Starting phenix.real_space_refine on Wed Jul 24 04:47:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/07_2024/7uuw_26805_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/07_2024/7uuw_26805.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/07_2024/7uuw_26805.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/07_2024/7uuw_26805.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/07_2024/7uuw_26805_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7uuw_26805/07_2024/7uuw_26805_neut.cif" } resolution = 3.36 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= 0.066 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 12 5.49 5 Mg 6 5.21 5 S 192 5.16 5 C 15654 2.51 5 N 4242 2.21 5 O 4746 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 25": "OD1" <-> "OD2" Residue "A ARG 28": "NH1" <-> "NH2" Residue "A GLU 93": "OE1" <-> "OE2" Residue "A ASP 184": "OD1" <-> "OD2" Residue "A GLU 205": "OE1" <-> "OE2" Residue "A ARG 206": "NH1" <-> "NH2" Residue "A GLU 224": "OE1" <-> "OE2" Residue "A TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 270": "OE1" <-> "OE2" Residue "A GLU 361": "OE1" <-> "OE2" Residue "A ASP 363": "OD1" <-> "OD2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B ARG 28": "NH1" <-> "NH2" Residue "B GLU 93": "OE1" <-> "OE2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 205": "OE1" <-> "OE2" Residue "B ARG 206": "NH1" <-> "NH2" Residue "B GLU 224": "OE1" <-> "OE2" Residue "B TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 270": "OE1" <-> "OE2" Residue "B GLU 361": "OE1" <-> "OE2" Residue "B ASP 363": "OD1" <-> "OD2" Residue "C ASP 25": "OD1" <-> "OD2" Residue "C ARG 28": "NH1" <-> "NH2" Residue "C GLU 93": "OE1" <-> "OE2" Residue "C ASP 184": "OD1" <-> "OD2" Residue "C GLU 205": "OE1" <-> "OE2" Residue "C ARG 206": "NH1" <-> "NH2" Residue "C GLU 224": "OE1" <-> "OE2" Residue "C TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 270": "OE1" <-> "OE2" Residue "C GLU 361": "OE1" <-> "OE2" Residue "C ASP 363": "OD1" <-> "OD2" Residue "D ASP 25": "OD1" <-> "OD2" Residue "D ARG 28": "NH1" <-> "NH2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "D ASP 184": "OD1" <-> "OD2" Residue "D GLU 205": "OE1" <-> "OE2" Residue "D ARG 206": "NH1" <-> "NH2" Residue "D GLU 224": "OE1" <-> "OE2" Residue "D TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 270": "OE1" <-> "OE2" Residue "D GLU 361": "OE1" <-> "OE2" Residue "D ASP 363": "OD1" <-> "OD2" Residue "E ASP 25": "OD1" <-> "OD2" Residue "E ARG 28": "NH1" <-> "NH2" Residue "E GLU 93": "OE1" <-> "OE2" Residue "E ASP 184": "OD1" <-> "OD2" Residue "E GLU 205": "OE1" <-> "OE2" Residue "E ARG 206": "NH1" <-> "NH2" Residue "E GLU 224": "OE1" <-> "OE2" Residue "E TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "E GLU 361": "OE1" <-> "OE2" Residue "E ASP 363": "OD1" <-> "OD2" Residue "F ASP 25": "OD1" <-> "OD2" Residue "F ARG 28": "NH1" <-> "NH2" Residue "F GLU 93": "OE1" <-> "OE2" Residue "F ASP 184": "OD1" <-> "OD2" Residue "F GLU 205": "OE1" <-> "OE2" Residue "F ARG 206": "NH1" <-> "NH2" Residue "F GLU 224": "OE1" <-> "OE2" Residue "F TYR 240": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 270": "OE1" <-> "OE2" Residue "F GLU 361": "OE1" <-> "OE2" Residue "F ASP 363": "OD1" <-> "OD2" Residue "G ARG 750": "NH1" <-> "NH2" Residue "G ARG 873": "NH1" <-> "NH2" Residue "H ARG 750": "NH1" <-> "NH2" Residue "H ARG 873": "NH1" <-> "NH2" Residue "I ARG 750": "NH1" <-> "NH2" Residue "I ARG 873": "NH1" <-> "NH2" Residue "K ARG 750": "NH1" <-> "NH2" Residue "K ARG 873": "NH1" <-> "NH2" Residue "L ARG 750": "NH1" <-> "NH2" Residue "L ARG 873": "NH1" <-> "NH2" Residue "Z ARG 750": "NH1" <-> "NH2" Residue "Z ARG 873": "NH1" <-> "NH2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 24852 Number of models: 1 Model: "" Number of chains: 18 Chain: "A" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 2888 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 2888 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 19, 'TRANS': 350} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'HIC:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "H" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "I" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "K" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "L" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 3 Chain: "Z" Number of atoms: 1226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1226 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 5, 'TRANS': 153} Chain breaks: 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} Chain: "F" 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: 13.82, per 1000 atoms: 0.56 Number of scatterers: 24852 At special positions: 0 Unit cell: (102.384, 120.528, 222.912, 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 192 16.00 P 12 15.00 Mg 6 11.99 O 4746 8.00 N 4242 7.00 C 15654 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 9.05 Conformation dependent library (CDL) restraints added in 4.2 seconds 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5940 Finding SS restraints... Secondary structure from input PDB file: 168 helices and 36 sheets defined 59.4% alpha, 8.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.88 Creating SS restraints... Processing helix chain 'A' and resid 56 through 61 removed outlier: 3.762A pdb=" N LYS A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.513A pdb=" N LEU A 65 " --> pdb=" O ARG A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET A 82 " --> pdb=" O ASN A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 97 through 101 Processing helix chain 'A' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG A 116 " --> pdb=" O PRO A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 145 Processing helix chain 'A' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE A 175 " --> pdb=" O PRO A 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 172 through 175' Processing helix chain 'A' and resid 181 through 194 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 222 through 233 Processing helix chain 'A' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG A 256 " --> pdb=" O ASN A 252 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N CYS A 257 " --> pdb=" O GLU A 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 252 through 257' Processing helix chain 'A' and resid 258 through 261 Processing helix chain 'A' and resid 273 through 283 Processing helix chain 'A' and resid 284 through 285 No H-bonds generated for 'chain 'A' and resid 284 through 285' Processing helix chain 'A' and resid 286 through 288 No H-bonds generated for 'chain 'A' and resid 286 through 288' Processing helix chain 'A' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA A 295 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR A 304 " --> pdb=" O GLY A 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR A 306 " --> pdb=" O THR A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 334 through 336 No H-bonds generated for 'chain 'A' and resid 334 through 336' Processing helix chain 'A' and resid 337 through 348 Processing helix chain 'A' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN A 353 " --> pdb=" O SER A 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN A 354 " --> pdb=" O THR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 366 Processing helix chain 'A' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG A 372 " --> pdb=" O SER A 368 " (cutoff:3.500A) Processing helix chain 'B' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 65 removed outlier: 3.513A pdb=" N LEU B 65 " --> pdb=" O ARG B 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 62 through 65' Processing helix chain 'B' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET B 82 " --> pdb=" O ASN B 78 " (cutoff:3.500A) Processing helix chain 'B' and resid 97 through 101 Processing helix chain 'B' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG B 116 " --> pdb=" O PRO B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 145 Processing helix chain 'B' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE B 175 " --> pdb=" O PRO B 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 172 through 175' Processing helix chain 'B' and resid 181 through 194 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 222 through 233 Processing helix chain 'B' and resid 252 through 257 removed outlier: 3.784A pdb=" N ARG B 256 " --> pdb=" O ASN B 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 257 " --> pdb=" O GLU B 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 252 through 257' Processing helix chain 'B' and resid 258 through 261 Processing helix chain 'B' and resid 273 through 283 Processing helix chain 'B' and resid 284 through 285 No H-bonds generated for 'chain 'B' and resid 284 through 285' Processing helix chain 'B' and resid 286 through 288 No H-bonds generated for 'chain 'B' and resid 286 through 288' Processing