Starting phenix.real_space_refine on Thu Feb 15 10:47:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds9_27686/02_2024/8ds9_27686_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds9_27686/02_2024/8ds9_27686.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds9_27686/02_2024/8ds9_27686.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds9_27686/02_2024/8ds9_27686.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds9_27686/02_2024/8ds9_27686_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ds9_27686/02_2024/8ds9_27686_updated.pdb" } resolution = 3.17 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= 0.064 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 97 5.16 5 C 8030 2.51 5 N 1877 2.21 5 O 2033 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 102": "OD1" <-> "OD2" Residue "A PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 258": "OD1" <-> "OD2" Residue "A TYR 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 275": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 298": "OD1" <-> "OD2" Residue "A PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 25": "OD1" <-> "OD2" Residue "B PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 100": "OD1" <-> "OD2" Residue "B TYR 124": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 292": "OD1" <-> "OD2" Residue "C PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 100": "OD1" <-> "OD2" Residue "C ASP 102": "OD1" <-> "OD2" Residue "C TYR 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 115": "OE1" <-> "OE2" Residue "C GLU 236": "OE1" <-> "OE2" Residue "C GLU 238": "OE1" <-> "OE2" Residue "C GLU 255": "OE1" <-> "OE2" Residue "C TYR 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 298": "OD1" <-> "OD2" Residue "C TYR 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 354": "OE1" <-> "OE2" Residue "C TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 371": "OD1" <-> "OD2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 386": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 396": "OE1" <-> "OE2" Residue "D ASP 29": "OD1" <-> "OD2" Residue "D ASP 100": "OD1" <-> "OD2" Residue "D TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 255": "OE1" <-> "OE2" Residue "D ASP 292": "OD1" <-> "OD2" Residue "D PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 364": "OD1" <-> "OD2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ASP 383": "OD1" <-> "OD2" Residue "D PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 396": "OE1" <-> "OE2" Residue "E PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 50": "OD1" <-> "OD2" Residue "E TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 144": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 294": "OD1" <-> "OD2" Residue "E GLU 300": "OE1" <-> "OE2" Residue "E TYR 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 146": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 339": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12039 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "B" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "C" Number of atoms: 2685 Number of conformers: 1 Conformer: "" Number of residues, atoms: 320, 2685 Classifications: {'peptide': 320} Link IDs: {'PTRANS': 9, 'TRANS': 310} Chain breaks: 2 Chain: "D" Number of atoms: 2646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 316, 2646 Classifications: {'peptide': 316} Link IDs: {'PTRANS': 9, 'TRANS': 306} Chain breaks: 2 Chain: "E" Number of atoms: 1662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1662 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 5, 'TRANS': 191} Chain breaks: 2 Chain: "F" Number of atoms: 1599 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1599 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 3, 'TRANS': 187} Chain breaks: 2 Chain: "C" Number of atoms: 22 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 22 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 90 Unresolved non-hydrogen dihedrals: 78 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'PEE:plan-2': 2} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 95 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 95 Unusual residues: {'PEE': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.62, per 1000 atoms: 0.55 Number of scatterers: 12039 At special positions: 0 Unit cell: (105.848, 98.512, 137.288, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 97 16.00 P 2 15.00 O 2033 8.00 N 1877 7.00 C 8030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=17, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 310 " distance=2.02 Simple disulfide: pdb=" SG CYS A 57 " - pdb=" SG CYS A 65 " distance=2.03 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 295 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 310 " distance=2.03 Simple disulfide: pdb=" SG CYS B 57 " - pdb=" SG CYS B 65 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 295 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 310 " distance=2.03 Simple disulfide: pdb=" SG CYS C 57 " - pdb=" SG CYS C 