Starting phenix.real_space_refine on Fri Feb 16 05:59:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvp_11467/02_2024/6zvp_11467_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvp_11467/02_2024/6zvp_11467.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvp_11467/02_2024/6zvp_11467.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvp_11467/02_2024/6zvp_11467.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvp_11467/02_2024/6zvp_11467_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zvp_11467/02_2024/6zvp_11467_updated.pdb" } resolution = 4.0 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= 0.005 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 Fe 4 7.16 5 S 40 5.16 5 C 9232 2.51 5 N 2532 2.21 5 O 2744 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "D PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 166": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 199": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 261": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 388": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 432": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 14552 Number of models: 1 Model: "" Number of chains: 8 Chain: "D" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3626 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 429} Chain: "A" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3626 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 429} Chain: "B" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3626 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 429} Chain: "C" Number of atoms: 3626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3626 Classifications: {'peptide': 458} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 429} Chain: "D" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 12 Unusual residues: {' FE': 1, 'LDP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.27, per 1000 atoms: 0.57 Number of scatterers: 14552 At special positions: 0 Unit cell: (106.05, 131.25, 120.75, 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) Fe 4 26.01 S 40 16.00 O 2744 8.00 N 2532 7.00 C 9232 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 6.07 Conformation dependent library (CDL) restraints added in 2.9 seconds 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3472 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 20 sheets defined 45.9% alpha, 9.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.22 Creating SS restraints... Processing helix chain 'D' and resid 41 through 57 Processing helix chain 'D' and resid 95 through 106 removed outlier: 3.549A pdb=" N PHE D 103 " --> pdb=" O VAL D 100 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU D 104 " --> pdb=" O LYS D 101 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE D 106 " --> pdb=" O PHE D 103 " (cutoff:3.500A) Processing helix chain 'D' and resid 138 through 150 removed outlier: 4.134A pdb=" N ALA D 142 " --> pdb=" O ARG D 138 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA D 143 " --> pdb=" O GLY D 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY D 147 " --> pdb=" O ALA D 143 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN D 150 " --> pdb=" O SER D 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 170 through 179 removed outlier: 3.736A pdb=" N HIS D 177 " --> pdb=" O LEU D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 211 Processing helix chain 'D' and resid 226 through 243 removed outlier: 3.680A pdb=" N LEU D 242 " --> pdb=" O THR D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 249 through 261 Processing helix chain 'D' and resid 273 through 282 Processing helix chain 'D' and resid 296 through 304 Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 328 through 333 Processing helix chain 'D' and resid 336 through 340 Processing helix chain 'D' and resid 342 through 355 Processing helix chain 'D' and resid 360 through 373 Processing helix chain 'D' and resid 396 through 402 Processing helix chain 'D' and resid 414 through 419 Processing helix chain 'D' and resid 437 through 450 Processing helix chain 'D' and resid 472 through 495 removed outlier: 3.550A pdb=" N GLY D 481 " --> pdb=" O ARG D 477 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 57 Processing helix chain 'A' and resid 95 through 106 removed outlier: 3.549A pdb=" N PHE A 103 " --> pdb=" O VAL A 100 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU A 104 " --> pdb=" O LYS A 101 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE A 106 " --> pdb=" O PHE A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.134A pdb=" N ALA A 142 " --> pdb=" O ARG A 138 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA A 143 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY A 147 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN A 150 " --> pdb=" O SER A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 179 removed outlier: 3.736A pdb=" N HIS A 177 " --> pdb=" O LEU A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 211 Processing helix chain 'A' and resid 226 through 243 removed outlier: 3.680A pdb=" N LEU A 242 " --> pdb=" O THR A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 