Starting phenix.real_space_refine on Mon Sep 30 09:18:37 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/09_2024/7e51_30989.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/09_2024/7e51_30989.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.23 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/09_2024/7e51_30989.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/09_2024/7e51_30989.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/09_2024/7e51_30989.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e51_30989/09_2024/7e51_30989.cif" } resolution = 3.23 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.006 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 8 5.49 5 Mg 16 5.21 5 S 56 5.16 5 C 15608 2.51 5 N 4320 2.21 5 O 5024 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 115 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 25032 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "B" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "C" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "D" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "E" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "F" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "G" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "H" Number of atoms: 3117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 423, 3117 Classifications: {'peptide': 423} Link IDs: {'PTRANS': 18, 'TRANS': 404} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 12 Unusual residues: {' MG': 2, 'PEP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 14.74, per 1000 atoms: 0.59 Number of scatterers: 25032 At special positions: 0 Unit cell: (159.43, 159.43, 72.76, 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 56 16.00 P 8 15.00 Mg 16 11.99 O 5024 8.00 N 4320 7.00 C 15608 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.53 Conformation dependent library (CDL) restraints added in 3.3 seconds 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6000 Finding SS restraints... Secondary structure from input PDB file: 136 helices and 37 sheets defined 46.5% alpha, 12.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.13 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 Processing helix chain 'A' and resid 63 through 73 Processing helix chain 'A' and resid 73 through 79 removed outlier: 3.521A pdb=" N VAL A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 108 through 124 removed outlier: 4.005A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.537A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N GLY A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 194 removed outlier: 3.755A pdb=" N SER A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LYS A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 4.059A pdb=" N ALA A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 243 through 246 Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.613A pdb=" N GLY A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.789A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.772A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.734A pdb=" N ILE A 339 " --> pdb=" O VAL A 336 " (cutoff:3.500A) Processing helix chain 'A' and resid 341 through 354 Processing helix chain 'A' and resid 371 through 380 removed outlier: 3.935A pdb=" N ASP A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 removed outlier: 4.028A pdb=" N TYR A 399 " --> pdb=" O ARG A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 413 No H-bonds generated for 'chain 'A' and resid 411 through 413' Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.502A pdb=" N GLY B 59 " --> pdb=" O ASP B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 63 through 73 Processing helix chain 'B' and resid 73 through 79 Processing helix chain 'B' and resid 85 through 98 Processing helix chain 'B' and resid 108 through 122 removed outlier: 3.952A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.670A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.647A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLY B 229 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 243 through 246 Processing helix chain 'B' and resid 262 through 277 Processing helix chain 'B' and resid 290 through 302 Processing helix chain 'B' and resid 316 through 326 removed outlier: 3.698A pdb=" N GLU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.701A pdb=" N ILE B 339 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 removed outlier: 3.528A pdb=" N THR B 345 " --> pdb=" O THR B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.940A pdb=" N ASP B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 removed outlier: 4.023A pdb=" N TYR B 399 " --> pdb=" O ARG B 395 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 413 No H-bonds generated for 'chain 'B' and resid 411 through 413' Processing helix chain 'C' and resid 56 through 61 Processing helix chain 'C' and resid 63 through 73 Processing helix chain 'C' and resid 73 through 79 removed outlier: 3.555A pdb=" N VAL C 78 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 85 through 98 removed outlier: 3.792A pdb=" N GLN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 removed outlier: 3.535A pdb=" N ILE C 110 " --> pdb=" O GLY C 106 " (cutoff:3.500A) Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 173 through 194 removed outlier: 3.606A pdb=" N SER C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.556A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.633A pdb=" N PHE C 248 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.663A pdb=" N ALA C 276 " --> pdb=" O GLY C 272 " (cutoff:3.500A) Processing helix chain 'C' and resid 290 through 302 Processing helix chain 'C' and resid 316 through 326 removed outlier: 3.886A pdb=" N GLU C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.782A pdb=" N ILE C 339 " --> pdb=" O VAL C 336 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 354 Processing helix chain 'C' and resid 371 through 380 removed outlier: 4.003A pdb=" N ASP C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 removed outlier: 3.908A pdb=" N TYR C 399 " --> pdb=" O ARG C 395 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 413 No H-bonds generated for 'chain 'C' and resid 411 through 413' Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.545A pdb=" N GLY D 59 " --> pdb=" O ASP D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 73 Processing helix chain 'D' and resid 73 through 79 Processing helix chain 'D' and resid 85 through 98 Processing helix chain 'D' and resid 106 through 125 removed outlier: 