Starting phenix.real_space_refine on Mon Mar 11 09:12:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjh_33227/03_2024/7xjh_33227_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjh_33227/03_2024/7xjh_33227.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjh_33227/03_2024/7xjh_33227.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjh_33227/03_2024/7xjh_33227.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjh_33227/03_2024/7xjh_33227_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xjh_33227/03_2024/7xjh_33227_updated.pdb" } resolution = 3.3 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= 0.011 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 46 5.16 5 C 4962 2.51 5 N 1378 2.21 5 O 1446 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "G GLU 58": "OE1" <-> "OE2" Residue "N GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7832 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 1884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 1884 Classifications: {'peptide': 231} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 1 Unresolved non-hydrogen bonds: 40 Unresolved non-hydrogen angles: 49 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 6, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 30 Chain: "B" Number of atoms: 2543 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2543 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 5, 'TRANS': 334} Unresolved non-hydrogen bonds: 73 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 58 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 4, 'ARG:plan': 6, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 63 Chain: "G" Number of atoms: 393 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 393 Classifications: {'peptide': 52} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 47} 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: "N" Number of atoms: 950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 950 Classifications: {'peptide': 128} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 5, 'TRANS': 122} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 30 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 15 Chain: "R" Number of atoms: 2062 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2062 Unusual residues: {'5FW': 1} Classifications: {'peptide': 276, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 16, 'TRANS': 259, None: 1} Not linked: pdbres="LEU R 360 " pdbres="5FW R 401 " Chain breaks: 2 Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 63 Unresolved non-hydrogen dihedrals: 45 Planarities with less than four sites: {'GLU:plan': 1, 'HIS:plan': 2, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 40 Time building chain proxies: 4.61, per 1000 atoms: 0.59 Number of scatterers: 7832 At special positions: 0 Unit cell: (96.3829, 120.479, 86.5255, 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 46 16.00 O 1446 8.00 N 1378 7.00 C 4962 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 196 " distance=2.03 Simple disulfide: pdb=" SG CYS R 189 " - pdb=" SG CYS R 195 " 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1926 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 30 helices and 10 sheets defined 38.7% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid 10 through 39 removed outlier: 4.056A pdb=" N ALA A 39 " --> pdb=" O GLN A 35 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 56 No H-bonds generated for 'chain 'A' and resid 53 through 56' Processing helix chain 'A' and resid 236 through 238 No H-bonds generated for 'chain 'A' and resid 236 through 238' Processing helix chain 'A' and resid 253 through 255 No H-bonds generated for 'chain 'A' and resid 253 through 255' Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 284 through 293 Processing helix chain 'A' and resid 298 through 300 No H-bonds generated for 'chain 'A' and resid 298 through 300' Processing helix chain 'A' and resid 303 through 307 removed outlier: 3.662A pdb=" N ALA A 306 " --> pdb=" O PRO A 303 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ARG A 307 " --> pdb=" O GLU A 304 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 303 through 307' Processing helix chain 'A' and resid 322 through 340 Processing helix chain 'A' and resid 361 through 380 removed outlier: 3.884A pdb=" N ILE A 365 " --> pdb=" O ASN A 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 2 through 24 Processing helix chain 'B' and resid 30 through 36 removed outlier: 3.957A