Starting phenix.real_space_refine on Mon Sep 30 08:02:09 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4x_30988/09_2024/7e4x_30988.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4x_30988/09_2024/7e4x_30988.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4x_30988/09_2024/7e4x_30988.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4x_30988/09_2024/7e4x_30988.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4x_30988/09_2024/7e4x_30988.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e4x_30988/09_2024/7e4x_30988.cif" } resolution = 3.08 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= 0.007 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: 4 Type Number sf(0) Gaussians S 56 5.16 5 C 15584 2.51 5 N 4320 2.21 5 O 4976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 111 residue(s): 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 24936 Number of models: 1 Model: "" Number of chains: 8 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} Time building chain proxies: 14.89, per 1000 atoms: 0.60 Number of scatterers: 24936 At special positions: 0 Unit cell: (159.43, 160.5, 71.69, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 56 16.00 O 4976 8.00 N 4320 7.00 C 15584 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: 5.78 Conformation dependent library (CDL) restraints added in 3.4 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 38 sheets defined 46.5% alpha, 12.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.28 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 Processing helix chain 'A' and resid 85 through 98 Processing helix chain 'A' and resid 108 through 124 removed outlier: 3.984A pdb=" N VAL A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 135 removed outlier: 3.504A pdb=" N VAL A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY A 134 " --> pdb=" O PHE A 130 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 194 removed outlier: 3.847A pdb=" N SER A 190 " --> pdb=" O HIS A 186 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS A 193 " --> pdb=" O LYS A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 212 through 229 removed outlier: 4.039A pdb=" N ALA A 216 " --> pdb=" O ALA A 212 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N GLY A 229 " --> pdb=" O ILE A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 244 through 246 No H-bonds generated for 'chain 'A' and resid 244 through 246' Processing helix chain 'A' and resid 262 through 277 removed outlier: 3.637A pdb=" N GLY A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ALA A 276 " --> pdb=" O GLY A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 301 removed outlier: 3.940A pdb=" N ALA A 299 " --> pdb=" O ALA A 295 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N SER A 300 " --> pdb=" O ALA A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 316 through 326 removed outlier: 3.725A pdb=" N GLU A 322 " --> pdb=" O GLU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 339 removed outlier: 3.700A 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: 3.902A pdb=" N ASP A 375 " --> pdb=" O THR A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 410 removed outlier: 4.006A 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: 3.507A 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: 3.904A pdb=" N VAL B 113 " --> pdb=" O ALA B 109 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA B 120 " --> pdb=" O ALA B 116 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 135 removed outlier: 3.627A pdb=" N VAL B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLY B 134 " --> pdb=" O PHE B 130 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 195 removed outlier: 3.529A pdb=" N LYS B 193 " --> pdb=" O LYS B 189 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 229 removed outlier: 3.539A pdb=" N ALA B 217 " --> pdb=" O GLY B 213 " (cutoff:3.500A) removed outlier: 3.737A 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: 3.725A pdb=" N GLU B 322 " --> pdb=" O GLU B 318 " (cutoff:3.500A) Processing helix chain 'B' and resid 335 through 339 removed outlier: 3.693A pdb=" N ILE B 339 " --> pdb=" O VAL B 336 " (cutoff:3.500A) Processing helix chain 'B' and resid 341 through 354 Processing helix chain 'B' and resid 371 through 380 removed outlier: 3.895A pdb=" N ASP B 375 " --> pdb=" O THR B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 395 through 410 removed outlier: 3.967A 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 Processing helix chain 'C' and resid 85 through 98 removed outlier: 3.630A pdb=" N GLN C 91 " --> pdb=" O ARG C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 124 Processing helix chain 'C' and resid 128 through 135 Processing helix chain 'C' and resid 173 through 194 removed outlier: 3.608A pdb=" N SER C 190 " --> pdb=" O HIS C 186 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 229 removed outlier: 3.597A pdb=" N GLY C 229 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 243 through 248 removed outlier: 3.651A pdb=" N PHE C 248 " --> pdb=" O THR C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 262 through 277 removed outlier: 3.624A 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: 3.905A pdb=" N GLU C 322 " --> pdb=" O GLU C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 335 through 339 removed outlier: 3.875A 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: 3.937A pdb=" N ASP C 375 " --> pdb=" O THR C 371 " (cutoff:3.500A) Processing helix chain 'C' and resid 395 through 410 removed outlier: 3.845A 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: 3.530A 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 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: 3.724A 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: 3.786A pdb=" N GLU D 322 " --> pdb=" O GLU D 318 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ARG D 326 " --> pdb=" O GLU D 322 " (cutoff:3.500A) Processing helix chain 'D' and resid 335 through 339 removed outlier: 3.679A 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: 