Starting phenix.real_space_refine on Fri Sep 27 03:41:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/09_2024/7bti_30179.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/09_2024/7bti_30179.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/09_2024/7bti_30179.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/09_2024/7bti_30179.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/09_2024/7bti_30179.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bti_30179/09_2024/7bti_30179.cif" } resolution = 3.6 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= 0.001 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 10 5.49 5 Mg 5 5.21 5 S 108 5.16 5 C 9239 2.51 5 N 2475 2.21 5 O 2813 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 14650 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 2855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2855 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "C" Number of atoms: 2868 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2868 Classifications: {'peptide': 369} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 19, 'TRANS': 349} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 369, 2880 Classifications: {'peptide': 369} Link IDs: {'PTRANS': 19, 'TRANS': 349} Chain: "E" Number of atoms: 2862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2862 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 19, 'TRANS': 346} Chain breaks: 1 Chain: "X" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Y" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "Z" Number of atoms: 55 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 55 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'HYP:plan-1': 1, 'ALO:plan-1': 1, 'G5G:plan-1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 9.80, per 1000 atoms: 0.67 Number of scatterers: 14650 At special positions: 0 Unit cell: (95.22, 95.22, 193.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 108 16.00 P 10 15.00 Mg 5 11.99 O 2813 8.00 N 2475 7.00 C 9239 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.56 Conformation dependent library (CDL) restraints added in 1.7 seconds 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3440 Finding SS restraints... Secondary structure from input PDB file: 83 helices and 30 sheets defined 40.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 55 through 61 removed outlier: 3.579A pdb=" N GLN A 59 " --> pdb=" O GLY A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 79 through 95 removed outlier: 4.046A pdb=" N GLU A 93 " --> pdb=" O THR A 89 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.195A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 146 removed outlier: 3.657A pdb=" N SER A 141 " --> pdb=" O GLN A 137 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU A 142 " --> pdb=" O ALA A 138 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 193 removed outlier: 3.698A pdb=" N LYS A 191 " --> pdb=" O ASP A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.792A pdb=" N ILE A 208 " --> pdb=" O ALA A 204 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N ASP A 211 " --> pdb=" O GLU A 207 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N LYS A 215 " --> pdb=" O ASP A 211 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N CYS A 217 " --> pdb=" O LYS A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 257 through 262 removed outlier: 3.598A pdb=" N THR A 260 " --> pdb=" O CYS A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 267 removed outlier: 3.523A pdb=" N PHE A 266 " --> pdb=" O GLN A 263 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N ILE A 267 " --> pdb=" O PRO A 264 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 263 through 267' Processing helix chain 'A' and resid 273 through 284 removed outlier: 4.106A pdb=" N TYR A 279 " --> pdb=" O HIS A 275 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 294 Processing helix chain 'A' and resid 308 through 318 removed outlier: 4.015A pdb=" N THR A 318 " --> pdb=" O GLN A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 347 Processing helix chain 'A' and resid 349 through 354 removed outlier: 3.981A pdb=" N GLN A 354 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 364 removed outlier: 3.685A pdb=" N GLU A 364 " --> pdb=" O GLN A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 372 removed outlier: 3.829A pdb=" N VAL A 370 " --> pdb=" O PRO A 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 Processing helix chain 'B' and resid 79 through 91 removed outlier: 4.125A pdb=" N ILE B 85 " --> pdb=" O ASP B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.142A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 146 removed outlier: 3.949A pdb=" N LEU B 142 " --> pdb=" O ALA B 138 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 193 removed outlier: 3.627A pdb=" N LEU B 185 " --> pdb=" O ALA B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.822A pdb=" N ILE B 208 " --> pdb=" O ALA B 204 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP B 211 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N LYS B 215 " --> pdb=" O ASP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 230 Processing helix chain 'B' and resid 273 through 284 removed outlier: 3.679A pdb=" N TYR B 279 " --> pdb=" O HIS B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 294 removed outlier: 3.943A pdb=" N LYS B 291 " --> pdb=" O ILE B 287 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N ASP B 292 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 305 removed outlier: 3.721A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 311 Processing helix chain 'B' and resid 312 through 319 Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 351 through 355 removed outlier: 4.057A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 removed outlier: 3.699A pdb=" N ASP B 363 " --> pdb=" O LYS B 359 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU B 364 " --> pdb=" O GLN B 360 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 365 " --> pdb=" O GLU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 369 through 374 removed outlier: 3.558A pdb=" N CYS B 374 " --> pdb=" O VAL B 370 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.877A pdb=" N