65 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 295 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 310 " distance=2.02 Simple disulfide: pdb=" SG CYS D 57 " - pdb=" SG CYS D 65 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 295 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 310 " distance=2.03 Simple disulfide: pdb=" SG CYS E 57 " - pdb=" SG CYS E 65 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 295 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 308 " distance=2.03 Simple disulfide: pdb=" SG CYS F 115 " - pdb=" SG CYS F 293 " distance=2.03 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: 4.78 Conformation dependent library (CDL) restraints added in 2.1 seconds 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2754 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 51 helices and 6 sheets defined 66.1% alpha, 4.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 23 through 48 Processing helix chain 'A' and resid 103 through 116 Processing helix chain 'A' and resid 120 through 140 Proline residue: A 126 - end of helix Processing helix chain 'A' and resid 259 through 288 removed outlier: 4.844A pdb=" N HIS A 287 " --> pdb=" O VAL A 283 " (cutoff:3.500A) removed outlier: 5.201A pdb=" N ASN A 288 " --> pdb=" O TYR A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 344 Processing helix chain 'B' and resid 17 through 20 Processing helix chain 'B' and resid 23 through 49 Processing helix chain 'B' and resid 103 through 115 Processing helix chain 'B' and resid 120 through 140 Proline residue: B 126 - end of helix Processing helix chain 'B' and resid 142 through 145 No H-bonds generated for 'chain 'B' and resid 142 through 145' Processing helix chain 'B' and resid 259 through 288 removed outlier: 3.849A pdb=" N TYR B 285 " --> pdb=" O TYR B 281 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N HIS B 287 " --> pdb=" O VAL B 283 " (cutoff:3.500A) removed outlier: 5.715A pdb=" N ASN B 288 " --> pdb=" O TYR B 284 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 344 removed outlier: 4.230A pdb=" N THR B 316 " --> pdb=" O PRO B 313 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N LEU B 317 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 4.485A pdb=" N SER B 323 " --> pdb=" O ILE B 320 " (cutoff:3.500A) Processing helix chain 'C' and resid 17 through 20 Processing helix chain 'C' and resid 23 through 48 Processing helix chain 'C' and resid 103 through 116 Processing helix chain 'C' and resid 120 through 140 Proline residue: C 126 - end of helix Processing helix chain 'C' and resid 142 through 145 No H-bonds generated for 'chain 'C' and resid 142 through 145' Processing helix chain 'C' and resid 147 through 164 removed outlier: 3.928A pdb=" N LYS C 152 " --> pdb=" O ARG C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 167 through 174 Processing helix chain 'C' and resid 234 through 255 Processing helix chain 'C' and resid 259 through 288 removed outlier: 4.570A pdb=" N HIS C 287 " --> pdb=" O VAL C 283 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N ASN C 288 " --> pdb=" O TYR C 284 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 345 removed outlier: 3.542A pdb=" N ALA C 322 " --> pdb=" O PHE C 318 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 Processing helix chain 'C' and resid 370 through 382 Processing helix chain 'C' and resid 384 through 394 removed outlier: 4.136A pdb=" N VAL C 392 " --> pdb=" O LYS C 388 " (cutoff:3.500A) removed outlier: 4.613A pdb=" N PHE C 393 " --> pdb=" O ARG C 389 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 410 Processing helix chain 'D' and resid 23 through 48 Processing helix chain 'D' and resid 103 through 115 removed outlier: 3.548A pdb=" N ASN D 107 " --> pdb=" O ARG D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 145 Proline residue: D 126 - end of helix removed outlier: 4.828A pdb=" N TRP D 143 " --> pdb=" O CYS D 139 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N PHE D 144 " --> pdb=" O SER D 140 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 165 removed outlier: 4.149A pdb=" N LYS D 152 " --> pdb=" O ARG D 148 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ASP D 165 " --> pdb=" O LEU D 161 " (cutoff:3.500A) Processing helix chain 'D' and resid 167 through 174 Processing helix chain 'D' and resid 234 through 255 Processing helix chain 'D' and resid 259 through 288 removed outlier: 4.804A pdb=" N HIS D 287 " --> pdb=" O VAL D 283 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ASN D 288 " --> pdb=" O TYR D 284 " (cutoff:3.500A) Processing helix chain 'D' and resid 315 through 345 Processing helix chain 'D' and resid 354 through 359 Processing helix chain 'D' and resid 370 through 382 Processing helix chain 'D' and resid 384 through 394 removed outlier: 4.360A pdb=" N VAL D 392 " --> pdb=" O LYS D 388 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N PHE D 393 " --> pdb=" O ARG D 389 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N LEU D 394 " --> pdb=" O PHE D 390 " (cutoff:3.500A) Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'E' and resid 23 through 49 Processing helix chain 'E' and resid 103 through 116 Processing helix chain 'E' and resid 120 through 123 No H-bonds generated for 'chain 'E' and resid 120 through 123' Processing helix chain 'E' and resid 125 through 140 Processing helix chain 'E' and resid 142 through 145 No H-bonds generated for 'chain 'E' and resid 142 through 145' Processing helix chain 'E' and resid 259 through 288 removed outlier: 5.240A pdb=" N HIS E 287 " --> pdb=" O VAL E 283 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ASN E 288 " --> pdb=" O TYR E 284 " (cutoff:3.500A) Processing helix chain 'E' and resid 300 through 303 No H-bonds generated for 'chain 'E' and resid 300 through 303' Processing helix chain 'E' and resid 316 through 343 Processing helix chain 'F' and resid 23 through 47 Processing helix chain 'F' and resid 105 through 118 Processing helix chain 'F' and resid 122 through 142 Proline residue: F 128 - end of helix Processing helix chain 'F' and resid 257 through 286 removed outlier: 5.205A pdb=" N SER F 285 " --> pdb=" O SER F 281 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N LYS F 286 " --> pdb=" O ALA F 282 " (cutoff:3.500A) Processing helix chain 'F' and resid 313 through 343 Processing sheet with id= A, first strand: chain 'A' and resid 53 through 56 removed outlier: 3.879A pdb=" N LEU A 55 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 52 through 56 removed outlier: 3.701A pdb=" N LEU B 55 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 53 through 56 Processing sheet with id= D, first strand: chain 'D' and resid 52 through 56 Processing sheet with id= E, first strand: chain 'E' and resid 292 through 296 Processing sheet with id= F, first strand: chain 'F' and resid 52 through 56 735 hydrogen bonds defined for protein. 2109 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: 3.10 Time building geometry restraints manager: 5.21 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2565 1.33 - 1.46: 3178 1.46 - 1.58: 6500 1.58 - 1.70: 2 1.70 - 1.82: 140 Bond restraints: 12385 Sorted by residual: bond pdb=" C10 PEE C 902 " pdb=" O4 PEE C 902 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C10 PEE C 901 " pdb=" O4 PEE C 901 " ideal model delta sigma weight residual 1.206 1.357 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" O4P PEE D 902 " pdb=" P PEE D 902 " ideal model delta sigma weight residual 1.653 1.777 -0.124 2.00e-02 2.50e+03 3.82e+01 bond pdb=" O4P PEE D 901 " pdb=" P PEE D 901 " ideal model delta sigma weight residual 1.653 1.776 -0.123 2.00e-02 2.50e+03 3.79e+01 bond pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 1.332 1.215 0.117 2.00e-02 2.50e+03 3.41e+01 ... (remaining 12380 not shown) Histogram of bond angle deviations from ideal: 90.81 - 99.50: 6 99.50 - 108.20: 486 108.20 - 116.89: 7795 116.89 - 125.59: 8237 125.59 - 134.28: 249 Bond angle restraints: 16773 Sorted by residual: angle pdb=" O1P PEE D 902 " pdb=" P PEE D 902 " pdb=" O2P PEE D 902 " ideal model delta sigma weight residual 119.43 133.28 -13.85 3.00e+00 1.11e-01 2.13e+01 angle pdb=" O1P PEE D 901 " pdb=" P PEE D 901 " pdb=" O2P PEE D 901 " ideal model delta sigma weight residual 119.43 133.19 -13.76 3.00e+00 1.11e-01 2.10e+01 angle pdb=" C11 PEE C 901 " pdb=" C10 PEE C 901 " pdb=" O2 PEE C 901 " ideal model delta sigma weight residual 111.70 124.69 -12.99 3.00e+00 1.11e-01 1.87e+01 angle pdb=" C11 PEE C 902 " pdb=" C10 PEE C 902 " pdb=" O2 PEE C 902 " ideal model delta sigma weight residual 111.70 124.67 -12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" CA GLU C 245 " pdb=" CB GLU C 245 " pdb=" CG GLU C 245 " ideal model delta sigma weight residual 114.10 121.71 -7.61 2.00e+00 2.50e-01 1.45e+01 ... (remaining 16768 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.75: 6964 34.75 - 69.50: 257 69.50 - 104.25: 13 104.25 - 139.00: 2 139.00 - 173.75: 2 Dihedral angle restraints: 7238 sinusoidal: 2971 harmonic: 4267 Sorted by residual: dihedral pdb=" CB CYS D 113 " pdb=" SG CYS D 113 " pdb=" SG CYS D 295 " pdb=" CB CYS D 295 " ideal model delta sinusoidal sigma weight residual 93.00 37.93 55.07 1 1.00e+01 1.00e-02 4.10e+01 dihedral pdb=" CA GLU A 115 " pdb=" C GLU A 115 " pdb=" N ASN A 116 " pdb=" CA ASN A 116 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" N PEE D 902 " pdb=" C4 PEE D 902 " pdb=" C5 PEE D 902 " pdb=" O4P PEE D 902 " ideal model delta sinusoidal sigma weight residual -56.97 116.78 -173.75 1 3.00e+01 1.11e-03 2.13e+01 ... (remaining 7235 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.085: 1724 0.085 - 0.171: 117 0.171 - 0.256: 3 0.256 - 0.341: 0 0.341 - 0.426: 2 Chirality restraints: 1846 Sorted by residual: chirality pdb=" C2 PEE D 902 " pdb=" C1 PEE D 902 " pdb=" C3 PEE D 902 " pdb=" O2 PEE D 902 " both_signs ideal model delta sigma weight residual False -2.33 -2.75 0.43 2.00e-01 2.50e+01 4.55e+00 chirality pdb=" C2 PEE D 901 " pdb=" C1 PEE D 901 " pdb=" C3 PEE D 901 " pdb=" O2 PEE D 901 " both_signs ideal model