3.945A pdb=" N ASP D 375 " --> pdb=" O THR D 371 " (cutoff:3.500A) Processing helix chain 'D' and resid 395 through 410 removed outlier: 3.890A 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 Processing helix chain 'E' and resid 128 through 135 Processing helix chain 'E' and resid 173 through 195 removed outlier: 3.542A pdb=" N GLU E 195 " --> pdb=" O VAL E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 229 removed outlier: 3.722A 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: 3.786A pdb=" N GLU E 322 " --> pdb=" O GLU E 318 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ARG E 326 " --> pdb=" O GLU E 322 " (cutoff:3.500A) Processing helix chain 'E' and resid 335 through 339 removed outlier: 3.657A 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: 3.917A pdb=" N ASP E 375 " --> pdb=" O THR E 371 " (cutoff:3.500A) Processing helix chain 'E' and resid 395 through 410 removed outlier: 3.882A 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 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: 3.696A 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: 3.809A pdb=" N GLU F 322 " --> pdb=" O GLU F 318 " (cutoff:3.500A) Processing helix chain 'F' and resid 335 through 339 removed outlier: 3.660A 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: 3.929A pdb=" N ASP F 375 " --> pdb=" O THR F 371 " (cutoff:3.500A) Processing helix chain 'F' and resid 395 through 410 removed outlier: 3.883A 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 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: 3.714A 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: 4.014A pdb=" N GLU G 322 " --> pdb=" O GLU G 318 " (cutoff:3.500A) Processing helix chain 'G' and resid 335 through 339 removed outlier: 3.664A 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: 3.927A pdb=" N ASP G 375 " --> pdb=" O THR G 371 " (cutoff:3.500A) Processing helix chain 'G' and resid 395 through 410 removed outlier: 3.891A 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 126 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: 3.693A 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: 3.778A pdb=" N GLU H 322 " --> pdb=" O GLU H 318 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ARG H 326 " --> pdb=" O GLU H 322 " (cutoff:3.500A) Processing helix chain 'H' and resid 335 through 339 removed outlier: 3.651A 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: 3.905A pdb=" N ASP H 375 " --> pdb=" O THR H 371 " (cutoff:3.500A) Processing helix chain 'H' and resid 395 through 410 removed outlier: 3.877A 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: 5.942A pdb=" N VAL A 143 " --> pdb=" O ILE A 385 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N THR A 359 " --> pdb=" O GLN A 384 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N LYS A 386 " --> pdb=" O THR A 359 " (cutoff:3.500A) removed outlier: 6.527A 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: 5.478A pdb=" N ASN A 147 " --> pdb=" O VAL A 166 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A 166 " --> pdb=" O ASN A 147 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA A 167 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 5.983A pdb=" N LEU A 238 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.080A 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: 3.531A pdb=" N PHE A 256 " --> pdb=" O THR A 259 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 13 removed outlier: 3.522A pdb=" N GLN B 6 " --> pdb=" O ALA B 26 " (cutoff:3.500A) 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: 5.964A pdb=" N VAL B 143 " --> pdb=" O ILE B 385 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N THR B 359 " --> pdb=" O GLN B 384 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS B 386 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 6.565A 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: 7.173A pdb=" N PHE B 164 " --> pdb=" O ILE B 148 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ALA B 167 " --> pdb=" O ALA B 237 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N LEU B 238 " --> pdb=" O VAL B 280 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ILE B 282 " --> pdb=" O LEU B 238 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N LEU B 240 " --> pdb=" O ILE B 282 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 248 through 249 Processing sheet with id=AB2, first strand: chain 'C' and resid 4 through 6 removed outlier: 6.805A pdb=" N ALA C 26 " --> pdb=" O GLU C 5 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 9 through 13 Processing sheet with id=AB4, first strand: chain 'C' and resid 140 through 141 Processing sheet with id=AB5, first strand: chain 'C' and resid 331 through 332 removed outlier: 7.793A pdb=" N LEU C 238 " --> pdb=" O VAL C 280 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N ILE C 282 " --> pdb=" O LEU C 238 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N LEU C 240 " --> pdb=" O ILE C 282 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA C 167 " --> pdb=" O ALA C 237 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N PHE C 164 " --> pdb=" O ILE C 148 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE C 361 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 254 through 256 Processing sheet with id=AB7, first strand: chain 'D' and resid 4 through 13 Processing sheet with id=AB8, first strand: chain 'D' and resid 140 through 141 Processing sheet with id=AB9, first strand: chain 'D' and resid 143 through 144 removed outlier: 5.956A pdb=" N VAL D 143 " --> pdb=" O ILE D 385 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE D 361 " --> pdb=" O LYS D 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB9 Processing sheet with id=AC1, first strand: chain 'D' and resid 146 through 150 removed outlier: 7.013A pdb=" N PHE D 164 " --> pdb=" O ILE D 148 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N LEU D 238 " --> pdb=" O VAL D 280 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ILE D 282 " --> pdb=" O LEU D 238 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N