SER C 60 " --> pdb=" O ASP C 56 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 56 through 61' Processing helix chain 'C' and resid 78 through 91 removed outlier: 3.665A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.515A pdb=" N GLU C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N HIS C 101 " --> pdb=" O PRO C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.425A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLU C 117 " --> pdb=" O LYS C 113 " (cutoff:3.500A) Processing helix chain 'C' and resid 136 through 146 removed outlier: 3.642A pdb=" N LEU C 140 " --> pdb=" O ILE C 136 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N SER C 141 " --> pdb=" O GLN C 137 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N LEU C 142 " --> pdb=" O ALA C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 183 through 193 removed outlier: 3.647A pdb=" N LYS C 191 " --> pdb=" O ASP C 187 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 217 removed outlier: 3.683A pdb=" N GLU C 207 " --> pdb=" O THR C 203 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ILE C 208 " --> pdb=" O ALA C 204 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N LYS C 215 " --> pdb=" O ASP C 211 " (cutoff:3.500A) Processing helix chain 'C' and resid 222 through 230 removed outlier: 3.515A pdb=" N ALA C 228 " --> pdb=" O GLU C 224 " (cutoff:3.500A) Processing helix chain 'C' and resid 275 through 284 removed outlier: 3.800A pdb=" N TYR C 279 " --> pdb=" O HIS C 275 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ASN C 280 " --> pdb=" O GLU C 276 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER C 281 " --> pdb=" O THR C 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 295 removed outlier: 4.075A pdb=" N LYS C 291 " --> pdb=" O ILE C 287 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N ASP C 292 " --> pdb=" O ASP C 288 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 311 Processing helix chain 'C' and resid 312 through 317 Processing helix chain 'C' and resid 337 through 348 removed outlier: 3.684A pdb=" N GLY C 343 " --> pdb=" O VAL C 339 " (cutoff:3.500A) Processing helix chain 'C' and resid 352 through 356 removed outlier: 4.007A pdb=" N TRP C 356 " --> pdb=" O GLN C 353 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 removed outlier: 3.777A pdb=" N GLU C 364 " --> pdb=" O GLN C 360 " (cutoff:3.500A) Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'D' and resid 56 through 61 Processing helix chain 'D' and resid 78 through 91 removed outlier: 3.520A pdb=" N GLU D 83 " --> pdb=" O TRP D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 removed outlier: 3.531A pdb=" N GLU D 100 " --> pdb=" O ALA D 97 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N HIS D 101 " --> pdb=" O PRO D 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 97 through 101' Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.208A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) Processing helix chain 'D' and resid 136 through 146 removed outlier: 3.546A pdb=" N LEU D 140 " --> pdb=" O ILE D 136 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N LEU D 142 " --> pdb=" O ALA D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 193 removed outlier: 3.534A pdb=" N TYR D 188 " --> pdb=" O ASP D 184 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N LYS D 191 " --> pdb=" O ASP D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 205 through 217 removed outlier: 3.674A pdb=" N VAL D 209 " --> pdb=" O GLU D 205 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASP D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N LYS D 215 " --> pdb=" O ASP D 211 " (cutoff:3.500A) Processing helix chain 'D' and resid 222 through 230 removed outlier: 3.563A pdb=" N ALA D 228 " --> pdb=" O GLU D 224 " (cutoff:3.500A) Processing helix chain 'D' and resid 258 through 263 removed outlier: 4.378A pdb=" N PHE D 262 " --> pdb=" O PRO D 258 " (cutoff:3.500A) Processing helix chain 'D' and resid 264 through 268 removed outlier: 3.565A pdb=" N ILE D 267 " --> pdb=" O PRO D 264 " (cutoff:3.500A) Processing helix chain 'D' and resid 275 through 284 removed outlier: 4.162A pdb=" N SER D 281 " --> pdb=" O THR D 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 294 removed outlier: 4.152A pdb=" N LYS D 291 " --> pdb=" O ILE D 287 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N ASP D 292 " --> pdb=" O ASP D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 305 removed outlier: 3.859A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 removed outlier: 3.587A pdb=" N ALA D 319 " --> pdb=" O LYS D 315 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 347 Processing helix chain 'D' and resid 351 through 355 removed outlier: 4.067A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.797A pdb=" N GLU D 364 " --> pdb=" O GLN D 360 " (cutoff:3.500A) Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.298A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 55 through 61 removed outlier: 3.640A pdb=" N GLN E 59 " --> pdb=" O GLY E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 78 through 91 removed outlier: 4.122A pdb=" N LYS E 84 " --> pdb=" O ASP E 80 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 removed outlier: 3.855A pdb=" N HIS E 101 " --> pdb=" O PRO E 98 " (cutoff:3.500A) Processing helix chain 'E' and resid 113 through 126 removed outlier: 3.619A pdb=" N GLU E 117 " --> pdb=" O LYS E 113 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N THR E 120 " --> pdb=" O ARG E 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 138 through 145 removed outlier: 3.882A pdb=" N SER E 145 " --> pdb=" O SER E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 193 removed outlier: 3.644A pdb=" N TYR E 188 " --> pdb=" O ASP E 184 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N LYS E 191 " --> pdb=" O ASP E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 217 removed outlier: 3.773A pdb=" N ASP E 211 " --> pdb=" O GLU E 207 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LYS E 215 " --> pdb=" O ASP E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 222 through 230 Processing helix chain 'E' and resid 257 through 261 removed outlier: 3.764A pdb=" N THR E 260 " --> pdb=" O CYS