delta sigma weight residual False -2.33 -2.73 0.40 2.00e-01 2.50e+01 3.98e+00 chirality pdb=" CB VAL F 263 " pdb=" CA VAL F 263 " pdb=" CG1 VAL F 263 " pdb=" CG2 VAL F 263 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.16e+00 ... (remaining 1843 not shown) Planarity restraints: 1985 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 23 " 0.019 2.00e-02 2.50e+03 2.17e-02 1.18e+01 pdb=" CG TRP A 23 " -0.058 2.00e-02 2.50e+03 pdb=" CD1 TRP A 23 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 23 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 23 " 0.012 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 23 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 23 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP A 23 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 120 " 0.021 2.00e-02 2.50e+03 2.00e-02 9.99e+00 pdb=" CG TRP D 120 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 TRP D 120 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 120 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP D 120 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP D 120 " 0.010 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 120 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 120 " -0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP D 120 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 143 " -0.022 2.00e-02 2.50e+03 1.94e-02 9.44e+00 pdb=" CG TRP A 143 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP A 143 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 143 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 143 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 143 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 143 " -0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 143 " 0.001 2.00e-02 2.50e+03 ... (remaining 1982 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 855 2.74 - 3.28: 12390 3.28 - 3.82: 20831 3.82 - 4.36: 23514 4.36 - 4.90: 40934 Nonbonded interactions: 98524 Sorted by model distance: nonbonded pdb=" OD2 ASP A 50 " pdb=" OH TYR A 114 " model vdw 2.201 2.440 nonbonded pdb=" O ILE C 356 " pdb=" OG SER C 360 " model vdw 2.206 2.440 nonbonded pdb=" O THR E 44 " pdb=" OG1 THR E 48 " model vdw 2.221 2.440 nonbonded pdb=" OD2 ASP E 110 " pdb=" NE2 GLN F 106 " model vdw 2.251 2.520 nonbonded pdb=" OG1 THR C 316 " pdb=" OE2 GLU D 115 " model vdw 2.265 2.440 ... (remaining 98519 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 'E' } ncs_group { reference = (chain 'C' and (resid 15 through 407 or resid 901 through 902)) selection = (chain 'D' and (resid 15 through 407 or (resid 901 and (name C10 or name C11 or \ name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or name O2 \ or name O4 )) or (resid 902 and (name C10 or name C11 or name C12 or name C13 or \ name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name O2 \ or name O4 )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 15.570 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 34.000 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.060 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5913 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.151 12385 Z= 0.318 Angle : 0.805 13.851 16773 Z= 0.440 Chirality : 0.047 0.426 1846 Planarity : 0.006 0.054 1985 Dihedral : 17.316 173.749 4433 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.53 % Allowed : 23.59 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.22), residues: 1382 helix: 0.52 (0.16), residues: 962 sheet: 0.25 (0.54), residues: 102 loop : -1.23 (0.32), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP A 23 HIS 0.023 0.002 HIS E 119 PHE 0.039 0.002 PHE C 390 TYR 0.031 0.002 TYR E 325 ARG 0.014 0.001 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 225 time to evaluate : 1.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 5 residues processed: 231 average time/residue: 0.2596 time to fit residues: 84.7341 Evaluate side-chains 212 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 207 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 GLN Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain C residue 253 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 0.3980 chunk 105 optimal weight: 0.0170 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.7980 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 0.0570 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5917 moved from start: 0.1083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 12385 Z= 0.153 Angle : 0.480 6.803 16773 Z= 0.260 Chirality : 0.038 0.169 1846 Planarity : 0.004 0.043 1985 Dihedral : 9.711 177.160 1680 Min Nonbonded Distance : 2.137 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 3.42 % Allowed : 21.92 % Favored : 74.66 % 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: 1.06 (0.22), residues: 1382 helix: 1.36 (0.16), residues: 965 sheet: 0.44 (0.52), residues: 107 loop : -1.20 (0.33), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 23 HIS 0.008 0.001 HIS E 119 PHE 0.022 0.001 PHE D 390 TYR 0.023 0.001 