pdb=" N ASN B 35 " --> pdb=" O SER B 31 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ASN B 36 " --> pdb=" O GLN B 32 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 22 Processing helix chain 'G' and resid 30 through 47 removed outlier: 4.943A pdb=" N LYS G 46 " --> pdb=" O GLU G 42 " (cutoff:3.500A) removed outlier: 5.887A pdb=" N GLU G 47 " --> pdb=" O ALA G 43 " (cutoff:3.500A) 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 'R' and resid 38 through 63 removed outlier: 3.513A pdb=" N ALA R 42 " --> pdb=" O ALA R 38 " (cutoff:3.500A) Processing helix chain 'R' and resid 66 through 68 No H-bonds generated for 'chain 'R' and resid 66 through 68' Processing helix chain 'R' and resid 71 through 89 removed outlier: 4.303A pdb=" N PHE R 75 " --> pdb=" O MET R 71 " (cutoff:3.500A) Processing helix chain 'R' and resid 91 through 99 Processing helix chain 'R' and resid 107 through 140 removed outlier: 3.784A pdb=" N SER R 124 " --> pdb=" O CYS R 120 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 148 removed outlier: 4.398A pdb=" N GLY R 146 " --> pdb=" O PRO R 142 " (cutoff:3.500A) removed outlier: 5.292A pdb=" N ALA R 147 " --> pdb=" O LEU R 143 " (cutoff:3.500A) Processing helix chain 'R' and resid 151 through 169 Processing helix chain 'R' and resid 171 through 174 No H-bonds generated for 'chain 'R' and resid 171 through 174' Processing helix chain 'R' and resid 189 through 191 No H-bonds generated for 'chain 'R' and resid 189 through 191' Processing helix chain 'R' and resid 202 through 212 Processing helix chain 'R' and resid 214 through 242 Processing helix chain 'R' and resid 289 through 317 removed outlier: 3.538A pdb=" N TRP R 305 " --> pdb=" O PHE R 301 " (cutoff:3.500A) Proline residue: R 307 - end of helix Processing helix chain 'R' and resid 325 through 344 Proline residue: R 343 - end of helix Processing helix chain 'R' and resid 350 through 359 Processing sheet with id= A, first strand: chain 'A' and resid 349 through 353 removed outlier: 7.501A pdb=" N VAL A 277 " --> pdb=" O TYR A 350 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N HIS A 352 " --> pdb=" O VAL A 277 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N LEU A 279 " --> pdb=" O HIS A 352 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ASN A 218 " --> pdb=" O HIS A 41 " (cutoff:3.500A) removed outlier: 8.080A pdb=" N LEU A 43 " --> pdb=" O ASN A 218 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N HIS A 220 " --> pdb=" O LEU A 43 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N LEU A 45 " --> pdb=" O HIS A 220 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N PHE A 222 " --> pdb=" O LEU A 45 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 58 through 63 removed outlier: 7.071A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.403A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.341A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N HIS B 91 " --> pdb=" O ILE B 81 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ASP B 83 " --> pdb=" O LYS B 89 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N LYS B 89 " --> pdb=" O ASP B 83 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.970A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG B 137 " --> pdb=" O ILE B 123 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.230A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 146 through 150 removed outlier: 6.690A pdb=" N SER B 160 " --> pdb=" O SER B 147 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N CYS B 149 " --> pdb=" O VAL B 158 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N VAL B 158 " --> pdb=" O CYS B 149 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.777A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.728A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 250 through 254 Processing sheet with id= G, first strand: chain 'B' and resid 295 through 298 removed outlier: 4.259A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.569A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.526A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'N' and resid 3 through 7 Processing sheet with id= J, first strand: chain 'N' and resid 122 through 124 removed outlier: 6.244A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1086 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: 2.31 Time building geometry restraints manager: 3.36 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: 2581 1.34 - 1.46: 1625 1.46 - 1.58: 3719 