LEU D 240 " --> pdb=" O ILE D 282 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 248 through 249 Processing sheet with id=AC3, first strand: chain 'E' and resid 4 through 13 Processing sheet with id=AC4, first strand: chain 'E' and resid 140 through 141 Processing sheet with id=AC5, first strand: chain 'E' and resid 306 through 308 removed outlier: 7.746A pdb=" N LEU E 238 " --> pdb=" O VAL E 280 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 282 " --> pdb=" O LEU E 238 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU E 240 " --> pdb=" O ILE E 282 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N PHE E 164 " --> pdb=" O ILE E 148 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE E 361 " --> pdb=" O LYS E 386 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 248 through 249 Processing sheet with id=AC7, first strand: chain 'F' and resid 4 through 13 Processing sheet with id=AC8, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AC9, first strand: chain 'F' and resid 143 through 144 removed outlier: 5.958A pdb=" N VAL F 143 " --> pdb=" O ILE F 385 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE F 361 " --> pdb=" O LYS F 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'F' and resid 146 through 150 removed outlier: 7.010A pdb=" N PHE F 164 " --> pdb=" O ILE F 148 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N LEU F 238 " --> pdb=" O VAL F 280 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ILE F 282 " --> pdb=" O LEU F 238 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N LEU F 240 " --> pdb=" O ILE F 282 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'F' and resid 248 through 249 Processing sheet with id=AD3, first strand: chain 'G' and resid 4 through 13 Processing sheet with id=AD4, first strand: chain 'G' and resid 140 through 141 Processing sheet with id=AD5, first strand: chain 'G' and resid 331 through 332 removed outlier: 7.746A pdb=" N LEU G 238 " --> pdb=" O VAL G 280 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ILE G 282 " --> pdb=" O LEU G 238 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N LEU G 240 " --> pdb=" O ILE G 282 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N PHE G 164 " --> pdb=" O ILE G 148 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ILE G 361 " --> pdb=" O LYS G 386 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 248 through 249 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 143 through 144 removed outlier: 5.933A pdb=" N VAL H 143 " --> pdb=" O ILE H 385 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 361 " --> pdb=" O LYS H 386 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD9 Processing sheet with id=AE1, first strand: chain 'H' and resid 146 through 150 removed outlier: 6.888A pdb=" N PHE H 164 " --> pdb=" O ILE H 148 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N LEU H 238 " --> pdb=" O VAL H 280 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N ILE H 282 " --> pdb=" O LEU H 238 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N LEU H 240 " --> pdb=" O ILE H 282 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 248 through 249 removed outlier: 3.830A pdb=" N PHE H 256 " --> pdb=" O THR H 259 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3486 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: 8.52 Time building geometry restraints manager: 6.74 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: 8762 1.34 - 1.45: 2923 1.45 - 1.57: 13539 1.57 - 1.69: 0 1.69 - 1.81: 112 Bond restraints: 25336 Sorted by residual: bond pdb=" N ASP D 418 " pdb=" CA ASP D 418 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.23e-02 6.61e+03 1.11e+01 bond pdb=" N ASP B 418 " pdb=" CA ASP B 418 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.23e-02 6.61e+03 1.05e+01 bond pdb=" N ASP G 418 " pdb=" CA ASP G 418 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.29e-02 6.01e+03 9.49e+00 bond pdb=" N ARG E 8 " pdb=" CA ARG E 8 " ideal model delta sigma weight residual 1.453 1.489 -0.036 1.22e-02 6.72e+03 8.53e+00 bond pdb=" N VAL E 7 " pdb=" CA VAL E 7 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.79e+00 ... (remaining 25331 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.45: 33229 1.45 - 2.90: 1071 2.90 - 4.36: 140 4.36 - 5.81: 23 5.81 - 7.26: 1 Bond angle restraints: 34464 Sorted by residual: angle pdb=" CA GLY D 417 " pdb=" C GLY D 417 " pdb=" O GLY D 417 " ideal model delta sigma weight residual 120.91 116.90 4.01 8.70e-01 1.32e+00 2.12e+01 angle pdb=" CA GLY G 417 " pdb=" C GLY G 417 " pdb=" O GLY G 417 " ideal model delta sigma weight residual 120.89 117.09 3.80 9.20e-01 1.18e+00 1.71e+01 angle pdb=" N LEU D 419 " pdb=" CA LEU D 419 " pdb=" C LEU D 419 " ideal model delta sigma weight residual 112.72 108.10 4.62 1.14e+00 7.69e-01 1.64e+01 angle pdb=" N LEU G 419 " pdb=" CA LEU G 419 " pdb=" C LEU G 419 " ideal model delta sigma weight residual 112.72 108.18 4.54 1.14e+00 7.69e-01 1.59e+01 angle pdb=" O GLY G 417 " pdb=" C GLY G 417 " pdb=" N ASP G 418 " ideal model delta sigma weight residual 122.99 126.39 -3.40 8.60e-01 1.35e+00 1.56e+01 ... (remaining 34459 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.39: 13806 17.39 - 34.79: 1076 34.79 - 52.18: 134 52.18 - 69.58: 41 69.58 - 86.97: 39 Dihedral angle restraints: 15096 sinusoidal: 5648 harmonic: 9448 Sorted by residual: dihedral pdb=" C ASP G 418 " pdb=" N ASP G 418 " pdb=" CA ASP G 418 " pdb=" CB ASP G 418 " ideal model delta harmonic sigma weight residual -122.60 -133.26 10.66 0 2.50e+00 1.60e-01 1.82e+01 dihedral pdb=" C ASP D 418 " pdb=" N ASP D 418 " pdb=" CA ASP D 418 " pdb=" CB ASP D 418 " ideal model delta harmonic sigma weight residual -122.60 -133.12 10.52 0 2.50e+00 1.60e-01 1.77e+01 dihedral pdb=" N ASP G 418 " pdb=" C ASP G 418 " pdb=" CA ASP G 418 " pdb=" CB ASP G 418 " ideal model delta harmonic sigma weight residual 122.80 133.16 -10.36 0 2.50e+00 1.60e-01 1.72e+01 ... (remaining 15093 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 3506 0.070 - 0.139: 477 0.139 - 0.209: 6 0.209 - 