Starting phenix.real_space_refine on Fri Jan 19 16:39:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsa_27687/01_2024/8dsa_27687_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsa_27687/01_2024/8dsa_27687.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsa_27687/01_2024/8dsa_27687.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsa_27687/01_2024/8dsa_27687.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsa_27687/01_2024/8dsa_27687_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dsa_27687/01_2024/8dsa_27687_updated.pdb" } resolution = 3.48 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= 0.041 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: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 6.47, per 1000 atoms: 0.54 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: 4.61 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: 2.09 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: 3.20 Time building geometry restraints manager: 4.97 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: 4.770 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 16.170 Check model and map are aligned: 0.170 Set scattering table: 0.100 Process input model: 34.210 Find NCS groups from input model: 0.640 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6116 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 : 7.06 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 357 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 350 time to evaluate : 1.402 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ILE cc_start: 0.8039 (mt) cc_final: 0.7503 (mm) REVERT: A 131 LEU cc_start: 0.8425 (tt) cc_final: 0.8175 (tt) REVERT: A 143 TRP cc_start: 0.6701 (p90) cc_final: 0.6445 (p90) REVERT: B 35 MET cc_start: 0.6908 (mtp) cc_final: 0.6583 (mtt) REVERT: C 125 PHE cc_start: 0.7655 (t80) cc_final: 0.7378 (t80) REVERT: C 171 ARG cc_start: 0.8139 (tmt-80) cc_final: 0.7890 (tmt-80) REVERT: E 110 ASP cc_start: 0.5993 (m-30) cc_final: 0.5372 (m-30) REVERT: F 96 MET cc_start: 0.5211 (mpp) cc_final: 0.4965 (mmm) outliers start: 7 outliers final: 3 residues processed: 354 average time/residue: 0.2579 time to fit residues: 126.6812 Evaluate side-chains 242 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 239 time to evaluate : 1.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 126 optimal weight: 0.6980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 288 ASN ** C 404 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 406 ASN ** C 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 106 GLN ** F 112 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.2797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 12385 Z= 0.254 Angle : 0.608 8.189 16773 Z= 0.320 Chirality : 0.042 0.241 1846 Planarity : 0.004 0.047 1985 Dihedral : 9.867 179.843 1676 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 5.33 % Allowed : 21.16 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.22), residues: 1382 helix: 1.14 (0.16), residues: 958 sheet: 0.40 (0.51), residues: 107 loop : -1.25 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP A 23 HIS 0.006 0.001 HIS C 104 PHE 0.023 0.002 PHE E 291 TYR 0.028 0.002 TYR F 262 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 327 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 257 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5666 (p90) cc_final: 0.4886 (p90) REVERT: A 131 LEU cc_start: 0.8400 (OUTLIER) cc_final: 0.8073 (tt) REVERT: B 35 MET cc_start: 0.6981 (mtp) cc_final: 0.6637 (mtt) REVERT: B 275 PHE cc_start: 0.7220 (OUTLIER) cc_final: 0.6795 (t80) REVERT: B 337 MET cc_start: 0.7458 (tmm) cc_final: 0.6531 (tmm) REVERT: C 104 HIS cc_start: 0.6706 (OUTLIER) cc_final: 0.6137 (t70) REVERT: C 110 ASP cc_start: 0.7013 (m-30) cc_final: 0.6699 (m-30) REVERT: C 161 LEU cc_start: 0.7251 (OUTLIER) cc_final: 0.7033 (mp) REVERT: C 171 ARG cc_start: 0.8294 (tmt-80) cc_final: 0.7986 (tmt-80) REVERT: D 18 ARG cc_start: 0.6470 (OUTLIER) cc_final: 0.5743 (tpt90) REVERT: D 157 VAL cc_start: 0.8140 (t) cc_final: 0.7820 (p) REVERT: D 243 LEU cc_start: 0.7436 (mt) cc_final: 0.7006 (mt) REVERT: E 136 PHE cc_start: 0.4654 (OUTLIER) cc_final: 0.4209 (m-80) REVERT: E 291 PHE cc_start: 0.4612 (m-10) cc_final: 0.3908 (p90) REVERT: F 96 MET cc_start: 0.4543 (mpp) cc_final: 0.4331 (mmm) outliers