1.58 - 1.69: 0 1.69 - 1.81: 61 Bond restraints: 7986 Sorted by residual: bond pdb=" CA SER N 21 " pdb=" CB SER N 21 " ideal model delta sigma weight residual 1.532 1.486 0.046 1.74e-02 3.30e+03 6.99e+00 bond pdb=" CAO 5FW R 401 " pdb=" OAC 5FW R 401 " ideal model delta sigma weight residual 1.351 1.400 -0.049 2.00e-02 2.50e+03 6.06e+00 bond pdb=" CAM 5FW R 401 " pdb=" OAB 5FW R 401 " ideal model delta sigma weight residual 1.353 1.401 -0.048 2.00e-02 2.50e+03 5.66e+00 bond pdb=" C LEU R 306 " pdb=" N PRO R 307 " ideal model delta sigma weight residual 1.335 1.354 -0.018 1.30e-02 5.92e+03 2.00e+00 bond pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 1.454 1.470 -0.016 1.19e-02 7.06e+03 1.79e+00 ... (remaining 7981 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.34: 124 105.34 - 112.53: 4154 112.53 - 119.71: 2640 119.71 - 126.90: 3842 126.90 - 134.09: 98 Bond angle restraints: 10858 Sorted by residual: angle pdb=" N PHE A 222 " pdb=" CA PHE A 222 " pdb=" C PHE A 222 " ideal model delta sigma weight residual 108.55 113.15 -4.60 1.62e+00 3.81e-01 8.07e+00 angle pdb=" N GLU A 16 " pdb=" CA GLU A 16 " pdb=" CB GLU A 16 " ideal model delta sigma weight residual 110.28 114.64 -4.36 1.55e+00 4.16e-01 7.90e+00 angle pdb=" CA SER N 21 " pdb=" C SER N 21 " pdb=" O SER N 21 " ideal model delta sigma weight residual 121.16 118.03 3.13 1.13e+00 7.83e-01 7.66e+00 angle pdb=" C LEU N 20 " pdb=" N SER N 21 " pdb=" CA SER N 21 " ideal model delta sigma weight residual 122.87 118.94 3.93 1.61e+00 3.86e-01 5.95e+00 angle pdb=" C LEU R 89 " pdb=" N VAL R 90 " pdb=" CA VAL R 90 " ideal model delta sigma weight residual 122.63 119.81 2.82 1.19e+00 7.06e-01 5.60e+00 ... (remaining 10853 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 4301 17.97 - 35.93: 382 35.93 - 53.90: 58 53.90 - 71.87: 9 71.87 - 89.83: 8 Dihedral angle restraints: 4758 sinusoidal: 1782 harmonic: 2976 Sorted by residual: dihedral pdb=" CB CYS R 189 " pdb=" SG CYS R 189 " pdb=" SG CYS R 195 " pdb=" CB CYS R 195 " ideal model delta sinusoidal sigma weight residual -86.00 -133.54 47.54 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS N 99 " pdb=" SG CYS N 99 " pdb=" SG CYS N 107 " pdb=" CB CYS N 107 " ideal model delta sinusoidal sigma weight residual 93.00 134.21 -41.21 1 1.00e+01 1.00e-02 2.38e+01 dihedral pdb=" CA CYS N 107 " pdb=" C CYS N 107 " pdb=" N PHE N 108 " pdb=" CA PHE N 108 " ideal model delta harmonic sigma weight residual -180.00 -157.03 -22.97 0 5.00e+00 4.00e-02 2.11e+01 ... (remaining 4755 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 967 0.045 - 0.090: 220 0.090 - 0.134: 67 0.134 - 0.179: 2 0.179 - 0.224: 2 Chirality restraints: 1258 Sorted by residual: chirality pdb=" CAE 5FW R 401 " pdb=" CAF 5FW R 401 " pdb=" CAH 5FW R 401 " pdb=" OAA 5FW R 401 " both_signs ideal model delta sigma weight residual False -2.29 -2.52 0.22 2.00e-01 2.50e+01 1.25e+00 chirality pdb=" CB THR A 315 " pdb=" CA THR A 315 " pdb=" OG1 THR A 315 " pdb=" CG2 THR A 315 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.94e-01 chirality pdb=" CA ILE N 58 " pdb=" N ILE N 58 " pdb=" C ILE N 58 " pdb=" CB ILE N 58 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.37e-01 ... (remaining 1255 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU R 215 " -0.030 5.00e-02 4.00e+02 4.50e-02 3.24e+00 pdb=" N PRO R 216 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO R 216 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 216 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL R 323 " 0.027 5.00e-02 4.00e+02 4.17e-02 2.78e+00 pdb=" N PRO R 324 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO R 324 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO R 324 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN R 192 " 0.026 5.00e-02 4.00e+02 3.99e-02 2.55e+00 pdb=" N PRO R 193 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO R 193 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO R 193 " 0.022 5.00e-02 4.00e+02 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1017 2.75 - 3.29: 7572 3.29 - 3.83: 13248 3.83 - 4.36: 15315 4.36 - 4.90: 27158 Nonbonded interactions: 64310 Sorted by model distance: nonbonded pdb=" OG1 THR B 128 " pdb=" O ASN B 132 " model vdw 2.218 2.440 nonbonded pdb=" OD2 ASP A 33 " pdb=" NZ LYS B 78 " model vdw 2.223 2.520 nonbonded pdb=" OG SER B 161 " pdb=" OD1 ASP B 163 " model vdw 2.226 2.440 nonbonded pdb=" OG SER B 281 " pdb=" OD2 ASP G 48 " model vdw 2.228 2.440 nonbonded pdb=" O GLU B 226 " pdb=" NH2 ARG N 98 " model vdw 2.252 2.520 ... (remaining 64305 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: 0.220 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: 1.190 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 24.370 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.040 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:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 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 0.049 7986 Z= 0.193 Angle : 0.584 7.667 10858 Z= 0.315 Chirality : 0.042 0.224 1258 Planarity : 0.004 0.045 1390 Dihedral : 14.021 89.834 2820 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 0.45 (0.27), residues: 1011 helix: 2.43 (0.26), residues: 377 sheet: -0.72 (0.33), residues: 212 loop : -1.14 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 82 HIS 0.003 0.001 HIS A 347 PHE 0.023 0.002 PHE A 222 TYR 0.011 0.001 TYR B 59 ARG 0.007 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 164 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: A 28 LYS cc_start: 0.7055 (mtmt) cc_final: 0.6774 (mtmt) REVERT: A 32 LYS cc_start: 0.7857 (mtpt) cc_final: 0.7353 (mtpt) REVERT: A 34 LYS cc_start: 0.8052 (ttpp) cc_final: 0.7769 (tttt) REVERT: A 213 GLN cc_start: 0.7742 (tt0) cc_final: 0.7514 (tt0) REVERT: A 252 ASP cc_start: 0.7055 (t70) cc_final: 0.6826 (t70) REVERT: A 304 GLU cc_start: 0.7674 (pm20) cc_final: 0.7462 (pm20) REVERT: B 42 ARG cc_start: 0.7577 (tmt170) cc_final: 0.6922 (tpt170) REVERT: B 175 GLN cc_start: 0.7772 (mt0) cc_final: 0.7544 (mt0) REVERT: B 226 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8450 (mt-10) REVERT: N 20 LEU cc_start: 0.8027 (mt) cc_final: 0.7764 (mt) REVERT: N 21 SER cc_start: 0.8305 (m) cc_final: 0.7963 (p) REVERT: N 77 ASN cc_start: 0.6830 (m-40) cc_final: 0.6525 (m-40) REVERT: R 236 ARG cc_start: 0.6685 (mtm110) cc_final: 0.6406 (mtm110) REVERT: R 240 ARG cc_start: 0.7363 (tmm-80) cc_final: 0.7003 (ttm170) outliers start: 0 outliers final: 0 residues processed: 164 average time/residue: 0.2347 time to fit residues: 49.8818 Evaluate side-chains 129 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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: 0.5980 chunk 76 optimal weight: 0.0570 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 40 optimal weight: 0.0970 chunk 79 optimal weight: 0.8980 chunk 30 optimal weight: 7.9990 chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN G 59 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 332 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7486 moved from start: 0.0861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7986 Z= 0.134 Angle : 0.491 7.918 10858 Z= 0.253 Chirality : 0.040 0.147 1258 Planarity : 0.004 0.042 1390 Dihedral : 4.018 28.897 1122 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 0.25 % Allowed : 7.36 % Favored : 92.39 % 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: 0.71 (0.27), residues: 1011 helix: 2.52 (0.26), residues: 379 sheet: -0.48 (0.33), residues: 218 loop : -0.94 (0.31), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.005 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 137 time to evaluate : 0.846 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7957 (mtpt) cc_final: 0.7454 (mtpt) REVERT: A 34 LYS cc_start: 0.8001 (ttpp) cc_final: 0.7758 (tttt) REVERT: A 229 ASP cc_start: 0.6843 (p0) cc_final: 0.6641 (p0) REVERT: A 252 ASP cc_start: 0.7109 (t70) cc_final: 0.6865 (t70) REVERT: A 299 GLU cc_start: 0.7854 (mp0) cc_final: 0.7642 (mp0) REVERT: A 304 GLU cc_start: 0.7680 (pm20) cc_final: 0.7454 (pm20) REVERT: A 308 TYR cc_start: 0.7208 (t80) cc_final: 0.6728 (t80) REVERT: B 42 ARG cc_start: 0.7596 (tmt170) cc_final: 0.6952 (tpt170) REVERT: B 175 GLN cc_start: 0.7728 (mt0) cc_final: 0.7500 (mt0) REVERT: B 226 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8417 (mt-10) REVERT: N 20 LEU cc_start: 0.7996 (mt) cc_final: 0.7768 (mt) REVERT: N 77 ASN cc_start: 0.6771 (m-40) cc_final: 0.6530 (m-40) REVERT: R 240 ARG cc_start: 0.7310 (tmm-80) cc_final: 0.7045 (ttm170) outliers start: 2 outliers final: 1 residues processed: 137 average time/residue: 0.2361 time to fit residues: 42.1892 Evaluate side-chains 127 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 126 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 89 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 76 optimal weight: 0.6980 chunk 62 optimal weight: 10.0000 chunk 25 optimal weight: 30.0000 chunk 91 optimal