: K 250 GLU cc_start: 0.8252 (tp30) cc_final: 0.7920 (tp30) REVERT: K 269 GLN cc_start: 0.8948 (tp40) cc_final: 0.8406 (tp-100) REVERT: K 270 GLU cc_start: 0.7897 (tm-30) cc_final: 0.7445 (tm-30) REVERT: K 271 VAL cc_start: 0.8875 (t) cc_final: 0.8392 (p) REVERT: X 10 TRP cc_start: 0.8205 (p-90) cc_final: 0.7997 (p-90) REVERT: X 11 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8349 (pp) REVERT: X 79 GLN cc_start: 0.8400 (mp10) cc_final: 0.8154 (pm20) REVERT: X 84 MET cc_start: 0.7566 (mtt) cc_final: 0.7273 (mtt) REVERT: Y 3 GLU cc_start: 0.6588 (OUTLIER) cc_final: 0.6317 (pt0) REVERT: Y 22 LEU cc_start: 0.8310 (tt) cc_final: 0.7986 (tp) REVERT: Y 35 LEU cc_start: 0.8824 (pt) cc_final: 0.8500 (pp) REVERT: Y 53 TRP cc_start: 0.9034 (m-10) cc_final: 0.8705 (m100) REVERT: Y 64 GLN cc_start: 0.8368 (mm-40) cc_final: 0.7861 (mm-40) REVERT: Y 79 GLN cc_start: 0.8653 (mp10) cc_final: 0.8415 (mp10) REVERT: Y 83 GLN cc_start: 0.8606 (mt0) cc_final: 0.8236 (mt0) REVERT: Y 137 GLN cc_start: 0.7675 (mm-40) cc_final: 0.7252 (mm-40) REVERT: Y 142 MET cc_start: 0.7035 (tpp) cc_final: 0.6809 (tpp) outliers start: 146 outliers final: 95 residues processed: 1175 average time/residue: 0.4176 time to fit residues: 753.6371 Evaluate side-chains 1185 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1079 time to evaluate : 2.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 269 GLN Chi-restraints excluded: chain A residue 270 GLU Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 215 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 180 ILE Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 199 LEU Chi-restraints excluded: chain D residue 207 THR Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 140 MET Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 221 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 241 ILE Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 238 GLU Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 21 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 124 ASP Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain G residue 263 ILE Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 180 ILE Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 227 LYS Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 181 LYS Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 226 SER Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 62 SER Chi-restraints excluded: chain J residue 129 THR Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 246 GLU Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain Y residue 3 GLU Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 320 random chunks: chunk 246 optimal weight: 2.9990 chunk 279 optimal weight: 4.9990 chunk 105 optimal weight: 4.9990 chunk 131 optimal weight: 0.0000 chunk 180 optimal weight: 5.9990 chunk 251 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 36 optimal weight: 0.5980 chunk 144 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 130 optimal weight: 0.6980 overall best weight: 1.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 38 GLN B 206 ASN C 38 GLN D 81 GLN D 98 GLN ** f 577 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 38 GLN K 38 GLN Y 34 HIS ** Y 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.113066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.094866 restraints weight = 55903.