3.565A pdb=" N ILE D 110 " --> pdb=" O GLY D 106 " (cutoff:3.500A) Processing helix chain 'D' and resid 128 through 135 Processing helix chain 'D' and resid 173 through 195 Processing helix chain 'D' and resid 213 through 229 removed outlier: 3.691A pdb=" N GLY D 229 " --> pdb=" O ILE D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 243 through 246 Processing helix chain 'D' and resid 262 through 277 Processing helix chain 'D' and resid 290 through 302 Processing helix chain 'D' and resid 316 through 326 removed outlier: 3.747A pdb=" N GLU D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ARG D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.717A pdb=" N ILE D 339 " --> pdb=" O VAL D 336 " (cutoff:3.500A) Processing helix chain 'D' and resid 341 through 354 Processing helix chain 'D' and resid 371 through 380 removed outlier: 4.041A pdb=" N ASP D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.899A pdb=" N TYR D 399 " --> pdb=" O ARG D 395 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 413 No H-bonds generated for 'chain 'D' and resid 411 through 413' Processing helix chain 'E' and resid 56 through 61 Processing helix chain 'E' and resid 63 through 73 Processing helix chain 'E' and resid 73 through 79 Processing helix chain 'E' and resid 85 through 98 Processing helix chain 'E' and resid 106 through 125 removed outlier: 3.533A pdb=" N ILE E 110 " --> pdb=" O GLY E 106 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 173 through 195 Processing helix chain 'E' and resid 213 through 229 removed outlier: 3.679A pdb=" N GLY E 229 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing helix chain 'E' and resid 243 through 246 Processing helix chain 'E' and resid 262 through 277 Processing helix chain 'E' and resid 290 through 302 Processing helix chain 'E' and resid 316 through 326 removed outlier: 3.703A pdb=" N GLU E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.717A pdb=" N ILE E 339 " --> pdb=" O VAL E 336 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 354 Processing helix chain 'E' and resid 371 through 380 removed outlier: 3.945A pdb=" N ASP E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 410 removed outlier: 3.901A pdb=" N TYR E 399 " --> pdb=" O ARG E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 413 No H-bonds generated for 'chain 'E' and resid 411 through 413' Processing helix chain 'F' and resid 56 through 61 Processing helix chain 'F' and resid 63 through 73 Processing helix chain 'F' and resid 73 through 79 Processing helix chain 'F' and resid 85 through 98 Processing helix chain 'F' and resid 106 through 125 removed outlier: 3.560A pdb=" N ILE F 110 " --> pdb=" O GLY F 106 " (cutoff:3.500A) Processing helix chain 'F' and resid 128 through 135 Processing helix chain 'F' and resid 173 through 195 Processing helix chain 'F' and resid 213 through 229 removed outlier: 3.698A pdb=" N GLY F 229 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing helix chain 'F' and resid 243 through 246 Processing helix chain 'F' and resid 262 through 277 Processing helix chain 'F' and resid 290 through 302 Processing helix chain 'F' and resid 316 through 326 removed outlier: 3.751A pdb=" N GLU F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.683A pdb=" N ILE F 339 " --> pdb=" O VAL F 336 " (cutoff:3.500A) Processing helix chain 'F' and resid 341 through 354 Processing helix chain 'F' and resid 371 through 380 removed outlier: 3.981A pdb=" N ASP F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 removed outlier: 3.897A pdb=" N TYR F 399 " --> pdb=" O ARG F 395 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 413 No H-bonds generated for 'chain 'F' and resid 411 through 413' Processing helix chain 'G' and resid 56 through 61 Processing helix chain 'G' and resid 63 through 73 Processing helix chain 'G' and resid 73 through 79 Processing helix chain 'G' and resid 85 through 98 Processing helix chain 'G' and resid 106 through 125 removed outlier: 3.557A pdb=" N ILE G 110 " --> pdb=" O GLY G 106 " (cutoff:3.500A) Processing helix chain 'G' and resid 128 through 135 Processing helix chain 'G' and resid 173 through 195 Processing helix chain 'G' and resid 213 through 229 removed outlier: 3.737A pdb=" N GLY G 229 " --> pdb=" O ILE G 225 " (cutoff:3.500A) Processing helix chain 'G' and resid 243 through 246 Processing helix chain 'G' and resid 262 through 277 Processing helix chain 'G' and resid 290 through 302 Processing helix chain 'G' and resid 316 through 326 removed outlier: 3.926A pdb=" N GLU G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 339 removed outlier: 3.677A pdb=" N ILE G 339 " --> pdb=" O VAL G 336 " (cutoff:3.500A) Processing helix chain 'G' and resid 341 through 354 Processing helix chain 'G' and resid 371 through 380 removed outlier: 4.004A pdb=" N ASP G 375 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 410 removed outlier: 3.909A pdb=" N TYR G 399 " --> pdb=" O ARG G 395 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 413 No H-bonds generated for 'chain 'G' and resid 411 through 413' Processing helix chain 'H' and resid 56 through 61 Processing helix chain 'H' and resid 63 through 73 Processing helix chain 'H' and resid 73 through 79 Processing helix chain 'H' and resid 85 through 98 Processing helix chain 'H' and resid 106 through 125 removed outlier: 3.561A pdb=" N ILE H 110 " --> pdb=" O GLY H 106 " (cutoff:3.500A) Processing helix chain 'H' and resid 128 through 135 Processing helix chain 'H' and resid 173 through 195 Processing helix chain 'H' and resid 213 through 229 removed outlier: 3.692A pdb=" N GLY H 229 " --> pdb=" O ILE H 225 " (cutoff:3.500A) Processing helix chain 'H' and resid 243 through 246 Processing helix chain 'H' and resid 262 through 277 Processing helix chain 'H' and resid 290 through 302 Processing helix chain 'H' and resid 316 through 326 removed outlier: 3.744A pdb=" N GLU H 322 " --> pdb=" O GLU H 318 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ARG H 326 " --> pdb=" O GLU H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 339 removed outlier: 3.688A pdb=" N ILE H 339 " --> pdb=" O VAL H 336 " (cutoff:3.500A) Processing helix chain 'H' and resid 341 through 354 Processing helix chain 'H' and resid 371 through 380 removed outlier: 3.949A pdb=" N ASP H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 410 removed outlier: 3.920A pdb=" N TYR H 399 " --> pdb=" O ARG H 395 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 413 No H-bonds generated for 'chain 'H' and resid 411 through 413' Processing sheet with id=AA1, first strand: chain 'A' and resid 4 through 13 Processing sheet with id=AA2, first strand: chain 'A' and resid 140 through 141 Processing sheet with id=AA3, first strand: chain 'A' and resid 143 through 144 removed outlier: 5.983A pdb=" N VAL A 143 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N THR A 359 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 7.965A pdb=" N LYS A 386 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ILE A 361 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 146 through 150 removed outlier: 5.586A pdb=" N ASN A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 7.057A pdb=" N VAL A 166 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N ALA A 167 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N LEU A 238 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N SER A 281 " --> pdb=" O LEU A 238 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 248 through 249 removed outlier: 3.619A pdb=" N THR A 249 " --> pdb=" O GLY A 253 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 13 Processing sheet with id=AA7, first strand: chain 'B' and resid 140 through 141 Processing sheet with id=AA8, first strand: chain 'B' and resid 143 through 144 removed outlier: 5.944A pdb=" N VAL B 143 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N THR B 359 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N LYS B 386 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE B 361 " --> pdb=" O LYS B 386 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 146 through 150 removed outlier: 5.539A pdb=" N ASN B 147 " --> pdb=" O VAL B 166 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N VAL B 166 " --> pdb=" O ASN B 147 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU B 149 " --> pdb=" O PHE B 164 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA B 167 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N LEU B 238 " --> pdb=" O LEU B 279 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N SER B 281 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL B 280 " --> pdb=" O GLN B 306 " (cutoff:3.500A) removed outlier: 7.788A pdb=" N VAL B 308 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N ILE B 282 " --> pdb=" O VAL B 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 249 removed outlier: 3.627A pdb=" N THR B 249 " --> pdb=" O GLY B 253 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 13 removed outlier: 3.588A pdb=" N ARG C 8 " --> pdb=" O GLU C 24 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB4, first strand: chain 'C' and resid 331 through 332 removed outlier: 6.994A pdb=" N VAL C 280 " --> pdb=" O GLN C 306 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N VAL C 308 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N ILE C 282 " --> pdb=" O VAL C 308 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N LEU C 238 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 282 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N LEU C 240 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA C 167 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LEU C 149 " --> pdb=" O PHE C 164 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N VAL C 166 " --> pdb=" O ASN C 147 " (cutoff:3.500A) removed outlier: 5.612A pdb=" N ASN C 147 " --> pdb=" O VAL C 166 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N ILE C 361 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 254 through 256 Processing sheet with id=AB6, first strand: chain 'D' and resid 4 through 13 Processing sheet with id=AB7, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB8, first strand: chain 'D' and resid 306 through 308 removed outlier: 7.016A pdb=" N VAL D 280 " --> pdb=" O GLN D 306 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N VAL D 308 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE D 282 " --> pdb=" O VAL D 308 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N LEU D 238 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ILE D 282 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU D 240 " --> pdb=" O ILE D 282 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N PHE D 164 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N ILE D 361 " --> pdb=" O LYS D 386 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 248 through 249 removed outlier: 3.820A pdb=" N THR D 249 " --> pdb=" O GLY D 253 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 4 through 13 Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AC3, first strand: chain 'E' and resid 143 through 144 removed outlier: 5.933A pdb=" N VAL E 143 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ILE E 361 " --> pdb=" O LYS E 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC3 Processing sheet with id=AC4, first strand: chain 'E' and resid 146 through 150 removed outlier: 7.007A pdb=" N PHE E 164 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 7.793A pdb=" N LEU E 238 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE E 282 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N LEU E 240 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.028A pdb=" N VAL E 280 " --> pdb=" O GLN E 306 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL E 308 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE E 282 " --> pdb=" O VAL E 308 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 248 through 249 removed outlier: 3.581A pdb=" N THR E 249 " --> pdb=" O GLY E 253 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 4 through 13 Processing sheet with id=AC7, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AC8, first strand: chain 'F' and resid 143 through 144 removed outlier: 5.966A pdb=" N VAL F 143 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N ILE F 361 " --> pdb=" O LYS F 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'F' and resid 146 through 150 removed outlier: 7.042A pdb=" N PHE F 164 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 8.490A pdb=" N VAL F 280 " --> pdb=" O VAL F 236 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N LEU F 238 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE F 282 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU F 240 " --> pdb=" O ILE F 282 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N VAL F 280 " --> pdb=" O GLN F 306 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL F 308 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N ILE F 282 " --> pdb=" O VAL F 308 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 248 through 249 removed outlier: 3.736A pdb=" N THR F 249 " --> pdb=" O GLY F 253 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 