weight: 0.8980 chunk 99 optimal weight: 0.7980 chunk 81 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 73 optimal weight: 7.9990 chunk 90 optimal weight: 0.6980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN B 220 GLN B 230 ASN B 340 ASN G 59 ASN N 82 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7554 moved from start: 0.1229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 7986 Z= 0.191 Angle : 0.507 8.013 10858 Z= 0.259 Chirality : 0.040 0.155 1258 Planarity : 0.004 0.044 1390 Dihedral : 4.097 30.775 1122 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 1.96 % Allowed : 9.69 % Favored : 88.34 % 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 (0.27), residues: 1011 helix: 2.45 (0.26), residues: 380 sheet: -0.42 (0.33), residues: 224 loop : -0.79 (0.32), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.005 0.001 HIS A 347 PHE 0.018 0.002 PHE N 108 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 130 time to evaluate : 0.845 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7975 (mtpt) cc_final: 0.7508 (mtpt) REVERT: A 34 LYS cc_start: 0.8107 (ttpp) cc_final: 0.7841 (tttt) REVERT: A 35 GLN cc_start: 0.7484 (pt0) cc_final: 0.7256 (pt0) REVERT: A 213 GLN cc_start: 0.7974 (tt0) cc_final: 0.7474 (tt0) REVERT: A 252 ASP cc_start: 0.7085 (t70) cc_final: 0.6863 (t70) REVERT: B 42 ARG cc_start: 0.7588 (tmt170) cc_final: 0.6925 (tpt170) REVERT: B 175 GLN cc_start: 0.7678 (mt0) cc_final: 0.7438 (mt0) REVERT: B 226 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8404 (mt-10) REVERT: B 259 GLN cc_start: 0.7987 (mm-40) cc_final: 0.7627 (mm-40) REVERT: N 20 LEU cc_start: 0.8015 (mt) cc_final: 0.7761 (mt) REVERT: N 65 LYS cc_start: 0.6502 (ttmm) cc_final: 0.6241 (tptp) REVERT: R 353 ARG cc_start: 0.6218 (mtt90) cc_final: 0.5871 (mtt180) outliers start: 16 outliers final: 10 residues processed: 138 average time/residue: 0.2269 time to fit residues: 41.3055 Evaluate side-chains 135 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 125 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 338 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 6.9990 chunk 10 optimal weight: 0.3980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 92 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 87 optimal weight: 5.9990 chunk 26 optimal weight: 0.0370 chunk 81 optimal weight: 0.9990 overall best weight: 0.8862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN N 82 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7533 moved from start: 0.1420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7986 Z= 0.143 Angle : 0.478 8.099 10858 Z= 0.245 Chirality : 0.039 0.145 1258 Planarity : 0.003 0.042 1390 Dihedral : 3.920 26.747 1122 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.09 % Allowed : 11.17 % Favored : 86.75 % 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: 0.90 (0.27), residues: 1011 helix: 2.63 (0.26), residues: 374 sheet: -0.26 (0.33), residues: 228 loop : -0.82 (0.31), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 234 HIS 0.004 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.002 0.000 ARG N 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 129 time to evaluate : 0.799 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7977 (mtpt) cc_final: 0.7515 (mtpt) REVERT: A 34 LYS cc_start: 0.8086 (ttpp) cc_final: 0.7825 (tttt) REVERT: A 35 GLN cc_start: 0.7459 (pt0) cc_final: 0.7221 (pt0) REVERT: A 252 ASP cc_start: 0.7085 (t70) cc_final: 0.6836 (t70) REVERT: A 308 TYR cc_start: 0.7293 (t80) cc_final: 0.6779 (t80) REVERT: B 42 ARG cc_start: 0.7581 (tmt170) cc_final: 0.6917 (tpt170) REVERT: B 175 GLN cc_start: 0.7673 (mt0) cc_final: 0.7439 (mt0) REVERT: B 226 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8394 (mt-10) REVERT: B 259 GLN cc_start: 0.8049 (mm-40) cc_final: 0.7658 (mm-40) REVERT: N 20 LEU cc_start: 0.8033 (mt) cc_final: 0.7769 (mt) REVERT: N 65 LYS cc_start: 0.6500 (ttmm) cc_final: 0.6259 (tptp) REVERT: R 353 ARG cc_start: 0.6195 (mtt90) cc_final: 0.5885 (mtt180) outliers start: 17 outliers final: 11 residues processed: 137 average time/residue: 0.2286 time to fit residues: 41.2086 Evaluate side-chains 137 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 126 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 0.3980 chunk 1 optimal weight: 0.9980 chunk 72 optimal weight: 0.0770 chunk 40 optimal weight: 0.0270 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 0 optimal weight: 30.0000 chunk 49 optimal weight: 9.9990 