Starting phenix.real_space_refine on Mon Mar 11 11:54:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f76_28896/03_2024/8f76_28896_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f76_28896/03_2024/8f76_28896.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f76_28896/03_2024/8f76_28896.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f76_28896/03_2024/8f76_28896.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f76_28896/03_2024/8f76_28896_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8f76_28896/03_2024/8f76_28896_updated.pdb" } resolution = 3.1 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= 0.015 sd= 0.111 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: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 5195 2.51 5 N 1428 2.21 5 O 1490 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 190": "OD1" <-> "OD2" Residue "N TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 89": "OE1" <-> "OE2" Residue "N TYR 117": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 21": "OE1" <-> "OE2" Residue "X GLU 27": "OE1" <-> "OE2" Residue "X ASP 49": "OD1" <-> "OD2" Residue "X TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 318": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 212": "OD1" <-> "OD2" Residue "Y GLU 226": "OE1" <-> "OE2" Residue "Y PHE 253": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 254": "OD1" <-> "OD2" Residue "Y GLU 260": "OE1" <-> "OE2" Residue "Y TYR 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8170 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 302, 2363 Classifications: {'peptide': 302} Link IDs: {'PTRANS': 14, 'TRANS': 287} Chain: "N" Number of atoms: 961 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 961 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 5, 'TRANS': 120} Chain: "X" Number of atoms: 1818 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1818 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 5, 'TRANS': 210} Chain breaks: 4 Chain: "Y" Number of atoms: 2594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2594 Classifications: {'peptide': 338} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 5, 'TRANS': 332} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "Z" Number of atoms: 429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 429 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "A" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PPI': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.78, per 1000 atoms: 0.59 Number of scatterers: 8170 At special positions: 0 Unit cell: (82.62, 98.82, 136.89, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 1490 8.00 N 1428 7.00 C 5195 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 4 " - pdb=" SG CYS A 168 " distance=2.03 Simple disulfide: pdb=" SG CYS A 96 " - pdb=" SG CYS A 178 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.05 Conformation dependent library (CDL) restraints added in 1.5 seconds 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1956 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 12 sheets defined 38.3% alpha, 21.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.60 Creating SS restraints... Processing helix chain 'A' and resid 23 through 48 Proline residue: A 29 - end of helix removed outlier: 3.932A pdb=" N SER A 32 " --> pdb=" O PHE A 28 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N VAL A 44 " --> pdb=" O GLY A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 57 through 86 Proline residue: A 78 - end of helix Processing helix chain 'A' and resid 93 through 126 Processing helix chain 'A' and resid 128 through 134 removed outlier: 3.733A pdb=" N HIS A 131 " --> pdb=" O PRO A 128 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N ALA A 132 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA A 133 " --> pdb=" O ARG A 130 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL A 134 " --> pdb=" O HIS A 131 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 128 through 134' Processing helix chain 'A' and resid 137 through 162 Proline residue: A 157 - end of helix Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 192 through 226 removed outlier: 4.039A pdb=" N GLN A 226 " --> pdb=" O ARG A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 262 Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 269 through 280 Processing helix chain 'A' and resid 283 through 291 Proline residue: A 288 - end of helix Processing helix chain 'A' and resid 296 through 304 Processing helix chain 'N' and resid 29 through 31 No H-bonds generated for 'chain 'N' and resid 29 through 31' Processing helix chain 'N' and resid 88 through 90 No