E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 263 through 268 removed outlier: 3.652A pdb=" N PHE E 266 " --> pdb=" O GLN E 263 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ILE E 267 " --> pdb=" O PRO E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 278 through 283 Processing helix chain 'E' and resid 289 through 294 Processing helix chain 'E' and resid 301 through 305 removed outlier: 3.973A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) Processing helix chain 'E' and resid 311 through 318 removed outlier: 3.506A pdb=" N LYS E 315 " --> pdb=" O ASP E 311 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 347 Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 373 removed outlier: 4.199A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 3.665A pdb=" N ALA A 29 " --> pdb=" O ALA A 19 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA A 19 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.458A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.534A pdb=" N VAL A 35 " --> pdb=" O LYS A 68 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG A 37 " --> pdb=" O THR A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 4.107A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'A' and resid 176 through 178 removed outlier: 3.589A pdb=" N ASN A 162 " --> pdb=" O MET A 176 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ASN A 297 " --> pdb=" O ILE A 330 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 239 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 Processing sheet with id=AA8, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.551A pdb=" N ARG B 37 " --> pdb=" O THR B 66 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 42 removed outlier: 4.178A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AB2, first strand: chain 'B' and resid 176 through 178 removed outlier: 3.826A pdb=" N ASP B 154 " --> pdb=" O HIS B 161 " (cutoff:3.500A) removed outlier: 5.963A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.647A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN B 297 " --> pdb=" O ILE B 330 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 removed outlier: 3.573A pdb=" N LYS B 238 " --> pdb=" O ILE B 250 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 8 through 9 removed outlier: 6.720A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 11 through 12 Processing sheet with id=AB6, first strand: chain 'C' and resid 53 through 54 Processing sheet with id=AB7, first strand: chain 'C' and resid 71 through 72 Processing sheet with id=AB8, first strand: chain 'C' and resid 176 through 178 removed outlier: 6.299A pdb=" N ASN C 297 " --> pdb=" O ILE C 330 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'C' and resid 239 through 241 Processing sheet with id=AC1, first strand: chain 'D' and resid 29 through 31 removed outlier: 3.520A pdb=" N VAL D 9 " --> pdb=" O GLY D 20 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 53 through 54 Processing sheet with id=AC3, first strand: chain 'D' and resid 71 through 72 Processing sheet with id=AC4, first strand: chain 'D' and resid 176 through 179 Processing sheet with id=AC5, first strand: chain 'D' and resid 238 through 241 removed outlier: 3.558A pdb=" N LYS D 238 " --> pdb=" O ILE D 250 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ILE D 250 " --> pdb=" O LYS D 238 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 29 through 32 removed outlier: 3.514A pdb=" N PHE E 31 " --> pdb=" O VAL E 17 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.797A pdb=" N LYS E 68 " --> pdb=" O VAL E 35 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 71 through 72 Processing sheet with id=AC9, first strand: chain 'E' and resid 150 through 151 Processing sheet with id=AD1, first strand: chain 'E' and resid 160 through 161 Processing sheet with id=AD2, first strand: chain 'E' and resid 240 through 242 removed outlier: 3.852A pdb=" N GLN E 246 " --> pdb=" O LEU E 242 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'E' and resid 297 through 298 removed outlier: 5.983A pdb=" N ASN E 297 " --> pdb=" O ILE E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD3 511 hydrogen bonds defined for protein. 1350 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: 4.49 Time building geometry restraints manager: 4.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 2443 1.30 - 1.43: 3806 1.43 - 1.56: 8510 1.56 - 1.68: 21 1.68 - 1.81: 189 Bond restraints: 14969 Sorted by residual: bond pdb=" C1' ADP D 402 " pdb=" C2' ADP D 402 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP E 402 " pdb=" C2' ADP E 402 " ideal model delta sigma weight residual 1.524 1.295 0.229 2.00e-02 2.50e+03 1.32e+02 bond pdb=" C1' ADP C 402 " pdb=" C2' ADP C 402 " ideal model delta sigma weight residual 1.524 1.296 0.228 2.00e-02 2.50e+03 1.30e+02 bond pdb=" C1' ADP A 402 " pdb=" C2' ADP A 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.28e+02 bond pdb=" C1' ADP B 402 " pdb=" C2' ADP B 402 " ideal model delta sigma weight residual 1.524 1.298 0.226 2.00e-02 2.50e+03 1.27e+02 ... (remaining 14964 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 19825 2.17 - 4.35: 395 4.35 - 6.52: 50 6.52 - 8.69: 23 8.69 - 10.86: 26 Bond angle restraints: 20319 Sorted by residual: angle pdb=" C GLY C 308 " pdb=" N ILE C 309 " pdb=" CA ILE C 309 " ideal model delta sigma weight residual 121.97 131.32 -9.35 1.80e+00 3.09e-01 2.70e+01 angle pdb=" C GLY E 308 " pdb=" N ILE E 309 " pdb=" CA ILE E 309 " ideal model delta sigma weight residual 121.97 131.14 -9.17 1.80e+00 3.09e-01 2.60e+01 angle pdb=" C GLY B 308 " pdb=" N ILE B 309 " pdb=" CA ILE B 309 " ideal model delta sigma weight residual 121.97 131.11 -9.14 1.80e+00 3.09e-01 2.58e+01 angle pdb=" N HYP X 1 " pdb=" CA HYP X 1 " pdb=" CB HYP X 1 " ideal model delta sigma weight residual 103.00 108.56 -5.56 1.10e+00 8.26e-01 2.55e+01 angle pdb=" N HYP Z 1 " pdb=" CA HYP Z 1 " pdb=" CB HYP Z 1 " ideal model delta sigma weight residual 103.00 108.45 -5.45 1.10e+00 8.26e-01 2.46e+01 ... (remaining 20314 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.53: 8489 27.53 - 55.07: 468 55.07 - 82.60: 53 82.60 - 110.13: 8 110.13 - 137.66: 10 Dihedral angle restraints: 9028 sinusoidal: 3658 harmonic: 5370 Sorted