helix chain 'B' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA B 295 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR B 304 " --> pdb=" O GLY B 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR B 306 " --> pdb=" O THR B 303 " (cutoff:3.500A) Processing helix chain 'B' and resid 308 through 319 Processing helix chain 'B' and resid 334 through 336 No H-bonds generated for 'chain 'B' and resid 334 through 336' Processing helix chain 'B' and resid 337 through 348 Processing helix chain 'B' and resid 350 through 355 removed outlier: 3.737A pdb=" N GLN B 353 " --> pdb=" O SER B 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN B 354 " --> pdb=" O THR B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 366 Processing helix chain 'B' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG B 372 " --> pdb=" O SER B 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU C 65 " --> pdb=" O ARG C 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 62 through 65' Processing helix chain 'C' and resid 78 through 92 removed outlier: 3.582A pdb=" N MET C 82 " --> pdb=" O ASN C 78 " (cutoff:3.500A) Processing helix chain 'C' and resid 97 through 101 Processing helix chain 'C' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG C 116 " --> pdb=" O PRO C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 137 through 145 Processing helix chain 'C' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE C 175 " --> pdb=" O PRO C 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 172 through 175' Processing helix chain 'C' and resid 181 through 194 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 222 through 233 Processing helix chain 'C' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG C 256 " --> pdb=" O ASN C 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS C 257 " --> pdb=" O GLU C 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 252 through 257' Processing helix chain 'C' and resid 258 through 261 Processing helix chain 'C' and resid 273 through 283 Processing helix chain 'C' and resid 284 through 285 No H-bonds generated for 'chain 'C' and resid 284 through 285' Processing helix chain 'C' and resid 286 through 288 No H-bonds generated for 'chain 'C' and resid 286 through 288' Processing helix chain 'C' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA C 295 " --> pdb=" O LYS C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 301 through 306 removed outlier: 3.590A pdb=" N THR C 304 " --> pdb=" O GLY C 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR C 306 " --> pdb=" O THR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 308 through 319 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 337 through 348 Processing helix chain 'C' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN C 353 " --> pdb=" O SER C 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN C 354 " --> pdb=" O THR C 351 " (cutoff:3.500A) Processing helix chain 'C' and resid 359 through 366 Processing helix chain 'C' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG C 372 " --> pdb=" O SER C 368 " (cutoff:3.500A) Processing helix chain 'D' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS D 61 " --> pdb=" O GLU D 57 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU D 65 " --> pdb=" O ARG D 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 62 through 65' Processing helix chain 'D' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET D 82 " --> pdb=" O ASN D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 97 through 101 Processing helix chain 'D' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG D 116 " --> pdb=" O PRO D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 137 through 145 Processing helix chain 'D' and resid 172 through 175 removed outlier: 3.780A pdb=" N ILE D 175 " --> pdb=" O PRO D 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 172 through 175' Processing helix chain 'D' and resid 181 through 194 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 222 through 233 Processing helix chain 'D' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG D 256 " --> pdb=" O ASN D 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS D 257 " --> pdb=" O GLU D 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 252 through 257' Processing helix chain 'D' and resid 258 through 261 Processing helix chain 'D' and resid 273 through 283 Processing helix chain 'D' and resid 284 through 285 No H-bonds generated for 'chain 'D' and resid 284 through 285' Processing helix chain 'D' and resid 286 through 288 No H-bonds generated for 'chain 'D' and resid 286 through 288' Processing helix chain 'D' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA D 295 " --> pdb=" O LYS D 291 " (cutoff:3.500A) Processing helix chain 'D' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR D 304 " --> pdb=" O GLY D 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR D 306 " --> pdb=" O THR D 303 " (cutoff:3.500A) Processing helix chain 'D' and resid 308 through 319 Processing helix chain 'D' and resid 334 through 336 No H-bonds generated for 'chain 'D' and resid 334 through 336' Processing helix chain 'D' and resid 337 through 348 Processing helix chain 'D' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN D 353 " --> pdb=" O SER D 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN D 354 " --> pdb=" O THR D 351 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 Processing helix chain 'D' and resid 368 through 374 removed outlier: 4.069A pdb=" N ARG D 372 " --> pdb=" O SER D 368 " (cutoff:3.500A) Processing helix chain 'E' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS E 61 " --> pdb=" O GLU E 57 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU E 65 " --> pdb=" O ARG E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET E 82 " --> pdb=" O ASN E 78 " (cutoff:3.500A) Processing helix chain 'E' and resid 97 through 101 Processing helix chain 'E' and resid 112 through 126 removed outlier: 4.016A pdb=" N ARG E 116 " --> pdb=" O PRO E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 137 through 145 Processing helix chain 'E' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE E 175 " --> pdb=" O PRO E 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 172 through 175' Processing helix chain 'E' and resid 181 through 194 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 222 through 233 Processing helix chain 'E' and resid 252 through 257 removed outlier: 3.783A pdb=" N ARG E 256 " --> pdb=" O ASN E 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS E 257 " --> pdb=" O GLU E 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 252 through 257' Processing helix chain 'E' and resid 258 through 261 Processing helix chain 'E' and resid 273 through 283 Processing helix chain 'E' and resid 284 through 285 No H-bonds generated for 'chain 'E' and resid 284 through 285' Processing helix chain 'E' and resid 286 through 288 No H-bonds generated for 'chain 'E' and resid 286 through 288' Processing helix chain 'E' and resid 289 through 295 removed outlier: 3.581A pdb=" N ALA E 295 " --> pdb=" O LYS E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 301 through 306 removed outlier: 3.589A pdb=" N THR E 304 " --> pdb=" O GLY E 301 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N TYR E 306 " --> pdb=" O THR E 303 " (cutoff:3.500A) Processing helix chain 'E' and resid 308 through 319 Processing helix chain 'E' and resid 334 through 336 No H-bonds generated for 'chain 'E' and resid 334 through 336' Processing helix chain 'E' and resid 337 through 348 Processing helix chain 'E' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN E 353 " --> pdb=" O SER E 350 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLN E 354 " --> pdb=" O THR E 351 " (cutoff:3.500A) Processing helix chain 'E' and resid 359 through 366 Processing helix chain 'E' and resid 368 through 374 removed outlier: 4.068A pdb=" N ARG E 372 " --> pdb=" O SER E 368 " (cutoff:3.500A) Processing helix chain 'F' and resid 56 through 61 removed outlier: 3.761A pdb=" N LYS F 61 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 65 removed outlier: 3.514A pdb=" N LEU F 65 " --> pdb=" O ARG F 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 62 through 65' Processing helix chain 'F' and resid 78 through 92 removed outlier: 3.581A pdb=" N MET F 82 " --> pdb=" O ASN F 78 " (cutoff:3.500A) Processing helix chain 'F' and resid 97 through 101 Processing helix chain 'F' and resid 112 through 126 removed outlier: 4.017A pdb=" N ARG F 116 " --> pdb=" O PRO F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 137 through 145 Processing helix chain 'F' and resid 172 through 175 removed outlier: 3.781A pdb=" N ILE F 175 " --> pdb=" O PRO F 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 172 through 175' Processing helix chain 'F' and resid 181 through 194 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 222 through 233 