249 through 261 Processing helix chain 'A' and resid 273 through 282 Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 336 through 340 Processing helix chain 'A' and resid 342 through 355 Processing helix chain 'A' and resid 360 through 373 Processing helix chain 'A' and resid 396 through 402 Processing helix chain 'A' and resid 414 through 419 Processing helix chain 'A' and resid 437 through 450 Processing helix chain 'A' and resid 472 through 495 removed outlier: 3.551A pdb=" N GLY A 481 " --> pdb=" O ARG A 477 " (cutoff:3.500A) Processing helix chain 'B' and resid 41 through 57 Processing helix chain 'B' and resid 95 through 106 removed outlier: 3.549A pdb=" N PHE B 103 " --> pdb=" O VAL B 100 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU B 104 " --> pdb=" O LYS B 101 " (cutoff:3.500A) removed outlier: 4.004A pdb=" N PHE B 106 " --> pdb=" O PHE B 103 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 150 removed outlier: 4.134A pdb=" N ALA B 142 " --> pdb=" O ARG B 138 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY B 147 " --> pdb=" O ALA B 143 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN B 150 " --> pdb=" O SER B 146 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 179 removed outlier: 3.736A pdb=" N HIS B 177 " --> pdb=" O LEU B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 211 Processing helix chain 'B' and resid 226 through 243 removed outlier: 3.680A pdb=" N LEU B 242 " --> pdb=" O THR B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 249 through 261 Processing helix chain 'B' and resid 273 through 282 Processing helix chain 'B' and resid 296 through 304 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 328 through 333 Processing helix chain 'B' and resid 336 through 340 Processing helix chain 'B' and resid 342 through 355 Processing helix chain 'B' and resid 360 through 373 Processing helix chain 'B' and resid 396 through 402 Processing helix chain 'B' and resid 414 through 419 Processing helix chain 'B' and resid 437 through 450 Processing helix chain 'B' and resid 472 through 495 removed outlier: 3.550A pdb=" N GLY B 481 " --> pdb=" O ARG B 477 " (cutoff:3.500A) Processing helix chain 'C' and resid 41 through 57 Processing helix chain 'C' and resid 95 through 106 removed outlier: 3.549A pdb=" N PHE C 103 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 4.002A pdb=" N GLU C 104 " --> pdb=" O LYS C 101 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N PHE C 106 " --> pdb=" O PHE C 103 " (cutoff:3.500A) Processing helix chain 'C' and resid 138 through 150 removed outlier: 4.134A pdb=" N ALA C 142 " --> pdb=" O ARG C 138 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ALA C 143 " --> pdb=" O GLY C 139 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLY C 147 " --> pdb=" O ALA C 143 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLN C 150 " --> pdb=" O SER C 146 " (cutoff:3.500A) Processing helix chain 'C' and resid 170 through 179 removed outlier: 3.736A pdb=" N HIS C 177 " --> pdb=" O LEU C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 211 Processing helix chain 'C' and resid 226 through 243 removed outlier: 3.680A pdb=" N LEU C 242 " --> pdb=" O THR C 238 " (cutoff:3.500A) Processing helix chain 'C' and resid 249 through 261 Processing helix chain 'C' and resid 273 through 282 Processing helix chain 'C' and resid 296 through 304 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 328 through 333 Processing helix chain 'C' and resid 336 through 340 Processing helix chain 'C' and resid 342 through 355 Processing helix chain 'C' and resid 360 through 373 Processing helix chain 'C' and resid 396 through 402 Processing helix chain 'C' and resid 414 through 419 Processing helix chain 'C' and resid 437 through 450 Processing helix chain 'C' and resid 472 through 495 removed outlier: 3.551A pdb=" N GLY C 481 " --> pdb=" O ARG C 477 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'D' and resid 73 through 76 removed outlier: 6.225A pdb=" N GLU D 135 " --> pdb=" O ILE D 110 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE D 110 " --> pdb=" O GLU D 135 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'D' and resid 286 through 289 Processing sheet with id= C, first strand: chain 'D' and resid 378 through 381 Processing sheet with id= D, first strand: chain 'D' and resid 408 through 411 Processing sheet with id= E, first strand: chain 'D' and resid 456 through 460 Processing sheet with id= F, first strand: chain 'A' and resid 73 through 76 removed outlier: 6.225A pdb=" N GLU A 135 " --> pdb=" O ILE A 110 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 110 " --> pdb=" O GLU A 135 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 286 through 289 Processing sheet with id= H, first strand: chain 'A' and resid 378 through 381 Processing sheet with id= I, first strand: chain 'A' and resid 408 through 411 Processing sheet with id= J, first strand: chain 'A' and resid 456 through 460 Processing sheet with id= K, first strand: chain 'B' and resid 73 through 76 removed outlier: 6.225A pdb=" N GLU B 135 " --> pdb=" O ILE B 110 " (cutoff:3.500A) removed outlier: 4.729A pdb=" N ILE B 110 " --> pdb=" O