chunk 87 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 220 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7986 Z= 0.119 Angle : 0.462 8.159 10858 Z= 0.234 Chirality : 0.039 0.141 1258 Planarity : 0.003 0.040 1390 Dihedral : 3.700 21.801 1122 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.96 % Allowed : 12.27 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.27), residues: 1011 helix: 2.77 (0.26), residues: 374 sheet: -0.24 (0.33), residues: 231 loop : -0.82 (0.31), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR A 37 ARG 0.003 0.000 ARG R 240 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 127 time to evaluate : 0.855 Fit side-chains revert: symmetry clash REVERT: A 32 LYS cc_start: 0.7964 (mtpt) cc_final: 0.7509 (mtpt) REVERT: A 34 LYS cc_start: 0.8093 (ttpp) cc_final: 0.7842 (tttt) REVERT: A 213 GLN cc_start: 0.7892 (tt0) cc_final: 0.7409 (tt0) REVERT: A 252 ASP cc_start: 0.7057 (t70) cc_final: 0.6766 (t70) REVERT: A 308 TYR cc_start: 0.7252 (t80) cc_final: 0.6759 (t80) REVERT: B 42 ARG cc_start: 0.7546 (tmt170) cc_final: 0.6823 (tpt170) REVERT: B 175 GLN cc_start: 0.7657 (mt0) cc_final: 0.7419 (mt0) REVERT: B 226 GLU cc_start: 0.8647 (mt-10) cc_final: 0.8370 (mt-10) REVERT: B 259 GLN cc_start: 0.8113 (mm-40) cc_final: 0.7750 (mm-40) REVERT: N 20 LEU cc_start: 0.7989 (mt) cc_final: 0.7694 (mt) REVERT: N 65 LYS cc_start: 0.6497 (ttmm) cc_final: 0.6281 (tptp) outliers start: 16 outliers final: 11 residues processed: 136 average time/residue: 0.2166 time to fit residues: 39.0056 Evaluate side-chains 131 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 2.9990 chunk 97 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 32 optimal weight: 7.9990 chunk 51 optimal weight: 4.9990 chunk 94 optimal weight: 6.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 268 ASN B 220 GLN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.1985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 7986 Z= 0.336 Angle : 0.578 9.009 10858 Z= 0.298 Chirality : 0.043 0.155 1258 Planarity : 0.004 0.046 1390 Dihedral : 4.377 25.420 1122 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 3.44 % Allowed : 12.15 % Favored : 84.42 % 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: 1011 helix: 2.13 (0.26), residues: 386 sheet: -0.24 (0.34), residues: 220 loop : -0.89 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.019 0.002 PHE R 308 TYR 0.014 0.002 TYR A 329 ARG 0.008 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 120 time to evaluate : 0.884 Fit side-chains REVERT: A 32 LYS cc_start: 0.7971 (mtpt) cc_final: 0.7497 (mtpt) REVERT: A 34 LYS cc_start: 0.8248 (ttpp) cc_final: 0.7906 (tttt) REVERT: A 213 GLN cc_start: 0.8168 (tt0) cc_final: 0.7781 (tt0) REVERT: A 252 ASP cc_start: 0.7088 (t70) cc_final: 0.6844 (t70) REVERT: A 308 TYR cc_start: 0.7417 (t80) cc_final: 0.6982 (t80) REVERT: B 42 ARG cc_start: 0.7588 (tmt170) cc_final: 0.6876 (tpt170) REVERT: B 175 GLN cc_start: 0.7753 (mt0) cc_final: 0.7494 (mt0) REVERT: B 259 GLN cc_start: 0.8124 (mm-40) cc_final: 0.7748 (mm-40) REVERT: N 20 LEU cc_start: 0.8003 (mt) cc_final: 0.7658 (mt) REVERT: N 65 LYS cc_start: 0.6588 (ttmm) cc_final: 0.6321 (tptp) outliers start: 28 outliers final: 21 residues processed: 139 average time/residue: 0.2212 time to fit residues: 40.5793 Evaluate side-chains 137 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 SER Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 243 THR Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 82 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 97 optimal weight: 0.0770 chunk 60 optimal weight: 10.0000 chunk 59 optimal weight: 9.9990 chunk 44 optimal weight: 0.0980 chunk 38 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 77 ASN ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7540 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 7986 Z= 0.124 Angle : 0.479 8.637 10858 Z= 0.245 Chirality : 0.039 0.209 1258 Planarity : 0.004 0.042 1390 Dihedral : 3.922 21.621 1122 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.70 % Allowed : 13.37 % Favored : 83.93 % 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: 0.86 (0.27), residues: 1011 helix: 2.53 (0.26), residues: 380 sheet: -0.15 (0.33), residues: 230 loop : -0.93 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG R 240 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 126 time to evaluate : 0.926 Fit side-chains REVERT: A 32 LYS cc_start: 0.7989 (mtpt) cc_final: 0.7495 (mtpt) REVERT: A 34 LYS cc_start: 0.8156 (ttpp) cc_final: 0.7856 (tttt) REVERT: A 213 GLN cc_start: 0.8118 (tt0) cc_final: 0.7730 (tt0) REVERT: A 252 ASP cc_start: 0.7009 (t70) cc_final: 0.6759 (t70) REVERT: A 308 TYR cc_start: 0.7186 (t80) cc_final: 0.6675 (t80) REVERT: B 42 ARG cc_start: 0.7613 (tmt170) cc_final: 0.6911 (tpt170) REVERT: B 175 GLN cc_start: 0.7737 (mt0) cc_final: 0.7490 (mt0) REVERT: B 256 ARG cc_start: 0.8067 (mtm110) cc_final: 0.7700 (mtm110) REVERT: B 259 GLN cc_start: 0.8060 (mm-40) cc_final: 0.7814 (mm-40) REVERT: N 20 LEU cc_start: 0.7996 (mt) cc_final: 0.7746 (mt) REVERT: N 65 LYS cc_start: 0.6528 (ttmm) cc_final: 0.6264 (tptp) outliers start: 22 outliers final: 16 residues processed: 136 average time/residue: 0.2339 time to fit residues: 41.7296 Evaluate side-chains 137 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 121 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 61 optimal weight: 0.0010 chunk 66 optimal weight: 4.9990 chunk 48 optimal weight: 9.9990 chunk 9 optimal weight: 5.9990 chunk 76 optimal weight: 0.8980 chunk 88 optimal weight: 8.9990 chunk 93 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 overall best weight: 0.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7536 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 7986 Z= 0.136 Angle : 0.474 8.350 10858 Z= 0.242 Chirality : 0.039 0.161 1258 Planarity : 0.003 0.042 1390 Dihedral : 3.789 20.204 1122 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.21 % Allowed : 14.11 % Favored : 83.68 % 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 (0.27), residues: 1011 helix: 2.62 (0.26), residues: 379 sheet: -0.12 (0.33), residues: 230 loop : -0.86 (0.31), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 234 HIS 0.003 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG R 240 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 0.911 Fit side-chains REVERT: A 32 LYS cc_start: 0.7974 (mtpt) cc_final: 0.7485 (mtpt) REVERT: A 34 LYS cc_start: 0.8153 (ttpp) cc_final: 0.7864 (tttt) REVERT: A 213 GLN cc_start: 0.8101 (tt0) cc_final: 0.7788 (tt0) REVERT: A 252 ASP cc_start: 0.7017 (t70) cc_final: 0.6775 (t70) REVERT: A 308 TYR cc_start: 0.7226 (t80) cc_final: 0.6766 (t80) REVERT: B 42 ARG cc_start: 0.7589 (tmt170) cc_final: 0.6859 (tpt170) REVERT: B 175 GLN cc_start: 0.7737 (mt0) cc_final: 0.7492 (mt0) REVERT: B 256 ARG cc_start: 0.8011 (mtm110) cc_final: 0.7324 (mtm110) REVERT: B 259 GLN cc_start: 0.8105 (mm-40) cc_final: 0.7863 (mm-40) REVERT: N 20 LEU cc_start: 0.8015 (mt) cc_final: 0.7744 (mt) REVERT: N 65 LYS cc_start: 0.6507 (ttmm) cc_final: 0.6249 (tptp) outliers start: 18 outliers final: 17 residues processed: 135 average time/residue: 0.2359 time to fit residues: 41.5665 Evaluate side-chains 140 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 123 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 4.9990 chunk 93 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 81 optimal weight: 6.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 20.0000 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.3980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7579 moved from start: 0.2051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 7986 Z= 0.202 Angle : 0.508 8.100 10858 Z= 0.260 Chirality : 0.040 0.160 1258 Planarity : 0.004 0.043 1390 Dihedral : 3.974 21.518 1122 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 2.70 % Allowed : 14.11 % Favored : 83.19 % 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: 0.90 (0.27), residues: 1011 helix: 2.52 (0.26), residues: 379 sheet: -0.15 (0.34), residues: 219 loop : -0.81 (0.30), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 99 HIS 0.006 0.001 HIS A 347 PHE 0.014 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG N 98 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 121 time to evaluate : 0.801 Fit side-chains REVERT: A 32 LYS cc_start: 0.7982 (mtpt) cc_final: 0.7501 (mtpt) REVERT: A 34 LYS cc_start: 0.8213 (ttpp) cc_final: 0.7893 (ttmt) REVERT: A 213 GLN cc_start: 0.8141 (tt0) cc_final: 0.7764 (tt0) REVERT: A 252 ASP cc_start: 0.7062 (t70) cc_final: 0.6815 (t70) REVERT: A 308 TYR cc_start: 0.7303 (t80) cc_final: 0.6881 (t80) REVERT: B 42 ARG cc_start: 0.7624 (tmt170) cc_final: 0.6883 (tpt170) REVERT: B 175 GLN cc_start: 0.7719 (mt0) cc_final: 0.7475 (mt0) REVERT: B 256 ARG cc_start: 0.8000 (mtm110) cc_final: 0.7277 (mtm110) REVERT: B 259 GLN cc_start: 0.8095 (mm-40) cc_final: 0.7874 (mm-40) REVERT: N 20 LEU cc_start: 