0.279: 0 0.279 - 0.348: 3 Chirality restraints: 3992 Sorted by residual: chirality pdb=" CA ASP G 418 " pdb=" N ASP G 418 " pdb=" C ASP G 418 " pdb=" CB ASP G 418 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.03e+00 chirality pdb=" CA ASP D 418 " pdb=" N ASP D 418 " pdb=" C ASP D 418 " pdb=" CB ASP D 418 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" CA ASP B 418 " pdb=" N ASP B 418 " pdb=" C ASP B 418 " pdb=" CB ASP B 418 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.73e+00 ... (remaining 3989 not shown) Planarity restraints: 4616 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY C 75 " 0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO C 76 " -0.094 5.00e-02 4.00e+02 pdb=" CA PRO C 76 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO C 76 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 75 " -0.035 5.00e-02 4.00e+02 5.34e-02 4.57e+00 pdb=" N PRO A 76 " 0.092 5.00e-02 4.00e+02 pdb=" CA PRO A 76 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 76 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 75 " 0.033 5.00e-02 4.00e+02 4.96e-02 3.93e+00 pdb=" N PRO E 76 " -0.086 5.00e-02 4.00e+02 pdb=" CA PRO E 76 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO E 76 " 0.028 5.00e-02 4.00e+02 ... (remaining 4613 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2577 2.74 - 3.28: 25365 3.28 - 3.82: 41571 3.82 - 4.36: 51080 4.36 - 4.90: 89231 Nonbonded interactions: 209824 Sorted by model distance: nonbonded pdb=" OD2 ASP C 90 " pdb=" OG1 THR C 343 " model vdw 2.196 3.040 nonbonded pdb=" OG1 THR F 245 " pdb=" OE1 GLU F 288 " model vdw 2.208 3.040 nonbonded pdb=" OG1 THR G 245 " pdb=" OE1 GLU G 288 " model vdw 2.209 3.040 nonbonded pdb=" OE2 GLU H 73 " pdb=" NH2 ARG H 104 " model vdw 2.210 3.120 nonbonded pdb=" OG1 THR C 245 " pdb=" OE1 GLU C 288 " model vdw 2.219 3.040 ... (remaining 209819 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: 4.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.920 Check model and map are aligned: 0.180 Set scattering table: 0.220 Process input model: 54.680 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.120 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 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 : 0.006 0.041 25336 Z= 0.397 Angle : 0.611 7.260 34464 Z= 0.354 Chirality : 0.045 0.348 3992 Planarity : 0.004 0.054 4616 Dihedral : 13.516 86.971 9096 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 9.87 Ramachandran Plot: Outliers : 0.24 % Allowed : 6.89 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Cbeta Deviations : 0.10 % 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: -3.25 (0.12), residues: 3368 helix: -1.03 (0.12), residues: 1360 sheet: -2.54 (0.20), residues: 536 loop : -3.07 (0.13), residues: 1472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 294 HIS 0.008 0.001 HIS H 363 PHE 0.011 0.002 PHE A 247 TYR 0.010 0.002 TYR B 415 ARG 0.008 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 365 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 2.871 Fit side-chains REVERT: B 288 GLU cc_start: 0.7023 (tm-30) cc_final: 0.6720 (tm-30) REVERT: B 294 TRP cc_start: 0.7491 (m100) cc_final: 0.6873 (m100) REVERT: C 294 TRP cc_start: 0.7481 (m100) cc_final: 0.6899 (m100) REVERT: D 294 TRP cc_start: 0.7517 (m100) cc_final: 0.6956 (m100) REVERT: E 247 PHE cc_start: 0.8046 (p90) cc_final: 0.7473 (p90) REVERT: E 294 TRP cc_start: 0.7558 (m100) cc_final: 0.7037 (m100) REVERT: E 414 ARG cc_start: 0.8086 (mmt-90) cc_final: 0.7885 (tpp80) REVERT: F 294 TRP cc_start: 0.7476 (m100) cc_final: 0.7239 (m100) REVERT: G 294 TRP cc_start: 0.7527 (m100) cc_final: 0.6924 (m100) REVERT: H 294 TRP cc_start: 0.7662 (m100) cc_final: 0.7007 (m100) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.3863 time to fit residues: 217.4501 Evaluate side-chains 231 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 231 time to evaluate : 3.025 ------------------------------------------------------------------------------- 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: 2.9990 chunk 254 optimal weight: 0.8980 chunk 141 optimal weight: 9.9990 chunk 86 optimal weight: 2.9990 chunk 171 optimal weight: 2.9990 chunk 136 optimal weight: 0.9990 chunk 263 optimal weight: 0.7980 chunk 101 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 chunk 196 optimal weight: 7.9990 chunk 305 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 GLN A 64 GLN A 147 ASN A 186 HIS A 363 HIS B 147 ASN B 306 GLN B 363 HIS C 186 HIS ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 6 GLN D 147 ASN D 363 HIS E 6 GLN E 147 ASN E 363 HIS F 6 GLN F 147 ASN F 363 HIS G 6 GLN G 147 ASN G 150 ASN G 363 HIS H 6 GLN H 68 GLN H 147 ASN H 363 HIS Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 25336 Z= 0.189 Angle : 0.531 5.937 34464 Z= 0.281 Chirality : 0.041 0.179 3992 Planarity : 0.004 0.036 4616 Dihedral : 4.605 23.570 3632 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.43 % Allowed : 7.48 % Favored : 91.08 % 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: -1.58 (0.14), residues: 3368 helix: 0.73 (0.13), residues: 1408 sheet: -2.11 (0.21), residues: 536 loop : -2.48 (0.14), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 294 HIS 0.006 0.001 HIS F 363 PHE 0.025 0.002 PHE C 247 TYR 0.029 0.001 TYR A 357 ARG 0.003 0.000 ARG A 34 *********************** 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 287 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 251 time to evaluate : 2.801 Fit side-chains REVERT: B 82 ASN cc_start: 0.8073 (t0) cc_final: 0.7812 (t0) REVERT: B 288 GLU cc_start: 0.6988 (tm-30) cc_final: 0.6581 (tm-30) REVERT: B 294 TRP cc_start: 0.7347 (m100) cc_final: 0.6810 (m100) REVERT: C 294 TRP cc_start: 0.7497 (m100) cc_final: 0.7127 (m100) REVERT: D 294 TRP cc_start: 0.7581 (m100) cc_final: 0.6850 (m100) REVERT: E 266 MET cc_start: 0.7183 (mmm) cc_final: 0.6982 (mmm) REVERT: E 294 TRP cc_start: 0.7593 (m100) cc_final: 0.6865 (m100) REVERT: F 247 PHE cc_start: 0.7656 (p90) cc_final: 0.7387 (p90) REVERT: G 294 TRP cc_start: 0.7561 (m100) cc_final: 0.7089 (m100) REVERT: G 419 LEU cc_start: 0.8682 (OUTLIER) cc_final: 0.8475 (mp) REVERT: H 294 TRP cc_start: 0.7534 (m100) cc_final: 0.7026 (m100) outliers start: 36 outliers final: 15 residues processed: 275 average time/residue: 0.3428 time to fit residues: 152.0172 Evaluate side-chains 239 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 2.