Processing helix chain 'F' and resid 252 through 257 removed outlier: 3.782A pdb=" N ARG F 256 " --> pdb=" O ASN F 252 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS F 257 " --> pdb=" O GLU F 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 252 through 257' Processing helix chain 'F' and resid 258 through 261 Processing helix chain 'F' and resid 273 through 283 Processing helix chain 'F' and resid 284 through 285 No H-bonds generated for 'chain 'F' and resid 284 through 285' Processing helix chain 'F' and resid 286 through 288 No H-bonds generated for 'chain 'F' and resid 286 through 288' Processing helix chain 'F' and resid 289 through 295 removed outlier: 3.582A pdb=" N ALA F 295 " --> pdb=" O LYS F 291 " (cutoff:3.500A) Processing helix chain 'F' and resid 301 through 306 removed outlier: 3.588A pdb=" N THR F 304 " --> pdb=" O GLY F 301 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N TYR F 306 " --> pdb=" O THR F 303 " (cutoff:3.500A) Processing helix chain 'F' and resid 308 through 319 Processing helix chain 'F' and resid 334 through 336 No H-bonds generated for 'chain 'F' and resid 334 through 336' Processing helix chain 'F' and resid 337 through 348 Processing helix chain 'F' and resid 350 through 355 removed outlier: 3.736A pdb=" N GLN F 353 " --> pdb=" O SER F 350 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLN F 354 " --> pdb=" O THR F 351 " (cutoff:3.500A) Processing helix chain 'F' and resid 359 through 366 Processing helix chain 'F' and resid 368 through 374 removed outlier: 4.067A pdb=" N ARG F 372 " --> pdb=" O SER F 368 " (cutoff:3.500A) Processing helix chain 'G' and resid 691 through 696 Processing helix chain 'G' and resid 714 through 738 Processing helix chain 'G' and resid 744 through 773 Processing helix chain 'G' and resid 776 through 810 removed outlier: 3.621A pdb=" N LYS G 780 " --> pdb=" O SER G 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY G 810 " --> pdb=" O VAL G 806 " (cutoff:3.500A) Processing helix chain 'G' and resid 818 through 848 removed outlier: 4.250A pdb=" N SER G 823 " --> pdb=" O ASP G 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU G 824 " --> pdb=" O SER G 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN G 837 " --> pdb=" O THR G 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR G 838 " --> pdb=" O ALA G 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS G 840 " --> pdb=" O VAL G 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA G 841 " --> pdb=" O GLN G 837 " (cutoff:3.500A) Processing helix chain 'H' and resid 691 through 696 Processing helix chain 'H' and resid 714 through 738 Processing helix chain 'H' and resid 744 through 773 Processing helix chain 'H' and resid 776 through 810 removed outlier: 3.621A pdb=" N LYS H 780 " --> pdb=" O SER H 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY H 810 " --> pdb=" O VAL H 806 " (cutoff:3.500A) Processing helix chain 'H' and resid 818 through 848 removed outlier: 4.252A pdb=" N SER H 823 " --> pdb=" O ASP H 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU H 824 " --> pdb=" O SER H 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN H 837 " --> pdb=" O THR H 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR H 838 " --> pdb=" O ALA H 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS H 840 " --> pdb=" O VAL H 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA H 841 " --> pdb=" O GLN H 837 " (cutoff:3.500A) Processing helix chain 'I' and resid 691 through 696 Processing helix chain 'I' and resid 714 through 738 Processing helix chain 'I' and resid 744 through 773 Processing helix chain 'I' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS I 780 " --> pdb=" O SER I 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY I 810 " --> pdb=" O VAL I 806 " (cutoff:3.500A) Processing helix chain 'I' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER I 823 " --> pdb=" O ASP I 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU I 824 " --> pdb=" O SER I 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN I 837 " --> pdb=" O THR I 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR I 838 " --> pdb=" O ALA I 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS I 840 " --> pdb=" O VAL I 836 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA I 841 " --> pdb=" O GLN I 837 " (cutoff:3.500A) Processing helix chain 'K' and resid 691 through 696 Processing helix chain 'K' and resid 714 through 738 Processing helix chain 'K' and resid 744 through 773 Processing helix chain 'K' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS K 780 " --> pdb=" O SER K 776 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N GLY K 810 " --> pdb=" O VAL K 806 " (cutoff:3.500A) Processing helix chain 'K' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER K 823 " --> pdb=" O ASP K 819 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N LEU K 824 " --> pdb=" O SER K 820 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN K 837 " --> pdb=" O THR K 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR K 838 " --> pdb=" O ALA K 834 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LYS K 840 " --> pdb=" O VAL K 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA K 841 " --> pdb=" O GLN K 837 " (cutoff:3.500A) Processing helix chain 'L' and resid 691 through 696 Processing helix chain 'L' and resid 714 through 738 Processing helix chain 'L' and resid 744 through 773 Processing helix chain 'L' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS L 780 " --> pdb=" O SER L 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY L 810 " --> pdb=" O VAL L 806 " (cutoff:3.500A) Processing helix chain 'L' and resid 818 through 848 removed outlier: 4.250A pdb=" N SER L 823 " --> pdb=" O ASP L 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU L 824 " --> pdb=" O SER L 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN L 837 " --> pdb=" O THR L 833 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR L 838 " --> pdb=" O ALA L 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS L 840 " --> pdb=" O VAL L 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA L 841 " --> pdb=" O GLN L 837 " (cutoff:3.500A) Processing helix chain 'Z' and resid 691 through 696 Processing helix chain 'Z' and resid 714 through 738 Processing helix chain 'Z' and resid 744 through 773 Processing helix chain 'Z' and resid 776 through 810 removed outlier: 3.622A pdb=" N LYS Z 780 " --> pdb=" O SER Z 776 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY Z 810 " --> pdb=" O VAL Z 806 " (cutoff:3.500A) Processing helix chain 'Z' and resid 818 through 848 removed outlier: 4.251A pdb=" N SER Z 823 " --> pdb=" O ASP Z 819 " (cutoff:3.500A) removed outlier: 4.507A pdb=" N LEU Z 824 " --> pdb=" O SER Z 820 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N GLN Z 837 " --> pdb=" O THR Z 833 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N THR Z 838 " --> pdb=" O ALA Z 834 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LYS Z 840 " --> pdb=" O VAL Z 836 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA Z 841 " --> pdb=" O GLN Z 837 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU A 8 " --> pdb=" O LEU A 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR A 106 " --> pdb=" O LEU A 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS A 10 " --> pdb=" O THR A 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR A 103 " --> pdb=" O TYR A 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA A 135 " --> pdb=" O THR A 103 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU A 105 " --> pdb=" O ALA A 135 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA3, first strand: chain 'A' and resid 41 through 42 removed outlier: 3.521A pdb=" N GLN A 41 " --> pdb=" O ALA C 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL C 298 " --> pdb=" O THR C 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE C 151 " --> pdb=" O VAL C 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER C 300 " --> pdb=" O ILE C 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU C 153 " --> pdb=" O SER C 300 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 169 through 170 removed outlier: 7.129A pdb=" N VAL A 298 " --> pdb=" O THR A 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE A 151 " --> pdb=" O VAL A 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER A 300 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU A 153 " --> pdb=" O SER A 300 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 160 through 162 removed outlier: 3.520A pdb=" N MET A 176 " --> pdb=" O ASN A 162 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 238 through 241 Processing sheet with id=AA7, first strand: chain 'B' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU B 8 " --> pdb=" O LEU B 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR B 106 " --> pdb=" O LEU B 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS B 10 " --> pdb=" O THR B 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR B 103 " --> pdb=" O TYR B 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA B 135 " --> pdb=" O THR B 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU B 105 " --> pdb=" O ALA B 135 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'B' and resid 41 through 42 removed outlier: 3.550A pdb=" N GLN B 41 " --> pdb=" O ALA D 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL D 298 " --> pdb=" O THR D 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE D 151 " --> pdb=" O VAL D 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER D 300 " --> pdb=" O ILE D 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU D 153 " --> pdb=" O SER D 300 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 169 through 170 removed outlier: 7.130A pdb=" N VAL B 298 " --> pdb=" O THR B 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE B 151 " --> pdb=" O VAL B 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER B 300 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU B 153 " --> pdb=" O SER B 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET B 176 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 238 through 241 Processing sheet with id=AB4, first strand: chain 'C' and resid 29 through 32 removed outlier: 7.064A pdb=" N LEU C 8 " --> pdb=" O LEU C 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR C 106 " --> pdb=" O LEU C 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS C 10 " --> pdb=" O THR C 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR C 103 " --> pdb=" O TYR C 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA C 135 " --> pdb=" O THR C 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU C 105 " --> pdb=" O ALA C 135 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 35 through 36 Processing sheet with id=AB6, first strand: chain 'C' and resid 41 through 42 removed outlier: 3.510A pdb=" N GLN C 41 " --> pdb=" O ALA E 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL E 298 " --> pdb=" O THR E 149 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N ILE E 151 " --> pdb=" O VAL E 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER E 300 " --> pdb=" O ILE E 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 153 " --> pdb=" O SER E 300 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'C' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET C 176 " --> pdb=" O ASN C 162 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 238 through 241 Processing sheet with id=AB9, first strand: chain 'D' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU D 8 " --> pdb=" O LEU D 104 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N THR D 106 " --> pdb=" O LEU D 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS D 10 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR D 103 " --> pdb=" O TYR D 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA D 135 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N LEU D 105 " --> pdb=" O ALA D 135 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 35 through 36 Processing sheet with id=AC2, first strand: chain 'D' and resid 41 through 42 removed outlier: 3.528A pdb=" N GLN D 41 " --> pdb=" O ALA F 170 " (cutoff:3.500A) removed outlier: 7.129A pdb=" N VAL F 298 " --> pdb=" O THR F 149 " (cutoff:3.500A) removed outlier: 5.942A pdb=" N ILE F 151 " --> pdb=" O VAL F 298 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N SER F 300 " --> pdb=" O ILE F 151 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU F 153 " --> pdb=" O SER F 300 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET D 176 " --> pdb=" O ASN D 162 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 238 through 241 Processing sheet with id=AC5, first strand: chain 'E' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU E 8 " --> pdb=" O LEU E 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR E 106 " --> pdb=" O LEU E 8 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N CYS E 10 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR E 103 " --> pdb=" O TYR E 133 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N ALA E 135 " --> pdb=" O THR E 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU E 105 " --> pdb=" O ALA E 135 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 35 through 36 Processing sheet with id=AC7, first strand: chain 'E' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET E 176 " --> pdb=" O ASN E 162 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 238 through 241 Processing sheet with id=AC9, first strand: chain 'F' and resid 29 through 32 removed outlier: 7.065A pdb=" N LEU F 8 " --> pdb=" O LEU F 104 " (cutoff:3.500A) removed outlier: 8.608A pdb=" N THR F 106 " --> pdb=" O LEU F 8 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N CYS F 10 " --> pdb=" O THR F 106 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N THR F 103 " --> pdb=" O TYR F 133 " (cutoff:3.500A) removed outlier: 7.848A pdb=" N ALA F 135 " --> pdb=" O THR F 103 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 105 " --> pdb=" O ALA F 135 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'F' and resid 35 through 36 Processing sheet with id=AD2, first strand: chain 'F' and resid 160 through 162 removed outlier: 3.519A pdb=" N MET F 176 " --> pdb=" O ASN F 162 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'F' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 697 through 698 Processing sheet with id=AD5, first strand: chain 'H' and resid 697 through 698 Processing sheet with id=AD6, first strand: chain 'I' and resid 697 through 698 Processing sheet with id=AD7, first strand: chain 'K' and resid 697 through 698 Processing sheet with id=AD8, first strand: chain 'L' and resid 697 through 698 Processing sheet with id=AD9, first strand: chain 'Z' and resid 697 through 698 1300 hydrogen bonds defined for protein. 3684 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: 9.72 Time building geometry restraints manager: 9.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 8112 1.34 - 1.46: 5463 1.46 - 1.58: 11373 1.58 - 1.70: 18 1.70 - 1.82: 330 Bond restraints: 25296 Sorted by residual: bond pdb=" CE1 HIC F 73 " pdb=" NE2 HIC F 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.34e+00 bond pdb=" CE1 HIC E 73 " pdb=" NE2 HIC E 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.20e+00 bond pdb=" CE1 HIC D 73 " pdb=" NE2 HIC D 73 " ideal model delta sigma weight residual 1.347 1.401 -0.054 2.00e-02 2.50e+03 7.19e+00 bond pdb=" CE1 HIC A 73 " pdb=" NE2 HIC A 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.15e+00 bond pdb=" CE1 HIC B 73 " pdb=" NE2 HIC B 73 " ideal model delta sigma weight residual 1.347 1.400 -0.053 2.00e-02 2.50e+03 7.11e+00 ... (remaining 25291 not shown) Histogram of bond angle deviations from ideal: 98.78 - 106.14: 726 106.14 - 113.50: 14411 113.50 - 120.86: 11993 120.86 - 128.22: 6932 128.22 - 135.58: 180 Bond angle restraints: 34242 Sorted by residual: angle pdb=" CB MET F 325 " pdb=" CG MET F 325 " pdb=" SD MET F 325 " ideal model delta sigma weight residual 112.70 98.78 13.92 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET B 325 " pdb=" CG MET B 325 " pdb=" SD MET B 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET D 325 " pdb=" CG MET D 325 " pdb=" SD MET D 325 " ideal model delta sigma weight residual 112.70 98.80 13.90 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET C 325 " pdb=" CG MET C 325 " pdb=" SD MET C 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.15e+01 angle pdb=" CB MET A 325 " pdb=" CG MET A 325 " pdb=" SD MET A 325 " ideal model delta sigma weight residual 112.70 98.81 13.89 3.00e+00 1.11e-01 2.14e+01 ... (remaining 34237 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.41: 14910 34.41 - 68.82: 444 68.82 - 103.24: 48 103.24 - 137.65: 6 137.65 - 172.06: 12 Dihedral angle restraints: 15420 sinusoidal: 6222 harmonic: 9198 Sorted by residual: dihedral pdb=" O2A ADP B 401 " pdb=" O3A ADP B 401 " pdb=" PA ADP B 401 " pdb=" PB ADP B 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP C 401 " pdb=" O3A ADP C 401 " pdb=" PA ADP C 401 " pdb=" PB ADP C 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.06 -172.06 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP E 401 " pdb=" O3A ADP E 401 " pdb=" PA ADP E 401 " pdb=" PB ADP E 401 " ideal model delta sinusoidal sigma weight residual -60.00 112.04 -172.04 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 15417 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 2192 0.034 - 0.068: 1232 0.068 - 0.103: 352 0.103 - 0.137: 113 0.137 - 0.171: 23 Chirality restraints: 3912 Sorted by residual: chirality pdb=" CA MET E 325 " pdb=" N MET E 325 " pdb=" C MET E 325 " pdb=" CB MET E 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.33e-01 chirality pdb=" CA MET C 325 " pdb=" N MET C 325 " pdb=" C MET C 325 " pdb=" CB