4 through 13 Processing sheet with id=AD3, first strand: chain 'G' and resid 140 through 141 Processing sheet with id=AD4, first strand: chain 'G' and resid 143 through 144 removed outlier: 5.896A pdb=" N VAL G 143 " --> pdb=" O ILE G 385 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N ILE G 361 " --> pdb=" O LYS G 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'G' and resid 146 through 150 removed outlier: 6.970A pdb=" N PHE G 164 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 7.801A pdb=" N LEU G 238 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE G 282 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N LEU G 240 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N VAL G 280 " --> pdb=" O GLN G 306 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N VAL G 308 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE G 282 " --> pdb=" O VAL G 308 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 248 through 249 removed outlier: 4.371A pdb=" N THR G 249 " --> pdb=" O GLY G 253 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N GLY G 253 " --> pdb=" O THR G 249 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 4 through 13 Processing sheet with id=AD8, first strand: chain 'H' and resid 140 through 141 Processing sheet with id=AD9, first strand: chain 'H' and resid 306 through 308 removed outlier: 7.806A pdb=" N LEU H 238 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE H 282 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU H 240 " --> pdb=" O ILE H 282 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N PHE H 164 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ILE H 361 " --> pdb=" O LYS H 386 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 248 through 249 removed outlier: 3.876A pdb=" N THR H 249 " --> pdb=" O GLY H 253 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N PHE H 256 " --> pdb=" O THR H 259 " (cutoff:3.500A) 1215 hydrogen bonds defined for protein. 3411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.61 Time building geometry restraints manager: 7.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8750 1.34 - 1.45: 2681 1.45 - 1.57: 13857 1.57 - 1.69: 8 1.69 - 1.81: 112 Bond restraints: 25408 Sorted by residual: bond pdb=" N GLU E 45 " pdb=" CA GLU E 45 " ideal model delta sigma weight residual 1.457 1.499 -0.042 1.29e-02 6.01e+03 1.05e+01 bond pdb=" N GLU E 47 " pdb=" CA GLU E 47 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.32e-02 5.74e+03 9.64e+00 bond pdb=" N THR G 43 " pdb=" CA THR G 43 " ideal model delta sigma weight residual 1.455 1.489 -0.034 1.21e-02 6.83e+03 7.83e+00 bond pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta sigma weight residual 1.448 1.476 -0.028 1.04e-02 9.25e+03 7.13e+00 bond pdb=" N THR H 43 " pdb=" CA THR H 43 " ideal model delta sigma weight residual 1.454 1.488 -0.033 1.27e-02 6.20e+03 6.92e+00 ... (remaining 25403 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 33621 1.79 - 3.58: 798 3.58 - 5.37: 124 5.37 - 7.16: 15 7.16 - 8.95: 10 Bond angle restraints: 34568 Sorted by residual: angle pdb=" C2 PEP C 501 " pdb=" C1 PEP C 501 " pdb=" O2' PEP C 501 " ideal model delta sigma weight residual 113.54 120.43 -6.89 1.21e+00 6.82e-01 3.24e+01 angle pdb=" C2 PEP E 501 " pdb=" C1 PEP E 501 " pdb=" O2' PEP E 501 " ideal model delta sigma weight residual 113.54 120.42 -6.88 1.21e+00 6.82e-01 3.23e+01 angle pdb=" C2 PEP G 501 " pdb=" C1 PEP G 501 " pdb=" O2' PEP G 501 " ideal model delta sigma weight residual 113.54 120.37 -6.83 1.21e+00 6.82e-01 3.18e+01 angle pdb=" C2 PEP A 501 " pdb=" C1 PEP A 501 " pdb=" O2' PEP A 501 " ideal model delta sigma weight residual 113.54 120.31 -6.77 1.21e+00 6.82e-01 3.13e+01 angle pdb=" C1 PEP H 501 " pdb=" C2 PEP H 501 " pdb=" O2 PEP H 501 " ideal model delta sigma weight residual 111.24 120.19 -8.95 1.68e+00 3.56e-01 2.85e+01 ... (remaining 34563 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.89: 13815 17.89 - 35.78: 1086 35.78 - 53.66: 132 53.66 - 71.55: 57 71.55 - 89.44: 38 Dihedral angle restraints: 15128 sinusoidal: 5680 harmonic: 9448 Sorted by residual: dihedral pdb=" CA ARG D 392 " pdb=" C ARG D 392 " pdb=" N SER D 393 " pdb=" CA SER D 393 " ideal model delta harmonic sigma weight residual -180.00 -159.01 -20.99 0 5.00e+00 4.00e-02 1.76e+01 dihedral pdb=" CA ARG F 392 " pdb=" C ARG F 392 " pdb=" N SER F 393 " pdb=" CA SER F 393 " ideal model delta harmonic sigma weight residual 180.00 -159.07 -20.93 0 5.00e+00 4.00e-02 1.75e+01 dihedral pdb=" CA ARG E 392 " pdb=" C ARG E 392 " pdb=" N SER E 393 " pdb=" CA SER E 393 " ideal model delta harmonic sigma weight residual -180.00 -159.10 -20.90 0 5.00e+00 4.00e-02 1.75e+01 ... (remaining 15125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 3065 0.051 - 0.103: 808 0.103 - 0.154: 111 0.154 - 0.206: 6 0.206 - 0.257: 2 Chirality restraints: 3992 Sorted by residual: chirality pdb=" CA GLU E 45 " pdb=" N GLU E 45 " pdb=" C GLU E 45 " pdb=" CB GLU E 45 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.66e+00 chirality pdb=" CA VAL B 328 " pdb=" N VAL B 328 " pdb=" C VAL B 328 " pdb=" CB VAL B 328 " both_signs ideal model delta sigma weight residual False 2.44 2.68 -0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CB VAL A 305 " pdb=" CA VAL A 305 " pdb=" CG1 VAL A 305 " pdb=" CG2 VAL A 305 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 3989 not shown) Planarity restraints: 4632 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 47 " 0.012 2.00e-02 2.50e+03 2.50e-02 6.27e+00 pdb=" C GLU E 47 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU E 47 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA E 48 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 328 " 0.011 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C VAL B 328 " -0.042 2.00e-02 2.50e+03 pdb=" O VAL B 328 " 0.016 2.00e-02 2.50e+03 pdb=" N ALA B 329 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 189 " -0.012 2.00e-02 2.50e+03 2.39e-02 5.71e+00 pdb=" C LYS B 189 " 0.041 2.00e-02 2.50e+03 pdb=" O LYS B 189 " -0.015 2.00e-02 2.50e+03 pdb=" N SER B 190 " -0.014 2.00e-02 2.50e+03 ... (remaining 4629 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 383 2.62 - 3.19: 22985 3.19 - 3.76: 38630 3.76 - 4.33: 55540 4.33 - 4.90: 92117 Nonbonded interactions: 209655 Sorted by model distance: nonbonded pdb=" OE2 GLU B 283 " pdb="MG MG B 503 " model vdw 2.055 2.170 nonbonded pdb=" O2P PEP F 501 " pdb="MG MG F 502 " model vdw 2.069 2.170 nonbonded pdb=" OG SER H 42 " pdb="MG MG H 502 " model vdw 2.069 2.170 nonbonded pdb=" O2P PEP D 