GLU B 135 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'B' and resid 286 through 289 Processing sheet with id= M, first strand: chain 'B' and resid 378 through 381 Processing sheet with id= N, first strand: chain 'B' and resid 408 through 411 Processing sheet with id= O, first strand: chain 'B' and resid 456 through 460 Processing sheet with id= P, first strand: chain 'C' and resid 73 through 76 removed outlier: 6.225A pdb=" N GLU C 135 " --> pdb=" O ILE C 110 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE C 110 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'C' and resid 286 through 289 Processing sheet with id= R, first strand: chain 'C' and resid 378 through 381 Processing sheet with id= S, first strand: chain 'C' and resid 408 through 411 Processing sheet with id= T, first strand: chain 'C' and resid 456 through 460 624 hydrogen bonds defined for protein. 1752 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.23 Time building geometry restraints manager: 6.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4892 1.34 - 1.46: 3290 1.46 - 1.58: 6670 1.58 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 14904 Sorted by residual: bond pdb=" C3 LDP B 502 " pdb=" O1 LDP B 502 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C3 LDP D 502 " pdb=" O1 LDP D 502 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C3 LDP A 502 " pdb=" O1 LDP A 502 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C3 LDP C 502 " pdb=" O1 LDP C 502 " ideal model delta sigma weight residual 1.353 1.400 -0.047 2.00e-02 2.50e+03 5.45e+00 bond pdb=" C4 LDP D 502 " pdb=" O2 LDP D 502 " ideal model delta sigma weight residual 1.355 1.399 -0.044 2.00e-02 2.50e+03 4.94e+00 ... (remaining 14899 not shown) Histogram of bond angle deviations from ideal: 100.67 - 107.33: 624 107.33 - 113.99: 8240 113.99 - 120.64: 5788 120.64 - 127.30: 5383 127.30 - 133.96: 169 Bond angle restraints: 20204 Sorted by residual: angle pdb=" C VAL C 336 " pdb=" CA VAL C 336 " pdb=" CB VAL C 336 " ideal model delta sigma weight residual 113.70 110.24 3.46 9.50e-01 1.11e+00 1.33e+01 angle pdb=" C VAL A 336 " pdb=" CA VAL A 336 " pdb=" CB VAL A 336 " ideal model delta sigma weight residual 113.70 110.24 3.46 9.50e-01 1.11e+00 1.33e+01 angle pdb=" C VAL B 336 " pdb=" CA VAL B 336 " pdb=" CB VAL B 336 " ideal model delta sigma weight residual 113.70 110.30 3.40 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL D 336 " pdb=" CA VAL D 336 " pdb=" CB VAL D 336 " ideal model delta sigma weight residual 113.70 110.30 3.40 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C HIS D 335 " pdb=" N VAL D 336 " pdb=" CA VAL D 336 " ideal model delta sigma weight residual 120.43 123.38 -2.95 9.60e-01 1.09e+00 9.47e+00 ... (remaining 20199 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.74: 8082 13.74 - 27.49: 602 27.49 - 41.23: 236 41.23 - 54.97: 72 54.97 - 68.72: 20 Dihedral angle restraints: 9012 sinusoidal: 3648 harmonic: 5364 Sorted by residual: dihedral pdb=" CA HIS B 177 " pdb=" C HIS B 177 " pdb=" N HIS B 178 " pdb=" CA HIS B 178 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA HIS D 177 " pdb=" C HIS D 177 " pdb=" N HIS D 178 " pdb=" CA HIS D 178 " ideal model delta harmonic sigma weight residual 180.00 161.42 18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA HIS C 177 " pdb=" C HIS C 177 " pdb=" N HIS C 178 " pdb=" CA HIS C 178 " ideal model delta harmonic sigma weight residual 180.00 161.48 18.52 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 9009 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 1316 0.025 - 0.049: 494 0.049 - 0.074: 214 0.074 - 0.099: 106 0.099 - 0.123: 42 Chirality restraints: 2172 Sorted by residual: chirality pdb=" CA VAL A 132 " pdb=" N VAL A 132 " pdb=" C VAL A 132 " pdb=" CB VAL A 132 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL C 132 " pdb=" N VAL C 132 " pdb=" C VAL C 132 " pdb=" CB VAL C 132 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.80e-01 chirality pdb=" CA VAL D 132 " pdb=" N VAL D 132 " pdb=" C VAL D 132 " pdb=" CB VAL D 132 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.61e-01 ... (remaining 2169 not shown) Planarity restraints: 2676 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY D 125 " -0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO D 126 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO D 126 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO D 126 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 125 " 0.046 5.00e-02 4.00e+02 6.94e-02 7.70e+00 pdb=" N PRO B 126 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO B 126 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO B 126 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 125 " 0.046 5.00e-02 4.00e+02 6.91e-02 7.65e+00 pdb=" N PRO A 126 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " 0.038 5.00e-02 4.00e+02 ... (remaining 2673 not shown) Histogram of nonbonded interaction distances: 1.74 - 2.38: 120 2.38 - 3.01: 8824 3.01 - 3.64: 24966 3.64 - 4.27: 34734 4.27 - 4.90: 54286 Nonbonded interactions: 122930 Sorted by model distance: nonbonded pdb=" CE1 HIS C 330 " pdb="FE FE C 501 " model vdw 1.744 2.480 nonbonded pdb=" CE1 