by residual: dihedral pdb=" O2A ADP B 402 " pdb=" O3A ADP B 402 " pdb=" PA ADP B 402 " pdb=" PB ADP B 402 " ideal model delta sinusoidal sigma weight residual -60.00 77.67 -137.66 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP C 402 " pdb=" O3A ADP C 402 " pdb=" PA ADP C 402 " pdb=" PB ADP C 402 " ideal model delta sinusoidal sigma weight residual -60.00 77.62 -137.62 1 2.00e+01 2.50e-03 4.17e+01 dihedral pdb=" O2A ADP E 402 " pdb=" O3A ADP E 402 " pdb=" PA ADP E 402 " pdb=" PB ADP E 402 " ideal model delta sinusoidal sigma weight residual -60.00 75.56 -135.56 1 2.00e+01 2.50e-03 4.11e+01 ... (remaining 9025 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.143: 2242 0.143 - 0.287: 18 0.287 - 0.430: 0 0.430 - 0.574: 0 0.574 - 0.717: 3 Chirality restraints: 2263 Sorted by residual: chirality pdb=" CA G5G X 4 " pdb=" N G5G X 4 " pdb=" C G5G X 4 " pdb=" CB G5G X 4 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" CA G5G Z 4 " pdb=" N G5G Z 4 " pdb=" C G5G Z 4 " pdb=" CB G5G Z 4 " both_signs ideal model delta sigma weight residual False 2.51 1.80 0.71 2.00e-01 2.50e+01 1.26e+01 chirality pdb=" CA G5G Y 4 " pdb=" N G5G Y 4 " pdb=" C G5G Y 4 " pdb=" CB G5G Y 4 " both_signs ideal model delta sigma weight residual False 2.51 1.81 0.70 2.00e-01 2.50e+01 1.23e+01 ... (remaining 2260 not shown) Planarity restraints: 2586 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 306 " 0.045 5.00e-02 4.00e+02 6.81e-02 7.43e+00 pdb=" N PRO E 307 " -0.118 5.00e-02 4.00e+02 pdb=" CA PRO E 307 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 307 " 0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " -0.045 5.00e-02 4.00e+02 6.79e-02 7.37e+00 pdb=" N PRO D 243 " 0.117 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN B 111 " 0.039 5.00e-02 4.00e+02 5.89e-02 5.56e+00 pdb=" N PRO B 112 " -0.102 5.00e-02 4.00e+02 pdb=" CA PRO B 112 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 112 " 0.033 5.00e-02 4.00e+02 ... (remaining 2583 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.65: 243 2.65 - 3.21: 12209 3.21 - 3.77: 22506 3.77 - 4.34: 31095 4.34 - 4.90: 52487 Nonbonded interactions: 118540 Sorted by model distance: nonbonded pdb="MG MG B 401 " pdb=" O2B ADP B 402 " model vdw 2.083 2.170 nonbonded pdb="MG MG D 401 " pdb=" O2B ADP D 402 " model vdw 2.098 2.170 nonbonded pdb="MG MG E 401 " pdb=" O2B ADP E 402 " model vdw 2.109 2.170 nonbonded pdb="MG MG A 401 " pdb=" O3B ADP A 402 " model vdw 2.126 2.170 nonbonded pdb="MG MG C 401 " pdb=" O3B ADP C 402 " model vdw 2.127 2.170 ... (remaining 118535 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' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 374 or r \ esid 401 through 402)) selection = (chain 'B' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or resid 236 through 308 or (resid 309 through 310 and (name N or na \ me CA or name C or name O or name CB )) or resid 311 through 374 or resid 401 th \ rough 402)) selection = (chain 'C' and (resid 6 through 212 or (resid 213 and (name N or name CA or name \ C or name O or name CB )) or resid 214 through 232 or resid 236 through 308 or \ (resid 309 through 310 and (name N or name CA or name C or name O or name CB )) \ or resid 311 through 374 or resid 401 through 402)) selection = (chain 'D' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 232 or resid 236 through 308 or (resid 309 through 310 and (name N or na \ me CA or name C or name O or name CB )) or resid 311 through 374 or resid 401 th \ rough 402)) selection = (chain 'E' and (resid 6 through 48 or (resid 49 through 50 and (name N or name C \ A or name C or name O or name CB )) or resid 51 through 166 or (resid 167 and (n \ ame N or name CA or name C or name O or name CB )) or resid 168 through 212 or ( \ resid 213 and (name N or name CA or name C or name O or name CB )) or resid 214 \ through 308 or (resid 309 through 310 and (name N or name CA or name C or name O \ or name CB )) or resid 311 through 374 or resid 401 through 402)) } ncs_group { reference = chain 'X' selection = chain 'Y' selection = chain 'Z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.820 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: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 34.460 Find NCS groups from input model: 0.770 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 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 : 0.010 0.231 14969 Z= 0.709 Angle : 0.858 10.863 20319 Z= 0.439 Chirality : 0.057 0.717 2263 Planarity : 0.007 0.068 2586 Dihedral : 17.054 137.664 5588 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.70 % Favored : 94.08 % Rotamer: Outliers : 10.93 % Allowed : 11.06 % Favored : 78.01 % 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: -4.46 (0.16), residues: 1825 helix: -3.24 (0.13), residues: 687 sheet: -3.03 (0.24), residues: 312 loop : -2.51 (0.19), residues: 826 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP E 340 HIS 0.005 0.001 HIS D 87 PHE 0.015 0.002 PHE E 255 TYR 0.012 0.001 TYR C 143 ARG 0.004 0.000 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 170 poor density : 116 time to evaluate : 1.605 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 82 MET cc_start: 0.8615 (tpp) cc_final: 0.8371 (tpt) REVERT: A 291 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8705 (mptt) REVERT: A 311 ASP cc_start: 0.8259 (OUTLIER) cc_final: 0.8034 (t0) REVERT: A 313 MET cc_start: 0.8224 (mmm) cc_final: 0.8015 (mmm) REVERT: A 369 ILE cc_start: 0.9149 (OUTLIER) cc_final: 0.8231 (tt) REVERT: B 49 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7416 (pt0) REVERT: B 62 ARG cc_start: 0.8981 (OUTLIER) cc_final: 0.7742 (ptt180) REVERT: B 180 LEU cc_start: 0.8811 (OUTLIER) cc_final: 0.8581 (tt) REVERT: B 291 LYS cc_start: 0.9226 (OUTLIER) cc_final: 0.8178 (mmtt) REVERT: B 328 LYS cc_start: 0.8464 (OUTLIER) cc_final: 0.8145 (tttm) REVERT: B 335 ARG cc_start: 0.9038 (OUTLIER) cc_final: 0.8717 (ptp-170) REVERT: C 51 ASP cc_start: 0.6253 (OUTLIER) cc_final: 0.6053 (m-30) REVERT: C 195 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.6888 (pp20) REVERT: C 370 VAL cc_start: 0.9206 (OUTLIER) cc_final: 0.9001 (p) REVERT: D 50 LYS cc_start: 0.7685 (OUTLIER) cc_final: 0.7441 (ttpp) REVERT: D 140 LEU cc_start: 0.9355 (OUTLIER) cc_final: 0.9123 (mt) REVERT: D 194 THR cc_start: 0.9298 (OUTLIER) cc_final: 0.9079 (p) REVERT: D 260 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8866 (p) REVERT: E 12 ASN cc_start: 0.8865 (t0) cc_final: 0.8533 (p0) REVERT: E 44 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8451 (mpt) REVERT: E 103 THR cc_start: 0.9229 (OUTLIER) cc_final: 0.8966 (m) REVERT: E 227 MET cc_start: 0.8545 (mmm) cc_final: 0.8263 (mmm) outliers start: 170 outliers final: 55 residues processed: 280 average time/residue: 0.2299 time to fit residues: 98.1238 Evaluate side-chains 162 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 89 time to evaluate : 1.