501 " pdb="MG MG D 502 " model vdw 2.074 2.170 nonbonded pdb=" O2P PEP E 501 " pdb="MG MG E 502 " model vdw 2.077 2.170 ... (remaining 209650 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.990 Check model and map are aligned: 0.180 Set scattering table: 0.240 Process input model: 55.360 Find NCS groups from input model: 1.030 Set up NCS constraints: 0.130 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: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8184 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 : 0.005 0.058 25408 Z= 0.337 Angle : 0.689 8.951 34568 Z= 0.403 Chirality : 0.045 0.257 3992 Planarity : 0.004 0.052 4632 Dihedral : 14.036 89.439 9128 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.09 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % 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: -3.14 (0.12), residues: 3368 helix: -1.02 (0.12), residues: 1368 sheet: -2.52 (0.20), residues: 536 loop : -2.92 (0.13), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 294 HIS 0.007 0.001 HIS D 363 PHE 0.015 0.002 PHE B 247 TYR 0.009 0.001 TYR C 132 ARG 0.006 0.001 ARG A 34 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 360 time to evaluate : 2.812 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7960 (pm20) cc_final: 0.7592 (pm20) REVERT: B 65 LYS cc_start: 0.8844 (ptpt) cc_final: 0.8498 (ptmt) REVERT: C 47 GLU cc_start: 0.7782 (pm20) cc_final: 0.7572 (pm20) REVERT: C 264 ASP cc_start: 0.7355 (m-30) cc_final: 0.7126 (p0) REVERT: C 288 GLU cc_start: 0.7331 (pm20) cc_final: 0.6973 (pp20) REVERT: D 119 LYS cc_start: 0.8235 (mtpt) cc_final: 0.7856 (mttp) REVERT: E 288 GLU cc_start: 0.7353 (pm20) cc_final: 0.7048 (pp20) REVERT: G 145 MET cc_start: 0.8833 (mmm) cc_final: 0.8608 (mmt) REVERT: G 321 GLU cc_start: 0.7134 (mm-30) cc_final: 0.6883 (mm-30) REVERT: H 288 GLU cc_start: 0.7223 (pm20) cc_final: 0.6884 (pp20) outliers start: 0 outliers final: 0 residues processed: 360 average time/residue: 0.4439 time to fit residues: 239.0468 Evaluate side-chains 216 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 2.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 283 optimal weight: 0.8980 chunk 254 optimal weight: 0.9980 chunk 141 optimal weight: 20.0000 chunk 86 optimal weight: 0.8980 chunk 171 optimal weight: 5.9990 chunk 136 optimal weight: 0.9990 chunk 263 optimal weight: 0.9990 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 3.9990 chunk 196 optimal weight: 0.0370 chunk 305 optimal weight: 0.7980 overall best weight: 0.7258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** B 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 363 HIS E 6 GLN E 154 HIS F 6 GLN G 6 GLN ** G 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN H 363 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 25408 Z= 0.175 Angle : 0.532 7.211 34568 Z= 0.281 Chirality : 0.041 0.156 3992 Planarity : 0.004 0.034 4632 Dihedral : 5.305 70.909 3664 Min Nonbonded Distance : 2.004 Molprobity Statistics. All-atom Clashscore : 7.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.04 % Allowed : 7.29 % Favored : 91.68 % 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: -1.49 (0.14), residues: 3368 helix: 0.79 (0.13), residues: 1416 sheet: -2.25 (0.20), residues: 544 loop : -2.34 (0.14), residues: 1408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.000 TRP F 294 HIS 0.006 0.001 HIS D 363 PHE 0.022 0.002 PHE D 32 TYR 0.017 0.001 TYR A 357 ARG 0.002 0.000 ARG D 364 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 2.784 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7904 (pm20) cc_final: 0.7601 (pm20) REVERT: A 282 ILE cc_start: 0.8721 (OUTLIER) cc_final: 0.8509 (pt) REVERT: B 65 LYS cc_start: 0.8528 (ptpt) cc_final: 0.8318 (ptmt) REVERT: D 119 LYS cc_start: 0.8139 (mtpt) cc_final: 0.7702 (mttp) REVERT: D 264 ASP cc_start: 0.7310 (m-30) cc_final: 0.7059 (p0) REVERT: F 119 LYS cc_start: 0.8120 (mtpt) cc_final: 0.7644 (mttp) REVERT: G 119 LYS cc_start: 0.8074 (mtpt) cc_final: 0.7804 (mttp) REVERT: G 145 MET cc_start: 0.8801 (mmm) cc_final: 0.8578 (mmm) REVERT: G 264 ASP cc_start: 0.7593 (m-30) cc_final: 0.7358 (p0) REVERT: G 326 ARG cc_start: 0.6783 (OUTLIER) cc_final: 0.6574 (mtm180) REVERT: G 351 LEU cc_start: 0.8646 (mp) cc_final: 0.8426 (mp) REVERT: H 288 GLU cc_start: 0.7242 (pm20) cc_final: 0.6708 (pp20) outliers start: 26 outliers final: 8 residues processed: 272 average time/residue: 0.3515 time to fit residues: 150.9129 Evaluate side-chains 218 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 208 time to evaluate : 2.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.5980 chunk 94 optimal weight: 6.9990 chunk 253 optimal weight: 0.7980 chunk 207 optimal weight: 0.6980 chunk 84 optimal weight: 5.9990 chunk 305 optimal weight: 4.9990 chunk 330 optimal weight: 3.9990 chunk 272 optimal weight: 5.9990 chunk 303 optimal weight: 7.9990 chunk 104 optimal weight: 8.9990 chunk 245 optimal weight: 5.9990 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 363 HIS C 363 HIS G 363 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.1544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 25408 Z= 0.329 Angle : 0.557 7.439 34568 Z= 0.294 Chirality : 0.043 0.147 3992 Planarity : 0.005 0.072 4632 Dihedral : 5.336 73.487 3664 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 1.11 % Allowed : 10.43 % Favored : 88.46 % 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: -1.04 (0.14), residues: 3368 helix: 1.18 (0.14), residues: 1424 sheet: -2.11 (0.20), residues: 544 loop : -2.08 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 294 HIS 0.007 0.001 HIS G 363 PHE 0.023 0.002 PHE G 32 TYR 0.026 0.002 TYR G 357 ARG 0.004 0.000 ARG H 10 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 202 time to evaluate : 2.695 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8099 (pm20) cc_final: 0.7742 (pm20) REVERT: A 282 ILE cc_start: 0.8780 (OUTLIER) cc_final: 0.8572 (pt) REVERT: B 145 MET cc_start: 0.8814 (mmm) cc_final: 0.8371 (mmt) REVERT: D 119 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7707 (mttp) REVERT: E 145 MET cc_start: 0.8780 (mmm) cc_final: 0.8367 (mmt) REVERT: E 256 PHE cc_start: 0.5741 (t80) cc_final: 0.5499 (t80) REVERT: G 119 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7808 (mttp) REVERT: G 264 ASP cc_start: 0.7622 (m-30) cc_final: 0.7305 (p0) REVERT: G 322 GLU cc_start: 0.7210 (tt0) cc_final: 0.6784 (tp30) REVERT: H 282 ILE cc_start: 0.8768 (OUTLIER) cc_final: 0.8539 (pt) REVERT: H 288 GLU cc_start: 0.7305 (pm20) cc_final: 0.6890 (pp20) outliers start: 28 outliers final: 16 residues processed: 225 average time/residue: 0.3777 time to fit residues: 133.7637 Evaluate side-chains 203 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 185 time to evaluate : 2.