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 84 ASP Chi-restraints excluded: chain C residue 84 ASP Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 84 ASP Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 419 LEU Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 8.9990 chunk 253 optimal weight: 0.0470 chunk 207 optimal weight: 0.5980 chunk 84 optimal weight: 6.9990 chunk 305 optimal weight: 3.9990 chunk 330 optimal weight: 3.9990 chunk 272 optimal weight: 0.0980 chunk 303 optimal weight: 7.9990 chunk 104 optimal weight: 10.0000 chunk 245 optimal weight: 2.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 147 ASN B 147 ASN B 150 ASN B 306 GLN C 150 ASN ** C 363 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 147 ASN E 147 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 68 GLN H 147 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 25336 Z= 0.175 Angle : 0.490 7.626 34464 Z= 0.257 Chirality : 0.040 0.186 3992 Planarity : 0.003 0.056 4616 Dihedral : 4.324 23.052 3632 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.27 % Allowed : 9.79 % Favored : 88.93 % 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: -0.81 (0.14), residues: 3368 helix: 1.49 (0.13), residues: 1408 sheet: -1.79 (0.22), residues: 528 loop : -2.17 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP F 294 HIS 0.005 0.000 HIS C 363 PHE 0.019 0.002 PHE G 247 TYR 0.021 0.002 TYR C 357 ARG 0.003 0.000 ARG G 326 *********************** 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 275 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 243 time to evaluate : 2.777 Fit side-chains REVERT: B 288 GLU cc_start: 0.6998 (tm-30) cc_final: 0.6577 (tm-30) REVERT: B 294 TRP cc_start: 0.7381 (m100) cc_final: 0.6836 (m100) REVERT: C 290 ASP cc_start: 0.7463 (t0) cc_final: 0.7178 (t0) REVERT: C 294 TRP cc_start: 0.7526 (m100) cc_final: 0.7122 (m100) REVERT: D 290 ASP cc_start: 0.7480 (t0) cc_final: 0.7135 (t0) REVERT: D 294 TRP cc_start: 0.7509 (m100) cc_final: 0.6745 (m100) REVERT: E 294 TRP cc_start: 0.7575 (m100) cc_final: 0.6840 (m100) REVERT: F 294 TRP cc_start: 0.7484 (m100) cc_final: 0.7241 (m100) REVERT: G 245 THR cc_start: 0.8615 (OUTLIER) cc_final: 0.8354 (m) REVERT: G 294 TRP cc_start: 0.7545 (m100) cc_final: 0.7138 (m100) REVERT: H 68 GLN cc_start: 0.8213 (tp40) cc_final: 0.7993 (tp-100) REVERT: H 290 ASP cc_start: 0.7451 (t0) cc_final: 0.7148 (t0) REVERT: H 294 TRP cc_start: 0.7417 (m100) cc_final: 0.6805 (m100) outliers start: 32 outliers final: 15 residues processed: 261 average time/residue: 0.3294 time to fit residues: 142.1467 Evaluate side-chains 239 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 223 time to evaluate : 2.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 297 LEU 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: 5.9990 chunk 229 optimal weight: 3.9990 chunk 158 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 145 optimal weight: 6.9990 chunk 205 optimal weight: 3.9990 chunk 306 optimal weight: 6.9990 chunk 324 optimal weight: 10.0000 chunk 160 optimal weight: 1.9990 chunk 290 optimal weight: 5.9990 chunk 87 optimal weight: 6.9990 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 150 ASN C 68 GLN C 363 HIS D 147 ASN D 186 HIS E 68 GLN E 86 GLN E 147 ASN E 186 HIS F 68 GLN F 147 ASN F 150 ASN F 186 HIS G 147 ASN G 150 ASN G 186 HIS H 147 ASN H 186 HIS Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 25336 Z= 0.442 Angle : 0.604 6.913 34464 Z= 0.320 Chirality : 0.046 0.161 3992 Planarity : 0.005 0.042 4616 Dihedral : 4.597 20.320 3632 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 8.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 1.91 % Allowed : 11.31 % Favored : 86.78 % 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: -1.03 (0.14), residues: 3368 helix: 1.09 (0.13), residues: 1408 sheet: -1.73 (0.22), residues: 528 loop : -2.12 (0.15), residues: 1432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 294 HIS 0.012 0.001 HIS C 363 PHE 0.013 0.002 PHE C 130 TYR 0.029 0.002 TYR G 357 ARG 0.006 0.001 ARG G 326 *********************** 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 278 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 230 time to evaluate : 2.650 Fit side-chains REVERT: B 288 GLU cc_start: 0.7101 (tm-30) cc_final: 0.6712 (tm-30) REVERT: B 294 TRP cc_start: 0.7378 (m100) cc_final: 0.6793 (m100) REVERT: C 294 TRP cc_start: 0.7571 (m100) cc_final: 0.7139 (m100) REVERT: D 294 TRP cc_start: 0.7516 (m100) cc_final: 0.6780 (m100) REVERT: E 294 TRP cc_start: 0.7609 (m100) cc_final: 0.6925 (m100) REVERT: F 294 TRP cc_start: 0.7676 (m100) cc_final: 0.7456 (m100) REVERT: G 294 TRP cc_start: 0.7580 (m100) cc_final: 0.7124 (m100) REVERT: H 294 TRP cc_start: 0.7547 (m100) cc_final: 0.6923 (m100) outliers start: 48 outliers final: 30 residues processed: 256 average time/residue: 0.3279 time to fit residues: 138.4080 Evaluate side-chains 241 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 2.