start: 70 outliers final: 39 residues processed: 305 average time/residue: 0.2528 time to fit residues: 109.1817 Evaluate side-chains 266 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 221 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain B residue 23 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 120 TRP Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 155 HIS Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 161 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 18 ARG Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 102 ASP Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 314 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 343 MET Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 343 TYR 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: 1.9990 chunk 105 optimal weight: 2.9990 chunk 85 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 126 optimal weight: 0.5980 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 10.0000 chunk 125 optimal weight: 0.7980 chunk 43 optimal weight: 0.2980 chunk 101 optimal weight: 20.0000 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 406 ASN ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6369 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 12385 Z= 0.212 Angle : 0.563 9.193 16773 Z= 0.296 Chirality : 0.040 0.183 1846 Planarity : 0.003 0.039 1985 Dihedral : 9.362 174.745 1675 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 5.86 % Allowed : 21.77 % Favored : 72.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.22), residues: 1382 helix: 1.32 (0.16), residues: 955 sheet: 0.73 (0.52), residues: 105 loop : -1.16 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP E 24 HIS 0.005 0.001 HIS D 104 PHE 0.027 0.002 PHE E 291 TYR 0.035 0.002 TYR F 262 ARG 0.004 0.000 ARG B 345 *********************** 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 303 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 226 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5639 (p90) cc_final: 0.5070 (p90) REVERT: A 37 MET cc_start: 0.7637 (ptm) cc_final: 0.7428 (ptm) REVERT: A 131 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8343 (tt) REVERT: B 35 MET cc_start: 0.6899 (mtp) cc_final: 0.6623 (mtt) REVERT: B 275 PHE cc_start: 0.7146 (OUTLIER) cc_final: 0.6721 (t80) REVERT: B 331 PHE cc_start: 0.6193 (OUTLIER) cc_final: 0.5952 (t80) REVERT: C 104 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.5970 (t70) REVERT: C 110 ASP cc_start: 0.7020 (m-30) cc_final: 0.6635 (m-30) REVERT: C 171 ARG cc_start: 0.8376 (tmt-80) cc_final: 0.7996 (tmt-80) REVERT: E 291 PHE cc_start: 0.5162 (m-80) cc_final: 0.4080 (p90) REVERT: E 343 MET cc_start: 0.1598 (mtp) cc_final: 0.0571 (ptp) REVERT: F 96 MET cc_start: 0.4440 (mpp) cc_final: 0.4181 (mmm) REVERT: F 318 LYS cc_start: 0.7908 (mmmt) cc_final: 0.7633 (mmmt) outliers start: 77 outliers final: 37 residues processed: 278 average time/residue: 0.2518 time to fit residues: 99.5296 Evaluate side-chains 247 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 206 time to evaluate : 1.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 331 PHE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 368 VAL Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 253 HIS Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 41 PHE Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.0030 chunk 95 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 2.9990 chunk 126 optimal weight: 0.7980 chunk 134 optimal weight: 2.9990 chunk 66 optimal weight: 0.5980 chunk 120 optimal weight: 0.9980 chunk 36 optimal weight: 0.9980 overall best weight: 0.6590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 239 GLN ** 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 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 12385 Z= 0.208 Angle : 0.555 8.714 16773 Z= 0.292 Chirality : 0.040 0.187 1846 Planarity : 0.003 0.036 1985 Dihedral : 8.839 166.419 1673 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 10.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.48 % Allowed : 22.68 % Favored : 71.