MET C 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.21e-01 chirality pdb=" CA MET B 325 " pdb=" N MET B 325 " pdb=" C MET B 325 " pdb=" CB MET B 325 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.16e-01 ... (remaining 3909 not shown) Planarity restraints: 4338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 242 " -0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO E 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO E 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO E 243 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU D 242 " 0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO D 243 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO D 243 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO D 243 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU B 242 " -0.026 5.00e-02 4.00e+02 3.98e-02 2.54e+00 pdb=" N PRO B 243 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 243 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 243 " -0.022 5.00e-02 4.00e+02 ... (remaining 4335 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 2987 2.74 - 3.28: 24061 3.28 - 3.82: 39496 3.82 - 4.36: 49656 4.36 - 4.90: 88228 Nonbonded interactions: 204428 Sorted by model distance: nonbonded pdb=" O GLY A 156 " pdb=" OG1 THR A 303 " model vdw 2.202 2.440 nonbonded pdb=" O GLY D 156 " pdb=" OG1 THR D 303 " model vdw 2.203 2.440 nonbonded pdb=" O GLY B 156 " pdb=" OG1 THR B 303 " model vdw 2.203 2.440 nonbonded pdb=" O GLY C 156 " pdb=" OG1 THR C 303 " model vdw 2.203 2.440 nonbonded pdb=" O GLY E 156 " pdb=" OG1 THR E 303 " model vdw 2.204 2.440 ... (remaining 204423 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.440 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: 0.000 Extract box with map and model: 0.290 Check model and map are aligned: 0.200 Set scattering table: 0.250 Process input model: 67.290 Find NCS groups from input model: 2.020 Set up NCS constraints: 0.130 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 78.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 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 : 0.007 0.054 25296 Z= 0.463 Angle : 0.750 13.916 34242 Z= 0.392 Chirality : 0.046 0.171 3912 Planarity : 0.004 0.040 4338 Dihedral : 17.000 172.062 9480 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.34 % Allowed : 3.53 % Favored : 95.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.15), residues: 3096 helix: 0.48 (0.13), residues: 1656 sheet: -1.68 (0.27), residues: 366 loop : -0.22 (0.20), residues: 1074 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 340 HIS 0.003 0.001 HIS C 87 PHE 0.013 0.001 PHE Z 697 TYR 0.014 0.002 TYR D 279 ARG 0.004 0.001 ARG A 206 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 329 time to evaluate : 2.384 Fit side-chains REVERT: A 118 LYS cc_start: 0.8375 (mttm) cc_final: 0.7909 (mmmt) REVERT: A 119 MET cc_start: 0.8288 (mtm) cc_final: 0.7662 (mtp) REVERT: A 157 ASP cc_start: 0.8839 (t0) cc_final: 0.8633 (t0) REVERT: A 176 MET cc_start: 0.8479 (OUTLIER) cc_final: 0.8123 (mtt) REVERT: A 211 ASP cc_start: 0.8633 (t0) cc_final: 0.8254 (t0) REVERT: A 227 MET cc_start: 0.8660 (mmm) cc_final: 0.8231 (mmt) REVERT: B 123 MET cc_start: 0.8667 (mmt) cc_final: 0.8386 (mmm) REVERT: B 191 LYS cc_start: 0.7348 (tttp) cc_final: 0.6910 (tttt) REVERT: B 313 MET cc_start: 0.8219 (ttt) cc_final: 0.7841 (ttt) REVERT: B 349 LEU cc_start: 0.8477 (mt) cc_final: 0.8178 (mt) REVERT: C 82 MET cc_start: 0.8551 (tpt) cc_final: 0.8341 (tpt) REVERT: C 211 ASP cc_start: 0.8594 (t0) cc_final: 0.8265 (t0) REVERT: C 313 MET cc_start: 0.8000 (ttt) cc_final: 0.7738 (ttm) REVERT: D 119 MET cc_start: 0.8108 (mtm) cc_final: 0.7901 (mtm) REVERT: D 313 MET cc_start: 0.8358 (ttt) cc_final: 0.7942 (ttt) REVERT: D 325 MET cc_start: 0.8023 (mmt) cc_final: 0.7807 (mmt) REVERT: E 100 GLU cc_start: 0.7838 (mt-10) cc_final: 0.7636 (mt-10) REVERT: E 118 LYS cc_start: 0.8579 (mttm) cc_final: 0.8072 (mmmt) REVERT: E 123 MET cc_start: 0.8764 (mmt) cc_final: 0.8548 (mmt) REVERT: E 292 ASP cc_start: 0.7333 (m-30) cc_final: 0.7126 (m-30) REVERT: F 57 GLU cc_start: 0.8328 (pt0) cc_final: 0.8036 (pt0) REVERT: F 299 MET cc_start: 0.8766 (mtm) cc_final: 0.8554 (mtp) REVERT: G 746 MET cc_start: 0.7497 (OUTLIER) cc_final: 0.7198 (mmm) REVERT: G 863 MET cc_start: 0.7720 (mtm) cc_final: 0.6798 (ptp) REVERT: H 725 MET cc_start: 0.7749 (mtt) cc_final: 0.7359 (mtt) REVERT: H 822 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8180 (mmp) REVERT: H 863 MET cc_start: 0.8121 (mtm) cc_final: 0.7618 (mtm) REVERT: I 732 MET cc_start: 0.8281 (mtp) cc_final: 0.8017 (mtp) REVERT: K 869 GLN cc_start: 0.8795 (mm110) cc_final: 0.8505 (mm-40) REVERT: L 732 MET cc_start: 0.8189 (mtp) cc_final: 0.7969 (mtm) REVERT: L 746 MET cc_start: 0.7743 (OUTLIER) cc_final: 0.7456 (tpt) REVERT: L 794 GLN cc_start: 0.8655 (tp-100) cc_final: 0.8341 (tp40) REVERT: Z 732 MET cc_start: 0.8243 (mtp) cc_final: 0.7921 (mtp) REVERT: Z 746 MET cc_start: 0.7789 (OUTLIER) cc_final: 0.7560 (mmm) REVERT: Z 794 GLN cc_start: 0.9079 (tp40) cc_final: 0.8828 (tp40) REVERT: Z 822 MET cc_start: 0.8039 (OUTLIER) cc_final: 0.7687 (mmm) REVERT: Z 863 MET cc_start: 0.7501 (mtm) cc_final: 0.7142 (mtm) outliers start: 36 outliers final: 7 residues processed: 335 average time/residue: 0.3622 time to fit residues: 194.6692 Evaluate side-chains 270 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 257 time to evaluate : 2.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain A residue 232 SER Chi-restraints excluded: chain C residue 232 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 232 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 232 SER Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain G residue 746 MET Chi-restraints excluded: chain H residue 822 MET Chi-restraints excluded: chain L residue 746 MET Chi-restraints excluded: chain Z residue 746 MET Chi-restraints excluded: chain Z residue 822 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 263 optimal weight: 0.9980 chunk 236 optimal weight: 0.0970 chunk 131 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 159 optimal weight: 0.3980 chunk 126 optimal weight: 0.9980 chunk 244 optimal weight: 10.0000 chunk 94 optimal weight: 0.7980 chunk 148 optimal weight: 5.9990 chunk 182 optimal weight: 0.7980 chunk 283 optimal weight: 9.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 353 GLN K 794 GLN L 837 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 25296 Z= 0.168 Angle : 0.535 7.608 34242 Z= 0.266 Chirality : 0.040 0.148 3912 Planarity : 0.004 0.038 4338 Dihedral : 12.268 174.297 3511 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.16 % Favored : 98.84 % Rotamer: Outliers : 0.82 % Allowed : 5.88 % Favored : 93.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.16), residues: 3096 helix: 1.11 (0.13), residues: 1686 sheet: -1.23 (0.27), residues: 378 loop : -0.14 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 340 HIS 0.006 0.001 HIS C 40 PHE 0.007 0.001 PHE B 127 TYR 0.011 0.001 TYR F 143 ARG 0.005 0.000 ARG B 206 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 272 time to evaluate : 2.527 Fit side-chains REVERT: A 118 LYS cc_start: 0.8191 (mttm) cc_final: 0.7750 (mmmt) REVERT: A 119 MET cc_start: 0.8084 (mtm) cc_final: 0.7753 (mtp) REVERT: A 176 MET cc_start: 0.8321 (OUTLIER) cc_final: 0.7988 (mtt) REVERT: A 364 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7268 (mt-10) REVERT: B 123 MET cc_start: 0.8580 (mmt) cc_final: 0.8284 (mmm) REVERT: B 191 LYS cc_start: 0.7325 (tttp) cc_final: 0.6930 (tttt) REVERT: B 205 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7820 (mt-10) REVERT: B 313 MET cc_start: 0.8143 (ttt) cc_final: 0.7758 (ttt) REVERT: C 82 MET cc_start: 0.8469 (tpt) cc_final: 0.8258 (tpt) REVERT: C 211 ASP cc_start: 0.8538 (t0) cc_final: 0.8202 (t0) REVERT: C 313 MET cc_start: 0.7867 (ttt) cc_final: 0.7594 (ttm) REVERT: D 311 ASP cc_start: 0.7796 (m-30) cc_final: 0.7545 (m-30) REVERT: D 313 MET cc_start: 0.8303 (ttt) cc_final: 0.7920 (ttt) REVERT: E 72 GLU cc_start: 0.7368 (tt0) cc_final: 0.7028 (tt0) REVERT: F 44 MET cc_start: 0.8416 (mtt) cc_final: 0.8187 (mtp) REVERT: F 57 GLU cc_start: 0.8307 (pt0) cc_final: 0.8067 (pt0) REVERT: F 283 MET cc_start: 0.8066 (mmm) cc_final: 0.7852 (mmt) REVERT: F 344 SER cc_start: 0.8573 (m) cc_final: 0.8176 (p) REVERT: G 805 ASP cc_start: 0.6997 (m-30) cc_final: 0.6678 (m-30) REVERT: H 729 MET cc_start: 0.8423 (tpt) cc_final: 0.7575 (tpt) REVERT: H 822 MET cc_start: 0.8353 (mmm) cc_final: 0.8110 (mmm) REVERT: I 732 MET cc_start: 0.8310 (mtm) cc_final: 0.8061 (mtp) REVERT: I 822 MET cc_start: 0.8522 (mmm) cc_final: 0.7814 (mmt) REVERT: K 746 MET cc_start: 0.7809 (mmm) cc_final: 0.7314 (tpp) REVERT: K 869 GLN cc_start: 0.8833 (mm110) cc_final: 0.8511 (mm-40) REVERT: L 729 MET cc_start: 0.7537 (tpt) cc_final: 0.7311 (tpt) REVERT: L 732 MET cc_start: 0.8268 (mtm) cc_final: 0.8059 (mtm) REVERT: L 746 MET cc_start: 0.7293 (tpp) cc_final: 0.7010 (tpt) REVERT: Z 732 MET cc_start: 0.8338 (mtm) cc_final: 0.7854 (mtp) REVERT: Z 863 MET cc_start: 0.7507 (mtm) cc_final: 0.7098 (mtm) outliers start: 22 outliers final: 18 residues processed: 284 average time/residue: 0.3159 time to fit residues: 149.1747 Evaluate side-chains 276 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 257 time to evaluate : 2.