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 99 THR Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain C residue 314 VAL Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 86 GLN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 266 MET Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain G residue 314 VAL Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 270 optimal weight: 0.6980 chunk 184 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 241 optimal weight: 3.9990 chunk 134 optimal weight: 0.6980 chunk 277 optimal weight: 7.9990 chunk 224 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 chunk 165 optimal weight: 1.9990 chunk 291 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN B 150 ASN C 150 ASN D 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 68 GLN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 25336 Z= 0.152 Angle : 0.488 5.906 34464 Z= 0.258 Chirality : 0.040 0.175 3992 Planarity : 0.003 0.032 4616 Dihedral : 4.319 23.196 3632 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.83 % Favored : 96.17 % Rotamer: Outliers : 1.23 % Allowed : 13.02 % Favored : 85.75 % 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: -0.43 (0.15), residues: 3368 helix: 1.77 (0.14), residues: 1416 sheet: -1.52 (0.22), residues: 528 loop : -1.98 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 294 HIS 0.001 0.000 HIS C 139 PHE 0.022 0.001 PHE G 247 TYR 0.024 0.002 TYR E 357 ARG 0.003 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 266 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 235 time to evaluate : 2.551 Fit side-chains REVERT: A 68 GLN cc_start: 0.8418 (tp-100) cc_final: 0.8050 (tp-100) REVERT: A 204 GLU cc_start: 0.7843 (mm-30) cc_final: 0.7535 (mm-30) REVERT: A 294 TRP cc_start: 0.7558 (m-10) cc_final: 0.7100 (m-10) REVERT: B 288 GLU cc_start: 0.7056 (tm-30) cc_final: 0.6671 (tm-30) REVERT: B 294 TRP cc_start: 0.7388 (m100) cc_final: 0.6856 (m100) REVERT: C 290 ASP cc_start: 0.7462 (t0) cc_final: 0.7188 (t0) REVERT: C 294 TRP cc_start: 0.7501 (m100) cc_final: 0.7088 (m100) REVERT: D 294 TRP cc_start: 0.7503 (m100) cc_final: 0.6771 (m100) REVERT: E 68 GLN cc_start: 0.8314 (tp40) cc_final: 0.8066 (tp-100) REVERT: E 294 TRP cc_start: 0.7499 (m100) cc_final: 0.6826 (m100) REVERT: F 294 TRP cc_start: 0.7585 (m100) cc_final: 0.7376 (m100) REVERT: G 68 GLN cc_start: 0.8345 (tp40) cc_final: 0.8051 (tp-100) REVERT: G 294 TRP cc_start: 0.7479 (m100) cc_final: 0.7099 (m100) REVERT: H 290 ASP cc_start: 0.7458 (t0) cc_final: 0.7154 (t0) REVERT: H 294 TRP cc_start: 0.7428 (m100) cc_final: 0.6848 (m100) outliers start: 31 outliers final: 19 residues processed: 251 average time/residue: 0.3330 time to fit residues: 136.1335 Evaluate side-chains 240 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 221 time to evaluate : 2.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 109 optimal weight: 9.9990 chunk 292 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 190 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 325 optimal weight: 5.9990 chunk 269 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 27 optimal weight: 0.6980 chunk 107 optimal weight: 3.9990 chunk 170 optimal weight: 6.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN B 150 ASN D 147 ASN E 86 GLN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 25336 Z= 0.350 Angle : 0.556 6.376 34464 Z= 0.294 Chirality : 0.044 0.170 3992 Planarity : 0.004 0.036 4616 Dihedral : 4.408 20.600 3632 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.06 % Allowed : 5.70 % Favored : 94.24 % Rotamer: Outliers : 1.51 % Allowed : 13.57 % Favored : 84.91 % 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: -0.51 (0.14), residues: 3368 helix: 1.60 (0.13), residues: 1400 sheet: -1.42 (0.22), residues: 528 loop : -1.92 (0.16), residues: 1440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 294 HIS 0.006 0.001 HIS A 363 PHE 0.014 0.002 PHE G 247 TYR 0.025 0.002 TYR B 357 ARG 0.005 0.000 ARG A 34 *********************** 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 267 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 229 time to evaluate : 2.685 Fit side-chains REVERT: A 68 GLN cc_start: 0.8493 (tp-100) cc_final: 0.8160 (tp-100) REVERT: A 204 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7473 (mm-30) REVERT: B 288 GLU cc_start: 0.7211 (tm-30) cc_final: 0.6802 (tm-30) REVERT: B 294 TRP cc_start: 0.7363 (m100) cc_final: 0.6819 (m100) REVERT: C 68 GLN cc_start: 0.8443 (tp-100) cc_final: 0.8196 (tp-100) REVERT: C 294 TRP cc_start: 0.7561 (m100) cc_final: 0.7147 (m100) REVERT: D 294 TRP cc_start: 0.7526 (m100) cc_final: 0.6817 (m100) REVERT: E 68 GLN cc_start: 0.8407 (tp40) cc_final: 0.8160 (tp-100) REVERT: E 294 TRP cc_start: 0.7551 (m100) cc_final: 0.6893 (m100) REVERT: F 294 TRP cc_start: 0.7659 (m100) cc_final: 0.7438 (m100) REVERT: G 294 TRP cc_start: 0.7560 (m100) cc_final: 0.7152 (m100) REVERT: H 294 TRP cc_start: 0.7494 (m100) cc_final: 0.6925 (m100) outliers start: 38 outliers final: 32 residues processed: 249 average time/residue: 0.3268 time to fit residues: 133.9449 Evaluate side-chains 247 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 215 time to evaluate : 2.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 1 MET Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 259 THR Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain F residue 314 VAL Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 314 VAL Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 313 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 185 optimal weight: 1.9990 chunk 237 optimal weight: 0.0970 chunk 183 optimal weight: 9.9990 chunk 273 optimal weight: 0.0970 chunk 181 optimal weight: 0.6980 chunk 323 optimal weight: 0.8980 chunk 202 optimal weight: 0.9990 chunk 197 optimal weight: 0.7980 chunk 149 optimal weight: 4.9990 overall best weight: 0.5176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN B 150 ASN C 150 ASN D 68 GLN D 147 ASN E 150 ASN F 150 ASN G 150 ASN H 68 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 0.1848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 25336 Z= 0.138 Angle : 0.481 5.860 34464 Z= 0.254 Chirality : 0.040 0.174 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.224 23.134 3632 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.15 % Allowed : 14.57 % Favored : 84.28 % 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: -0.13 (0.15), residues: 3368 helix: 1.94 (0.14), residues: 1432 sheet: -1.42 (0.22), residues: 544 loop : -1.74 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP A 294 HIS 0.002 0.000 HIS B 353 PHE 0.019 0.001 PHE G 247 TYR 0.022 0.001 TYR F 357 ARG 0.002 0.000 ARG G 326 *********************** 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 264 