TYR D 284 ARG 0.005 0.000 ARG B 345 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 274 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 229 time to evaluate : 1.378 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.4772 (OUTLIER) cc_final: 0.4512 (m-10) REVERT: B 46 GLN cc_start: 0.7803 (tm-30) cc_final: 0.7488 (tm-30) REVERT: B 117 ARG cc_start: 0.7110 (mmm160) cc_final: 0.6716 (tpt90) REVERT: B 275 PHE cc_start: 0.6738 (OUTLIER) cc_final: 0.6289 (t80) REVERT: C 275 PHE cc_start: 0.7625 (OUTLIER) cc_final: 0.7250 (t80) REVERT: D 324 PHE cc_start: 0.6258 (t80) cc_final: 0.6049 (t80) REVERT: D 375 MET cc_start: 0.6669 (mtt) cc_final: 0.6376 (mtt) REVERT: E 343 MET cc_start: 0.2006 (OUTLIER) cc_final: 0.1735 (mtt) outliers start: 45 outliers final: 20 residues processed: 258 average time/residue: 0.2453 time to fit residues: 90.3246 Evaluate side-chains 232 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 208 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 233 ASP Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 37 MET Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 95 GLU Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 3.9990 chunk 85 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 0.5980 chunk 136 optimal weight: 0.9980 chunk 112 optimal weight: 8.9990 chunk 125 optimal weight: 0.5980 chunk 43 optimal weight: 5.9990 chunk 101 optimal weight: 20.0000 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN C 155 HIS ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6137 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 12385 Z= 0.345 Angle : 0.604 7.357 16773 Z= 0.324 Chirality : 0.043 0.148 1846 Planarity : 0.004 0.044 1985 Dihedral : 9.499 170.505 1676 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 11.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.63 % Allowed : 21.61 % Favored : 72.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.70 (0.22), residues: 1382 helix: 1.21 (0.16), residues: 949 sheet: 0.04 (0.51), residues: 107 loop : -1.53 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP D 120 HIS 0.009 0.002 HIS C 104 PHE 0.032 0.002 PHE D 390 TYR 0.033 0.002 TYR D 284 ARG 0.008 0.001 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 222 time to evaluate : 1.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.7118 (OUTLIER) cc_final: 0.6887 (t70) REVERT: A 136 PHE cc_start: 0.5287 (OUTLIER) cc_final: 0.4955 (m-10) REVERT: A 343 MET cc_start: 0.6088 (OUTLIER) cc_final: 0.5655 (mtm) REVERT: B 100 ASP cc_start: 0.7998 (t0) cc_final: 0.7529 (t0) REVERT: B 275 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6286 (t80) REVERT: C 104 HIS cc_start: 0.6410 (OUTLIER) cc_final: 0.6072 (t70) REVERT: C 275 PHE cc_start: 0.7772 (OUTLIER) cc_final: 0.7376 (t80) REVERT: C 300 GLU cc_start: 0.7456 (tt0) cc_final: 0.7083 (tt0) REVERT: D 153 LEU cc_start: 0.7722 (OUTLIER) cc_final: 0.7459 (mp) REVERT: D 305 TYR cc_start: 0.8124 (m-80) cc_final: 0.7798 (m-80) REVERT: E 299 ILE cc_start: 0.3906 (OUTLIER) cc_final: 0.2482 (pt) REVERT: E 343 MET cc_start: 0.2610 (OUTLIER) cc_final: 0.2229 (mtt) REVERT: F 300 MET cc_start: 0.4666 (mmt) cc_final: 0.4385 (mmt) REVERT: F 315 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.7099 (tp) outliers start: 74 outliers final: 44 residues processed: 276 average time/residue: 0.2215 time to fit residues: 88.6388 Evaluate side-chains 261 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 207 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 330 ILE Chi-restraints excluded: chain E residue 343 MET Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Chi-restraints excluded: chain F residue 315 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 chunk 60 optimal weight: 0.4980 chunk 84 optimal weight: 3.9990 chunk 126 optimal weight: 0.5980 chunk 134 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 120 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN C 49 GLN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6057 moved from start: 0.2175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12385 Z= 0.193 Angle : 0.494 5.730 16773 Z= 0.270 Chirality : 0.039 0.164 1846 Planarity : 0.003 0.039 1985 Dihedral : 8.900 169.474 1674 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 4.26 % Allowed : 23.21 % Favored : 72.53 % 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: 1.10 (0.22), residues: 1382 helix: 1.48 (0.16), residues: 948 sheet: 0.20 (0.52), residues: 107 loop : -1.26 (0.33), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP D 120 HIS 0.006 0.001 HIS E 119 PHE 0.032 0.002 PHE F 27 TYR 0.027 0.001 TYR D 284 ARG 0.005 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 224 time to evaluate : 1.438 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.6837 (OUTLIER) cc_final: 0.6566 (t70) REVERT: A 136 PHE cc_start: 0.5218 (OUTLIER) cc_final: 0.4663 (m-80) REVERT: A 319 LYS cc_start: 0.5570 (tptm) cc_final: 0.5153 (mtpt) REVERT: A 343 MET cc_start: 0.6154 (OUTLIER) cc_final: 0.5716 (mtm) REVERT: B 275 PHE cc_start: 0.6517 (OUTLIER) cc_final: 0.5949 (t80) REVERT: C 104 HIS cc_start: 0.6565 (OUTLIER) cc_final: 0.6078 (t70) REVERT: C 275 PHE cc_start: 0.7724 (OUTLIER) cc_final: 0.7372 (t80) REVERT: D 305 TYR cc_start: 0.8036 (m-80) cc_final: 0.7783 (m-80) REVERT: E 299 ILE cc_start: 0.3837 (OUTLIER) cc_final: 0.2479 (tp) outliers start: 56 outliers final: 41 residues processed: 265 average time/residue: 0.2435 time to fit residues: 91.9245 Evaluate side-chains 257 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 209 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 294 ASP Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.6980 chunk 76 optimal weight: 0.6980 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 114 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 312 HIS B 66 ASN C 49 GLN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6075 moved from start: 0.2424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12385 Z= 0.216 Angle : 0.508 5.713 16773 Z= 0.277 Chirality : 0.039 0.135 1846 Planarity : 0.003 0.037 1985 Dihedral : 8.614 164.077 1674 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 10.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 5.10 % Allowed : 22.98 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.22), residues: 1382 helix: 1.52 (0.16), residues: 948 sheet: 0.29 (0.52), residues: 105 loop : -1.26 (0.33), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP D 120 HIS 0.005 0.001 HIS E 119 PHE 0.025 0.002 PHE E 331 TYR 0.029 0.002 TYR D 284 ARG 0.004 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 216 time to evaluate : 1.260 Fit side-chains revert: symmetry clash REVERT: A 136 PHE cc_start: 0.5272 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: A 319 LYS cc_start: 0.5613 (tptm) cc_final: 0.5180 (mtpt) REVERT: A 343 MET cc_start: 0.6017 (OUTLIER) cc_final: 0.5591 (mtm) REVERT: B 275 PHE cc_start: 0.6504 (OUTLIER) cc_final: 0.5908 (t80) REVERT: C 275 PHE cc_start: 0.7738 (OUTLIER) cc_final: 0.7397 (t80) REVERT: D 305 TYR cc_start: 0.8047 (m-80) cc_final: 0.7809 (m-80) REVERT: E 299 ILE cc_start: 0.3904 (OUTLIER) cc_final: 0.2494 (tp) outliers start: 67 outliers final: 47 residues processed: 267 average time/residue: 0.2458 time to fit residues: 93.1553 Evaluate side-chains 252 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 200 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 296 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 47 VAL Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 0.3980 chunk 26 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 33 optimal weight: 0.9990 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 70 optimal weight: 6.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 107 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6029 moved from start: 0.2561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 12385 Z= 0.176 Angle : 0.490 6.329 16773 Z= 0.267 Chirality : 0.039 0.142 1846 Planarity : 0.003 0.037 1985 Dihedral : 8.322 156.427 1674 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.79 % Allowed : 23.44 % Favored : 71.77 % 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: 1.37 (0.23), residues: 1382 helix: 1.67 (0.17), residues: 947 sheet: 0.41 (0.52), residues: 105 loop : -1.13 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 120 HIS 0.004 0.001 HIS D 104 PHE 0.026 0.001 PHE E 331 TYR 0.028 0.001 TYR D 284 ARG 0.003 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 63 poor density : 210 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5577 (tptm) cc_final: 0.5226 (mtpt) REVERT: B 27 PHE cc_start: 0.5143 (m-10) cc_final: 0.4751 (m-10) REVERT: B 275 PHE cc_start: 0.6450 (OUTLIER) cc_final: 0.5738 (t80) REVERT: C 275 PHE cc_start: 0.7691 (OUTLIER) cc_final: 0.7368 (t80) REVERT: D 305 TYR cc_start: 0.7956 (m-80) cc_final: 0.7723 (m-80) REVERT: E 299 ILE cc_start: 0.3898 (OUTLIER) cc_final: 0.2528 (tp) outliers start: 63 outliers final: 50 residues processed: 257 average time/residue: 0.2224 time to fit residues: 83.4649 Evaluate side-chains 253 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 200 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 116 ASN Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 19 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 131 LEU Chi-restraints excluded: chain D residue 153 LEU Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 76 optimal weight: 0.7980 chunk 98 optimal weight: 0.5980 chunk 113 optimal weight: 4.