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 176 MET Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 176 MET Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 176 MET Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 311 ASP Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 157 optimal weight: 3.9990 chunk 87 optimal weight: 3.9990 chunk 235 optimal weight: 0.7980 chunk 192 optimal weight: 0.7980 chunk 78 optimal weight: 3.9990 chunk 283 optimal weight: 9.9990 chunk 306 optimal weight: 3.9990 chunk 252 optimal weight: 9.9990 chunk 281 optimal weight: 2.9990 chunk 96 optimal weight: 0.9980 chunk 227 optimal weight: 6.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 837 GLN L 794 GLN Z 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8270 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 25296 Z= 0.368 Angle : 0.597 6.735 34242 Z= 0.295 Chirality : 0.044 0.171 3912 Planarity : 0.004 0.035 4338 Dihedral : 10.861 157.728 3492 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.12 % Allowed : 7.92 % Favored : 90.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.16), residues: 3096 helix: 1.04 (0.13), residues: 1680 sheet: -1.18 (0.27), residues: 378 loop : -0.18 (0.20), residues: 1038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP E 340 HIS 0.005 0.001 HIS E 88 PHE 0.012 0.001 PHE C 255 TYR 0.016 0.002 TYR K 792 ARG 0.004 0.000 ARG D 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 259 time to evaluate : 3.026 Fit side-chains REVERT: A 118 LYS cc_start: 0.8222 (mttm) cc_final: 0.7863 (mmmt) REVERT: A 119 MET cc_start: 0.7844 (mtm) cc_final: 0.7587 (mtp) REVERT: A 369 ILE cc_start: 0.8703 (tp) cc_final: 0.8479 (tp) REVERT: B 123 MET cc_start: 0.8583 (mmt) cc_final: 0.8243 (mmm) REVERT: B 176 MET cc_start: 0.7964 (mtt) cc_final: 0.7632 (mtt) REVERT: B 191 LYS cc_start: 0.7565 (tttp) cc_final: 0.7095 (tttt) REVERT: B 305 MET cc_start: 0.8861 (mtp) cc_final: 0.8635 (mmm) REVERT: C 211 ASP cc_start: 0.8687 (t0) cc_final: 0.8350 (t0) REVERT: C 313 MET cc_start: 0.7882 (ttt) cc_final: 0.7650 (ttm) REVERT: E 72 GLU cc_start: 0.7445 (tt0) cc_final: 0.7108 (tt0) REVERT: E 118 LYS cc_start: 0.8553 (mttm) cc_final: 0.8058 (mmmt) REVERT: F 57 GLU cc_start: 0.8360 (pt0) cc_final: 0.7979 (pt0) REVERT: F 61 LYS cc_start: 0.8535 (mttm) cc_final: 0.8251 (mttm) REVERT: F 325 MET cc_start: 0.8844 (mmp) cc_final: 0.8479 (mmp) REVERT: G 746 MET cc_start: 0.7012 (mmm) cc_final: 0.6808 (mmm) REVERT: G 863 MET cc_start: 0.8515 (mtm) cc_final: 0.8085 (mtp) REVERT: H 729 MET cc_start: 0.8384 (tpt) cc_final: 0.7430 (tpt) REVERT: H 822 MET cc_start: 0.8377 (mmm) cc_final: 0.8161 (mmp) REVERT: I 822 MET cc_start: 0.8551 (mmm) cc_final: 0.8079 (mmt) REVERT: L 746 MET cc_start: 0.7282 (tpp) cc_final: 0.6995 (tpt) REVERT: L 822 MET cc_start: 0.8433 (mmp) cc_final: 0.8226 (mmt) REVERT: Z 732 MET cc_start: 0.8322 (mtm) cc_final: 0.7702 (mtp) REVERT: Z 863 MET cc_start: 0.7803 (mtm) cc_final: 0.7277 (mtm) outliers start: 30 outliers final: 26 residues processed: 279 average time/residue: 0.3443 time to fit residues: 156.3129 Evaluate side-chains 276 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 250 time to evaluate : 2.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 229 THR Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 863 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 280 optimal weight: 4.9990 chunk 213 optimal weight: 0.3980 chunk 147 optimal weight: 4.9990 chunk 31 optimal weight: 3.9990 chunk 135 optimal weight: 0.9990 chunk 190 optimal weight: 2.9990 chunk 284 optimal weight: 5.9990 chunk 301 optimal weight: 4.9990 chunk 148 optimal weight: 5.9990 chunk 269 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 173 HIS I 837 GLN K 794 GLN L 794 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.1351 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 25296 Z= 0.247 Angle : 0.531 6.663 34242 Z= 0.260 Chirality : 0.041 0.147 3912 Planarity : 0.003 0.037 4338 Dihedral : 9.876 142.623 3480 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.00 % Allowed : 9.45 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.16), residues: 3096 helix: 1.21 (0.13), residues: 1692 sheet: -1.13 (0.28), residues: 324 loop : -0.24 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 PHE 0.009 0.001 PHE C 255 TYR 0.011 0.001 TYR B 143 ARG 0.002 0.000 ARG B 256 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 258 time to evaluate : 3.084 Fit side-chains REVERT: A 72 GLU cc_start: 0.7361 (tt0) cc_final: 0.6943 (mt-10) REVERT: A 118 LYS cc_start: 0.8210 (mttm) cc_final: 0.7798 (mmmt) REVERT: A 119 MET cc_start: 0.7731 (mtm) cc_final: 0.7408 (mtp) REVERT: A 369 ILE cc_start: 0.8719 (tp) cc_final: 0.8463 (tp) REVERT: B 123 MET cc_start: 0.8584 (mmt) cc_final: 0.8328 (mmm) REVERT: B 176 MET cc_start: 0.7776 (mtt) cc_final: 0.7483 (mtt) REVERT: B 191 LYS cc_start: 0.7472 (tttp) cc_final: 0.7159 (tttt) REVERT: B 305 MET cc_start: 0.8811 (mtp) cc_final: 0.8590 (mmm) REVERT: C 211 ASP cc_start: 0.8648 (t0) cc_final: 0.8285 (t0) REVERT: C 313 MET cc_start: 0.7819 (ttt) cc_final: 0.7594 (ttm) REVERT: D 132 MET cc_start: 0.8180 (ptm) cc_final: 0.7969 (ttp) REVERT: D 353 GLN cc_start: 0.9173 (mm-40) cc_final: 0.8774 (mm110) REVERT: E 72 GLU cc_start: 0.7383 (tt0) cc_final: 0.6897 (tt0) REVERT: F 57 GLU cc_start: 0.8424 (pt0) cc_final: 0.8045 (pt0) REVERT: F 61 LYS cc_start: 0.8522 (mttm) cc_final: 0.8245 (mttm) REVERT: F 325 MET cc_start: 0.8841 (mmp) cc_final: 0.8612 (mmp) REVERT: G 863 MET cc_start: 0.8551 (mtm) cc_final: 0.8127 (mtp) REVERT: H 729 MET cc_start: 0.8338 (tpt) cc_final: 0.7450 (tpt) REVERT: I 822 MET cc_start: 0.8591 (mmm) cc_final: 0.8256 (mmt) REVERT: L 729 MET cc_start: 0.7636 (tpt) cc_final: 0.7053 (tpt) REVERT: L 746 MET cc_start: 0.7172 (tpp) cc_final: 0.6876 (tpt) REVERT: Z 732 MET cc_start: 0.8324 (mtm) cc_final: 0.8047 (mtm) REVERT: Z 863 MET cc_start: 0.7856 (mtm) cc_final: 0.7293 (mtm) outliers start: 27 outliers final: 27 residues processed: 277 average time/residue: 0.3288 time to fit residues: 149.9042 Evaluate side-chains 276 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 249 time to evaluate : 2.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 251 optimal weight: 7.9990 chunk 171 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 224 optimal weight: 2.9990 chunk 124 optimal weight: 0.5980 chunk 257 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 153 optimal weight: 0.0770 chunk 270 optimal weight: 4.9990 chunk 76 optimal weight: 1.9990 overall best weight: 1.1142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 837 GLN L 763 ASN L 794 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8233 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25296 Z= 0.230 Angle : 0.520 6.662 34242 Z= 0.253 Chirality : 0.041 0.166 3912 Planarity : 0.003 0.035 4338 Dihedral : 9.514 138.231 3480 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.12 % Allowed : 10.12 % Favored : 88.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.16), residues: 3096 helix: 1.34 (0.13), residues: 1692 sheet: -1.02 (0.28), residues: 324 loop : -0.15 (0.20), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 340 HIS 0.003 0.001 HIS E 88 PHE 0.008 0.001 PHE F 31 TYR 0.010 0.001 TYR B 143 ARG 0.002 0.000 ARG D 147 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 258 time to evaluate : 2.921 Fit side-chains REVERT: A 72 GLU cc_start: 0.7299 (tt0) cc_final: 0.6853 (mt-10) REVERT: A 118 LYS cc_start: 0.8266 (mttm) cc_final: 0.7830 (mmmt) REVERT: A 326 LYS cc_start: 0.8491 (tttp) cc_final: 0.8176 (tttm) REVERT: A 369 ILE cc_start: 0.8714 (tp) cc_final: 0.8445 (tp) REVERT: B 176 MET cc_start: 0.7769 (mtt) cc_final: 0.7539 (mtt) REVERT: B 191 LYS cc_start: 0.7446 (tttp) cc_final: 0.7079 (tttt) REVERT: B 205 GLU cc_start: 0.8063 (mt-10) cc_final: 0.7860 (mt-10) REVERT: B 305 MET cc_start: 0.8805 (mtp) cc_final: 0.8576 (mmm) REVERT: C 211 ASP cc_start: 0.8644 (t0) cc_final: 0.8301 (t0) REVERT: D 353 GLN cc_start: 0.9154 (mm-40) cc_final: 0.8705 (mm110) REVERT: E 72 GLU cc_start: 0.7321 (tt0) cc_final: 0.6835 (tt0) REVERT: F 57 GLU cc_start: 0.8337 (pt0) cc_final: 0.7991 (pt0) REVERT: F 61 LYS cc_start: 0.8509 (mttm) cc_final: 0.8244 (mttm) REVERT: G 805 ASP cc_start: 0.6796 (m-30) cc_final: 0.6466 (m-30) REVERT: G 863 MET cc_start: 0.8732 (mtm) cc_final: 0.8405 (mtp) REVERT: H 729 MET cc_start: 0.8380 (tpt) cc_final: 0.7584 (tpt) REVERT: I 729 MET cc_start: 0.8058 (tpt) cc_final: 0.7854 (tpt) REVERT: I 732 MET