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.22), residues: 1382 helix: 1.48 (0.16), residues: 956 sheet: 0.61 (0.50), residues: 105 loop : -1.17 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 24 HIS 0.012 0.001 HIS D 104 PHE 0.026 0.002 PHE F 27 TYR 0.037 0.001 TYR F 330 ARG 0.005 0.000 ARG D 103 *********************** 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 293 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 72 poor density : 221 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5670 (p90) cc_final: 0.5220 (p90) REVERT: A 37 MET cc_start: 0.7439 (ptm) cc_final: 0.7229 (ptm) REVERT: A 104 HIS cc_start: 0.6980 (OUTLIER) cc_final: 0.6708 (t70) REVERT: A 131 LEU cc_start: 0.8647 (OUTLIER) cc_final: 0.8337 (tt) REVERT: B 23 TRP cc_start: 0.6844 (p-90) cc_final: 0.6537 (p-90) REVERT: B 35 MET cc_start: 0.6825 (mtp) cc_final: 0.6585 (mtt) REVERT: B 275 PHE cc_start: 0.7067 (OUTLIER) cc_final: 0.6697 (t80) REVERT: B 308 TYR cc_start: 0.7661 (OUTLIER) cc_final: 0.7005 (m-80) REVERT: C 104 HIS cc_start: 0.6802 (OUTLIER) cc_final: 0.6263 (t70) REVERT: C 110 ASP cc_start: 0.7015 (m-30) cc_final: 0.6628 (m-30) REVERT: D 157 VAL cc_start: 0.8348 (t) cc_final: 0.8041 (p) REVERT: E 25 ASP cc_start: 0.5094 (m-30) cc_final: 0.4865 (m-30) REVERT: E 52 MET cc_start: 0.4645 (ppp) cc_final: 0.3609 (ttp) REVERT: E 299 ILE cc_start: 0.3512 (OUTLIER) cc_final: 0.2593 (pt) REVERT: E 343 MET cc_start: 0.1470 (mtp) cc_final: 0.1248 (mtp) REVERT: F 51 LYS cc_start: 0.6152 (OUTLIER) cc_final: 0.5562 (pttp) REVERT: F 145 TRP cc_start: 0.4988 (t-100) cc_final: 0.4712 (t-100) REVERT: F 300 MET cc_start: 0.6493 (mmt) cc_final: 0.6051 (mmp) REVERT: F 318 LYS cc_start: 0.8029 (mmmt) cc_final: 0.7713 (mmmt) REVERT: F 328 SER cc_start: 0.6783 (t) cc_final: 0.6205 (p) outliers start: 72 outliers final: 49 residues processed: 268 average time/residue: 0.2599 time to fit residues: 100.5225 Evaluate side-chains 262 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 206 time to evaluate : 1.704 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 52 MET Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU Chi-restraints excluded: chain B residue 136 PHE Chi-restraints excluded: chain B residue 275 PHE Chi-restraints excluded: chain B residue 308 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain C residue 368 VAL 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 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 51 LYS Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 7.9990 chunk 76 optimal weight: 0.9980 chunk 1 optimal weight: 5.9990 chunk 100 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 114 optimal weight: 0.0470 chunk 92 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 68 optimal weight: 0.6980 chunk 120 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 overall best weight: 0.4678 ------------------------------------------------------------------------------- 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 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6358 moved from start: 0.4137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12385 Z= 0.182 Angle : 0.536 9.240 16773 Z= 0.278 Chirality : 0.039 0.179 1846 Planarity : 0.003 0.034 1985 Dihedral : 8.323 149.043 1673 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.10 % Allowed : 23.29 % Favored : 71.61 % 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: 1.35 (0.22), residues: 1382 helix: 1.59 (0.16), residues: 958 sheet: 0.80 (0.51), residues: 105 loop : -1.18 (0.34), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 24 HIS 0.012 0.001 HIS D 104 PHE 0.019 0.001 PHE D 156 TYR 0.031 0.001 TYR F 262 ARG 0.005 0.000 ARG D 103 *********************** 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 294 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 227 time to evaluate : 1.495 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5660 (p90) cc_final: 0.5315 (p90) REVERT: A 37 MET cc_start: 0.7509 (ptm) cc_final: 0.7285 (ptm) REVERT: A 104 HIS cc_start: 0.6962 (OUTLIER) cc_final: 0.6665 (t70) REVERT: A 131 LEU cc_start: 0.8648 (OUTLIER) cc_final: 0.8339 (tt) REVERT: A 144 PHE cc_start: 0.6848 (OUTLIER) cc_final: 0.6351 (m-80) REVERT: B 35 MET cc_start: 0.6830 (mtp) cc_final: 0.6562 (mtt) REVERT: B 275 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6807 (t80) REVERT: B 308 TYR cc_start: 0.7721 (OUTLIER) cc_final: 0.7002 (m-80) REVERT: C 104 HIS cc_start: 0.6705 (OUTLIER) cc_final: 0.5941 (t70) REVERT: C 110 ASP cc_start: 0.7075 (m-30) cc_final: 0.6651 (m-30) REVERT: D 239 GLN cc_start: 0.7415 (pm20) cc_final: 0.7048 (pm20) REVERT: D 374 PHE cc_start: 0.6994 (OUTLIER) cc_final: 0.6023 (m-80) REVERT: E 52 MET cc_start: 0.4698 (ppp) cc_final: 0.3776 (ttp) REVERT: E 136 PHE cc_start: 0.4492 (OUTLIER) cc_final: 0.4105 (m-80) REVERT: E 299 ILE cc_start: 0.3269 (OUTLIER) cc_final: 0.2398 (pt) REVERT: E 343 MET cc_start: 0.1235 (mtp) cc_final: 0.0803 (mtp) REVERT: F 300 MET cc_start: 0.6653 (mmt) cc_final: 0.6268 (mmp) REVERT: F 328 SER cc_start: 0.6824 (t) cc_final: 0.6385 (p) outliers start: 67 outliers final: 45 residues processed: 275 average time/residue: 0.2508 time to fit residues: 99.6344 Evaluate side-chains 269 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 215 time to evaluate : 1.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP 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 115 GLU 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 B residue 308 TYR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 327 SER Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 38 ILE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 17 TYR Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 292 ASP Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.1980 chunk 120 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 78 optimal weight: 0.4980 chunk 33 optimal weight: 0.7980 chunk 134 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 44 optimal weight: 0.4980 chunk 70 optimal weight: 6.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12385 Z= 0.185 Angle : 0.540 9.647 16773 Z= 0.281 Chirality : 0.039 0.179 1846 Planarity : 0.003 0.034 1985 Dihedral : 7.832 119.217 1673 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.33 % Allowed : 24.12 % Favored : 70.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.22), residues: 1382 helix: 1.67 (0.16), residues: 955 sheet: 0.90 (0.52), residues: 105 loop : -1.14 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP E 24 HIS 0.012 0.001 HIS D 104 PHE 0.027 0.001 PHE C 125 TYR 0.026 0.001 TYR F 262 ARG 0.004 0.000 ARG D 103 *********************** 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 300 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 230 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5877 (p90) cc_final: 0.5572 (p90) REVERT: A 37 MET cc_start: 0.7482 (ptm) cc_final: 0.7269 (ptm) REVERT: A 104 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6583 (t70) REVERT: A 131 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8350 (tt) REVERT: A 144 PHE cc_start: 0.6811 (OUTLIER) cc_final: 0.6389 (m-80) REVERT: A 337 MET cc_start: 0.5450 (tpt) cc_final: 0.5167 (tpt) REVERT: B 35 MET cc_start: 0.6783 (mtp) cc_final: 0.6502 (mtt) REVERT: B 275 PHE cc_start: 0.7254 (OUTLIER) cc_final: 0.6785 (t80) REVERT: B 308 TYR cc_start: 0.7729 (OUTLIER) cc_final: 0.6953 (m-80) REVERT: C 104 HIS cc_start: 0.6686 (OUTLIER) cc_final: 0.5920 (t70) REVERT: C 110 ASP cc_start: 0.7095 (m-30) cc_final: 0.6638 (m-30) REVERT: D 37 MET cc_start: 0.5358 (tmm) cc_final: 0.5065 (tpt) REVERT: D 156 PHE cc_start: 0.7733 (t80) cc_final: 0.7402 (t80) REVERT: D 157 VAL cc_start: 0.8429 (t) cc_final: 0.8111 (p) REVERT: D 374 PHE cc_start: 0.7042 (OUTLIER) cc_final: 0.5951 (m-80) REVERT: E 52 MET cc_start: 0.4645 (ppp) cc_final: 0.3842 (ttp) REVERT: E 136 PHE cc_start: 0.4461 (OUTLIER) cc_final: 0.4090 (m-80) REVERT: E 299 ILE cc_start: 0.3251 (OUTLIER) cc_final: 0.1572 (mm) REVERT: E 343 MET cc_start: 0.1593 (mtp) cc_final: 0.1373 (mtp) REVERT: F 300 MET cc_start: 0.6668 (mmt) cc_final: 0.6230 (mmp) REVERT: F 328 SER cc_start: 0.6635 (t) cc_final: 0.6132 (p) outliers start: 70 outliers final: 52 residues processed: 281 average time/residue: 0.2389 time to fit residues: 97.9998 Evaluate side-chains 272 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 211 time to evaluate : 1.