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 282 ILE Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 302 optimal weight: 0.9980 chunk 229 optimal weight: 0.0050 chunk 158 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 2.9990 chunk 205 optimal weight: 1.9990 chunk 306 optimal weight: 0.2980 chunk 324 optimal weight: 6.9990 chunk 160 optimal weight: 6.9990 chunk 290 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 overall best weight: 0.5594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25408 Z= 0.145 Angle : 0.479 6.417 34568 Z= 0.252 Chirality : 0.040 0.138 3992 Planarity : 0.003 0.033 4632 Dihedral : 5.168 75.310 3664 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.23 % Allowed : 10.91 % Favored : 87.86 % 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: -0.44 (0.14), residues: 3368 helix: 1.78 (0.14), residues: 1424 sheet: -1.74 (0.21), residues: 544 loop : -1.94 (0.15), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 294 HIS 0.002 0.000 HIS F 363 PHE 0.021 0.002 PHE G 256 TYR 0.015 0.001 TYR E 357 ARG 0.004 0.000 ARG H 10 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 209 time to evaluate : 2.602 Fit side-chains REVERT: A 301 ILE cc_start: 0.8073 (pt) cc_final: 0.7733 (mt) REVERT: B 194 LYS cc_start: 0.8855 (tmmt) cc_final: 0.8602 (ttpt) REVERT: C 47 GLU cc_start: 0.7842 (pm20) cc_final: 0.7563 (pm20) REVERT: C 351 LEU cc_start: 0.8504 (mp) cc_final: 0.8265 (mp) REVERT: D 119 LYS cc_start: 0.8160 (mtpt) cc_final: 0.7694 (mttp) REVERT: F 119 LYS cc_start: 0.8140 (mtpt) cc_final: 0.7674 (mttp) REVERT: G 119 LYS cc_start: 0.8128 (mtpt) cc_final: 0.7689 (mttp) REVERT: G 264 ASP cc_start: 0.7699 (m-30) cc_final: 0.7440 (p0) REVERT: G 322 GLU cc_start: 0.7184 (tt0) cc_final: 0.6780 (tp30) REVERT: G 351 LEU cc_start: 0.8619 (mp) cc_final: 0.8401 (mp) outliers start: 31 outliers final: 19 residues processed: 234 average time/residue: 0.3669 time to fit residues: 134.8794 Evaluate side-chains 202 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 183 time to evaluate : 2.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 5.9990 chunk 184 optimal weight: 3.9990 chunk 4 optimal weight: 0.0970 chunk 241 optimal weight: 9.9990 chunk 134 optimal weight: 0.7980 chunk 277 optimal weight: 20.0000 chunk 224 optimal weight: 0.5980 chunk 0 optimal weight: 5.9990 chunk 165 optimal weight: 2.9990 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25408 Z= 0.209 Angle : 0.494 7.017 34568 Z= 0.258 Chirality : 0.041 0.138 3992 Planarity : 0.004 0.032 4632 Dihedral : 5.136 78.563 3664 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.27 % Favored : 96.70 % Rotamer: Outliers : 1.71 % Allowed : 11.74 % Favored : 86.54 % 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: -0.24 (0.15), residues: 3368 helix: 1.92 (0.14), residues: 1424 sheet: -1.57 (0.21), residues: 544 loop : -1.82 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.000 TRP B 294 HIS 0.003 0.000 HIS F 363 PHE 0.023 0.002 PHE H 32 TYR 0.022 0.001 TYR G 357 ARG 0.006 0.000 ARG G 326 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 188 time to evaluate : 2.599 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.7967 (pm20) cc_final: 0.7632 (pm20) REVERT: A 145 MET cc_start: 0.8776 (mmm) cc_final: 0.8532 (mmt) REVERT: A 301 ILE cc_start: 0.8036 (pt) cc_final: 0.7739 (mt) REVERT: C 351 LEU cc_start: 0.8505 (mp) cc_final: 0.8264 (mp) REVERT: D 119 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7721 (mttp) REVERT: E 282 ILE cc_start: 0.9040 (OUTLIER) cc_final: 0.8819 (pt) REVERT: G 119 LYS cc_start: 0.8156 (mtpt) cc_final: 0.7702 (mttp) REVERT: G 252 THR cc_start: 0.6653 (OUTLIER) cc_final: 0.6398 (t) REVERT: G 264 ASP cc_start: 0.7679 (m-30) cc_final: 0.7403 (p0) REVERT: G 322 GLU cc_start: 0.7221 (tt0) cc_final: 0.6788 (tp30) REVERT: G 351 LEU cc_start: 0.8641 (mp) cc_final: 0.8419 (mp) REVERT: H 282 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8605 (pt) outliers start: 43 outliers final: 23 residues processed: 224 average time/residue: 0.3657 time to fit residues: 128.9457 Evaluate side-chains 206 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 180 time to evaluate : 2.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 65 LYS Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 313 PHE Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 10.0000 chunk 292 optimal weight: 2.9990 chunk 64 optimal weight: 0.3980 chunk 190 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 325 optimal weight: 0.6980 chunk 269 optimal weight: 0.5980 chunk 150 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 170 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.2113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 25408 Z= 0.142 Angle : 0.467 6.394 34568 Z= 0.244 Chirality : 0.039 0.137 3992 Planarity : 0.003 0.032 4632 Dihedral : 5.033 79.132 3664 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 1.51 % Allowed : 12.54 % Favored : 85.95 % 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: 0.09 (0.15), residues: 3368 helix: 2.25 (0.14), residues: 1424 sheet: -1.35 (0.21), residues: 544 loop : -1.74 (0.16), residues: 1400 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 294 HIS 0.002 0.000 HIS F 363 PHE 0.022 0.002 PHE G 256 TYR 0.017 0.001 TYR A 357 ARG 0.005 0.000 ARG B 10 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 192 time to evaluate : 2.594 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8017 (pm20) cc_final: 0.7627 (pm20) REVERT: A 145 MET cc_start: 0.8807 (mmm) cc_final: 0.8517 (mmt) REVERT: C 47 GLU cc_start: 0.7840 (pm20) cc_final: 0.7505 (pt0) REVERT: C 119 LYS cc_start: 0.8054 (mtpt) cc_final: 0.7652 (mttp) REVERT: C 264 ASP cc_start: 0.7642 (m-30) cc_final: 0.7355 (p0) REVERT: C 351 LEU cc_start: 0.8493 (mp) cc_final: 0.8246 (mp) REVERT: D 119 LYS cc_start: 0.8175 (mtpt) cc_final: 0.7723 (mttp) REVERT: E 282 ILE cc_start: 0.9065 (OUTLIER) cc_final: 0.8818 (pt) REVERT: F 119 LYS cc_start: 0.8165 (mtpt) cc_final: 0.7733 (mttp) REVERT: F 282 ILE cc_start: 0.8947 (OUTLIER) cc_final: 0.8740 (pt) REVERT: G 119 LYS cc_start: 0.8150 (mtpt) cc_final: 0.7696 (mttp) REVERT: G 252 THR cc_start: 0.6896 (OUTLIER) cc_final: 0.6650 (t) REVERT: G 264 ASP cc_start: 0.7694 (m-30) cc_final: 0.7449 (p0) REVERT: G 322 GLU cc_start: 0.7214 (tt0) cc_final: 0.6846 (tp30) outliers start: 38 outliers final: 26 residues processed: 222 average time/residue: 0.3837 time to fit residues: 131.6325 Evaluate side-chains 207 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 178 time to evaluate : 2.