cc_start: 0.8555 (mtm) cc_final: 0.8285 (mtp) REVERT: I 805 ASP cc_start: 0.7283 (m-30) cc_final: 0.6812 (m-30) REVERT: I 822 MET cc_start: 0.8560 (mmm) cc_final: 0.8299 (mmt) REVERT: K 746 MET cc_start: 0.7481 (mmm) cc_final: 0.7254 (tpp) REVERT: L 746 MET cc_start: 0.7108 (tpp) cc_final: 0.6748 (tpt) REVERT: L 794 GLN cc_start: 0.8665 (tp-100) cc_final: 0.8370 (tp40) REVERT: Z 732 MET cc_start: 0.8361 (mtm) cc_final: 0.8010 (mtp) outliers start: 30 outliers final: 29 residues processed: 277 average time/residue: 0.3279 time to fit residues: 150.0037 Evaluate side-chains 278 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 249 time to evaluate : 2.619 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 176 MET Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 101 optimal weight: 1.9990 chunk 271 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 177 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 301 optimal weight: 0.9990 chunk 250 optimal weight: 0.8980 chunk 139 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 158 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 HIS G 763 ASN G 826 GLN H 763 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 25296 Z= 0.188 Angle : 0.497 6.686 34242 Z= 0.240 Chirality : 0.040 0.148 3912 Planarity : 0.003 0.034 4338 Dihedral : 9.188 142.551 3480 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 0.93 % Allowed : 10.60 % Favored : 88.47 % 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: 1.16 (0.16), residues: 3096 helix: 1.64 (0.13), residues: 1656 sheet: -0.71 (0.27), residues: 354 loop : 0.06 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 340 HIS 0.002 0.001 HIS E 88 PHE 0.007 0.001 PHE F 31 TYR 0.009 0.001 TYR E 143 ARG 0.003 0.000 ARG K 829 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 252 time to evaluate : 2.875 Fit side-chains revert: symmetry clash REVERT: A 82 MET cc_start: 0.8315 (tpt) cc_final: 0.8041 (tpt) REVERT: A 118 LYS cc_start: 0.8318 (mttm) cc_final: 0.7908 (mmmt) REVERT: A 191 LYS cc_start: 0.7946 (tttp) cc_final: 0.7445 (tttp) REVERT: A 326 LYS cc_start: 0.8513 (tttp) cc_final: 0.8203 (tttm) REVERT: A 369 ILE cc_start: 0.8704 (tp) cc_final: 0.8403 (tp) REVERT: B 191 LYS cc_start: 0.7321 (tttp) cc_final: 0.6883 (tttt) REVERT: B 305 MET cc_start: 0.8778 (mtp) cc_final: 0.8543 (mmm) REVERT: B 372 ARG cc_start: 0.7727 (mtm180) cc_final: 0.7494 (mtp180) REVERT: C 211 ASP cc_start: 0.8628 (t0) cc_final: 0.8289 (t0) REVERT: D 353 GLN cc_start: 0.9137 (mm-40) cc_final: 0.8663 (mm110) REVERT: E 72 GLU cc_start: 0.7291 (tt0) cc_final: 0.6785 (tt0) REVERT: E 325 MET cc_start: 0.8264 (mmm) cc_final: 0.7989 (mmt) REVERT: F 57 GLU cc_start: 0.8309 (pt0) cc_final: 0.7944 (pt0) REVERT: F 61 LYS cc_start: 0.8468 (mttm) cc_final: 0.8063 (mtpp) REVERT: G 795 GLN cc_start: 0.8988 (mt0) cc_final: 0.8699 (mt0) REVERT: G 805 ASP cc_start: 0.6925 (m-30) cc_final: 0.6568 (m-30) REVERT: G 863 MET cc_start: 0.8679 (mtm) cc_final: 0.8401 (mtp) REVERT: H 729 MET cc_start: 0.8400 (tpt) cc_final: 0.7655 (tpt) REVERT: I 732 MET cc_start: 0.8478 (mtm) cc_final: 0.8203 (mtp) REVERT: I 805 ASP cc_start: 0.7245 (m-30) cc_final: 0.6807 (m-30) REVERT: I 822 MET cc_start: 0.8534 (mmm) cc_final: 0.7981 (mmt) REVERT: K 746 MET cc_start: 0.7403 (mmm) cc_final: 0.7187 (tpp) REVERT: L 729 MET cc_start: 0.7318 (tpt) cc_final: 0.7000 (tpt) REVERT: L 746 MET cc_start: 0.7002 (tpp) cc_final: 0.6617 (tpt) REVERT: Z 732 MET cc_start: 0.8334 (mtm) cc_final: 0.8002 (mtp) REVERT: Z 863 MET cc_start: 0.8199 (ttm) cc_final: 0.7823 (mtp) outliers start: 25 outliers final: 23 residues processed: 269 average time/residue: 0.3426 time to fit residues: 149.3298 Evaluate side-chains 268 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 245 time to evaluate : 2.681 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 324 THR Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 291 optimal weight: 2.9990 chunk 34 optimal weight: 0.0770 chunk 171 optimal weight: 3.9990 chunk 220 optimal weight: 3.9990 chunk 170 optimal weight: 3.9990 chunk 254 optimal weight: 4.9990 chunk 168 optimal weight: 1.9990 chunk 300 optimal weight: 8.9990 chunk 188 optimal weight: 4.9990 chunk 183 optimal weight: 0.9980 chunk 138 optimal weight: 1.9990 overall best weight: 1.6144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 40 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 25296 Z= 0.307 Angle : 0.550 7.151 34242 Z= 0.267 Chirality : 0.042 0.152 3912 Planarity : 0.003 0.033 4338 Dihedral : 9.058 147.025 3480 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 1.26 % Allowed : 10.75 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 3096 helix: 1.34 (0.13), residues: 1692 sheet: -0.92 (0.28), residues: 324 loop : -0.11 (0.19), residues: 1080 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.009 0.001 PHE C 31 TYR 0.013 0.001 TYR D 143 ARG 0.003 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 252 time to evaluate : 2.502 Fit side-chains REVERT: A 72 GLU cc_start: 0.7335 (tt0) cc_final: 0.7009 (mt-10) REVERT: A 118 LYS cc_start: 0.8322 (mttm) cc_final: 0.7919 (mmmt) REVERT: A 326 LYS cc_start: 0.8484 (tttp) cc_final: 0.8158 (tttm) REVERT: A 369 ILE cc_start: 0.8704 (tp) cc_final: 0.8411 (tp) REVERT: B 191 LYS cc_start: 0.7489 (tttp) cc_final: 0.7029 (tttt) REVERT: B 205 GLU cc_start: 0.8188 (mt-10) cc_final: 0.7827 (mt-10) REVERT: B 305 MET cc_start: 0.8828 (mtp) cc_final: 0.8595 (mmm) REVERT: C 211 ASP cc_start: 0.8691 (t0) cc_final: 0.8332 (t0) REVERT: C 313 MET cc_start: 0.7828 (ttt) cc_final: 0.7597 (ttm) REVERT: D 353 GLN cc_start: 0.9183 (mm-40) cc_final: 0.8713 (mm110) REVERT: E 47 MET cc_start: 0.7729 (mtp) cc_final: 0.7437 (mtt) REVERT: E 72 GLU cc_start: 0.7427 (tt0) cc_final: 0.6938 (tt0) REVERT: E 118 LYS cc_start: 0.8477 (mttm) cc_final: 0.7974 (mmmt) REVERT: E 325 MET cc_start: 0.8345 (OUTLIER) cc_final: 0.7888 (mmp) REVERT: F 61 LYS cc_start: 0.8480 (mttm) cc_final: 0.8053 (mtpp) REVERT: G 863 MET cc_start: 0.8760 (mtm) cc_final: 0.8469 (mtp) REVERT: H 729 MET cc_start: 0.8399 (tpt) cc_final: 0.7671 (tpt) REVERT: I 805 ASP cc_start: 0.7266 (m-30) cc_final: 0.6807 (m-30) REVERT: I 822 MET cc_start: 0.8530 (mmm) cc_final: 0.7997 (mmt) REVERT: L 746 MET cc_start: 0.7029 (tpp) cc_final: 0.6654 (tpt) REVERT: Z 732 MET cc_start: 0.8350 (mtm) cc_final: 0.8008 (mtp) REVERT: Z 863 MET cc_start: 0.8285 (ttm) cc_final: 0.7951 (mtp) outliers start: 34 outliers final: 29 residues processed: 276 average time/residue: 0.3286 time to fit residues: 147.8637 Evaluate side-chains 277 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 247 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 201 VAL Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 325 MET Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 323 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 186 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 179 optimal weight: 0.7980 chunk 90 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 191 optimal weight: 0.3980 chunk 204 optimal weight: 0.9990 chunk 148 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 236 optimal weight: 10.0000 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 40 HIS L 794 GLN Z 763 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 25296 Z= 0.177 Angle : 0.492 6.856 34242 Z= 0.237 Chirality : 0.040 0.148 3912 Planarity : 0.003 0.034 4338 Dihedral : 8.764 152.176 3480 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 1.15 % Allowed : 10.90 % Favored : 87.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.16), residues: 3096 helix: 1.73 (0.13), residues: 1656 sheet: -0.61 (0.27), residues: 354 loop : 0.10 (0.19), residues: 1086 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 340 HIS 0.002 0.001 HIS B 88 PHE 0.008 0.001 PHE F 31 TYR 0.008 0.001 TYR D 240 ARG 0.002 0.000 ARG C 210 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 249 time to evaluate : 2.978 Fit side-chains REVERT: A 118 LYS cc_start: 0.8323 (mttm) cc_final: 0.7902 (mmmt) REVERT: A 191 LYS cc_start: 0.7944 (tttp) cc_final: 0.7441 (tttp) REVERT: A 326 LYS cc_start: 0.8480 (tttp) cc_final: 0.8166 (tttm) REVERT: A 369 ILE cc_start: 0.8678 (tp) cc_final: 0.8384 (tp) REVERT: B 191 LYS cc_start: 0.7391 (tttp) cc_final: 0.6882 (tttt) REVERT: B 305 MET cc_start: 0.8768 (mtp) cc_final: 0.8530 (mmm) REVERT: C 211 ASP cc_start: 0.8625 (t0) cc_final: 0.8270 (t0) REVERT: C 313 MET cc_start: 0.7814 (ttt) cc_final: 0.7576 (ttm) REVERT: D 353 GLN cc_start: 0.9179 (mm-40) cc_final: 0.8696 (mm110) REVERT: E 72 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6882 (tt0) REVERT: G 863 MET cc_start: 0.8767 (mtm) cc_final: 0.8461 (mtm) REVERT: H 729 MET cc_start: 0.8395 (tpt) cc_final: 0.7715 (tpt) REVERT: I 732 MET cc_start: 0.8457 (mtm) cc_final: 0.8236 (mtp) REVERT: I 805 ASP cc_start: 0.7224 (m-30) cc_final: 0.6793 (m-30) REVERT: I 822 MET cc_start: 0.8497 (mmm) cc_final: 0.7987 (mmt) REVERT: K 746 MET cc_start: 0.7181 (mmm) cc_final: 0.6921 (tpp) REVERT: L 729 MET cc_start: 0.7343 (tpt) cc_final: 0.6956 (tpt) REVERT: L 746 MET cc_start: 0.6957 (tpp) cc_final: 0.6550 (tpt) REVERT: Z 732 MET cc_start: 0.8307 (mtm) cc_final: 0.7983 (mtp) REVERT: Z 863 MET cc_start: 0.8188 (ttm) cc_final: 0.7894 (mtp) outliers start: 31 outliers final: 28 residues processed: 270 average time/residue: 0.3314 time to fit residues: 146.1392 Evaluate side-chains 272 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 243 time to evaluate : 2.