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL 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 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 134 LEU 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 B residue 308 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 363 SER Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain E residue 300 GLU Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 0.9990 chunk 76 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 0.7980 chunk 81 optimal weight: 0.9980 chunk 61 optimal weight: 0.7980 chunk 82 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 49 GLN ** C 239 GLN ** 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 104 HIS ** D 288 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6428 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12385 Z= 0.238 Angle : 0.574 9.088 16773 Z= 0.300 Chirality : 0.041 0.169 1846 Planarity : 0.003 0.034 1985 Dihedral : 7.525 90.939 1673 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 11.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 5.40 % Allowed : 25.57 % Favored : 69.03 % 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: 1.38 (0.22), residues: 1382 helix: 1.61 (0.16), residues: 956 sheet: 0.86 (0.51), residues: 105 loop : -1.16 (0.35), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP E 24 HIS 0.015 0.001 HIS E 132 PHE 0.026 0.002 PHE C 125 TYR 0.024 0.001 TYR F 262 ARG 0.003 0.000 ARG D 103 *********************** 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 277 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 206 time to evaluate : 1.481 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 24 TRP cc_start: 0.5870 (p90) cc_final: 0.5642 (p90) REVERT: A 37 MET cc_start: 0.7370 (ptm) cc_final: 0.7144 (ptm) REVERT: A 104 HIS cc_start: 0.7206 (OUTLIER) cc_final: 0.6876 (t70) REVERT: A 131 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8378 (tt) REVERT: A 337 MET cc_start: 0.5628 (tpt) cc_final: 0.5428 (tpt) REVERT: B 35 MET cc_start: 0.6789 (mtp) cc_final: 0.6521 (mtt) REVERT: B 52 MET cc_start: 0.6600 (ptm) cc_final: 0.6396 (ptm) REVERT: B 275 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6846 (t80) REVERT: B 308 TYR cc_start: 0.7787 (OUTLIER) cc_final: 0.7035 (m-80) REVERT: B 337 MET cc_start: 0.7578 (tmm) cc_final: 0.6695 (tpt) REVERT: C 104 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6194 (t70) REVERT: C 110 ASP cc_start: 0.7096 (m-30) cc_final: 0.6636 (m-30) REVERT: D 157 VAL cc_start: 0.8432 (t) cc_final: 0.8122 (p) REVERT: D 356 ILE cc_start: 0.4403 (OUTLIER) cc_final: 0.3668 (mt) REVERT: D 374 PHE cc_start: 0.6921 (OUTLIER) cc_final: 0.5812 (m-80) REVERT: E 52 MET cc_start: 0.4807 (ppp) cc_final: 0.3594 (ttp) REVERT: E 136 PHE cc_start: 0.4429 (OUTLIER) cc_final: 0.4050 (m-80) REVERT: E 299 ILE cc_start: 0.3487 (OUTLIER) cc_final: 0.2580 (pt) REVERT: E 343 MET cc_start: 0.1711 (mtp) cc_final: 0.1200 (mtp) REVERT: F 114 MET cc_start: 0.6562 (tpt) cc_final: 0.6309 (tpt) REVERT: F 300 MET cc_start: 0.7272 (mmt) cc_final: 0.6852 (mmp) outliers start: 71 outliers final: 55 residues processed: 259 average time/residue: 0.2311 time to fit residues: 86.4864 Evaluate side-chains 258 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 194 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL Chi-restraints excluded: chain A residue 104 HIS Chi-restraints excluded: chain A residue 119 HIS Chi-restraints excluded: chain A residue 131 LEU Chi-restraints excluded: chain A residue 136 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 47 VAL Chi-restraints excluded: chain B residue 102 ASP Chi-restraints excluded: chain B residue 103 ARG Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 LEU 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 B residue 308 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 158 SER Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 104 HIS Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 1.9990 chunk 80 optimal weight: 0.6980 chunk 40 optimal weight: 0.5980 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.9980 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.4773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12385 Z= 0.202 Angle : 0.579 9.933 16773 Z= 0.302 Chirality : 0.040 0.185 1846 Planarity : 0.003 0.033 1985 Dihedral : 7.219 73.542 1673 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.63 % Allowed : 25.72 % Favored : 68.65 % 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: 1.39 (0.23), residues: 1382 helix: 1.61 (0.16), residues: 964 sheet: 0.88 (0.51), residues: 105 loop : -1.23 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP E 24 HIS 0.009 0.001 HIS E 132 PHE 0.024 0.001 PHE C 125 TYR 0.022 0.001 TYR F 262 ARG 0.002 0.000 ARG E 117 *********************** 