HIS B 330 " pdb="FE FE B 501 " model vdw 1.744 2.480 nonbonded pdb=" CE1 HIS D 330 " pdb="FE FE D 501 " model vdw 1.744 2.480 nonbonded pdb=" CE1 HIS A 330 " pdb="FE FE A 501 " model vdw 1.744 2.480 nonbonded pdb=" OE2 GLU A 375 " pdb=" O2 LDP A 502 " model vdw 2.008 2.440 ... (remaining 122925 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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=0.00 max=1.00 mean=0.84 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 2.120 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 41.960 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.090 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6014 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 : 0.003 0.047 14904 Z= 0.172 Angle : 0.610 10.393 20204 Z= 0.347 Chirality : 0.037 0.123 2172 Planarity : 0.005 0.069 2676 Dihedral : 12.579 68.716 5540 Min Nonbonded Distance : 1.744 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 5.87 % Allowed : 10.05 % Favored : 84.07 % 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: -0.21 (0.21), residues: 1824 helix: 1.07 (0.18), residues: 896 sheet: -1.68 (0.51), residues: 104 loop : -1.29 (0.22), residues: 824 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 371 HIS 0.002 0.000 HIS C 330 PHE 0.008 0.001 PHE A 347 TYR 0.010 0.001 TYR D 370 ARG 0.002 0.000 ARG D 297 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 484 time to evaluate : 1.537 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 219 ILE cc_start: 0.9325 (mm) cc_final: 0.9045 (mt) REVERT: D 321 MET cc_start: 0.8919 (pmm) cc_final: 0.8331 (pmm) REVERT: D 451 ILE cc_start: 0.9029 (mt) cc_final: 0.8827 (mm) REVERT: A 219 ILE cc_start: 0.9323 (mm) cc_final: 0.9046 (mt) REVERT: A 321 MET cc_start: 0.8923 (pmm) cc_final: 0.8333 (pmm) REVERT: A 451 ILE cc_start: 0.9024 (mt) cc_final: 0.8823 (mm) REVERT: B 219 ILE cc_start: 0.9324 (mm) cc_final: 0.9047 (mt) REVERT: B 321 MET cc_start: 0.8922 (pmm) cc_final: 0.8335 (pmm) REVERT: B 451 ILE cc_start: 0.9025 (mt) cc_final: 0.8823 (mm) REVERT: C 219 ILE cc_start: 0.9325 (mm) cc_final: 0.9049 (mt) REVERT: C 321 MET cc_start: 0.8924 (pmm) cc_final: 0.8337 (pmm) REVERT: C 451 ILE cc_start: 0.9033 (mt) cc_final: 0.8831 (mm) outliers start: 90 outliers final: 24 residues processed: 566 average time/residue: 0.3017 time to fit residues: 235.9791 Evaluate side-chains 395 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 371 time to evaluate : 1.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 430 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 151 optimal weight: 1.9990 chunk 136 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 92 optimal weight: 40.0000 chunk 72 optimal weight: 10.0000 chunk 141 optimal weight: 8.9990 chunk 54 optimal weight: 6.9990 chunk 85 optimal weight: 7.9990 chunk 105 optimal weight: 6.9990 chunk 163 optimal weight: 40.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 246 HIS ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 246 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 HIS ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 346 GLN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 246 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 346 GLN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6149 moved from start: 0.3017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 14904 Z= 0.346 Angle : 0.765 10.149 20204 Z= 0.382 Chirality : 0.044 0.210 2172 Planarity : 0.006 0.067 2676 Dihedral : 6.449 51.866 2068 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 28.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 4.50 % Allowed : 20.76 % Favored : 74.74 % 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: -1.26 (0.19), residues: 1824 helix: 0.10 (0.16), residues: 920 sheet: -2.50 (0.42), residues: 128 loop : -1.62 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.003 TRP A 165 HIS 0.004 0.001 HIS B 191 PHE 0.021 0.002 PHE A 278 TYR 0.018 0.002 TYR B 313 ARG 0.006 0.001 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 419 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 350 time to evaluate : 1.728 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 451 ILE cc_start: 0.9055 (mt) cc_final: 0.8854 (mm) REVERT: B 451 ILE cc_start: 0.9050 (mt) cc_final: 0.8849 (mm) outliers start: 69 outliers final: 39 residues processed: 392 average time/residue: 0.2456 time to fit residues: 142.5080 Evaluate side-chains 341 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 302 time to evaluate : 1.