H-bonds generated for 'chain 'N' and resid 88 through 90' Processing helix chain 'X' and resid 16 through 39 Processing helix chain 'X' and resid 53 through 57 Processing helix chain 'X' and resid 234 through 239 removed outlier: 4.065A pdb=" N ASN X 239 " --> pdb=" O GLN X 236 " (cutoff:3.500A) Processing helix chain 'X' and resid 266 through 278 Processing helix chain 'X' and resid 280 through 282 No H-bonds generated for 'chain 'X' and resid 280 through 282' Processing helix chain 'X' and resid 294 through 302 Processing helix chain 'X' and resid 308 through 311 No H-bonds generated for 'chain 'X' and resid 308 through 311' Processing helix chain 'X' and resid 313 through 317 Processing helix chain 'X' and resid 332 through 350 Processing helix chain 'X' and resid 371 through 390 Processing helix chain 'Y' and resid 4 through 25 Processing helix chain 'Y' and resid 30 through 33 No H-bonds generated for 'chain 'Y' and resid 30 through 33' Processing helix chain 'Z' and resid 8 through 23 Processing helix chain 'Z' and resid 30 through 47 removed outlier: 5.078A pdb=" N LYS Z 46 " --> pdb=" O GLU Z 42 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N GLU Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 10 through 12 Processing sheet with id= B, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= C, first strand: chain 'N' and resid 122 through 124 removed outlier: 3.543A pdb=" N ASN N 35 " --> pdb=" O ALA N 97 " (cutoff:3.500A) removed outlier: 5.956A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 4.830A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'X' and resid 359 through 363 removed outlier: 7.194A pdb=" N VAL X 287 " --> pdb=" O TYR X 360 " (cutoff:3.500A) removed outlier: 7.703A pdb=" N HIS X 362 " --> pdb=" O VAL X 287 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU X 289 " --> pdb=" O HIS X 362 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ALA X 243 " --> pdb=" O ARG X 42 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N VAL X 224 " --> pdb=" O LEU X 45 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'Y' and resid 58 through 63 removed outlier: 6.778A pdb=" N ALA Y 73 " --> pdb=" O TYR Y 59 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N MET Y 61 " --> pdb=" O VAL Y 71 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N VAL Y 71 " --> pdb=" O MET Y 61 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N TRP Y 63 " --> pdb=" O LEU Y 69 " (cutoff:3.500A) removed outlier: 7.215A pdb=" N LEU Y 69 " --> pdb=" O TRP Y 63 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU Y 70 " --> pdb=" O TRP Y 82 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ASP Y 83 " --> pdb=" O LYS Y 89 " (cutoff:3.500A) removed outlier: 5.850A pdb=" N LYS Y 89 " --> pdb=" O ASP Y 83 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'Y' and resid 100 through 105 removed outlier: 6.631A pdb=" N GLY Y 115 " --> pdb=" O MET Y 101 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N CYS Y 103 " --> pdb=" O ALA Y 113 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ALA Y 113 " --> pdb=" O CYS Y 103 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N TYR Y 105 " --> pdb=" O TYR Y 111 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR Y 111 " --> pdb=" O TYR Y 105 " (cutoff:3.500A) removed outlier: 4.388A pdb=" N GLY Y 116 " --> pdb=" O ILE Y 120 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N ILE Y 120 " --> pdb=" O GLY Y 116 " (cutoff:3.500A) removed outlier: 6.032A pdb=" N ASN Y 125 " --> pdb=" O VAL Y 135 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL Y 135 " --> pdb=" O ASN Y 125 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'Y' and resid 146 through 151 removed outlier: 6.717A pdb=" N SER Y 160 " --> pdb=" O SER Y 147 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N CYS Y 149 " --> pdb=" O VAL Y 158 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N VAL Y 158 " --> pdb=" O CYS Y 149 " (cutoff:3.500A) removed outlier: 5.356A pdb=" N PHE Y 151 " --> pdb=" O GLN Y 156 " (cutoff:3.500A) removed outlier: 7.796A pdb=" N GLN Y 156 " --> pdb=" O PHE Y 151 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N THR Y 165 " --> pdb=" O SER Y 161 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ASP Y 170 " --> pdb=" O GLN Y 176 " (cutoff:3.500A) removed outlier: 5.920A pdb=" N GLN Y 176 " --> pdb=" O ASP Y 170 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'Y' and resid 187 through 192 removed outlier: 6.928A pdb=" N GLY Y 202 " --> pdb=" O MET Y 188 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N LEU Y 190 " --> pdb=" O VAL Y 200 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL Y 200 " --> pdb=" O LEU Y 190 " (cutoff:3.500A) removed outlier: 5.381A pdb=" N LEU Y 192 " --> pdb=" O LEU Y 198 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N LEU Y 198 " --> pdb=" O LEU Y 192 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N SER Y 207 " --> pdb=" O ALA Y 203 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N ASP Y 212 " --> pdb=" O CYS Y 218 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N CYS Y 218 " --> pdb=" O ASP Y 212 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'Y' and resid 229 through 234 removed outlier: 6.672A pdb=" N GLY Y 244 " --> pdb=" O ASN Y 230 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE Y 232 " --> pdb=" O ALA Y 242 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ALA Y 242 " --> pdb=" O ILE Y 232 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N PHE Y 234 " --> pdb=" O ALA Y 240 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N ALA Y 240 " --> pdb=" O PHE Y 234 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N ASP Y 254 " --> pdb=" O GLU Y 260 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N GLU Y 260 " --> pdb=" O ASP Y 254 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'Y' and resid 273 through 278 removed outlier: 6.535A pdb=" N GLY Y 288 " --> pdb=" O THR Y 274 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N VAL Y 276 " --> pdb=" O LEU Y 286 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N LEU Y 286 " --> pdb=" O VAL Y 276 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N PHE Y 278 " --> pdb=" O LEU Y 284 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LEU Y 284 " --> pdb=" O PHE Y 278 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASP Y 298 " --> pdb=" O ARG Y 304 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG Y 304 " --> pdb=" O ASP Y 298 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'Y' and resid 46 through 52 removed outlier: 6.679A pdb=" N ILE Y 338 " --> pdb=" O ARG Y 48 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N THR Y 50 " --> pdb=" O LEU Y 336 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LEU Y 336 " --> pdb=" O THR Y 50 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'Y' and resid 315 through 320 removed outlier: 7.136A pdb=" N GLY Y 330 " --> pdb=" O SER Y 316 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N LEU Y 318 " --> pdb=" O ALA Y 328 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ALA Y 328 " --> pdb=" O LEU Y 318 " (cutoff:3.500A) 391 hydrogen bonds defined for protein. 1128 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: 2.26 Time building geometry restraints manager: 3.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2320 1.34 - 1.45: 1421 1.45 - 1.57: 4512 1.57 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 8336 Sorted by residual: bond pdb=" CG1 ILE X 285 " pdb=" CD1 ILE X 285 " ideal model delta sigma weight residual 1.513 1.445 0.068 3.90e-02 6.57e+02 3.00e+00 bond pdb=" CB PHE A 101 " pdb=" CG PHE A 101 " ideal model delta sigma weight residual 1.502 1.540 -0.038 2.30e-02 1.89e+03 2.76e+00 bond pdb=" C2 PPI A 401 " pdb=" C3 PPI A 401 " ideal model delta sigma weight residual 1.519 1.487 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CB THR Y 274 " pdb=" CG2 THR Y 274 " ideal model delta sigma weight residual 1.521 1.469 0.052 3.30e-02 9.18e+02 2.48e+00 bond pdb=" CA THR Y 87 " pdb=" C THR Y 87 " ideal model delta sigma weight residual 1.523 1.541 -0.018 1.34e-02 5.57e+03 1.83e+00 ... (remaining 8331 not shown) Histogram of bond angle deviations from ideal: 96.16 - 103.73: 93 103.73 - 111.30: 3265 111.30 - 118.87: 3402 118.87 - 126.45: 4401 126.45 - 134.02: 126 Bond angle restraints: 11287 Sorted by residual: angle pdb=" C THR Y 86 " pdb=" N THR Y 87 " pdb=" CA THR Y 87 " ideal model delta sigma weight residual 121.54 128.77 -7.23 1.91e+00 2.74e-01 1.43e+01 angle pdb=" CA PRO A 283 " pdb=" C PRO A 283 " pdb=" N PRO A 284 " ideal model delta sigma weight residual 117.93 122.25 -4.32 1.20e+00 6.94e-01 1.29e+01 angle pdb=" C TYR A 188 " pdb=" N ALA A 189 " pdb=" CA ALA A 189 " ideal model delta sigma weight residual 121.54 128.36 -6.82 1.91e+00 2.74e-01 1.27e+01 angle pdb=" N PRO A 283 " pdb=" CA PRO A 283 " pdb=" C PRO A 283 " ideal model delta sigma weight residual 110.70 114.92 -4.22 1.22e+00 6.72e-01 1.20e+01 angle pdb=" CB MET A 77 " pdb=" CG MET A 77 " pdb=" SD MET A 77 " ideal model delta sigma weight residual 112.70 123.02 -10.32 3.00e+00 1.11e-01 1.18e+01 ... (remaining 11282 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 4450 17.96 - 35.92: 428 35.92 - 53.88: 78 53.88 - 71.84: 10 71.84 - 89.80: 10 Dihedral angle