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 276 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 202 time to evaluate : 1.507 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 104 HIS cc_start: 0.6987 (OUTLIER) cc_final: 0.6670 (t70) REVERT: A 131 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8337 (tt) REVERT: A 144 PHE cc_start: 0.6784 (OUTLIER) cc_final: 0.6393 (m-80) REVERT: A 337 MET cc_start: 0.5535 (tpt) cc_final: 0.5328 (tpt) REVERT: B 23 TRP cc_start: 0.6734 (p-90) cc_final: 0.6527 (p-90) REVERT: B 35 MET cc_start: 0.6807 (mtp) cc_final: 0.6521 (mtt) REVERT: B 275 PHE cc_start: 0.7259 (OUTLIER) cc_final: 0.6844 (t80) REVERT: B 308 TYR cc_start: 0.7790 (OUTLIER) cc_final: 0.6921 (m-80) REVERT: C 104 HIS cc_start: 0.6783 (OUTLIER) cc_final: 0.5990 (t70) REVERT: C 110 ASP cc_start: 0.7097 (m-30) cc_final: 0.6618 (m-30) REVERT: D 37 MET cc_start: 0.5270 (tmm) cc_final: 0.4963 (tpt) REVERT: D 156 PHE cc_start: 0.7735 (t80) cc_final: 0.7419 (t80) REVERT: D 157 VAL cc_start: 0.8487 (t) cc_final: 0.8154 (p) REVERT: D 279 ILE cc_start: 0.5310 (OUTLIER) cc_final: 0.4929 (mm) REVERT: D 356 ILE cc_start: 0.4449 (OUTLIER) cc_final: 0.3708 (mt) REVERT: D 374 PHE cc_start: 0.7068 (OUTLIER) cc_final: 0.5999 (m-80) REVERT: E 52 MET cc_start: 0.4837 (ppp) cc_final: 0.3706 (ttp) REVERT: E 136 PHE cc_start: 0.4536 (OUTLIER) cc_final: 0.4135 (m-80) REVERT: E 299 ILE cc_start: 0.3333 (OUTLIER) cc_final: 0.2442 (pt) REVERT: E 343 MET cc_start: 0.1922 (mtp) cc_final: 0.1407 (mtp) REVERT: F 114 MET cc_start: 0.6586 (tpt) cc_final: 0.6327 (tpt) REVERT: F 279 TYR cc_start: 0.4388 (t80) cc_final: 0.3994 (t80) REVERT: F 288 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.6253 (tp-100) REVERT: F 300 MET cc_start: 0.7245 (mmt) cc_final: 0.6876 (mmp) outliers start: 74 outliers final: 50 residues processed: 256 average time/residue: 0.2259 time to fit residues: 84.6577 Evaluate side-chains 259 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 197 time to evaluate : 1.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 VAL 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 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 44 THR 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 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 LEU 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 B residue 308 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 288 GLN Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 chunk 124 optimal weight: 0.0970 chunk 75 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 112 optimal weight: 9.9990 chunk 118 optimal weight: 0.8980 chunk 81 optimal weight: 0.7980 chunk 132 optimal weight: 3.9990 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 288 GLN ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6420 moved from start: 0.4914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12385 Z= 0.214 Angle : 0.600 10.540 16773 Z= 0.312 Chirality : 0.041 0.220 1846 Planarity : 0.003 0.032 1985 Dihedral : 7.054 69.774 1673 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 5.63 % Allowed : 25.80 % Favored : 68.57 % 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: 1.39 (0.23), residues: 1382 helix: 1.60 (0.16), residues: 955 sheet: 0.85 (0.51), residues: 105 loop : -1.05 (0.36), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.001 TRP A 24 HIS 0.009 0.001 HIS E 132 PHE 0.024 0.001 PHE C 125 TYR 0.027 0.001 TYR D 284 ARG 0.002 0.000 ARG E 117 *********************** 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 275 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 201 time to evaluate : 1.483 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8207 (mpp) cc_final: 0.7921 (mpp) REVERT: A 104 HIS cc_start: 0.6996 (OUTLIER) cc_final: 0.6630 (t70) REVERT: A 131 LEU cc_start: 0.8694 (OUTLIER) cc_final: 0.8377 (tt) REVERT: A 144 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.6463 (m-80) REVERT: A 265 MET cc_start: 0.6496 (ptp) cc_final: 0.6209 (ppp) REVERT: A 337 MET cc_start: 0.5344 (tpt) cc_final: 0.5126 (tpt) REVERT: B 23 TRP cc_start: 0.6734 (p-90) cc_final: 0.6343 (p-90) REVERT: B 35 MET cc_start: 0.6857 (mtp) cc_final: 0.6575 (mtt) REVERT: B 275 PHE cc_start: 0.7255 (OUTLIER) cc_final: 0.6857 (t80) REVERT: B 308 TYR cc_start: 0.7821 (OUTLIER) cc_final: 0.7014 (m-80) REVERT: B 337 MET cc_start: 0.7606 (tmm) cc_final: 0.6718 (tpt) REVERT: C 104 HIS cc_start: 0.6692 (OUTLIER) cc_final: 0.5919 (t70) REVERT: C 110 ASP cc_start: 0.7068 (m-30) cc_final: 0.6667 (m-30) REVERT: D 37 MET cc_start: 0.5281 (tmm) cc_final: 0.5002 (tpt) REVERT: D 156 PHE cc_start: 0.7749 (t80) cc_final: 0.7432 (t80) REVERT: D 157 VAL cc_start: 0.8431 (t) cc_final: 0.8120 (p) REVERT: D 356 ILE cc_start: 0.4220 (OUTLIER) cc_final: 0.3507 (mt) REVERT: D 374 PHE cc_start: 0.6963 (OUTLIER) cc_final: 0.5930 (m-80) REVERT: E 52 MET cc_start: 0.4731 (ppp) cc_final: 0.3511 (ttp) REVERT: E 136 PHE cc_start: 0.4578 (OUTLIER) cc_final: 0.4179 (m-80) REVERT: E 299 ILE cc_start: 0.3346 (OUTLIER) cc_final: 0.1646 (mm) REVERT: E 343 MET cc_start: 0.1869 (mtp) cc_final: 0.1473 (mtp) REVERT: F 35 MET cc_start: 0.6764 (mmt) cc_final: 0.6452 (mmt) REVERT: F 114 MET cc_start: 0.6573 (tpt) cc_final: 0.6297 (tpt) REVERT: F 279 TYR cc_start: 0.4597 (t80) cc_final: 0.4335 (t80) REVERT: F 300 MET cc_start: 0.7189 (mmt) cc_final: 0.6802 (mmp) outliers start: 74 outliers final: 57 residues processed: 255 average time/residue: 0.2271 time to fit residues: 84.6237 Evaluate side-chains 267 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 200 time to evaluate : 1.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 144 PHE Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP Chi-restraints excluded: chain B residue 38 ILE Chi-restraints excluded: chain B residue 44 THR 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 115 GLU Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 134 LEU 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 B residue 308 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain B residue 326 ILE Chi-restraints excluded: chain C residue 19 ILE Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 134 LEU Chi-restraints excluded: chain C residue 140 SER Chi-restraints excluded: chain C residue 149 THR Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 268 THR Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 283 VAL Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 356 ILE Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 273 PHE Chi-restraints excluded: chain F residue 330 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 0.1980 chunk 62 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 138 optimal weight: 8.9990 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 11 optimal weight: 6.9990 chunk 85 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 0.5980 chunk 117 optimal weight: 0.0040 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6373 moved from start: 0.5006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 12385 Z= 0.181 Angle : 0.581 10.385 16773 Z= 0.302 Chirality : 0.040 0.242 1846 Planarity : 0.003 0.032 1985 Dihedral : 6.781 68.988 1673 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 4.19 % Allowed : 27.25 % Favored : 68.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.23), residues: 1382 helix: 1.77 (0.16), residues: 940 sheet: 0.98 (0.52), residues: 105 loop : -0.96 (0.36), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.001 TRP A 24 HIS 0.003 0.001 HIS E 132 PHE 0.022 0.001 PHE C 125 TYR 0.020 0.001 TYR D 284 ARG 0.002 0.000 ARG B 345 ********************** 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 262 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 207 time to evaluate : 1.460 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 MET cc_start: 0.8180 (mpp) cc_final: 0.7870 (mpp) REVERT: A 104 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6559 (t70) REVERT: A 131 LEU cc_start: 0.8688 (OUTLIER) cc_final: 0.8368 (tt) REVERT: A 265 MET cc_start: 0.6456 (ptp) cc_final: 0.6174 (ppp) REVERT: A 337 MET cc_start: 0.5375 (tpt) cc_final: 0.5116 (tpt) REVERT: B 35 MET cc_start: 0.6836 (mtp) cc_final: 0.6561 (mtt) REVERT: B 275 PHE cc_start: 0.7253 (OUTLIER) cc_final: 0.6836 (t80) REVERT: B 308 TYR cc_start: 0.7756 (OUTLIER) cc_final: 0.6827 (m-80) REVERT: B 337 MET cc_start: 0.7594 (tmm) cc_final: 0.6531 (tpt) REVERT: C 104 HIS cc_start: 0.6632 (OUTLIER) cc_final: 0.5755 (t70) REVERT: C 110 ASP cc_start: 0.7069 (m-30) cc_final: 0.6667 (m-30) REVERT: C 349 LYS cc_start: 0.6184 (mtmt) cc_final: 0.5961 (mtmt) REVERT: D 37 MET cc_start: 0.5407 (tmm) cc_final: 0.5193 (tpt) REVERT: D 156 PHE cc_start: 0.7735 (t80) cc_final: 0.7408 (t80) REVERT: D 157 VAL cc_start: 0.8459 (t) cc_final: 0.8131 (p) REVERT: D 374 PHE cc_start: 0.6904 (OUTLIER) cc_final: 0.5925 (m-80) REVERT: E 52 MET cc_start: 0.4725 (ppp) cc_final: 0.3646 (ttp) REVERT: E 136 PHE cc_start: 0.4625 (OUTLIER) cc_final: 0.4221 (m-80) REVERT: E 299 ILE cc_start: 0.3437 (OUTLIER) cc_final: 0.1867 (mm) REVERT: E 343 MET cc_start: 0.1607 (mtp) cc_final: 0.1230 (mtp) REVERT: F 300 MET cc_start: 0.7180 (mmt) cc_final: 0.6807 (mmp) outliers start: 55 outliers final: 43 residues processed: 248 average time/residue: 0.2248 time to fit residues: 82.1087 Evaluate side-chains 252 residues out of total 1314 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 201 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 277 LEU Chi-restraints excluded: chain A residue 295 CYS Chi-restraints excluded: chain A residue 297 VAL Chi-restraints excluded: chain A residue 341 TRP 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 115 GLU Chi-restraints excluded: chain B residue 134 LEU 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 B residue 308 TYR Chi-restraints excluded: chain B residue 316 THR Chi-restraints excluded: chain C residue 52 MET Chi-restraints excluded: chain C residue 102 ASP Chi-restraints excluded: chain C residue 104 HIS Chi-restraints excluded: chain C residue 131 LEU Chi-restraints excluded: chain C residue 160 LEU Chi-restraints excluded: chain C residue 253 HIS Chi-restraints excluded: chain C residue 275 PHE Chi-restraints excluded: chain C residue 277 LEU Chi-restraints excluded: chain C residue 281 TYR Chi-restraints excluded: chain C residue 292 ASP Chi-restraints excluded: chain C residue 330 ILE Chi-restraints excluded: chain D residue 20 LEU Chi-restraints excluded: chain D residue 27 PHE Chi-restraints excluded: chain D residue 40 VAL Chi-restraints excluded: chain D residue 60 VAL Chi-restraints excluded: chain D residue 272 VAL Chi-restraints excluded: chain D residue 274 LYS Chi-restraints excluded: chain D residue 279 ILE Chi-restraints excluded: chain D residue 329 VAL Chi-restraints excluded: chain D residue 374 PHE Chi-restraints excluded: chain E residue 49 GLN Chi-restraints excluded: chain E residue 104 HIS Chi-restraints excluded: chain E residue 132 HIS Chi-restraints excluded: chain E residue 136 PHE Chi-restraints excluded: chain E residue 275 PHE Chi-restraints excluded: chain E residue 286 VAL Chi-restraints excluded: chain E residue 299 ILE Chi-restraints excluded: chain F residue 17 PHE Chi-restraints excluded: chain F residue 101 THR Chi-restraints excluded: chain F residue 104 ASP Chi-restraints excluded: chain F residue 106 GLN Chi-restraints excluded: chain F residue 137 VAL Chi-restraints excluded: chain F residue 145 TRP Chi-restraints excluded: chain F residue 273 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.0070 chunk 101 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 46 optimal weight: 0.0970 chunk 113 optimal weight: 1.9990 chunk 13 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 132 HIS ** E 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 298 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.208113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4151 r_free = 0.4151 target = 0.164515 restraints weight = 18239.276| |-----------------------------------------------------------------------------| r_work (start): 0.4129 rms_B_bonded: 3.27 r_work: 0.3944 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 moved from start: 0.5234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 12385 Z= 0.280 Angle : 0.649 10.835 16773 Z= 0.341 Chirality : 0.042 0.235 1846 Planarity : 0.004 0.032 1985 Dihedral : 6.962 60.992 1673 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 4.64 % Allowed : 27.32 % Favored : 68.04 % 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: 1.20 (0.23), residues: 1382 helix: 1.54 (0.16), residues: 939 sheet: 0.85 (0.50), residues: 104 loop : -1.32 (0.34), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.002 TRP A 24 HIS 0.006 0.001 HIS E 132 PHE 0.025 0.002 PHE C 125 TYR 0.029 0.002 TYR D 284 ARG 0.003 0.000 ARG E 117 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3165.62 seconds wall clock time: 57 minutes 51.25 seconds (3471.25 seconds total)