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 255 PHE Chi-restraints excluded: chain D residue 276 SER Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 311 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 255 PHE Chi-restraints excluded: chain A residue 275 VAL Chi-restraints excluded: chain A residue 276 SER Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 311 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 255 PHE Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 255 PHE Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 SER Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 311 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 484 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 90 optimal weight: 30.0000 chunk 50 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 45 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 176 optimal weight: 3.9990 chunk 145 optimal weight: 5.9990 chunk 162 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 131 optimal weight: 10.0000 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6094 moved from start: 0.3523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14904 Z= 0.226 Angle : 0.695 10.358 20204 Z= 0.333 Chirality : 0.043 0.159 2172 Planarity : 0.005 0.061 2676 Dihedral : 5.893 55.663 2056 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 22.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 3.66 % Allowed : 23.96 % Favored : 72.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.19), residues: 1824 helix: 0.32 (0.17), residues: 896 sheet: -2.30 (0.37), residues: 152 loop : -1.34 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 232 HIS 0.008 0.002 HIS D 251 PHE 0.020 0.002 PHE B 183 TYR 0.015 0.002 TYR A 370 ARG 0.004 0.001 ARG D 288 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 417 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 361 time to evaluate : 1.715 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 451 ILE cc_start: 0.9014 (mt) cc_final: 0.8813 (mm) REVERT: A 462 TYR cc_start: 0.9159 (m-80) cc_final: 0.8957 (m-80) REVERT: B 451 ILE cc_start: 0.9008 (mt) cc_final: 0.8808 (mm) REVERT: C 462 TYR cc_start: 0.9158 (m-80) cc_final: 0.8956 (m-80) outliers start: 56 outliers final: 36 residues processed: 405 average time/residue: 0.2714 time to fit residues: 163.0970 Evaluate side-chains 341 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 305 time to evaluate : 1.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 484 ASP Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 484 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 484 ASP Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 484 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 161 optimal weight: 6.9990 chunk 123 optimal weight: 5.9990 chunk 84 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 9.9990 chunk 164 optimal weight: 0.3980 chunk 173 optimal weight: 0.0980 chunk 85 optimal weight: 5.9990 chunk 155 optimal weight: 0.4980 chunk 46 optimal weight: 20.0000 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6111 moved from start: 0.3902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14904 Z= 0.224 Angle : 0.664 10.060 20204 Z= 0.326 Chirality : 0.042 0.153 2172 Planarity : 0.005 0.062 2676 Dihedral : 5.820 53.907 2056 Min Nonbonded Distance : 2.006 Molprobity Statistics. All-atom Clashscore : 23.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.15 % Favored : 94.85 % Rotamer: Outliers : 4.18 % Allowed : 23.89 % Favored : 71.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.93 (0.19), residues: 1824 helix: 0.34 (0.17), residues: 892 sheet: -2.55 (0.33), residues: 176 loop : -1.18 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 232 HIS 0.007 0.001 HIS D 491 PHE 0.016 0.002 PHE D 278 TYR 0.017 0.002 TYR A 370 ARG 0.006 0.001 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 400 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 336 time to evaluate : 1.755 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 462 TYR cc_start: 0.9217 (m-80) cc_final: 0.9009 (m-80) REVERT: C 462 TYR cc_start: 0.9221 (m-80) cc_final: 0.9010 (m-80) outliers start: 64 outliers final: 34 residues processed: 389 average time/residue: 0.2313 time to fit residues: 135.3004 Evaluate side-chains 333 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 299 time to evaluate : 1.599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 184 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 449 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 144 optimal weight: 20.0000 chunk 98 optimal weight: 50.0000 chunk 2 optimal weight: 0.4980 chunk 129 optimal weight: 20.0000 chunk 71 optimal weight: 5.9990 chunk 148 optimal weight: 0.2980 chunk 120 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 88 optimal weight: 1.9990 chunk 156 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6108 moved from start: 0.4242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 14904 Z= 0.216 Angle : 0.662 9.375 20204 Z= 0.323 Chirality : 0.042 0.147 2172 Planarity : 0.005 0.057 2676 Dihedral : 5.732 53.942 2052 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 3.92 % Allowed : 25.85 % Favored : 70.23 % 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: -0.98 (0.19), residues: 1824 helix: 0.26 (0.17), residues: 896 sheet: -2.45 (0.35), residues: 176 loop : -1.19 (0.22), residues: 752 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 371 HIS 0.011 0.002 HIS D 251 PHE 0.013 0.002 PHE D 347 TYR 0.012 0.002 TYR B 313 ARG 0.007 0.000 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 317 time to evaluate : 1.737 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: symmetry clash REVERT: A 290 VAL cc_start: 0.9095 (p) cc_final: 0.8864 (m) REVERT: B 290 VAL cc_start: 0.9100 (p) cc_final: 0.8867 (m) REVERT: C 290 VAL cc_start: 0.9095 (p) cc_final: 0.8858 (m) outliers start: 60 outliers final: 44 residues processed: 355 average time/residue: 0.2334 time to fit residues: 125.0834 Evaluate side-chains 342 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 298 time to evaluate : 1.