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN C 49 GLN C 116 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 HIS F 107 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6074 moved from start: 0.2778 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 12385 Z= 0.219 Angle : 0.517 6.614 16773 Z= 0.281 Chirality : 0.040 0.143 1846 Planarity : 0.003 0.036 1985 Dihedral : 8.235 141.077 1674 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.72 % Allowed : 24.58 % Favored : 70.70 % 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: 1.29 (0.23), residues: 1382 helix: 1.62 (0.16), residues: 947 sheet: 0.44 (0.52), residues: 105 loop : -1.23 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP D 120 HIS 0.004 0.001 HIS D 104 PHE 0.024 0.001 PHE E 331 TYR 0.029 0.001 TYR D 284 ARG 0.004 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 267 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 205 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 136 PHE cc_start: 0.5005 (OUTLIER) cc_final: 0.4743 (m-10) REVERT: A 319 LYS cc_start: 0.5667 (tptm) cc_final: 0.5251 (mtpt) REVERT: B 265 MET cc_start: 0.3309 (mmm) cc_final: 0.2963 (tpp) REVERT: B 275 PHE cc_start: 0.6420 (OUTLIER) cc_final: 0.5662 (t80) REVERT: C 275 PHE cc_start: 0.7729 (OUTLIER) cc_final: 0.7389 (t80) REVERT: D 305 TYR cc_start: 0.8036 (m-80) cc_final: 0.7821 (m-80) REVERT: E 299 ILE cc_start: 0.3919 (OUTLIER) cc_final: 0.2597 (pt) outliers start: 62 outliers final: 53 residues processed: 252 average time/residue: 0.2176 time to fit residues: 80.7341 Evaluate side-chains 254 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 197 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 336 CYS Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 25 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 91 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 105 optimal weight: 0.7980 chunk 121 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6069 moved from start: 0.2917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12385 Z= 0.214 Angle : 0.527 8.573 16773 Z= 0.286 Chirality : 0.040 0.151 1846 Planarity : 0.003 0.037 1985 Dihedral : 7.857 113.106 1674 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 4.64 % Allowed : 25.04 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.22), residues: 1382 helix: 1.58 (0.16), residues: 947 sheet: 0.39 (0.51), residues: 105 loop : -1.14 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP D 120 HIS 0.014 0.001 HIS E 132 PHE 0.027 0.001 PHE B 27 TYR 0.029 0.001 TYR D 284 ARG 0.003 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 204 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5668 (tptm) cc_final: 0.5220 (mtpt) REVERT: B 27 PHE cc_start: 0.5023 (m-10) cc_final: 0.4257 (m-80) REVERT: B 265 MET cc_start: 0.3277 (mmm) cc_final: 0.2944 (tpp) REVERT: B 275 PHE cc_start: 0.6389 (OUTLIER) cc_final: 0.5619 (t80) REVERT: C 275 PHE cc_start: 0.7725 (OUTLIER) cc_final: 0.7379 (t80) REVERT: D 305 TYR cc_start: 0.7999 (m-80) cc_final: 0.7781 (m-80) REVERT: E 299 ILE cc_start: 0.3914 (OUTLIER) cc_final: 0.2611 (pt) outliers start: 61 outliers final: 53 residues processed: 251 average time/residue: 0.2313 time to fit residues: 85.2032 Evaluate side-chains 259 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 203 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 283 VAL Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 55 LEU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.9990 chunk 117 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 75 optimal weight: 9.9990 chunk 54 optimal weight: 0.0980 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 10.0000 chunk 118 optimal weight: 0.7980 chunk 81 optimal weight: 0.5980 chunk 132 optimal weight: 0.8980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6066 moved from start: 0.3018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12385 Z= 0.206 Angle : 0.526 7.959 16773 Z= 0.285 Chirality : 0.039 0.144 1846 Planarity : 0.003 0.037 1985 Dihedral : 6.977 83.813 1674 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.72 % Allowed : 24.96 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.22), residues: 1382 helix: 1.57 (0.16), residues: 946 sheet: 0.39 (0.51), residues: 105 loop : -1.15 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP D 120 HIS 0.012 0.001 HIS E 132 PHE 0.025 0.001 PHE B 27 TYR 0.030 0.001 TYR D 284 ARG 0.004 0.000 ARG D 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 202 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5677 (tptm) cc_final: 0.5219 (mtpt) REVERT: B 27 PHE cc_start: 0.5027 (m-10) cc_final: 0.4267 (m-80) REVERT: B 46 GLN cc_start: 0.7736 (tm-30) cc_final: 0.7422 (tm-30) REVERT: B 265 MET cc_start: 0.3092 (mmm) cc_final: 0.2786 (tpp) REVERT: B 275 PHE cc_start: 0.6432 (OUTLIER) cc_final: 0.5738 (t80) REVERT: C 275 PHE cc_start: 0.7730 (OUTLIER) cc_final: 0.7398 (t80) REVERT: D 305 TYR cc_start: 0.7990 (m-80) cc_final: 0.7771 (m-80) REVERT: E 127 TYR cc_start: 0.3797 (m-10) cc_final: 0.3563 (m-10) REVERT: E 144 PHE cc_start: 0.5814 (m-10) cc_final: 0.5579 (m-80) REVERT: E 299 ILE cc_start: 0.3908 (OUTLIER) cc_final: 0.2621 (pt) outliers start: 62 outliers final: 50 residues processed: 248 average time/residue: 0.2173 time to fit residues: 79.3013 Evaluate side-chains 252 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 199 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.9990 chunk 62 optimal weight: 0.9990 chunk 91 optimal weight: 0.9990 chunk 138 optimal weight: 0.9990 chunk 127 optimal weight: 0.0770 chunk 110 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 