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 311 ASP Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain A residue 369 ILE Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 49 GLN Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 103 THR Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 249 THR Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 260 THR Chi-restraints excluded: chain B residue 291 LYS Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 51 ASP Chi-restraints excluded: chain C residue 111 ASN Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 246 GLN Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 25 ASP Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 56 ASP Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 140 LEU Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 151 ILE Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 193 LEU Chi-restraints excluded: chain D residue 194 THR Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 246 GLN Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 260 THR Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 286 ASP Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 335 ARG Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 25 ASP Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 44 MET Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain E residue 111 ASN Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 298 VAL Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 2.9990 chunk 136 optimal weight: 0.0040 chunk 75 optimal weight: 8.9990 chunk 46 optimal weight: 6.9990 chunk 92 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 141 optimal weight: 3.9990 chunk 54 optimal weight: 4.9990 chunk 85 optimal weight: 0.9980 chunk 105 optimal weight: 0.9990 chunk 163 optimal weight: 7.9990 overall best weight: 1.1996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 12 ASN A 115 ASN A 137 GLN A 161 HIS A 353 GLN A 354 GLN B 12 ASN B 49 GLN B 111 ASN B 115 ASN B 162 ASN B 246 GLN C 12 ASN ** C 111 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 115 ASN C 246 GLN C 314 GLN D 88 HIS D 92 ASN D 115 ASN D 137 GLN D 161 HIS D 246 GLN D 314 GLN E 111 ASN E 162 ASN E 314 GLN Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8681 moved from start: 0.1499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 14969 Z= 0.185 Angle : 0.637 8.077 20319 Z= 0.311 Chirality : 0.045 0.189 2263 Planarity : 0.005 0.051 2586 Dihedral : 13.939 138.829 2272 Min Nonbonded Distance : 2.032 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.57 % Allowed : 14.73 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.18), residues: 1825 helix: -1.96 (0.17), residues: 702 sheet: -2.28 (0.25), residues: 332 loop : -1.97 (0.21), residues: 791 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 340 HIS 0.006 0.001 HIS E 101 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.008 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 99 time to evaluate : 1.649 Fit side-chains REVERT: A 291 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8703 (mptt) REVERT: A 320 LEU cc_start: 0.9099 (OUTLIER) cc_final: 0.8864 (pp) REVERT: B 328 LYS cc_start: 0.8395 (OUTLIER) cc_final: 0.8156 (tttm) REVERT: C 195 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.6963 (pp20) REVERT: C 370 VAL cc_start: 0.9192 (OUTLIER) cc_final: 0.8987 (p) REVERT: D 50 LYS cc_start: 0.7267 (OUTLIER) cc_final: 0.6835 (tttm) REVERT: D 141 SER cc_start: 0.9410 (OUTLIER) cc_final: 0.9099 (t) REVERT: E 12 ASN cc_start: 0.8734 (t0) cc_final: 0.8241 (p0) REVERT: E 176 MET cc_start: 0.8680 (mmm) cc_final: 0.8309 (mmt) REVERT: E 227 MET cc_start: 0.8535 (mmm) cc_final: 0.8234 (mmm) REVERT: E 305 MET cc_start: 0.8375 (OUTLIER) cc_final: 0.8018 (mmt) outliers start: 71 outliers final: 38 residues processed: 165 average time/residue: 0.2611 time to fit residues: 67.0402 Evaluate side-chains 139 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 93 time to evaluate : 1.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 370 VAL Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 141 SER Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 136 optimal weight: 0.0570 chunk 111 optimal weight: 0.7980 chunk 45 optimal weight: 7.9990 chunk 163 optimal weight: 2.9990 chunk 176 optimal weight: 0.0570 chunk 145 optimal weight: 7.9990 chunk 162 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 131 optimal weight: 3.9990 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN C 137 GLN C 161 HIS D 115 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 14969 Z= 0.129 Angle : 0.583 6.948 20319 Z= 0.279 Chirality : 0.043 0.168 2263 Planarity : 0.004 0.046 2586 Dihedral : 12.277 139.551 2201 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.88 % Favored : 95.12 % Rotamer: Outliers : 3.47 % Allowed : 15.63 % Favored : 80.90 % 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: -2.47 (0.19), residues: 1825 helix: -1.30 (0.19), residues: 705 sheet: -1.86 (0.26), residues: 332 loop : -1.69 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 340 HIS 0.003 0.000 HIS D 87 PHE 0.007 0.001 PHE E 255 TYR 0.008 0.001 TYR E 166 ARG 0.006 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 98 time to evaluate : 1.655 Fit side-chains REVERT: A 291 LYS cc_start: 0.9044 (OUTLIER) cc_final: 0.8693 (mptt) REVERT: A 320 LEU cc_start: 0.9061 (OUTLIER) cc_final: 0.8825 (pp) REVERT: B 305 MET cc_start: 0.8747 (mmm) cc_final: 0.8467 (tpp) REVERT: B 328 LYS cc_start: 0.8332 (OUTLIER) cc_final: 0.8079 (tttm) REVERT: C 195 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.6922 (pp20) REVERT: C 325 MET cc_start: 0.8440 (mmt) cc_final: 0.8011 (tpt) REVERT: D 50 LYS cc_start: 0.7251 (OUTLIER) cc_final: 0.6759 (tttm) REVERT: D 313 MET cc_start: 0.7699 (mmm) cc_final: 0.7188 (mtp) REVERT: E 45 VAL cc_start: 0.8422 (OUTLIER) cc_final: 0.8064 (t) REVERT: E 227 MET cc_start: 0.8526 (mmm) cc_final: 0.8238 (mmm) outliers start: 54 outliers final: 38 residues processed: 150 average time/residue: 0.2192 time to fit residues: 52.0487 Evaluate side-chains 136 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 92 time to evaluate : 1.