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 392 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 184 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 392 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 184 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 392 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 449 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 58 optimal weight: 0.2980 chunk 156 optimal weight: 3.9990 chunk 34 optimal weight: 0.7980 chunk 102 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 174 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 80 optimal weight: 20.0000 chunk 14 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6112 moved from start: 0.4505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14904 Z= 0.220 Angle : 0.658 9.340 20204 Z= 0.321 Chirality : 0.042 0.145 2172 Planarity : 0.005 0.054 2676 Dihedral : 5.804 56.153 2052 Min Nonbonded Distance : 2.014 Molprobity Statistics. All-atom Clashscore : 22.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 4.05 % Allowed : 25.59 % Favored : 70.37 % 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: -0.78 (0.20), residues: 1824 helix: 0.41 (0.18), residues: 888 sheet: -2.26 (0.37), residues: 176 loop : -1.09 (0.22), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 371 HIS 0.012 0.001 HIS B 251 PHE 0.013 0.001 PHE B 347 TYR 0.016 0.002 TYR D 370 ARG 0.007 0.001 ARG C 445 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 326 time to evaluate : 1.665 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: symmetry clash REVERT: D 290 VAL cc_start: 0.9240 (p) cc_final: 0.8983 (m) REVERT: A 290 VAL cc_start: 0.9245 (p) cc_final: 0.8984 (m) REVERT: B 290 VAL cc_start: 0.9246 (p) cc_final: 0.8982 (m) REVERT: C 290 VAL cc_start: 0.9242 (p) cc_final: 0.8979 (m) outliers start: 62 outliers final: 43 residues processed: 366 average time/residue: 0.2610 time to fit residues: 147.1859 Evaluate side-chains 344 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 301 time to evaluate : 1.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 332 LEU Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 466 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 167 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 99 optimal weight: 4.9990 chunk 127 optimal weight: 1.9990 chunk 98 optimal weight: 20.0000 chunk 146 optimal weight: 4.9990 chunk 97 optimal weight: 0.0040 chunk 173 optimal weight: 2.9990 chunk 108 optimal weight: 4.9990 chunk 105 optimal weight: 0.9980 chunk 80 optimal weight: 10.0000 overall best weight: 1.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 312 GLN ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 312 GLN ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 312 GLN ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 312 GLN ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6095 moved from start: 0.4788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14904 Z= 0.206 Angle : 0.687 13.535 20204 Z= 0.325 Chirality : 0.042 0.141 2172 Planarity : 0.005 0.082 2676 Dihedral : 5.940 56.003 2052 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 24.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 3.92 % Allowed : 26.37 % Favored : 69.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.19), residues: 1824 helix: 0.30 (0.17), residues: 884 sheet: -2.18 (0.37), residues: 176 loop : -1.12 (0.22), residues: 764 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP D 371 HIS 0.010 0.001 HIS A 251 PHE 0.014 0.002 PHE D 344 TYR 0.012 0.002 TYR B 264 ARG 0.007 0.000 ARG D 282 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 60 poor density : 320 time to evaluate : 1.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 290 VAL cc_start: 0.9204 (p) cc_final: 0.8985 (m) REVERT: A 290 VAL cc_start: 0.9205 (p) cc_final: 0.8988 (m) REVERT: A 445 ARG cc_start: 0.9276 (tpp80) cc_final: 0.9013 (tpp-160) REVERT: B 290 VAL cc_start: 0.9202 (p) cc_final: 0.8981 (m) REVERT: C 290 VAL cc_start: 0.9204 (p) cc_final: 0.8986 (m) REVERT: C 445 ARG cc_start: 0.9274 (tpp80) cc_final: 0.9008 (tpp-160) outliers start: 60 outliers final: 44 residues processed: 366 average time/residue: 0.2314 time to fit residues: 129.1150 Evaluate side-chains 350 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 306 time to evaluate : 1.