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.097816 restraints weight = 24329.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.099657 restraints weight = 13313.828| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.5992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 28617 Z= 0.177 Angle : 0.649 12.425 38797 Z= 0.347 Chirality : 0.044 0.195 4282 Planarity : 0.005 0.149 4690 Dihedral : 15.712 150.914 4700 Min Nonbonded Distance : 1.861 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.97 % Allowed : 22.98 % Favored : 72.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.15), residues: 3239 helix: 1.33 (0.12), residues: 1841 sheet: 2.15 (0.31), residues: 253 loop : -0.33 (0.19), residues: 1145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP Y 114 HIS 0.006 0.001 HIS E 77 PHE 0.019 0.001 PHE G 204 TYR 0.017 0.001 TYR A 73 ARG 0.020 0.001 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.05218 ( 1345) hydrogen bonds : angle 4.62094 ( 3781) covalent geometry : bond 0.00394 (28609) covalent geometry : angle 0.64896 (38797) Misc. bond : bond 0.00452 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6478 Ramachandran restraints generated. 3239 Oldfield, 0 Emsley, 3239 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1249 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 1107 time to evaluate : 3.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 71 ASP cc_start: 0.8459 (m-30) cc_final: 0.8233 (m-30) REVERT: A 124 ASP cc_start: 0.8050 (m-30) cc_final: 0.7768 (m-30) REVERT: A 144 ASP cc_start: 0.7957 (m-30) cc_final: 0.7586 (m-30) REVERT: A 246 GLU cc_start: 0.6798 (tp30) cc_final: 0.6239 (tm-30) REVERT: a 573 TRP cc_start: 0.8241 (m-90) cc_final: 0.7163 (m-10) REVERT: B 66 LYS cc_start: 0.8122 (OUTLIER) cc_final: 0.7819 (pttp) REVERT: B 183 ASP cc_start: 0.7666 (t0) cc_final: 0.7382 (t0) REVERT: B 250 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8036 (tt0) REVERT: B 269 GLN cc_start: 0.7880 (mt0) cc_final: 0.7606 (mt0) REVERT: B 270 GLU cc_start: 0.8046 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 24 GLU cc_start: 0.8507 (mm-30) cc_final: 0.7900 (mm-30) REVERT: C 40 LYS cc_start: 0.8758 (tttt) cc_final: 0.8205 (ttpt) REVERT: C 78 LYS cc_start: 0.8133 (mmmm) cc_final: 0.7699 (tppt) REVERT: C 111 GLU cc_start: 0.7597 (tm-30) cc_final: 0.7246 (tm-30) REVERT: C 129 THR cc_start: 0.8732 (OUTLIER) cc_final: 0.8470 (m) REVERT: C 136 CYS cc_start: 0.7260 (t) cc_final: 0.7044 (t) REVERT: C 183 ASP cc_start: 0.7543 (t0) cc_final: 0.7227 (t0) REVERT: C 217 LYS cc_start: 0.7912 (mttp) cc_final: 0.7681 (mttp) REVERT: C 225 LYS cc_start: 0.8783 (pttt) cc_final: 0.8556 (pttm) REVERT: C 260 LEU cc_start: 0.8196 (mm) cc_final: 0.7992 (mp) REVERT: C 275 TYR cc_start: 0.8529 (m-80) cc_final: 0.8077 (m-80) REVERT: D 25 ILE cc_start: 0.7710 (mm) cc_final: 0.7359 (mm) REVERT: D 53 ARG cc_start: 0.8273 (mmt-90) cc_final: 0.7509 (mmt-90) REVERT: D 61 GLU cc_start: 0.8177 (mm-30) cc_final: 0.7667 (mm-30) REVERT: D 66 LYS cc_start: 0.8945 (mtmt) cc_final: 0.8715 (mttt) REVERT: D 89 VAL cc_start: 0.8896 (t) cc_final: 0.8588 (m) REVERT: D 139 GLU cc_start: 0.7864 (mm-30) cc_final: 0.7402 (mm-30) REVERT: D 144 ASP cc_start: 0.8561 (t0) cc_final: 0.8290 (m-30) REVERT: D 145 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7937 (mt-10) REVERT: D 182 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.7973 (mpp80) REVERT: D 229 MET cc_start: 0.7994 (mmm) cc_final: 0.7746 (mmm) REVERT: D 270 GLU cc_start: 0.8254 (OUTLIER) cc_final: 0.7926 (tt0) REVERT: E 49 LYS cc_start: 0.8361 (mmtt) cc_final: 0.8033 (mmtm) REVERT: E 89 VAL cc_start: 0.8820 (t) cc_final: 0.8466 (m) REVERT: E 163 ASP cc_start: 0.7837 (t70) cc_final: 0.7470 (t70) REVERT: E 164 LEU cc_start: 0.8589 (mt) cc_final: 0.8193 (mm) REVERT: E 177 ASP cc_start: 0.8294 (m-30) cc_final: 0.7967 (m-30) REVERT: E 186 VAL cc_start: 0.9012 (m) cc_final: 0.8764 (p) REVERT: E 189 ARG cc_start: 0.7427 (mpt-90) cc_final: 0.6853 (mtt-85) REVERT: E 203 ASP cc_start: 0.7528 (m-30) cc_final: 0.7285 (m-30) REVERT: E 204 PHE cc_start: 0.8404 (t80) cc_final: 0.8188 (t80) REVERT: E 250 GLU cc_start: 0.8337 (mm-30) cc_final: 0.8054 (mm-30) REVERT: F 33 ILE cc_start: 0.8672 (mp) cc_final: 0.8429 (mm) REVERT: F 41 THR cc_start: 0.8983 (m) cc_final: 0.8611 (p) REVERT: F 66 LYS cc_start: 0.8864 (mtmm) cc_final: 0.7810 (mtmm) REVERT: F 88 THR cc_start: 0.8527 (m) cc_final: 0.8031 (t) REVERT: F 95 ARG cc_start: 0.8632 (ttp-170) cc_final: 0.7988 (ttp80) REVERT: F 111 GLU cc_start: 0.7797 (mt-10) cc_final: 0.7239 (mt-10) REVERT: F 140 MET cc_start: 0.8029 (OUTLIER) cc_final: 0.7779 (ttp) REVERT: F 144 ASP cc_start: 0.8572 (t70) cc_final: 0.8152 (t0) REVERT: F 145 GLU cc_start: 0.7920 (mt-10) cc_final: 0.6713 (mt-10) REVERT: F 148 ARG cc_start: 0.8602 (mtt180) cc_final: 0.8184 (mtt180) REVERT: F 188 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7598 (mm-30) REVERT: F 274 GLU cc_start: 0.7969 (mt-10) cc_final: 0.7638 (mt-10) REVERT: G 38 GLN cc_start: 0.8112 (mm-40) cc_final: 0.7547 (mt0) REVERT: G 92 VAL cc_start: 0.9170 (t) cc_final: 0.8866 (p) REVERT: G 108 LYS cc_start: 0.8437 (tttm) cc_final: 0.8173 (tttm) REVERT: G 115 TYR cc_start: 0.8461 (t80) cc_final: 0.8038 (t80) REVERT: G 129 THR cc_start: 0.8937 (m) cc_final: 0.8577 (p) REVERT: G 183 ASP cc_start: 0.7681 (t0) cc_final: 0.7389 (t0) REVERT: G 268 LEU cc_start: 0.8765 (tp) cc_final: 0.8343 (tt) REVERT: G 274 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7843 (mt-10) REVERT: H 66 LYS cc_start: 0.8917 (mtmm) cc_final: 0.8683 (mttm) REVERT: H 89 VAL cc_start: 0.8962 (t) cc_final: 0.8644 (m) REVERT: H 144 ASP cc_start: 0.8853 (OUTLIER) cc_final: 0.7919 (t0) REVERT: H 215 VAL cc_start: 0.8471 (t) cc_final: 0.8200 (p) REVERT: H 245 ASP cc_start: 0.8384 (t0) cc_final: 0.7724 (t0) REVERT: H 269 GLN cc_start: 0.8125 (mt0) cc_final: 0.7659 (mt0) REVERT: I 42 LEU cc_start: 0.8933 (tp) cc_final: 0.8649 (tp) REVERT: I 46 LEU cc_start: 0.9000 (OUTLIER) cc_final: 0.8689 (mp) REVERT: I 128 ARG cc_start: 0.8661 (ttm170) cc_final: 0.8230 (mtm180) REVERT: I 139 GLU cc_start: 0.7768 (mt-10) cc_final: 0.7444 (mt-10) REVERT: I 162 GLU cc_start: 0.6664 (mt-10) cc_final: 0.6392 (mp0) REVERT: I 229 MET cc_start: 0.7868 (mmt) cc_final: 0.7536 (mmp) REVERT: I 230 LEU cc_start: 0.8635 (OUTLIER) cc_final: 0.8354 (mm) REVERT: I 245 ASP cc_start: 0.8426 (t70) cc_final: 0.8106 (t0) REVERT: J 28 LEU cc_start: 0.8670 (OUTLIER) cc_final: 