restraints: 4976 sinusoidal: 1957 harmonic: 3019 Sorted by residual: dihedral pdb=" CB CYS A 4 " pdb=" SG CYS A 4 " pdb=" SG CYS A 168 " pdb=" CB CYS A 168 " ideal model delta sinusoidal sigma weight residual -86.00 -136.74 50.74 1 1.00e+01 1.00e-02 3.52e+01 dihedral pdb=" CA ASN A 41 " pdb=" C ASN A 41 " pdb=" N CYS A 42 " pdb=" CA CYS A 42 " ideal model delta harmonic sigma weight residual -180.00 -154.37 -25.63 0 5.00e+00 4.00e-02 2.63e+01 dihedral pdb=" CA ALA Y 60 " pdb=" C ALA Y 60 " pdb=" N MET Y 61 " pdb=" CA MET Y 61 " ideal model delta harmonic sigma weight residual 180.00 158.11 21.89 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 4973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 906 0.050 - 0.100: 281 0.100 - 0.150: 80 0.150 - 0.200: 14 0.200 - 0.250: 4 Chirality restraints: 1285 Sorted by residual: chirality pdb=" CB VAL X 57 " pdb=" CA VAL X 57 " pdb=" CG1 VAL X 57 " pdb=" CG2 VAL X 57 " both_signs ideal model delta sigma weight residual False -2.63 -2.38 -0.25 2.00e-01 2.50e+01 1.57e+00 chirality pdb=" CA TYR Y 59 " pdb=" N TYR Y 59 " pdb=" C TYR Y 59 " pdb=" CB TYR Y 59 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.55e+00 chirality pdb=" CG LEU Y 286 " pdb=" CB LEU Y 286 " pdb=" CD1 LEU Y 286 " pdb=" CD2 LEU Y 286 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 1282 not shown) Planarity restraints: 1436 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 39 " 0.022 2.00e-02 2.50e+03 4.33e-02 1.87e+01 pdb=" C PHE A 39 " -0.075 2.00e-02 2.50e+03 pdb=" O PHE A 39 " 0.028 2.00e-02 2.50e+03 pdb=" N GLY A 40 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Y 59 " -0.035 2.00e-02 2.50e+03 2.41e-02 1.16e+01 pdb=" CG TYR Y 59 " 0.057 2.00e-02 2.50e+03 pdb=" CD1 TYR Y 59 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR Y 59 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR Y 59 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR Y 59 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR Y 59 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR Y 59 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PHE A 156 " 0.055 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO A 157 " -0.142 5.00e-02 4.00e+02 pdb=" CA PRO A 157 " 0.041 5.00e-02 4.00e+02 pdb=" CD PRO A 157 " 0.046 5.00e-02 4.00e+02 ... (remaining 1433 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1603 2.78 - 3.31: 7527 3.31 - 3.84: 14476 3.84 - 4.37: 17287 4.37 - 4.90: 29733 Nonbonded interactions: 70626 Sorted by model distance: nonbonded pdb=" OD1 ASP N 50 " pdb=" OG SER N 59 " model vdw 2.245 2.440 nonbonded pdb=" O PRO N 100 " pdb=" OG SER Y 227 " model vdw 2.276 2.440 nonbonded pdb=" OG1 THR Y 274 " pdb=" O VAL Y 315 " model vdw 2.279 2.440 nonbonded pdb=" OG SER Y 147 " pdb=" O VAL Y 187 " model vdw 2.285 2.440 nonbonded pdb=" O ILE Y 58 " pdb=" OG SER Y 316 " model vdw 2.288 2.440 ... (remaining 70621 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.430 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 25.530 Find NCS groups from input model: 0.220 Set up NCS constraints: 0.030 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 8336 Z= 0.324 Angle : 0.854 10.521 11287 Z= 0.451 Chirality : 0.055 0.250 1285 Planarity : 0.007 0.082 1436 Dihedral : 14.684 89.799 3014 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.19 (0.24), residues: 1020 helix: -0.63 (0.23), residues: 384 sheet: -0.65 (0.33), residues: 220 loop : -0.81 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP Y 99 HIS 0.005 0.001 HIS X 357 PHE 0.036 0.002 PHE A 101 TYR 0.057 0.003 TYR Y 59 ARG 0.016 0.001 ARG Y 197 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.909 Fit side-chains REVERT: X 27 GLU cc_start: 0.7099 (mt-10) cc_final: 0.6699 (mp0) REVERT: X 292 ASN cc_start: 0.7635 (m110) cc_final: 0.7412 (m110) outliers start: 0 outliers final: 0 residues processed: 116 average time/residue: 0.2498 time to fit residues: 37.8657 Evaluate side-chains 101 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 5.9990 chunk 76 optimal weight: 6.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 88 ASN Y 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.066 8336 Z= 0.523 Angle : 0.674 8.929 11287 Z= 0.354 Chirality : 0.048 0.164 1285 Planarity : 0.005 0.062 1436 Dihedral : 5.065 50.165 1129 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 11.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.01 % Allowed : 8.23 % Favored : 90.