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 148 VAL Chi-restraints excluded: chain D residue 151 VAL Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 283 THR Chi-restraints excluded: chain D residue 285 PHE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 151 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 151 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 285 PHE Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 148 VAL Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 466 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 107 optimal weight: 0.7980 chunk 69 optimal weight: 0.8980 chunk 103 optimal weight: 4.9990 chunk 52 optimal weight: 20.0000 chunk 34 optimal weight: 0.7980 chunk 33 optimal weight: 4.9990 chunk 110 optimal weight: 0.3980 chunk 118 optimal weight: 0.8980 chunk 85 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 136 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** D 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 483 GLN ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** B 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 312 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 483 GLN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6055 moved from start: 0.4947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14904 Z= 0.191 Angle : 0.713 11.166 20204 Z= 0.333 Chirality : 0.044 0.164 2172 Planarity : 0.005 0.059 2676 Dihedral : 5.953 54.997 2052 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 3.33 % Allowed : 26.50 % Favored : 70.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.88 (0.19), residues: 1824 helix: 0.28 (0.18), residues: 880 sheet: -2.06 (0.35), residues: 188 loop : -1.10 (0.22), residues: 756 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP D 371 HIS 0.008 0.001 HIS C 251 PHE 0.024 0.002 PHE B 459 TYR 0.023 0.002 TYR D 243 ARG 0.010 0.001 ARG B 282 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 394 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 343 time to evaluate : 1.732 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: D 232 TRP cc_start: 0.9547 (t60) cc_final: 0.9301 (t60) REVERT: D 462 TYR cc_start: 0.9220 (m-80) cc_final: 0.8926 (m-80) REVERT: A 232 TRP cc_start: 0.9550 (t60) cc_final: 0.9304 (t60) REVERT: B 232 TRP cc_start: 0.9550 (t60) cc_final: 0.9305 (t60) REVERT: B 462 TYR cc_start: 0.9203 (m-80) cc_final: 0.8887 (m-80) REVERT: C 232 TRP cc_start: 0.9543 (t60) cc_final: 0.9278 (t60) REVERT: C 462 TYR cc_start: 0.9209 (m-80) cc_final: 0.8915 (m-80) outliers start: 51 outliers final: 37 residues processed: 376 average time/residue: 0.2468 time to fit residues: 138.8288 Evaluate side-chains 345 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 308 time to evaluate : 1.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 449 SER Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 449 SER Chi-restraints excluded: chain C residue 466 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 157 optimal weight: 9.9990 chunk 166 optimal weight: 6.9990 chunk 151 optimal weight: 8.9990 chunk 161 optimal weight: 0.6980 chunk 97 optimal weight: 5.9990 chunk 70 optimal weight: 0.7980 chunk 126 optimal weight: 2.9990 chunk 49 optimal weight: 20.0000 chunk 146 optimal weight: 0.0980 chunk 152 optimal weight: 7.9990 chunk 106 optimal weight: 8.9990 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 428 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6089 moved from start: 0.5146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14904 Z= 0.224 Angle : 0.749 9.888 20204 Z= 0.362 Chirality : 0.046 0.214 2172 Planarity : 0.005 0.087 2676 Dihedral : 5.858 56.173 2051 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 26.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 3.00 % Allowed : 27.15 % Favored : 69.84 % 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: -0.96 (0.20), residues: 1824 helix: 0.24 (0.18), residues: 876 sheet: -2.19 (0.34), residues: 188 loop : -1.15 (0.23), residues: 760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.004 TRP C 371 HIS 0.007 0.001 HIS A 251 PHE 0.021 0.002 PHE D 278 TYR 0.047 0.002 TYR A 243 ARG 0.014 0.001 ARG D 49 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 324 time to evaluate : 1.826 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: symmetry clash REVERT: D 462 TYR cc_start: 0.9243 (m-80) cc_final: 0.8952 (m-80) REVERT: B 462 TYR cc_start: 0.9237 (m-80) cc_final: 0.8953 (m-80) REVERT: C 232 TRP cc_start: 0.9568 (t60) cc_final: 0.9315 (t60) REVERT: C 462 TYR cc_start: 0.9239 (m-80) cc_final: 0.8966 (m-80) outliers start: 46 outliers final: 36 residues processed: 350 average time/residue: 0.2389 time to fit residues: 126.4728 Evaluate side-chains 351 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 315 time to evaluate : 1.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 466 ILE Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 285 PHE Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 466 ILE Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 466 ILE Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 285 PHE Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 170 optimal weight: 0.8980 chunk 104 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 118 optimal weight: 0.0000 chunk 179 optimal weight: 0.9990 chunk 165 optimal weight: 0.0770 chunk 142 optimal weight: 8.9990 chunk 14 optimal weight: 20.0000 chunk 110 optimal weight: 9.9990 chunk 87 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 overall best weight: 0.9946 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 428 GLN D 483 GLN D 491 HIS ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 428 GLN ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 428 GLN B 483 GLN B 491 HIS ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 428 GLN ** C 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6050 moved from start: 0.5310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14904 Z= 0.195 Angle : 0.754 10.957 20204 Z= 0.360 Chirality : 0.045 0.177 2172 Planarity : 0.005 0.051 2676 Dihedral : 5.847 55.567 2051 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 23.