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 235 time to evaluate : 2.787 Fit side-chains REVERT: A 68 GLN cc_start: 0.8389 (tp-100) cc_final: 0.8050 (tp-100) REVERT: A 204 GLU cc_start: 0.7768 (mm-30) cc_final: 0.7393 (mm-30) REVERT: B 288 GLU cc_start: 0.7091 (tm-30) cc_final: 0.6703 (tm-30) REVERT: B 294 TRP cc_start: 0.7407 (m100) cc_final: 0.6746 (m100) REVERT: C 68 GLN cc_start: 0.8361 (tp-100) cc_final: 0.8112 (tp-100) REVERT: C 290 ASP cc_start: 0.7476 (t0) cc_final: 0.7201 (t0) REVERT: C 294 TRP cc_start: 0.7500 (m100) cc_final: 0.7108 (m100) REVERT: D 294 TRP cc_start: 0.7431 (m100) cc_final: 0.6807 (m100) REVERT: E 68 GLN cc_start: 0.8330 (tp40) cc_final: 0.8117 (tp-100) REVERT: E 294 TRP cc_start: 0.7540 (m100) cc_final: 0.6892 (m100) REVERT: G 68 GLN cc_start: 0.8305 (tp40) cc_final: 0.8079 (tp-100) REVERT: G 294 TRP cc_start: 0.7506 (m100) cc_final: 0.7117 (m100) REVERT: H 68 GLN cc_start: 0.8325 (tp40) cc_final: 0.8116 (tp-100) REVERT: H 290 ASP cc_start: 0.7462 (t0) cc_final: 0.7179 (t0) REVERT: H 294 TRP cc_start: 0.7413 (m100) cc_final: 0.6863 (m100) outliers start: 29 outliers final: 21 residues processed: 254 average time/residue: 0.3395 time to fit residues: 141.4887 Evaluate side-chains 242 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 221 time to evaluate : 2.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 200 optimal weight: 10.0000 chunk 129 optimal weight: 6.9990 chunk 193 optimal weight: 9.9990 chunk 97 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 62 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 220 optimal weight: 0.4980 chunk 160 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 chunk 254 optimal weight: 5.9990 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 25336 Z= 0.293 Angle : 0.526 6.280 34464 Z= 0.277 Chirality : 0.042 0.163 3992 Planarity : 0.004 0.032 4616 Dihedral : 4.259 21.275 3632 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 1.79 % Allowed : 14.57 % Favored : 83.64 % 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: -0.18 (0.15), residues: 3368 helix: 1.86 (0.14), residues: 1416 sheet: -1.20 (0.23), residues: 528 loop : -1.79 (0.16), residues: 1424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP F 294 HIS 0.005 0.001 HIS A 363 PHE 0.016 0.002 PHE G 247 TYR 0.025 0.002 TYR E 357 ARG 0.004 0.000 ARG A 34 *********************** 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 262 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 217 time to evaluate : 2.655 Fit side-chains REVERT: A 68 GLN cc_start: 0.8462 (tp-100) cc_final: 0.8132 (tp-100) REVERT: A 204 GLU cc_start: 0.7718 (mm-30) cc_final: 0.7379 (mm-30) REVERT: A 294 TRP cc_start: 0.7541 (m-10) cc_final: 0.7115 (m-10) REVERT: B 288 GLU cc_start: 0.7084 (tm-30) cc_final: 0.6688 (tm-30) REVERT: B 294 TRP cc_start: 0.7485 (m100) cc_final: 0.6828 (m100) REVERT: C 68 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8123 (tp-100) REVERT: C 294 TRP cc_start: 0.7512 (m100) cc_final: 0.7116 (m100) REVERT: D 294 TRP cc_start: 0.7471 (m100) cc_final: 0.6827 (m100) REVERT: E 68 GLN cc_start: 0.8367 (tp40) cc_final: 0.8110 (tp-100) REVERT: E 294 TRP cc_start: 0.7557 (m100) cc_final: 0.6955 (m100) REVERT: G 68 GLN cc_start: 0.8347 (tp40) cc_final: 0.8112 (tp-100) REVERT: G 245 THR cc_start: 0.8677 (OUTLIER) cc_final: 0.8320 (m) REVERT: G 288 GLU cc_start: 0.8393 (pm20) cc_final: 0.7759 (pm20) REVERT: G 294 TRP cc_start: 0.7541 (m100) cc_final: 0.7132 (m100) REVERT: H 294 TRP cc_start: 0.7487 (m100) cc_final: 0.6939 (m100) outliers start: 45 outliers final: 26 residues processed: 245 average time/residue: 0.3237 time to fit residues: 131.1299 Evaluate side-chains 238 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 211 time to evaluate : 2.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 81 LEU Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 245 THR Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 294 optimal weight: 5.9990 chunk 310 optimal weight: 3.9990 chunk 283 optimal weight: 4.9990 chunk 301 optimal weight: 0.8980 chunk 181 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 236 optimal weight: 0.9990 chunk 92 optimal weight: 4.9990 chunk 272 optimal weight: 0.3980 chunk 285 optimal weight: 10.0000 chunk 300 optimal weight: 2.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN C 150 ASN D 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 25336 Z= 0.202 Angle : 0.497 6.046 34464 Z= 0.261 Chirality : 0.040 0.165 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.190 22.080 3632 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 7.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.86 % Favored : 96.14 % Rotamer: Outliers : 1.35 % Allowed : 15.13 % Favored : 83.52 % 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: -0.03 (0.15), residues: 3368 helix: 1.95 (0.14), residues: 1432 sheet: -1.29 (0.23), residues: 544 loop : -1.64 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP F 294 HIS 0.003 0.000 HIS A 363 PHE 0.015 0.001 PHE G 247 TYR 0.017 0.001 TYR F 357 ARG 0.002 0.000 ARG G 326 *********************** 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 251 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 217 time to evaluate : 2.898 Fit side-chains REVERT: A 68 GLN cc_start: 0.8406 (tp-100) cc_final: 0.8072 (tp-100) REVERT: A 204 GLU cc_start: 0.7716 (mm-30) cc_final: 0.7385 (mm-30) REVERT: A 294 TRP cc_start: 0.7595 (m-10) cc_final: 0.7110 (m-10) REVERT: B 288 GLU cc_start: 0.7119 (tm-30) cc_final: 0.6727 (tm-30) REVERT: B 294 TRP cc_start: 0.7461 (m100) cc_final: 0.6818 (m100) REVERT: C 68 GLN cc_start: 0.8369 (tp-100) cc_final: 0.8091 (tp-100) REVERT: C 294 TRP cc_start: 0.7507 (m100) cc_final: 0.7129 (m100) REVERT: D 294 TRP cc_start: 0.7455 (m100) cc_final: 0.6824 (m100) REVERT: E 68 GLN cc_start: 0.8357 (tp40) cc_final: 0.8143 (tp-100) REVERT: E 294 TRP cc_start: 0.7558 (m100) cc_final: 0.6936 (m100) REVERT: G 68 GLN cc_start: 0.8305 (tp40) cc_final: 0.8080 (tp-100) REVERT: G 294 TRP cc_start: 0.7526 (m100) cc_final: 0.7116 (m100) REVERT: H 294 TRP cc_start: 0.7457 (m100) cc_final: 0.6929 (m100) outliers start: 34 outliers final: 28 residues processed: 239 average time/residue: 0.3268 time to fit residues: 129.2062 Evaluate side-chains 236 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 208 time to evaluate : 2.