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.49 (0.26), residues: 1020 helix: 0.25 (0.25), residues: 381 sheet: -0.70 (0.33), residues: 231 loop : -0.44 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP Y 99 HIS 0.005 0.001 HIS X 357 PHE 0.022 0.002 PHE X 246 TYR 0.043 0.003 TYR Y 59 ARG 0.004 0.001 ARG A 130 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 115 time to evaluate : 0.853 Fit side-chains revert: symmetry clash REVERT: Z 31 SER cc_start: 0.8050 (m) cc_final: 0.7814 (m) outliers start: 9 outliers final: 4 residues processed: 119 average time/residue: 0.2437 time to fit residues: 37.9665 Evaluate side-chains 106 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 102 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 189 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 99 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 31 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 90 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 23 ASN Y 259 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8336 Z= 0.194 Angle : 0.502 5.725 11287 Z= 0.265 Chirality : 0.041 0.136 1285 Planarity : 0.004 0.060 1436 Dihedral : 4.784 70.276 1129 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.92 % Allowed : 10.71 % Favored : 87.37 % 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: 0.04 (0.26), residues: 1020 helix: 0.99 (0.27), residues: 381 sheet: -0.66 (0.34), residues: 217 loop : -0.33 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.020 0.001 PHE A 155 TYR 0.020 0.001 TYR A 197 ARG 0.006 0.000 ARG Y 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 0.898 Fit side-chains REVERT: Y 43 ILE cc_start: 0.8204 (OUTLIER) cc_final: 0.7912 (mp) REVERT: Z 31 SER cc_start: 0.7957 (m) cc_final: 0.7716 (m) outliers start: 17 outliers final: 13 residues processed: 122 average time/residue: 0.2286 time to fit residues: 37.2489 Evaluate side-chains 119 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 105 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 276 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 0.7980 chunk 47 optimal weight: 0.0980 chunk 10 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9990 chunk 92 optimal weight: 3.9990 chunk 97 optimal weight: 7.9990 chunk 48 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 81 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8336 Z= 0.203 Angle : 0.493 6.615 11287 Z= 0.259 Chirality : 0.042 0.166 1285 Planarity : 0.004 0.057 1436 Dihedral : 4.538 64.532 1129 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.14 % Allowed : 11.95 % Favored : 85.91 % 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: 0.31 (0.26), residues: 1020 helix: 1.31 (0.27), residues: 381 sheet: -0.67 (0.33), residues: 217 loop : -0.18 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 220 PHE 0.017 0.001 PHE A 155 TYR 0.019 0.001 TYR A 197 ARG 0.004 0.000 ARG X 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 112 time to evaluate : 0.948 Fit side-chains REVERT: A 206 MET cc_start: 0.7909 (OUTLIER) cc_final: 0.6621 (mtm) REVERT: X 220 HIS cc_start: 0.8186 (t-170) cc_final: 0.7745 (t-90) REVERT: Y 43 ILE cc_start: 0.8180 (OUTLIER) cc_final: 0.7922 (mt) REVERT: Z 31 SER cc_start: 0.7985 (m) cc_final: 0.7742 (m) outliers start: 19 outliers final: 13 residues processed: 122 average time/residue: 0.2341 time to fit residues: 38.5390 Evaluate side-chains 123 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 77 ASN Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 333 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.8980 chunk 1 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 83 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 49 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 chunk 32 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 5 GLN Y 110 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8336 Z= 0.201 Angle : 0.488 6.657 11287 Z= 0.256 Chirality : 0.041 0.140 1285 Planarity : 0.004 0.056 1436 Dihedral : 4.438 62.963 1129 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.93 % Allowed : 12.74 % Favored : 84.33 % 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: 0.47 (0.27), residues: 1020 helix: 1.48 (0.27), residues: 381 sheet: -0.64 (0.33), residues: 223 loop : -0.10 (0.32), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 220 PHE 0.016 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 111 time to evaluate : 0.817 Fit side-chains REVERT: A 206 MET cc_start: 0.7891 (OUTLIER) cc_final: 0.6615 (mtm) REVERT: Y 43 ILE cc_start: 0.8183 (OUTLIER) cc_final: 0.7908 (mt) REVERT: Z 31 SER cc_start: 0.7992 (m) cc_final: 0.7750 (m) outliers start: 26 outliers final: 19 residues processed: 125 average time/residue: 0.2162 time to fit residues: 36.5147 Evaluate side-chains 129 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 108 