0.8202 (mm) REVERT: J 29 LYS cc_start: 0.8625 (ttpt) cc_final: 0.8150 (ttpt) REVERT: J 91 VAL cc_start: 0.9089 (t) cc_final: 0.8778 (p) REVERT: J 162 GLU cc_start: 0.6566 (mt-10) cc_final: 0.6300 (mt-10) REVERT: J 183 ASP cc_start: 0.7691 (t0) cc_final: 0.7459 (t0) REVERT: J 230 LEU cc_start: 0.8548 (OUTLIER) cc_final: 0.7867 (tp) REVERT: J 234 THR cc_start: 0.8467 (t) cc_final: 0.8042 (p) REVERT: J 246 GLU cc_start: 0.7628 (tt0) cc_final: 0.7321 (tt0) REVERT: J 275 TYR cc_start: 0.7389 (m-80) cc_final: 0.6604 (m-80) REVERT: j 581 GLU cc_start: 0.7995 (tp30) cc_final: 0.7715 (tp30) REVERT: K 91 VAL cc_start: 0.8847 (t) cc_final: 0.8594 (m) REVERT: K 124 ASP cc_start: 0.7602 (m-30) cc_final: 0.7318 (m-30) REVERT: K 145 GLU cc_start: 0.7937 (mt-10) cc_final: 0.7707 (mt-10) REVERT: K 164 LEU cc_start: 0.8533 (mt) cc_final: 0.8230 (mt) REVERT: K 233 LEU cc_start: 0.8468 (tp) cc_final: 0.8226 (tp) REVERT: K 245 ASP cc_start: 0.8646 (t70) cc_final: 0.8405 (t70) REVERT: K 250 GLU cc_start: 0.8158 (tp30) cc_final: 0.7726 (tp30) REVERT: K 264 ASP cc_start: 0.7933 (p0) cc_final: 0.7413 (t0) REVERT: K 269 GLN cc_start: 0.8901 (tp40) cc_final: 0.8345 (tp-100) REVERT: K 270 GLU cc_start: 0.7854 (tm-30) cc_final: 0.7512 (tm-30) REVERT: K 271 VAL cc_start: 0.8869 (t) cc_final: 0.8420 (p) REVERT: X 10 TRP cc_start: 0.8216 (p-90) cc_final: 0.8015 (p-90) REVERT: X 11 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8398 (pp) REVERT: X 80 ARG cc_start: 0.7769 (tpt170) cc_final: 0.7523 (tpm170) REVERT: Y 22 LEU cc_start: 0.8265 (tt) cc_final: 0.7961 (tp) REVERT: Y 53 TRP cc_start: 0.9063 (m-10) cc_final: 0.8495 (m-10) REVERT: Y 55 ARG cc_start: 0.7441 (mtp180) cc_final: 0.7238 (mtp180) REVERT: Y 64 GLN cc_start: 0.8266 (mm-40) cc_final: 0.7581 (mm-40) REVERT: Y 120 TRP cc_start: 0.7364 (p-90) cc_final: 0.7118 (p-90) REVERT: Y 137 GLN cc_start: 0.7725 (mm-40) cc_final: 0.7300 (mm-40) REVERT: Y 142 MET cc_start: 0.7047 (tpp) cc_final: 0.6726 (tpp) outliers start: 142 outliers final: 108 residues processed: 1163 average time/residue: 0.4269 time to fit residues: 760.6007 Evaluate side-chains 1194 residues out of total 2855 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 1074 time to evaluate : 2.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 TRP Chi-restraints excluded: chain A residue 47 ASP Chi-restraints excluded: chain A residue 58 VAL Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 136 CYS Chi-restraints excluded: chain A residue 143 ILE Chi-restraints excluded: chain A residue 153 THR Chi-restraints excluded: chain A residue 186 VAL Chi-restraints excluded: chain A residue 215 VAL Chi-restraints excluded: chain a residue 572 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 66 LYS Chi-restraints excluded: chain B residue 71 ASP Chi-restraints excluded: chain B residue 130 ILE Chi-restraints excluded: chain B residue 144 ASP Chi-restraints excluded: chain B residue 152 GLU Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 205 LYS Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 250 GLU Chi-restraints excluded: chain B residue 253 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 262 LYS Chi-restraints excluded: chain b residue 572 VAL Chi-restraints excluded: chain C residue 32 SER Chi-restraints