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 195 GLU Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain C residue 358 THR Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 9.9990 chunk 84 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 109 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 173 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 155 optimal weight: 3.9990 chunk 46 optimal weight: 0.3980 overall best weight: 2.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 14969 Z= 0.272 Angle : 0.610 7.548 20319 Z= 0.293 Chirality : 0.046 0.232 2263 Planarity : 0.004 0.048 2586 Dihedral : 11.926 138.479 2192 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 3.86 % Allowed : 15.76 % Favored : 80.39 % 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: -2.12 (0.19), residues: 1825 helix: -0.99 (0.19), residues: 705 sheet: -1.65 (0.26), residues: 332 loop : -1.53 (0.22), residues: 788 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.007 0.001 PHE D 266 TYR 0.007 0.001 TYR C 53 ARG 0.003 0.000 ARG B 372 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 90 time to evaluate : 1.668 Fit side-chains REVERT: A 291 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8697 (mptt) REVERT: A 320 LEU cc_start: 0.9078 (OUTLIER) cc_final: 0.8874 (pp) REVERT: B 30 VAL cc_start: 0.8976 (OUTLIER) cc_final: 0.8656 (p) REVERT: B 328 LYS cc_start: 0.8351 (OUTLIER) cc_final: 0.8072 (tttm) REVERT: D 330 ILE cc_start: 0.8767 (OUTLIER) cc_final: 0.8561 (pp) REVERT: E 45 VAL cc_start: 0.8468 (OUTLIER) cc_final: 0.8111 (t) REVERT: E 165 ILE cc_start: 0.9269 (OUTLIER) cc_final: 0.8994 (mm) REVERT: E 176 MET cc_start: 0.8626 (mmm) cc_final: 0.8226 (mmt) REVERT: E 227 MET cc_start: 0.8434 (mmm) cc_final: 0.8123 (mmm) REVERT: E 305 MET cc_start: 0.8322 (OUTLIER) cc_final: 0.8021 (mmt) outliers start: 60 outliers final: 39 residues processed: 147 average time/residue: 0.2275 time to fit residues: 52.8936 Evaluate side-chains 137 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 90 time to evaluate : 1.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 320 LEU Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 30 VAL Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 303 THR Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 10.0000 chunk 98 optimal weight: 6.9990 chunk 2 optimal weight: 9.9990 chunk 129 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 chunk 148 optimal weight: 0.7980 chunk 120 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 88 optimal weight: 5.9990 chunk 156 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 92 ASN ** E 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14969 Z= 0.262 Angle : 0.616 9.735 20319 Z= 0.294 Chirality : 0.046 0.220 2263 Planarity : 0.004 0.051 2586 Dihedral : 11.586 137.639 2185 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 3.86 % Allowed : 15.69 % Favored : 80.45 % 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: -1.90 (0.20), residues: 1825 helix: -0.85 (0.20), residues: 694 sheet: -1.45 (0.27), residues: 332 loop : -1.41 (0.23), residues: 799 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 89 time to evaluate : 1.759 Fit side-chains REVERT: A 180 LEU cc_start: 0.9206 (tp) cc_final: 0.8963 (tp) REVERT: A 291 LYS cc_start: 0.9088 (OUTLIER) cc_final: 0.8696 (mptt) REVERT: B 30 VAL cc_start: 0.8959 (OUTLIER) cc_final: 0.8679 (p) REVERT: B 305 MET cc_start: 0.8713 (mmm) cc_final: 0.8464 (tpp) REVERT: B 328 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.8039 (tttm) REVERT: C 320 LEU cc_start: 0.9184 (OUTLIER) cc_final: 0.8953 (pp) REVERT: D 50 LYS cc_start: 0.7553 (OUTLIER) cc_final: 0.6861 (tmtt) REVERT: D 227 MET cc_start: 0.8175 (mmm) cc_final: 0.7901 (mmm) REVERT: D 313 MET cc_start: 0.7750 (mmm) cc_final: 0.7454 (mtp) REVERT: D 330 ILE cc_start: 0.8820 (OUTLIER) cc_final: 0.8602 (pp) REVERT: E 165 ILE cc_start: 0.9284 (OUTLIER) cc_final: 0.9029 (mm) REVERT: E 176 MET cc_start: 0.8496 (mmm) cc_final: 0.7869 (mtp) REVERT: E 227 MET cc_start: 0.8425 (mmm) cc_final: 0.8119 (mmm) REVERT: E 275 HIS cc_start: 0.8997 (OUTLIER) cc_final: 0.7552 (p-80) REVERT: E 305 MET cc_start: 0.8337 (OUTLIER) cc_final: 0.7982 (mmt) outliers start: 60 outliers final: 37 residues processed: 146 average time/residue: 0.2018 time to fit residues: 46.8299 Evaluate side-chains 134 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 88 time to evaluate : 1.511 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 275 HIS Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 1.9990 chunk 156 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 42 optimal weight: 0.6980 chunk 174 optimal weight: 4.9990 chunk 144 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 3.9990 chunk 91 optimal weight: 5.