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 264 ASN Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 333 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 97 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 8 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8336 Z= 0.229 Angle : 0.509 8.541 11287 Z= 0.264 Chirality : 0.042 0.150 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.434 60.122 1129 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 3.16 % Allowed : 13.75 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.27), residues: 1020 helix: 1.53 (0.27), residues: 381 sheet: -0.57 (0.33), residues: 223 loop : -0.11 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.015 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 116 time to evaluate : 0.927 Fit side-chains REVERT: A 206 MET cc_start: 0.7907 (OUTLIER) cc_final: 0.6572 (mtm) REVERT: X 220 HIS cc_start: 0.8092 (t-90) cc_final: 0.7692 (t-90) REVERT: Y 43 ILE cc_start: 0.8199 (OUTLIER) cc_final: 0.7916 (mt) REVERT: Z 31 SER cc_start: 0.7990 (m) cc_final: 0.7746 (m) outliers start: 28 outliers final: 22 residues processed: 132 average time/residue: 0.2154 time to fit residues: 38.5012 Evaluate side-chains 134 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 110 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 264 ASN Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 59 TYR Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 322 ASP Chi-restraints excluded: chain Y residue 333 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 71 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 97 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 44 optimal weight: 6.9990 chunk 38 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8336 Z= 0.170 Angle : 0.485 8.875 11287 Z= 0.251 Chirality : 0.041 0.150 1285 Planarity : 0.003 0.057 1436 Dihedral : 4.330 61.856 1129 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.82 % Allowed : 13.75 % Favored : 83.43 % 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: 0.64 (0.27), residues: 1020 helix: 1.65 (0.27), residues: 381 sheet: -0.46 (0.33), residues: 221 loop : -0.09 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.016 0.001 PHE A 155 TYR 0.016 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 116 time to evaluate : 1.027 Fit side-chains REVERT: A 206 MET cc_start: 0.7818 (OUTLIER) cc_final: 0.6658 (mtm) REVERT: X 220 HIS cc_start: 0.8033 (t-90) cc_final: 0.7663 (t-90) REVERT: Y 43 ILE cc_start: 0.8129 (OUTLIER) cc_final: 0.7816 (mt) REVERT: Z 31 SER cc_start: 0.7974 (m) cc_final: 0.7735 (m) outliers start: 25 outliers final: 18 residues processed: 130 average time/residue: 0.2460 time to fit residues: 43.1066 Evaluate side-chains 132 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 112 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 61 optimal weight: 0.7980 chunk 66 optimal weight: 5.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 76 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 93 optimal weight: 9.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8336 Z= 0.233 Angle : 0.510 8.715 11287 Z= 0.264 Chirality : 0.042 0.217 1285 Planarity : 0.003 0.055 1436 Dihedral : 4.343 56.744 1129 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 10.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.93 % Allowed : 14.09 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.27), residues: 1020 helix: 1.62 (0.27), residues: 380 sheet: -0.46 (0.33), residues: 221 loop : -0.11 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.015 0.001 PHE X 212 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 115 time to evaluate : 0.958 Fit side-chains revert: symmetry clash REVERT: A 77 MET cc_start: 0.7868 (tpp) cc_final: 0.7661 (tpp) REVERT: A 206 MET cc_start: 0.7883 (OUTLIER) cc_final: 0.6618 (mtm) REVERT: Y 43 ILE cc_start: 0.8207 (OUTLIER) cc_final: 0.7896 (mt) REVERT: Z 31 SER cc_start: 0.7984 (m) cc_final: 0.7743 (m) outliers start: 26 outliers final: 22 residues processed: 131 average time/residue: 0.2335 time to fit residues: 40.5350 Evaluate side-chains 138 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain N residue 113 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 333 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 1.9990 chunk 93 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 259 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8336 Z= 0.272 Angle : 0.531 8.606 11287 Z= 0.274 Chirality : 0.043 0.192 1285 Planarity : 0.004 0.055 1436 Dihedral : 4.456 56.351 1129 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.93 % Allowed : 13.75 % Favored : 83.31 % 