excluded: chain C residue 62 SER Chi-restraints excluded: chain C residue 110 THR Chi-restraints excluded: chain C residue 129 THR Chi-restraints excluded: chain C residue 147 ASP Chi-restraints excluded: chain C residue 179 VAL Chi-restraints excluded: chain C residue 180 ILE Chi-restraints excluded: chain C residue 270 GLU Chi-restraints excluded: chain D residue 33 ILE Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 123 SER Chi-restraints excluded: chain D residue 160 ILE Chi-restraints excluded: chain D residue 177 ASP Chi-restraints excluded: chain D residue 179 VAL Chi-restraints excluded: chain D residue 182 ARG Chi-restraints excluded: chain D residue 215 VAL Chi-restraints excluded: chain D residue 256 LEU Chi-restraints excluded: chain D residue 270 GLU Chi-restraints excluded: chain D residue 271 VAL Chi-restraints excluded: chain E residue 32 SER Chi-restraints excluded: chain E residue 56 CYS Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 159 ASP Chi-restraints excluded: chain E residue 174 ASP Chi-restraints excluded: chain E residue 179 VAL Chi-restraints excluded: chain E residue 200 SER Chi-restraints excluded: chain E residue 232 ILE Chi-restraints excluded: chain E residue 274 GLU Chi-restraints excluded: chain e residue 572 VAL Chi-restraints excluded: chain F residue 27 ARG Chi-restraints excluded: chain F residue 55 SER Chi-restraints excluded: chain F residue 92 VAL Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 152 GLU Chi-restraints excluded: chain F residue 200 SER Chi-restraints excluded: chain F residue 241 ILE Chi-restraints excluded: chain F residue 268 LEU Chi-restraints excluded: chain G residue 28 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 222 SER Chi-restraints excluded: chain G residue 223 ASN Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 241 ILE Chi-restraints excluded: chain G residue 244 LEU Chi-restraints excluded: chain G residue 250 GLU Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 111 GLU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 119 LYS Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 136 CYS Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 220 VAL Chi-restraints excluded: chain H residue 255 SER Chi-restraints excluded: chain H residue 268 LEU Chi-restraints excluded: chain I residue 28 LEU Chi-restraints excluded: chain I residue 46 LEU Chi-restraints excluded: chain I residue 55 SER Chi-restraints excluded: chain I residue 56 CYS Chi-restraints excluded: chain I residue 159 ASP Chi-restraints excluded: chain I residue 213 GLN Chi-restraints excluded: chain I residue 230 LEU Chi-restraints excluded: chain J residue 28 LEU Chi-restraints excluded: chain J residue 31 LYS Chi-restraints excluded: chain J residue 36 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 220 VAL Chi-restraints excluded: chain J residue 225 LYS Chi-restraints excluded: chain J residue 230 LEU Chi-restraints excluded: chain J residue 233 LEU Chi-restraints excluded: chain J residue 247 ILE Chi-restraints excluded: chain J residue 255 SER Chi-restraints excluded: chain J residue 256 LEU Chi-restraints excluded: chain j residue 578 LEU Chi-restraints excluded: chain K residue 32 SER Chi-restraints excluded: chain K residue 41 THR Chi-restraints