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 12 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8689 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14969 Z= 0.216 Angle : 0.597 8.717 20319 Z= 0.283 Chirality : 0.045 0.189 2263 Planarity : 0.004 0.049 2586 Dihedral : 11.359 137.757 2183 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.73 % Allowed : 16.01 % Favored : 80.26 % 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: -1.71 (0.20), residues: 1825 helix: -0.67 (0.20), residues: 694 sheet: -1.32 (0.27), residues: 334 loop : -1.32 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 340 HIS 0.003 0.000 HIS D 87 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 90 time to evaluate : 1.802 Fit side-chains REVERT: A 132 MET cc_start: 0.8556 (tmm) cc_final: 0.8316 (tmm) REVERT: A 291 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8689 (mptt) REVERT: B 30 VAL cc_start: 0.8954 (OUTLIER) cc_final: 0.8699 (p) REVERT: B 305 MET cc_start: 0.8797 (mmm) cc_final: 0.8521 (tpp) REVERT: B 328 LYS cc_start: 0.8325 (OUTLIER) cc_final: 0.8035 (tttm) REVERT: C 132 MET cc_start: 0.8370 (ptm) cc_final: 0.8097 (tmm) REVERT: C 320 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8966 (pp) REVERT: D 50 LYS cc_start: 0.7444 (OUTLIER) cc_final: 0.6732 (tmtt) REVERT: D 330 ILE cc_start: 0.8888 (OUTLIER) cc_final: 0.8685 (pp) REVERT: E 165 ILE cc_start: 0.9277 (OUTLIER) cc_final: 0.9015 (mm) REVERT: E 176 MET cc_start: 0.8476 (mmm) cc_final: 0.7899 (mtp) REVERT: E 227 MET cc_start: 0.8436 (mmm) cc_final: 0.8108 (mmm) REVERT: E 305 MET cc_start: 0.8221 (OUTLIER) cc_final: 0.7892 (mmt) outliers start: 58 outliers final: 40 residues processed: 143 average time/residue: 0.2294 time to fit residues: 51.8867 Evaluate side-chains 136 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 88 time to evaluate : 1.789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 LEU Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain A residue 326 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 30 VAL Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 328 LYS Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 267 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 122 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 276 GLU Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 330 ILE Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 0.0870 chunk 19 optimal weight: 5.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 chunk 146 optimal weight: 0.9990 chunk 97 optimal weight: 0.9990 chunk 173 optimal weight: 4.9990 chunk 108 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 0.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 14969 Z= 0.140 Angle : 0.568 8.210 20319 Z= 0.267 Chirality : 0.044 0.169 2263 Planarity : 0.003 0.049 2586 Dihedral : 10.941 135.905 2183 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 6.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 3.73 % Allowed : 16.21 % Favored : 80.06 % 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: -1.55 (0.20), residues: 1825 helix: -0.48 (0.20), residues: 715 sheet: -1.23 (0.28), residues: 335 loop : -1.32 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 356 HIS 0.003 0.000 HIS D 87 PHE 0.007 0.001 PHE E 255 TYR 0.006 0.001 TYR C 69 ARG 0.002 0.000 ARG A 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 91 time to evaluate : 1.770 Fit side-chains revert: symmetry clash REVERT: A 291 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8693 (mptt) REVERT: B 305 MET cc_start: 0.8843 (mmm) cc_final: 0.8469 (tpp) REVERT: C 132 MET cc_start: 0.8402 (ptm) cc_final: 0.8166 (tmm) REVERT: D 50 LYS cc_start: 0.7293 (OUTLIER) cc_final: 0.6633 (tmtt) REVERT: D 313 MET cc_start: 0.7649 (mmm) cc_final: 0.7239 (mtp) REVERT: E 45 VAL cc_start: 0.8421 (OUTLIER) cc_final: 0.8051 (t) REVERT: E 165 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.9004 (mm) REVERT: E 227 MET cc_start: 0.8385 (mmm) cc_final: 0.8055 (mmm) outliers start: 58 outliers final: 36 residues processed: 143 average time/residue: 0.2336 time to fit residues: 52.7933 Evaluate side-chains 129 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 89 time to evaluate : 1.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 190 MET Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 0.0980 chunk 52 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 5.9990 chunk 85 optimal weight: 0.0670 chunk 16 optimal weight: 4.9990 chunk 136 optimal weight: 0.8980 overall best weight: 2.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14969 Z= 0.248 Angle : 0.603 8.832 20319 Z= 0.284 Chirality : 0.046 0.177 2263 Planarity : 0.004 0.052 2586 Dihedral : 10.777 133.453 2170 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 3.09 % Allowed : 16.53 % Favored : 80.39 % 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: -1.40 (0.20), residues: 1825 helix: -0.40 (0.21), residues: 694 sheet: -1.20 (0.28), residues: 337 loop : -1.15 (0.23), residues: 794 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 340 HIS 0.003 0.000 HIS D 87 PHE 0.007 0.001 PHE C 262 TYR 0.007 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 89 time to evaluate : 1.482 Fit side-chains REVERT: A 291 LYS cc_start: 0.9114 (OUTLIER) cc_final: 0.8674 (mptt) REVERT: B 305 MET cc_start: 0.8885 (mmm) cc_final: 0.8603 (tpp) REVERT: C 132 MET cc_start: 0.8378 (ptm) cc_final: 0.8115 (tmm) REVERT: D 50 LYS cc_start: 0.7376 (OUTLIER) cc_final: 0.6683 (tmtt) REVERT: D 313 MET cc_start: 0.7744 (mmm) cc_final: 0.7300 (mtp) REVERT: E 45 VAL cc_start: 0.8441 (OUTLIER) cc_final: 0.8067 (t) REVERT: E 165 ILE cc_start: 0.9257 (OUTLIER) cc_final: 0.9010 (mm) REVERT: E 227 MET cc_start: 0.8383 (mmm) cc_final: 0.8056 (mmm) outliers start: 48 outliers final: 39 residues processed: 130 average time/residue: 0.2362 time to fit residues: 49.1288 Evaluate side-chains 131 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 1.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 180 LEU Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 16 LEU Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 283 MET Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 1.9990 chunk 166 optimal weight: 3.9990 chunk 151 optimal weight: 4.9990 chunk 161 optimal weight: 6.9990 chunk 97 optimal weight: 0.5980 chunk 70 optimal weight: 5.9990 chunk 126 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 146 optimal weight: 0.9990 chunk 152 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 14969 Z= 0.256 Angle : 0.611 7.781 20319 Z= 0.290 Chirality : 0.046 0.184 2263 Planarity : 0.004 0.052 2586 Dihedral : 10.764 132.005 2170 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.02 % Allowed : 16.46 % Favored : 80.51 % 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: -1.36 (0.20), residues: 1825 helix: -0.38 (0.20), residues: 691 sheet: -1.14 (0.28), residues: 337 loop : -1.12 (0.23), residues: 797 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 340 HIS 0.003 0.001 HIS D 87 PHE 0.008 0.001 PHE E 255 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 89 time to evaluate : 1.540 Fit side-chains