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 3.33 % Allowed : 26.63 % Favored : 70.04 % 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: -1.03 (0.19), residues: 1824 helix: 0.19 (0.18), residues: 880 sheet: -2.28 (0.35), residues: 168 loop : -1.24 (0.22), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.003 TRP B 371 HIS 0.013 0.001 HIS B 251 PHE 0.018 0.002 PHE A 376 TYR 0.044 0.002 TYR D 243 ARG 0.011 0.001 ARG A 445 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3648 Ramachandran restraints generated. 1824 Oldfield, 0 Emsley, 1824 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 327 time to evaluate : 1.663 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: symmetry clash REVERT: D 232 TRP cc_start: 0.9558 (t60) cc_final: 0.9338 (t60) REVERT: A 232 TRP cc_start: 0.9559 (t60) cc_final: 0.9340 (t60) REVERT: A 445 ARG cc_start: 0.9289 (tpp80) cc_final: 0.8935 (tpp-160) REVERT: B 232 TRP cc_start: 0.9558 (t60) cc_final: 0.9329 (t60) REVERT: C 232 TRP cc_start: 0.9570 (t60) cc_final: 0.9319 (t60) REVERT: C 445 ARG cc_start: 0.9292 (tpp80) cc_final: 0.8938 (tpp-160) outliers start: 51 outliers final: 37 residues processed: 353 average time/residue: 0.2266 time to fit residues: 122.0152 Evaluate side-chains 353 residues out of total 1532 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 316 time to evaluate : 1.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 174 ASP Chi-restraints excluded: chain D residue 196 ASP Chi-restraints excluded: chain D residue 233 LYS Chi-restraints excluded: chain D residue 246 HIS Chi-restraints excluded: chain D residue 269 ILE Chi-restraints excluded: chain D residue 430 VAL Chi-restraints excluded: chain D residue 444 LEU Chi-restraints excluded: chain D residue 449 SER Chi-restraints excluded: chain D residue 468 VAL Chi-restraints excluded: chain A residue 174 ASP Chi-restraints excluded: chain A residue 196 ASP Chi-restraints excluded: chain A residue 233 LYS Chi-restraints excluded: chain A residue 246 HIS Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 332 LEU Chi-restraints excluded: chain A residue 430 VAL Chi-restraints excluded: chain A residue 444 LEU Chi-restraints excluded: chain A residue 468 VAL Chi-restraints excluded: chain B residue 174 ASP Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 LYS Chi-restraints excluded: chain B residue 246 HIS Chi-restraints excluded: chain B residue 283 THR Chi-restraints excluded: chain B residue 332 LEU Chi-restraints excluded: chain B residue 430 VAL Chi-restraints excluded: chain B residue 444 LEU Chi-restraints excluded: chain B residue 449 SER Chi-restraints excluded: chain B residue 468 VAL Chi-restraints excluded: chain C residue 174 ASP Chi-restraints excluded: chain C residue 196 ASP Chi-restraints excluded: chain C residue 233 LYS Chi-restraints excluded: chain C residue 246 HIS Chi-restraints excluded: chain C residue 283 THR Chi-restraints excluded: chain C residue 332 LEU Chi-restraints excluded: chain C residue 430 VAL Chi-restraints excluded: chain C residue 444 LEU Chi-restraints excluded: chain C residue 466 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 180 random chunks: chunk 152 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 21 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 143 optimal weight: 0.0030 chunk 59 optimal weight: 2.9990 chunk 146 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN ** A 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 491 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 483 GLN ** C 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 491 HIS ** 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 = 0.3797 r_free = 0.3797 target = 0.112822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.084852 restraints weight = 37466.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.087972 restraints weight = 24167.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.090306 restraints weight = 17504.634| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.5456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 14904 Z= 0.219 Angle : 0.759 10.682 20204 Z= 0.360 Chirality : 0.046 0.209 2172 Planarity : 0.005 0.054 2676 Dihedral : 5.858 55.192 2051 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 2.94 % Allowed : 27.48 % Favored : 69.58 % 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: -0.94 (0.20), residues: 1824 helix: 0.24 (0.18), residues: 876 sheet: -2.40 (0.34), residues: 168 loop : -1.10 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 371 HIS 0.017 0.002 HIS A 251 PHE 0.017 0.002 PHE A 376 TYR 0.029 0.002 TYR A 243 ARG 0.009 0.001 ARG C 445 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3364.34 seconds wall clock time: 61 minutes 36.95 seconds (3696.95 seconds total)