85 optimal weight: 0.8980 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 0.9990 chunk 117 optimal weight: 0.9980 overall best weight: 0.7340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 66 ASN C 49 GLN C 404 GLN C 408 ASN ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6076 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12385 Z= 0.221 Angle : 0.544 9.257 16773 Z= 0.294 Chirality : 0.040 0.172 1846 Planarity : 0.003 0.037 1985 Dihedral : 6.890 83.554 1674 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 4.57 % Allowed : 25.27 % Favored : 70.17 % 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 (0.22), residues: 1382 helix: 1.60 (0.16), residues: 935 sheet: 0.39 (0.52), residues: 105 loop : -1.07 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.001 TRP D 120 HIS 0.012 0.001 HIS E 132 PHE 0.024 0.001 PHE B 27 TYR 0.029 0.002 TYR D 284 ARG 0.004 0.000 ARG B 309 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2764 Ramachandran restraints generated. 1382 Oldfield, 0 Emsley, 1382 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 255 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 195 time to evaluate : 1.642 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 319 LYS cc_start: 0.5713 (tptm) cc_final: 0.5221 (mtpt) REVERT: B 27 PHE cc_start: 0.5023 (m-10) cc_final: 0.4398 (m-80) REVERT: B 265 MET cc_start: 0.2975 (mmm) cc_final: 0.2686 (tpp) REVERT: B 275 PHE cc_start: 0.6377 (OUTLIER) cc_final: 0.5657 (t80) REVERT: C 275 PHE cc_start: 0.7748 (OUTLIER) cc_final: 0.7403 (t80) REVERT: D 305 TYR cc_start: 0.8002 (m-80) cc_final: 0.7790 (m-80) REVERT: E 127 TYR cc_start: 0.3600 (m-10) cc_final: 0.3356 (m-10) REVERT: E 144 PHE cc_start: 0.5904 (m-10) cc_final: 0.5681 (m-80) REVERT: E 265 MET cc_start: 0.5318 (tpt) cc_final: 0.4968 (mmt) REVERT: E 299 ILE cc_start: 0.3904 (OUTLIER) cc_final: 0.2618 (pt) outliers start: 60 outliers final: 53 residues processed: 240 average time/residue: 0.2337 time to fit residues: 82.7052 Evaluate side-chains 249 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 193 time to evaluate : 1.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 SER Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 59 TRP Chi-restraints excluded: chain A residue 97 ILE Chi-restraints excluded: chain A residue 280 CYS Chi-restraints excluded: chain A residue 307 THR Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 343 MET Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 95 THR Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 259 ILE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 286 VAL Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 26 VAL Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 141 ASN Chi-restraints excluded: chain C residue 153 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 265 MET Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 294 ASP Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 28 THR Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 159 ILE Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 281 TYR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 317 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 400 ASN Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 278 ILE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 310 CYS Chi-restraints excluded: chain E residue 314 LEU Chi-restraints excluded: chain F residue 26 VAL Chi-restraints excluded: chain F residue 38 ILE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 293 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 2.9990 chunk 101 optimal weight: 20.0000 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 110 optimal weight: 7.9990 chunk 46 optimal weight: 0.6980 chunk 113 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 96 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 116 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 66 ASN C 49 GLN C 253 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.222896 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.182580 restraints weight = 15607.428| |-----------------------------------------------------------------------------| r_work (start): 0.4256 rms_B_bonded: 3.01 r_work: 0.4067 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.4067 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12385 Z= 0.221 Angle : 0.550 9.101 16773 Z= 0.296 Chirality : 0.040 0.162 1846 Planarity : 0.003 0.037 1985 Dihedral : 6.768 83.290 1674 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.64 % Allowed : 25.34 % Favored : 70.02 % 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 (0.22), residues: 1382 helix: 1.62 (0.16), residues: 935 sheet: 0.35 (0.52), residues: 105 loop : -1.14 (0.34), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.002 TRP D 120 HIS 0.012 0.001 HIS E 132 PHE 0.023 0.001 PHE B 27 TYR 0.027 0.001 TYR E 325 ARG 0.004 0.000 ARG D 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2970.59 seconds wall clock time: 54 minutes 36.71 seconds (3276.71 seconds total)