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 252 THR Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.0070 chunk 36 optimal weight: 0.8980 chunk 185 optimal weight: 5.9990 chunk 237 optimal weight: 4.9990 chunk 183 optimal weight: 0.1980 chunk 273 optimal weight: 8.9990 chunk 181 optimal weight: 0.0770 chunk 323 optimal weight: 9.9990 chunk 202 optimal weight: 3.9990 chunk 197 optimal weight: 8.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.0358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 25408 Z= 0.178 Angle : 0.477 6.771 34568 Z= 0.251 Chirality : 0.040 0.146 3992 Planarity : 0.003 0.032 4632 Dihedral : 5.013 80.617 3664 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.97 % Favored : 97.00 % Rotamer: Outliers : 1.51 % Allowed : 13.85 % Favored : 84.63 % 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: 0.20 (0.15), residues: 3368 helix: 2.37 (0.14), residues: 1408 sheet: -1.10 (0.23), residues: 480 loop : -1.75 (0.15), residues: 1480 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.000 TRP B 294 HIS 0.003 0.000 HIS F 363 PHE 0.025 0.002 PHE D 269 TYR 0.020 0.001 TYR C 357 ARG 0.003 0.000 ARG H 10 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 189 time to evaluate : 3.035 Fit side-chains revert: symmetry clash REVERT: A 47 GLU cc_start: 0.8093 (pm20) cc_final: 0.7702 (pm20) REVERT: A 145 MET cc_start: 0.8803 (mmm) cc_final: 0.8528 (mmt) REVERT: B 308 VAL cc_start: 0.8591 (OUTLIER) cc_final: 0.8332 (m) REVERT: B 325 GLU cc_start: 0.7586 (mm-30) cc_final: 0.7329 (mm-30) REVERT: C 47 GLU cc_start: 0.7878 (pm20) cc_final: 0.7590 (pm20) REVERT: C 264 ASP cc_start: 0.7626 (m-30) cc_final: 0.7347 (p0) REVERT: D 119 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7750 (mttp) REVERT: D 325 GLU cc_start: 0.7741 (mm-30) cc_final: 0.7513 (mm-30) REVERT: F 282 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8781 (pt) REVERT: G 119 LYS cc_start: 0.8171 (mtpt) cc_final: 0.7713 (mttp) REVERT: G 264 ASP cc_start: 0.7710 (m-30) cc_final: 0.7458 (p0) REVERT: G 322 GLU cc_start: 0.7251 (tt0) cc_final: 0.6879 (tp30) REVERT: G 351 LEU cc_start: 0.8576 (mp) cc_final: 0.8362 (mp) REVERT: H 282 ILE cc_start: 0.8817 (OUTLIER) cc_final: 0.8617 (pt) outliers start: 38 outliers final: 30 residues processed: 217 average time/residue: 0.3960 time to fit residues: 134.1362 Evaluate side-chains 205 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 172 time to evaluate : 2.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 326 ARG Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 192 LEU Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 192 LEU Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 0.0070 chunk 129 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 63 optimal weight: 10.0000 chunk 62 optimal weight: 0.0770 chunk 205 optimal weight: 2.9990 chunk 220 optimal weight: 5.9990 chunk 160 optimal weight: 4.9990 chunk 30 optimal weight: 4.9990 chunk 254 optimal weight: 3.9990 overall best weight: 2.2162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 25408 Z= 0.317 Angle : 0.543 12.584 34568 Z= 0.286 Chirality : 0.043 0.238 3992 Planarity : 0.004 0.034 4632 Dihedral : 5.213 80.455 3664 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.95 % Favored : 96.02 % Rotamer: Outliers : 1.67 % Allowed : 14.01 % Favored : 84.32 % 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: 0.07 (0.15), residues: 3368 helix: 2.19 (0.14), residues: 1400 sheet: -1.18 (0.23), residues: 480 loop : -1.71 (0.15), residues: 1488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 291 HIS 0.004 0.001 HIS F 363 PHE 0.027 0.003 PHE D 269 TYR 0.016 0.002 TYR F 357 ARG 0.003 0.000 ARG B 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 176 time to evaluate : 2.856 Fit side-chains REVERT: A 47 GLU cc_start: 0.8086 (pm20) cc_final: 0.7662 (pm20) REVERT: B 146 MET cc_start: 0.8943 (OUTLIER) cc_final: 0.8424 (mtt) REVERT: C 47 GLU cc_start: 0.8075 (pm20) cc_final: 0.7715 (pm20) REVERT: C 119 LYS cc_start: 0.8070 (mtpt) cc_final: 0.7631 (mttp) REVERT: C 146 MET cc_start: 0.9009 (OUTLIER) cc_final: 0.8497 (mtt) REVERT: D 119 LYS cc_start: 0.8255 (mtpt) cc_final: 0.7800 (mttp) REVERT: D 145 MET cc_start: 0.8813 (mmm) cc_final: 0.8452 (mmt) REVERT: F 119 LYS cc_start: 0.8214 (mtpt) cc_final: 0.7840 (mttp) REVERT: G 119 LYS cc_start: 0.8201 (mtpt) cc_final: 0.7821 (mttp) REVERT: G 264 ASP cc_start: 0.7604 (m-30) cc_final: 0.7382 (p0) REVERT: G 322 GLU cc_start: 0.7297 (tt0) cc_final: 0.6911 (tp30) REVERT: G 326 ARG cc_start: 0.7207 (OUTLIER) cc_final: 0.6788 (mtm180) REVERT: H 145 MET cc_start: 0.8862 (mmm) cc_final: 0.8438 (mmt) REVERT: H 282 ILE cc_start: 0.8826 (OUTLIER) cc_final: 0.8617 (pt) outliers start: 42 outliers final: 28 residues processed: 207 average time/residue: 0.3841 time to fit residues: 123.6843 Evaluate side-chains 202 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 170 time to evaluate : 2.710 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ILE Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 282 ILE Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 0.6980 chunk 310 optimal weight: 2.9990 chunk 283 optimal weight: 0.9980 chunk 301 optimal weight: 0.6980 chunk 181 optimal weight: 1.9990 chunk 131 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 92 optimal weight: 6.9990 chunk 272 optimal weight: 2.9990 chunk 285 optimal weight: 2.9990 chunk 300 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8168 moved from start: 0.2341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 25408 Z= 0.166 Angle : 0.485 7.843 34568 Z= 0.254 Chirality : 0.040 0.159 3992 Planarity : 0.003 0.032 4632 Dihedral : 5.021 75.860 3664 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.24 % Favored : 96.73 % Rotamer: Outliers : 1.35 % Allowed : 14.41 % Favored : 84.24 % 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: 0.27 (0.15), residues: 3368 helix: 2.37 (0.14), residues: 1416 sheet: -1.04 (0.23), residues: 480 loop : -1.68 (0.15), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 294 HIS 0.002 0.000 HIS E 363 PHE 0.030 0.002 PHE A 269 TYR 0.018 0.001 TYR F 357 ARG 0.003 0.000 ARG H 10 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 183 time to evaluate : 2.985 Fit side-chains REVERT: A 47 GLU cc_start: 0.8064 (pm20) cc_final: 0.7636 (pm20) REVERT: B 146 MET cc_start: 0.8974 (OUTLIER) cc_final: 0.8463 (mtt) REVERT: C 47 GLU cc_start: 0.8035 (pm20) cc_final: 