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: 0.54 (0.27), residues: 1020 helix: 1.54 (0.27), residues: 380 sheet: -0.52 (0.33), residues: 222 loop : -0.11 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 211 HIS 0.004 0.001 HIS X 220 PHE 0.014 0.001 PHE X 212 TYR 0.017 0.002 TYR A 197 ARG 0.004 0.000 ARG Y 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 114 time to evaluate : 0.949 Fit side-chains REVERT: A 77 MET cc_start: 0.7877 (tpp) cc_final: 0.7638 (tpp) REVERT: A 206 MET cc_start: 0.7935 (OUTLIER) cc_final: 0.6555 (mtm) REVERT: Y 43 ILE cc_start: 0.8242 (OUTLIER) cc_final: 0.7964 (mt) REVERT: Z 31 SER cc_start: 0.7983 (m) cc_final: 0.7738 (m) outliers start: 26 outliers final: 21 residues processed: 130 average time/residue: 0.2468 time to fit residues: 43.2070 Evaluate side-chains 134 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 111 time to evaluate : 0.920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 333 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 100 optimal weight: 0.5980 chunk 92 optimal weight: 3.9990 chunk 80 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 61 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 63 optimal weight: 9.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 GLN ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8336 Z= 0.218 Angle : 0.511 8.666 11287 Z= 0.265 Chirality : 0.042 0.195 1285 Planarity : 0.003 0.056 1436 Dihedral : 4.425 58.674 1129 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 2.71 % Allowed : 14.54 % Favored : 82.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.27), residues: 1020 helix: 1.58 (0.27), residues: 380 sheet: -0.50 (0.33), residues: 222 loop : -0.10 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 220 PHE 0.015 0.001 PHE A 155 TYR 0.017 0.001 TYR A 197 ARG 0.004 0.000 ARG Y 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2040 Ramachandran restraints generated. 1020 Oldfield, 0 Emsley, 1020 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 114 time to evaluate : 0.947 Fit side-chains REVERT: A 77 MET cc_start: 0.7850 (tpp) cc_final: 0.7625 (tpp) REVERT: A 206 MET cc_start: 0.7911 (OUTLIER) cc_final: 0.6634 (mtm) REVERT: Y 43 ILE cc_start: 0.8200 (OUTLIER) cc_final: 0.7905 (mt) outliers start: 24 outliers final: 22 residues processed: 130 average time/residue: 0.2212 time to fit residues: 38.7865 Evaluate side-chains 135 residues out of total 888 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 111 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 PHE Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 139 VAL Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 203 LEU Chi-restraints excluded: chain A residue 206 MET Chi-restraints excluded: chain A residue 279 TYR Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain N residue 5 GLN Chi-restraints excluded: chain N residue 69 THR Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 91 THR Chi-restraints excluded: chain X residue 54 SER Chi-restraints excluded: chain X residue 229 ASP Chi-restraints excluded: chain X residue 292 ASN Chi-restraints excluded: chain X residue 319 THR Chi-restraints excluded: chain Y residue 32 GLN Chi-restraints excluded: chain Y residue 43 ILE Chi-restraints excluded: chain Y residue 146 LEU Chi-restraints excluded: chain Y residue 186 ASP Chi-restraints excluded: chain Y residue 189 SER Chi-restraints excluded: chain Y residue 228 ASP Chi-restraints excluded: chain Y residue 276 VAL Chi-restraints excluded: chain Y residue 333 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 82 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 261 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 32 GLN ** Y 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.144008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.111795 restraints weight = 9498.259| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.95 r_work: 0.3128 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8336 Z= 0.197 Angle : 0.503 8.639 11287 Z= 0.259 Chirality : 0.042 0.194 1285 Planarity : 0.003 0.056 1436 Dihedral : 4.392 59.109 1129 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.71 % Allowed : 14.43 % Favored : 82.86 % 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: 0.65 (0.27), residues: 1020 helix: 1.64 (0.27), residues: 380 sheet: -0.43 (0.33), residues: 221 loop : -0.08 (0.32), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Y 211 HIS 0.003 0.001 HIS X 357 PHE 0.015 0.001 PHE A 155 TYR 0.023 0.001 TYR A 34 ARG 0.004 0.000 ARG Y 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2082.75 seconds wall clock time: 38 minutes 31.07 seconds (2311.07 seconds total)