excluded: chain K residue 58 VAL Chi-restraints excluded: chain K residue 89 VAL Chi-restraints excluded: chain K residue 94 ILE Chi-restraints excluded: chain K residue 117 VAL Chi-restraints excluded: chain K residue 140 MET Chi-restraints excluded: chain K residue 180 ILE Chi-restraints excluded: chain K residue 200 SER Chi-restraints excluded: chain K residue 226 SER Chi-restraints excluded: chain K residue 244 LEU Chi-restraints excluded: chain k residue 572 VAL Chi-restraints excluded: chain X residue 7 VAL Chi-restraints excluded: chain X residue 11 LEU Chi-restraints excluded: chain X residue 14 ILE Chi-restraints excluded: chain X residue 75 GLU Chi-restraints excluded: chain Y residue 14 ILE Chi-restraints excluded: chain Y residue 43 LEU Chi-restraints excluded: chain Y residue 112 ILE Chi-restraints excluded: chain Y residue 154 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/iotbx/cli_parser.py", line 994, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6551 > 50: distance: 47 - 119: 12.099 distance: 50 - 132: 21.552 distance: 65 - 135: 17.438 distance: 98 - 100: 13.944 distance: 100 - 101: 13.965 distance: 101 - 102: 7.413 distance: 101 - 104: 15.410 distance: 102 - 103: 20.415 distance: 102 - 107: 33.160 distance: 104 - 105: 21.254 distance: 104 - 106: 15.314 distance: 107 - 108: 16.721 distance: 108 - 109: 4.767 distance: 108 - 111: 7.287 distance: 109 - 110: 11.299 distance: 109 - 116: 8.120 distance: 111 - 112: 13.679 distance: 112 - 113: 6.104 distance: 113 - 115: 4.728 distance: 116 - 117: 4.891 distance: 117 - 118: 12.851 distance: 117 - 120: 15.698 distance: 118 - 119: 18.453 distance: 118 - 124: 35.596 distance: 120 - 121: 10.419 distance: 121 - 122: 4.292 distance: 122 - 123: 3.457 distance: 124 - 125: 5.807 distance: 125 - 126: 14.757 distance: 125 - 128: 31.136 distance: 126 - 132: 29.625 distance: 128 - 129: 20.095 distance: 129 - 130: 11.572 distance: 129 - 131: 11.174 distance: 132 - 133: 26.199 distance: 133 - 134: 17.916 distance: 133 - 136: 27.498 distance: 134 - 135: 29.967 distance: 134 - 140: 23.984 distance: 136 - 137: 25.298 distance: 136 - 138: 14.866 distance: 137 - 139: 4.124 distance: 140 - 141: 38.823 distance: 141 - 142: 15.201 distance: 141 - 144: 32.917 distance: 142 - 143: 33.643 distance: 142 - 148: 40.097 distance: 144 - 145: 46.555 distance: 144 - 146: 31.964 distance: 145 - 147: 22.729 distance: 148 - 149: 9.108 distance: 149 - 150: 25.808 distance: 149 - 152: 27.535 distance: 150 - 151: 24.847 distance: 150 - 156: 23.339 distance: 152 - 153: 30.156 distance: 153 - 154: 20.416 distance: 153 - 155: 25.408 distance: 156 - 157: 39.224 distance: 157 - 158: 40.934 distance: 157 - 160: 20.877 distance: 158 - 159: 16.844 distance: 158 - 165: 44.147 distance: 159 - 178: 19.678 distance: 160 - 161: 21.017 distance: 161 - 162: 12.579 distance: 162 - 163: 9.327 distance: 162 - 164: 17.316 distance: 165 - 166: 10.974 distance: 166 - 167: 30.777 distance: 166 - 169: 20.227 distance: 167 - 168: 33.345 distance: 167 - 170: 9.319 distance: 168 - 189: 24.295 distance: 170 - 171: 6.382 distance: 171 - 172: 8.796 distance: 171 - 174: 21.368 distance: 172 - 173: 38.016 distance: 172 - 178: 18.303 distance: 174 - 175: 15.853 distance: 175 - 176: 14.567 distance: 175 - 177: 24.110