REVERT: A 291 LYS cc_start: 0.9123 (OUTLIER) cc_final: 0.8690 (mptt) REVERT: B 305 MET cc_start: 0.8887 (mmm) cc_final: 0.8602 (tpp) REVERT: D 50 LYS cc_start: 0.7299 (OUTLIER) cc_final: 0.6687 (tmmm) REVERT: E 45 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8091 (t) REVERT: E 165 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9050 (mm) REVERT: E 176 MET cc_start: 0.8476 (mmm) cc_final: 0.7970 (mmt) REVERT: E 227 MET cc_start: 0.8313 (mmm) cc_final: 0.7988 (mmm) REVERT: E 305 MET cc_start: 0.8207 (OUTLIER) cc_final: 0.7862 (mmt) outliers start: 47 outliers final: 38 residues processed: 130 average time/residue: 0.2199 time to fit residues: 45.6435 Evaluate side-chains 131 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 88 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 16 LEU Chi-restraints excluded: chain B residue 180 LEU Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain D residue 325 MET Chi-restraints excluded: chain D residue 369 ILE Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 165 ILE Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain E residue 354 GLN Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 6.9990 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 0.8980 chunk 118 optimal weight: 0.7980 chunk 179 optimal weight: 0.0050 chunk 165 optimal weight: 0.2980 chunk 142 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 110 optimal weight: 0.9990 chunk 87 optimal weight: 7.9990 chunk 113 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 59 GLN D 252 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8637 moved from start: 0.2605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14969 Z= 0.133 Angle : 0.569 8.397 20319 Z= 0.267 Chirality : 0.044 0.169 2263 Planarity : 0.003 0.050 2586 Dihedral : 10.367 130.976 2170 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 2.70 % Allowed : 16.98 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.15 (0.20), residues: 1825 helix: -0.14 (0.21), residues: 679 sheet: -1.16 (0.27), residues: 361 loop : -0.97 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 356 HIS 0.002 0.000 HIS D 87 PHE 0.007 0.001 PHE E 255 TYR 0.006 0.001 TYR D 166 ARG 0.002 0.000 ARG E 256 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3650 Ramachandran restraints generated. 1825 Oldfield, 0 Emsley, 1825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 91 time to evaluate : 1.748 Fit side-chains REVERT: A 291 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8678 (mptt) REVERT: B 305 MET cc_start: 0.8819 (mmm) cc_final: 0.8462 (tpp) REVERT: C 132 MET cc_start: 0.8386 (ptm) cc_final: 0.8184 (tmm) REVERT: D 50 LYS cc_start: 0.7369 (OUTLIER) cc_final: 0.6778 (tmmm) REVERT: D 313 MET cc_start: 0.7693 (mmm) cc_final: 0.7268 (mtp) REVERT: E 45 VAL cc_start: 0.8406 (OUTLIER) cc_final: 0.8031 (t) REVERT: E 227 MET cc_start: 0.8370 (mmm) cc_final: 0.8031 (mmm) REVERT: E 305 MET cc_start: 0.7991 (OUTLIER) cc_final: 0.7406 (mmt) outliers start: 42 outliers final: 32 residues processed: 127 average time/residue: 0.2299 time to fit residues: 46.5420 Evaluate side-chains 125 residues out of total 1560 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 89 time to evaluate : 1.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 30 VAL Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 175 ILE Chi-restraints excluded: chain A residue 283 MET Chi-restraints excluded: chain A residue 291 LYS Chi-restraints excluded: chain B residue 14 SER Chi-restraints excluded: chain B residue 253 GLU Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain B residue 335 ARG Chi-restraints excluded: chain C residue 134 VAL Chi-restraints excluded: chain C residue 151 ILE Chi-restraints excluded: chain C residue 159 VAL Chi-restraints excluded: chain C residue 320 LEU Chi-restraints excluded: chain D residue 14 SER Chi-restraints excluded: chain D residue 50 LYS Chi-restraints excluded: chain D residue 64 ILE Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 134 VAL Chi-restraints excluded: chain D residue 236 LEU Chi-restraints excluded: chain D residue 253 GLU Chi-restraints excluded: chain D residue 267 ILE Chi-restraints excluded: chain D residue 305 MET Chi-restraints excluded: chain E residue 14 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 30 VAL Chi-restraints excluded: chain E residue 45 VAL Chi-restraints excluded: chain E residue 134 VAL Chi-restraints excluded: chain E residue 193 LEU Chi-restraints excluded: chain E residue 202 THR Chi-restraints excluded: chain E residue 253 GLU Chi-restraints excluded: chain E residue 303 THR Chi-restraints excluded: chain E residue 305 MET Chi-restraints excluded: chain E residue 355 MET Chi-restraints excluded: chain E residue 369 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 8.9990 chunk 43 optimal weight: 5.9990 chunk 131 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 143 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 146 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 10.0000 chunk 125 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.056272 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2623 r_free = 0.2623 target = 0.047331 restraints weight = 43426.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.048877 restraints weight = 22067.892| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.049890 restraints weight = 13846.403| |-----------------------------------------------------------------------------| r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 14969 Z= 0.285 Angle : 0.616 7.858 20319 Z= 0.292 Chirality : 0.046 0.180 2263 Planarity : 0.004 0.053 2586 Dihedral : 10.377 124.308 2165 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.57 % Allowed : 17.36 % Favored : 80.06 % 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: -1.28 (0.20), residues: 1825 helix: -0.30 (0.20), residues: 703 sheet: -1.01 (0.28), residues: 337 loop : -1.14 (0.23), residues: 785 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 340 HIS 0.003 0.001 HIS D 87 PHE 0.009 0.001 PHE C 262 TYR 0.008 0.001 TYR C 69 ARG 0.003 0.000 ARG A 256 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2325.28 seconds wall clock time: 44 minutes 46.33 seconds (2686.33 seconds total)