0.8016 (mt) cc_final: 0.7748 (mt) REVERT: N 65 LYS cc_start: 0.6557 (ttmm) cc_final: 0.6283 (tptp) outliers start: 22 outliers final: 18 residues processed: 134 average time/residue: 0.2217 time to fit residues: 39.0223 Evaluate side-chains 140 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 122 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain G residue 50 LEU Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 338 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 8.9990 chunk 66 optimal weight: 4.9990 chunk 100 optimal weight: 0.4980 chunk 92 optimal weight: 0.7980 chunk 80 optimal weight: 9.9990 chunk 8 optimal weight: 3.9990 chunk 61 optimal weight: 10.0000 chunk 49 optimal weight: 5.9990 chunk 63 optimal weight: 0.9980 chunk 85 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7986 Z= 0.259 Angle : 0.539 8.516 10858 Z= 0.278 Chirality : 0.042 0.155 1258 Planarity : 0.004 0.045 1390 Dihedral : 4.209 23.200 1122 Min Nonbonded Distance : 2.043 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.58 % Allowed : 14.11 % 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: 0.72 (0.27), residues: 1011 helix: 2.25 (0.26), residues: 384 sheet: -0.20 (0.34), residues: 220 loop : -0.86 (0.30), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.007 0.001 HIS A 347 PHE 0.016 0.002 PHE R 308 TYR 0.013 0.002 TYR A 329 ARG 0.006 0.000 ARG N 98 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2022 Ramachandran restraints generated. 1011 Oldfield, 0 Emsley, 1011 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 115 time to evaluate : 0.858 Fit side-chains REVERT: A 32 LYS cc_start: 0.7981 (mtpt) cc_final: 0.7496 (mtpt) REVERT: A 34 LYS cc_start: 0.8278 (ttpp) cc_final: 0.7952 (ttmt) REVERT: A 213 GLN cc_start: 0.8154 (tt0) cc_final: 0.7798 (tt0) REVERT: A 252 ASP cc_start: 0.7077 (t70) cc_final: 0.6794 (t0) REVERT: A 308 TYR cc_start: 0.7331 (t80) cc_final: 0.6895 (t80) REVERT: B 42 ARG cc_start: 0.7625 (tmt170) cc_final: 0.6880 (tpt170) REVERT: B 161 SER cc_start: 0.8604 (p) cc_final: 0.8316 (t) REVERT: B 175 GLN cc_start: 0.7744 (mt0) cc_final: 0.7493 (mt0) REVERT: B 256 ARG cc_start: 0.8025 (mtm110) cc_final: 0.7295 (mtm110) REVERT: B 259 GLN cc_start: 0.8083 (mm-40) cc_final: 0.7877 (mm-40) REVERT: N 20 LEU cc_start: 0.8039 (mt) cc_final: 0.7781 (mt) REVERT: N 65 LYS cc_start: 0.6631 (ttmm) cc_final: 0.6294 (tptp) outliers start: 21 outliers final: 18 residues processed: 129 average time/residue: 0.2293 time to fit residues: 39.0140 Evaluate side-chains 133 residues out of total 862 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 296 SER Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 74 SER Chi-restraints excluded: chain B residue 100 VAL Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 327 VAL Chi-restraints excluded: chain B residue 331 SER Chi-restraints excluded: chain N residue 99 CYS Chi-restraints excluded: chain N residue 104 THR Chi-restraints excluded: chain N residue 107 CYS Chi-restraints excluded: chain N residue 126 VAL Chi-restraints excluded: chain R residue 232 THR Chi-restraints excluded: chain R residue 288 HIS Chi-restraints excluded: chain R residue 338 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 33 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 10 optimal weight: 0.4980 chunk 14 optimal weight: 9.9990 chunk 70 optimal weight: 0.9990 chunk 4 optimal weight: 4.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 342 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.154835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.118508 restraints weight = 8990.699| |-----------------------------------------------------------------------------| r_work (start): 0.3276 rms_B_bonded: 1.94 r_work: 0.3134 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7986 Z= 0.139 Angle : 0.481 8.616 10858 Z= 0.247 Chirality : 0.039 0.149 1258 Planarity : 0.003 0.043 1390 Dihedral : 3.889 21.347 1122 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.96 % Allowed : 15.09 % Favored : 82.94 % 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: 0.85 (0.27), residues: 1011 helix: 2.49 (0.26), residues: 382 sheet: -0.13 (0.34), residues: 225 loop : -0.91 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 99 HIS 0.003 0.001 HIS A 347 PHE 0.015 0.001 PHE A 212 TYR 0.012 0.001 TYR A 37 ARG 0.004 0.000 ARG R 240 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1995.62 seconds wall clock time: 36 minutes 55.63 seconds (2215.63 seconds total)