0.7669 (pm20) REVERT: C 119 LYS cc_start: 0.8033 (mtpt) cc_final: 0.7616 (mttp) REVERT: C 146 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8494 (mtt) REVERT: D 119 LYS cc_start: 0.8191 (mtpt) cc_final: 0.7742 (mttp) REVERT: D 145 MET cc_start: 0.8827 (mmm) cc_final: 0.8365 (mmt) REVERT: D 146 MET cc_start: 0.8905 (OUTLIER) cc_final: 0.8431 (mtt) REVERT: D 325 GLU cc_start: 0.7722 (mm-30) cc_final: 0.7501 (mm-30) REVERT: F 119 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7737 (mttp) REVERT: G 119 LYS cc_start: 0.8163 (mtpt) cc_final: 0.7673 (mttp) REVERT: G 264 ASP cc_start: 0.7655 (m-30) cc_final: 0.7395 (p0) REVERT: G 282 ILE cc_start: 0.9114 (OUTLIER) cc_final: 0.8902 (pt) REVERT: G 322 GLU cc_start: 0.7263 (tt0) cc_final: 0.6885 (tp30) REVERT: G 351 LEU cc_start: 0.8645 (mp) cc_final: 0.8420 (mp) outliers start: 34 outliers final: 28 residues processed: 207 average time/residue: 0.3828 time to fit residues: 123.2085 Evaluate side-chains 209 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 177 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 266 MET Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 6.9990 chunk 319 optimal weight: 1.9990 chunk 194 optimal weight: 9.9990 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 0.8980 chunk 334 optimal weight: 0.9980 chunk 308 optimal weight: 0.9980 chunk 266 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 205 optimal weight: 0.8980 chunk 163 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 25408 Z= 0.172 Angle : 0.483 7.579 34568 Z= 0.253 Chirality : 0.040 0.161 3992 Planarity : 0.003 0.032 4632 Dihedral : 4.955 73.903 3664 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 1.47 % Allowed : 14.53 % Favored : 84.00 % 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: 0.47 (0.15), residues: 3368 helix: 2.44 (0.14), residues: 1416 sheet: -0.57 (0.26), residues: 416 loop : -1.58 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 294 HIS 0.003 0.000 HIS E 363 PHE 0.035 0.002 PHE A 269 TYR 0.011 0.001 TYR G 357 ARG 0.003 0.000 ARG H 10 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6736 Ramachandran restraints generated. 3368 Oldfield, 0 Emsley, 3368 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 181 time to evaluate : 3.041 Fit side-chains REVERT: A 47 GLU cc_start: 0.8030 (pm20) cc_final: 0.7604 (pm20) REVERT: A 145 MET cc_start: 0.8800 (mmm) cc_final: 0.8483 (mmt) REVERT: B 146 MET cc_start: 0.8982 (OUTLIER) cc_final: 0.8461 (mtt) REVERT: C 47 GLU cc_start: 0.8046 (pm20) cc_final: 0.7678 (pm20) REVERT: C 119 LYS cc_start: 0.8078 (mtpt) cc_final: 0.7727 (mttp) REVERT: C 146 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8508 (mtt) REVERT: C 282 ILE cc_start: 0.9109 (OUTLIER) cc_final: 0.8902 (pt) REVERT: D 119 LYS cc_start: 0.8200 (mtpt) cc_final: 0.7765 (mttp) REVERT: D 145 MET cc_start: 0.8821 (mmm) cc_final: 0.8353 (mmt) REVERT: D 146 MET cc_start: 0.8903 (OUTLIER) cc_final: 0.8422 (mtt) REVERT: D 325 GLU cc_start: 0.7712 (mm-30) cc_final: 0.7458 (mm-30) REVERT: F 119 LYS cc_start: 0.8216 (mtpt) cc_final: 0.7846 (mttp) REVERT: G 119 LYS cc_start: 0.8178 (mtpt) cc_final: 0.7722 (mttp) REVERT: G 264 ASP cc_start: 0.7633 (m-30) cc_final: 0.7373 (p0) REVERT: G 282 ILE cc_start: 0.9091 (OUTLIER) cc_final: 0.8879 (pt) REVERT: G 322 GLU cc_start: 0.7213 (tt0) cc_final: 0.6901 (tp30) REVERT: G 326 ARG cc_start: 0.7012 (OUTLIER) cc_final: 0.6601 (mtm180) REVERT: G 351 LEU cc_start: 0.8647 (mp) cc_final: 0.8427 (mp) REVERT: H 145 MET cc_start: 0.8853 (mmm) cc_final: 0.8385 (mmt) REVERT: H 146 MET cc_start: 0.8961 (OUTLIER) cc_final: 0.8483 (mtt) outliers start: 37 outliers final: 25 residues processed: 207 average time/residue: 0.3837 time to fit residues: 124.1342 Evaluate side-chains 205 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 173 time to evaluate : 2.753 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 255 VAL Chi-restraints excluded: chain A residue 283 GLU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 29 ASP Chi-restraints excluded: chain B residue 146 MET Chi-restraints excluded: chain B residue 259 THR Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain C residue 146 MET Chi-restraints excluded: chain C residue 211 VAL Chi-restraints excluded: chain C residue 255 VAL Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 39 SER Chi-restraints excluded: chain D residue 146 MET Chi-restraints excluded: chain D residue 211 VAL Chi-restraints excluded: chain D residue 252 THR Chi-restraints excluded: chain D residue 255 VAL Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 29 ASP Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 255 VAL Chi-restraints excluded: chain E residue 282 ILE Chi-restraints excluded: chain F residue 211 VAL Chi-restraints excluded: chain F residue 255 VAL Chi-restraints excluded: chain F residue 266 MET Chi-restraints excluded: chain G residue 255 VAL Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain G residue 326 ARG Chi-restraints excluded: chain H residue 146 MET Chi-restraints excluded: chain H residue 255 VAL Chi-restraints excluded: chain H residue 297 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.8980 chunk 283 optimal weight: 5.9990 chunk 81 optimal weight: 1.9990 chunk 245 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 74 optimal weight: 3.9990 chunk 266 optimal weight: 0.6980 chunk 111 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.128492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3260 r_free = 0.3260 target = 0.101699 restraints weight = 38271.393| |-----------------------------------------------------------------------------| r_work (start): 0.3254 rms_B_bonded: 2.17 r_work: 0.3129 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.2445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 25408 Z= 0.203 Angle : 0.492 6.907 34568 Z= 0.258 Chirality : 0.041 0.164 3992 Planarity : 0.004 0.032 4632 Dihedral : 4.954 73.105 3664 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.03 % Allowed : 3.30 % Favored : 96.67 % Rotamer: Outliers : 1.51 % Allowed : 14.65 % Favored : 83.84 % 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: 0.49 (0.15), residues: 3368 helix: 2.42 (0.14), residues: 1416 sheet: -0.54 (0.26), residues: 416 loop : -1.54 (0.15), residues: 1536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 294 HIS 0.003 0.000 HIS E 363 PHE 0.030 0.002 PHE D 269 TYR 0.011 0.001 TYR B 357 ARG 0.002 0.000 ARG H 10 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4657.20 seconds wall clock time: 83 minutes 52.65 seconds (5032.65 seconds total)