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 167 GLU Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 72 GLU Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 273 optimal weight: 3.9990 chunk 288 optimal weight: 5.9990 chunk 262 optimal weight: 2.9990 chunk 280 optimal weight: 2.9990 chunk 168 optimal weight: 0.8980 chunk 122 optimal weight: 1.9990 chunk 220 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 253 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 279 optimal weight: 3.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 296 ASN ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 25296 Z= 0.367 Angle : 0.579 7.408 34242 Z= 0.282 Chirality : 0.044 0.151 3912 Planarity : 0.004 0.033 4338 Dihedral : 8.789 159.740 3480 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.23 % Allowed : 11.27 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.15), residues: 3096 helix: 1.26 (0.13), residues: 1698 sheet: -0.83 (0.27), residues: 336 loop : -0.11 (0.20), residues: 1062 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 340 HIS 0.005 0.001 HIS D 87 PHE 0.011 0.001 PHE C 31 TYR 0.016 0.001 TYR B 143 ARG 0.004 0.000 ARG C 312 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 250 time to evaluate : 2.882 Fit side-chains REVERT: A 72 GLU cc_start: 0.7533 (tt0) cc_final: 0.7170 (mt-10) REVERT: A 118 LYS cc_start: 0.8327 (mttm) cc_final: 0.7925 (mmmt) REVERT: A 326 LYS cc_start: 0.8504 (tttp) cc_final: 0.8193 (tttm) REVERT: A 369 ILE cc_start: 0.8694 (tp) cc_final: 0.8405 (tp) REVERT: B 191 LYS cc_start: 0.7568 (tttp) cc_final: 0.7082 (tttt) REVERT: B 305 MET cc_start: 0.8839 (mtp) cc_final: 0.8617 (mmm) REVERT: C 211 ASP cc_start: 0.8723 (t0) cc_final: 0.8369 (t0) REVERT: D 49 GLN cc_start: 0.8524 (mm-40) cc_final: 0.8223 (mm-40) REVERT: D 353 GLN cc_start: 0.9193 (mm-40) cc_final: 0.8912 (mm-40) REVERT: E 72 GLU cc_start: 0.7455 (tt0) cc_final: 0.6972 (tt0) REVERT: E 118 LYS cc_start: 0.8449 (mttm) cc_final: 0.7958 (mmmt) REVERT: F 61 LYS cc_start: 0.8500 (mttm) cc_final: 0.8061 (mtpp) REVERT: G 863 MET cc_start: 0.8769 (mtm) cc_final: 0.8525 (mtm) REVERT: H 729 MET cc_start: 0.8406 (tpt) cc_final: 0.7703 (tpt) REVERT: I 732 MET cc_start: 0.8548 (mtm) cc_final: 0.8320 (mtp) REVERT: I 822 MET cc_start: 0.8508 (mmm) cc_final: 0.8002 (mmt) REVERT: K 746 MET cc_start: 0.7254 (mmm) cc_final: 0.6912 (tpp) REVERT: L 729 MET cc_start: 0.7380 (tpt) cc_final: 0.6935 (tpt) REVERT: L 746 MET cc_start: 0.6988 (tpp) cc_final: 0.6616 (tpt) REVERT: Z 732 MET cc_start: 0.8293 (mtm) cc_final: 0.7932 (mtp) outliers start: 33 outliers final: 30 residues processed: 275 average time/residue: 0.3350 time to fit residues: 149.6258 Evaluate side-chains 276 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 246 time to evaluate : 2.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 324 THR Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 184 optimal weight: 2.9990 chunk 296 optimal weight: 4.9990 chunk 180 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 310 optimal weight: 0.8980 chunk 286 optimal weight: 2.9990 chunk 247 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 151 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 25296 Z= 0.266 Angle : 0.534 7.202 34242 Z= 0.259 Chirality : 0.041 0.152 3912 Planarity : 0.003 0.035 4338 Dihedral : 8.755 171.664 3480 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.15 % Allowed : 11.38 % Favored : 87.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.16), residues: 3096 helix: 1.39 (0.13), residues: 1692 sheet: -0.73 (0.27), residues: 354 loop : -0.08 (0.20), residues: 1050 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 340 HIS 0.003 0.001 HIS E 88 PHE 0.009 0.001 PHE F 31 TYR 0.011 0.001 TYR D 143 ARG 0.003 0.000 ARG C 312 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6192 Ramachandran restraints generated. 3096 Oldfield, 0 Emsley, 3096 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 242 time to evaluate : 2.858 Fit side-chains REVERT: A 72 GLU cc_start: 0.7516 (tt0) cc_final: 0.7130 (mt-10) REVERT: A 118 LYS cc_start: 0.8365 (mttm) cc_final: 0.7920 (mmmt) REVERT: A 326 LYS cc_start: 0.8501 (tttp) cc_final: 0.8193 (tttm) REVERT: B 191 LYS cc_start: 0.7458 (tttp) cc_final: 0.6932 (tttt) REVERT: B 305 MET cc_start: 0.8802 (mtp) cc_final: 0.8575 (mmm) REVERT: C 211 ASP cc_start: 0.8685 (t0) cc_final: 0.8306 (t0) REVERT: D 353 GLN cc_start: 0.9175 (mm-40) cc_final: 0.8890 (mm-40) REVERT: E 72 GLU cc_start: 0.7420 (tt0) cc_final: 0.6946 (tt0) REVERT: E 118 LYS cc_start: 0.8447 (mttm) cc_final: 0.7954 (mmmt) REVERT: E 132 MET cc_start: 0.8376 (ttp) cc_final: 0.8067 (ttp) REVERT: F 61 LYS cc_start: 0.8493 (mttm) cc_final: 0.8058 (mtpp) REVERT: H 729 MET cc_start: 0.8423 (tpt) cc_final: 0.7761 (tpt) REVERT: I 732 MET cc_start: 0.8507 (mtm) cc_final: 0.8270 (mtp) REVERT: I 822 MET cc_start: 0.8490 (mmm) cc_final: 0.7990 (mmt) REVERT: K 746 MET cc_start: 0.7210 (mmm) cc_final: 0.6869 (tpp) REVERT: L 729 MET cc_start: 0.7405 (tpt) cc_final: 0.6909 (tpt) REVERT: L 746 MET cc_start: 0.6986 (tpp) cc_final: 0.6574 (tpt) REVERT: Z 732 MET cc_start: 0.8350 (mtp) cc_final: 0.8003 (mtp) outliers start: 31 outliers final: 30 residues processed: 266 average time/residue: 0.3563 time to fit residues: 154.6660 Evaluate side-chains 271 residues out of total 2688 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 241 time to evaluate : 2.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 MET Chi-restraints excluded: chain A residue 194 THR Chi-restraints excluded: chain A residue 234 SER Chi-restraints excluded: chain A residue 350 SER Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 148 THR Chi-restraints excluded: chain B residue 350 SER Chi-restraints excluded: chain B residue 351 THR Chi-restraints excluded: chain B residue 364 GLU Chi-restraints excluded: chain B residue 368 SER Chi-restraints excluded: chain C residue 6 THR Chi-restraints excluded: chain C residue 323 SER Chi-restraints excluded: chain C residue 350 SER Chi-restraints excluded: chain C residue 368 SER Chi-restraints excluded: chain D residue 145 SER Chi-restraints excluded: chain D residue 167 GLU Chi-restraints excluded: chain D residue 201 VAL Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain E residue 60 SER Chi-restraints excluded: chain E residue 234 SER Chi-restraints excluded: chain E residue 349 LEU Chi-restraints excluded: chain E residue 350 SER Chi-restraints excluded: chain E residue 351 THR Chi-restraints excluded: chain F residue 6 THR Chi-restraints excluded: chain F residue 99 GLU Chi-restraints excluded: chain F residue 232 SER Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 350 SER Chi-restraints excluded: chain I residue 833 THR Chi-restraints excluded: chain L residue 718 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 312 random chunks: chunk 196 optimal weight: 0.8980 chunk 263 optimal weight: 7.9990 chunk 75 optimal weight: 0.4980 chunk 228 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 3.9990 chunk 247 optimal weight: 2.9990 chunk 103 optimal weight: 0.9980 chunk 254 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 360 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 869 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.106593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.086496 restraints weight = 27744.735| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 0.94 r_work: 0.2672 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.2574 rms_B_bonded: 2.17 restraints_weight: 0.2500 r_work (final): 0.2574 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8323 moved from start: 0.1773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 25296 Z= 0.319 Angle : 0.560 7.429 34242 Z= 0.272 Chirality : 0.043 0.151 3912 Planarity : 0.004 0.034 4338 Dihedral : 8.751 173.746 3480 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.23 % Allowed : 11.42 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.78 (0.15), residues: 3096 helix: 1.30 (0.13), residues: 1692 sheet: -0.84 (0.27), residues: 336 loop : -0.15 (0.19), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP E 340 HIS 0.004 0.001 HIS D 87 PHE 0.010 0.001 PHE C 31 TYR 0.014 0.001 TYR D 143 ARG 0.003 0.000 ARG G 862 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4392.60 seconds wall clock time: 80 minutes 16.71 seconds (4816.71 seconds total)