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 147 ASN Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 147 ASN Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 147 ASN Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 147 ASN Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 198 optimal weight: 8.9990 chunk 319 optimal weight: 7.9990 chunk 194 optimal weight: 8.9990 chunk 151 optimal weight: 9.9990 chunk 221 optimal weight: 1.9990 chunk 334 optimal weight: 0.9990 chunk 308 optimal weight: 0.2980 chunk 266 optimal weight: 0.1980 chunk 27 optimal weight: 5.9990 chunk 205 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 147 ASN B 147 ASN D 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 25336 Z= 0.187 Angle : 0.493 6.908 34464 Z= 0.260 Chirality : 0.040 0.165 3992 Planarity : 0.003 0.031 4616 Dihedral : 4.152 22.180 3632 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.39 % Allowed : 15.21 % Favored : 83.40 % 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: 0.06 (0.15), residues: 3368 helix: 2.04 (0.14), residues: 1432 sheet: -1.23 (0.23), residues: 544 loop : -1.60 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 294 HIS 0.003 0.000 HIS A 363 PHE 0.015 0.001 PHE G 247 TYR 0.017 0.001 TYR A 357 ARG 0.002 0.000 ARG G 326 ********************** 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 248 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 213 time to evaluate : 2.760 Fit side-chains REVERT: A 68 GLN cc_start: 0.8403 (tp-100) cc_final: 0.8069 (tp-100) REVERT: A 204 GLU cc_start: 0.7705 (mm-30) cc_final: 0.7391 (mm-30) REVERT: A 294 TRP cc_start: 0.7585 (m-10) cc_final: 0.7123 (m-10) REVERT: B 288 GLU cc_start: 0.7018 (tm-30) cc_final: 0.6655 (tm-30) REVERT: B 294 TRP cc_start: 0.7400 (m100) cc_final: 0.6804 (m100) REVERT: C 68 GLN cc_start: 0.8363 (tp-100) cc_final: 0.8085 (tp-100) REVERT: C 290 ASP cc_start: 0.7492 (t0) cc_final: 0.7214 (t0) REVERT: C 294 TRP cc_start: 0.7503 (m100) cc_final: 0.7099 (m100) REVERT: D 294 TRP cc_start: 0.7439 (m100) cc_final: 0.6803 (m100) REVERT: E 68 GLN cc_start: 0.8352 (tp40) cc_final: 0.8140 (tp-100) REVERT: E 294 TRP cc_start: 0.7550 (m100) cc_final: 0.6930 (m100) REVERT: G 68 GLN cc_start: 0.8297 (tp40) cc_final: 0.8072 (tp-100) REVERT: G 294 TRP cc_start: 0.7520 (m100) cc_final: 0.7114 (m100) REVERT: H 294 TRP cc_start: 0.7451 (m100) cc_final: 0.6928 (m100) outliers start: 35 outliers final: 30 residues processed: 234 average time/residue: 0.3339 time to fit residues: 128.4075 Evaluate side-chains 240 residues out of total 2512 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 210 time to evaluate : 2.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 ASP Chi-restraints excluded: chain A residue 211 VAL Chi-restraints excluded: chain A residue 274 LEU Chi-restraints excluded: chain A residue 297 LEU Chi-restraints excluded: chain A residue 313 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain B residue 28 ILE Chi-restraints excluded: chain B residue 147 ASN Chi-restraints excluded: chain B residue 297 LEU Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 419 LEU Chi-restraints excluded: chain C residue 28 ILE Chi-restraints excluded: chain C residue 274 LEU Chi-restraints excluded: chain C residue 297 LEU Chi-restraints excluded: chain D residue 81 LEU Chi-restraints excluded: chain D residue 147 ASN Chi-restraints excluded: chain D residue 297 LEU Chi-restraints excluded: chain E residue 28 ILE Chi-restraints excluded: chain E residue 297 LEU Chi-restraints excluded: chain F residue 81 LEU Chi-restraints excluded: chain F residue 297 LEU Chi-restraints excluded: chain G residue 81 LEU Chi-restraints excluded: chain G residue 211 VAL Chi-restraints excluded: chain G residue 297 LEU Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 249 THR Chi-restraints excluded: chain H residue 261 ARG Chi-restraints excluded: chain H residue 297 LEU Chi-restraints excluded: chain H residue 368 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 336 random chunks: chunk 211 optimal weight: 0.5980 chunk 283 optimal weight: 0.3980 chunk 81 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 266 optimal weight: 0.9990 chunk 111 optimal weight: 0.0770 chunk 274 optimal weight: 2.9990 chunk 33 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 overall best weight: 0.5738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 150 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 147 ASN B 150 ASN D 147 ASN E 147 ASN E 150 ASN F 147 ASN F 150 ASN G 147 ASN G 150 ASN H 147 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.141876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.113664 restraints weight = 34327.255| |-----------------------------------------------------------------------------| r_work (start): 0.3310 rms_B_bonded: 2.03 r_work: 0.3179 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.3039 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8426 moved from start: 0.1943 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.096 25336 Z= 0.193 Angle : 0.776 59.197 34464 Z= 0.452 Chirality : 0.041 0.460 3992 Planarity : 0.003 0.040 4616 Dihedral : 4.181 23.967 3632 Min Nonbonded Distance : 1.808 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.19 % Allowed : 15.61 % Favored : 83.20 % Cbeta Deviations : 0.07 % 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: 0.08 (0.15), residues: 3368 helix: 2.06 (0.14), residues: 1432 sheet: -1.22 (0.23), residues: 544 loop : -1.59 (0.16), residues: 1392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 294 HIS 0.002 0.000 HIS A 363 PHE 0.013 0.001 PHE A 247 TYR 0.017 0.001 TYR F 357 ARG 0.002 0.000 ARG A 34 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4649.98 seconds wall clock time: 84 minutes 1.70 seconds (5041.70 seconds total)