Starting phenix.real_space_refine on Thu Jan 18 02:35:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/01_2024/8gbj_29917_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/01_2024/8gbj_29917.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/01_2024/8gbj_29917.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/01_2024/8gbj_29917.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/01_2024/8gbj_29917_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gbj_29917/01_2024/8gbj_29917_updated.pdb" } resolution = 3.11 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= 0.000 sd= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 15 5.49 5 S 50 5.16 5 C 4685 2.51 5 N 1296 2.21 5 O 1421 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B GLU 51": "OE1" <-> "OE2" Residue "C GLU 37": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "C PHE 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 197": "OE1" <-> "OE2" Residue "C GLU 232": "OE1" <-> "OE2" Residue "C GLU 303": "OE1" <-> "OE2" Residue "C TYR 327": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 348": "OD1" <-> "OD2" Residue "D ASP 174": "OD1" <-> "OD2" Residue "D ASP 180": "OD1" <-> "OD2" Residue "D GLU 184": "OE1" <-> "OE2" Residue "X GLU 26": "OE1" <-> "OE2" Residue "X GLU 75": "OE1" <-> "OE2" Residue "X PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 134": "OE1" <-> "OE2" Residue "X GLU 164": "OE1" <-> "OE2" Residue "X TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/modules/chem_data/mon_lib" Total number of atoms: 7467 Number of models: 1 Model: "" Number of chains: 8 Chain: "B" Number of atoms: 570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 570 Classifications: {'peptide': 73} Link IDs: {'PTRANS': 2, 'TRANS': 70} Chain: "C" Number of atoms: 2494 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2494 Classifications: {'peptide': 317} Link IDs: {'PTRANS': 11, 'TRANS': 305} Chain breaks: 2 Chain: "D" Number of atoms: 2318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 308, 2318 Classifications: {'peptide': 308} Link IDs: {'CIS': 1, 'PTRANS': 7, 'TRANS': 299} Chain breaks: 2 Chain: "X" Number of atoms: 1878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1878 Classifications: {'peptide': 232} Link IDs: {'CIS': 1, 'PTRANS': 5, 'TRANS': 225} Chain breaks: 3 Chain: "G" Number of atoms: 114 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 114 Classifications: {'DNA': 6} Link IDs: {'rna3p': 5} Chain: "C" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.47, per 1000 atoms: 0.60 Number of scatterers: 7467 At special positions: 0 Unit cell: (84.39, 81.78, 112.23, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 50 16.00 P 15 15.00 O 1421 8.00 N 1296 7.00 C 4685 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 27 " - pdb=" SG CYS B 60 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.36 Conformation dependent library (CDL) restraints added in 1.5 seconds 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1732 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 5 sheets defined 45.6% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.47 Creating SS restraints... Processing helix chain 'B' and resid 13 through 22 removed outlier: 3.573A pdb=" N HIS B 22 " --> pdb=" O ARG B 18 " (cutoff:3.500A) Processing helix chain 'B' and resid 27 through 31 Processing helix chain 'B' and resid 35 through 42 Processing helix chain 'B' and resid 46 through 59 removed outlier: 3.512A pdb=" N GLU B 51 " --> pdb=" O ARG B 47 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LEU B 52 " --> pdb=" O GLY B 48 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 74 Processing helix chain 'C' and resid 21 through 30 Processing helix chain 'C' and resid 35 through 38 Processing helix chain 'C' and resid 43 through 50 Processing helix chain 'C' and resid 54 through 66 Processing helix chain 'C' and resid 87 through 96 Processing helix chain 'C' and resid 105 through 110 Processing helix chain 'C' and resid 131 through 143 removed outlier: 4.323A pdb=" N GLN C 143 " --> pdb=" O ALA C 139 " (cutoff:3.500A) Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 166 through 187 Processing helix chain 'C' and resid 190 through 197 Processing helix chain 'C' and resid 201 through 206 Processing helix chain 'C' and resid 216 through 232 Proline residue: C 227 - end of helix Processing helix chain 'C' and resid 246 through 249 No H-bonds generated for 'chain 'C' and resid 246 through 249' Processing helix chain 'C' and resid 255 through 275 Processing helix chain 'C' and resid 304 through 307 Processing helix chain 'D' and resid 14 through 22 Processing helix chain 'D' and resid 28 through 33 Processing helix chain 'D' and resid 36 through 43 Processing helix chain 'D' and resid 47 through 61 Processing helix chain 'D' and resid 68 through 78 removed outlier: 3.915A pdb=" N THR D 77 " --> pdb=" O GLU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 92 Processing helix chain 'D' and resid 113 through 126 Processing helix chain 'D' and resid 143 through 153 Processing helix chain 'D' and resid 157 through 166 Processing helix chain 'D' and resid 175 through 192 Processing helix chain 'D' and resid 208 through 213 Processing helix chain 'D' and resid 222 through 238 Processing helix chain 'D' and resid 265 through 270 removed outlier: 3.735A pdb=" N PHE D 270 " --> pdb=" O ARG D 266 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 313 No H-bonds generated for 'chain 'D' and resid 311 through 313' Processing helix chain 'X' and resid 24 through 27 No H-bonds generated for 'chain 'X' and resid 24 through 27' Processing helix chain 'X' and resid 54 through 66 Processing helix chain 'X' and resid 89 through 99 Processing helix chain 'X' and resid 105 through 114 removed outlier: 3.798A pdb=" N ARG X 114 " --> pdb=" O TYR X 110 " (cutoff:3.500A) Processing helix chain 'X' and resid 123 through 137 removed outlier: 4.310A pdb=" N SER X 135 " --> pdb=" O TYR X 131 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET X 136 " --> pdb=" O SER X 132 " (cutoff:3.500A) Processing helix chain 'X' and resid 151 through 161 removed outlier: 4.333A pdb=" N PHE X 154 " --> pdb=" O LEU X 151 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N TRP X 156 " --> pdb=" O ALA X 153 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE X 157 " --> pdb=" O PHE X 154 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASN X 161 " --> pdb=" O ASP X 158 " (cutoff:3.500A) Processing helix chain 'X' and resid 166 through 169 No H-bonds generated for 'chain 'X' and resid 166 through 169' Processing helix chain 'X' and resid 171 through 186 Processing helix chain 'X' and resid 229 through 234 removed outlier: 4.446A pdb=" N LEU X 234 " --> pdb=" O ALA X 230 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'C' and resid 336 through 339 removed outlier: 4.150A pdb=" N ARG C 322 " --> pdb=" O PHE C 339 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N ARG C 312 " --> pdb=" O TYR C 327 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N GLU C 154 " --> pdb=" O ARG C 237 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N VAL C 239 " --> pdb=" O GLU C 154 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N VAL C 156 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 5.561A pdb=" N VAL C 241 " --> pdb=" O VAL C 156 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ILE C 158 " --> pdb=" O VAL C 241 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 340 through 342 Processing sheet with id= C, first strand: chain 'D' and resid 306 through 310 removed outlier: 6.539A pdb=" N ARG D 275 " --> pdb=" O ALA D 296 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N VAL D 245 " --> pdb=" O THR D 103 " (cutoff:3.500A) removed outlier: 7.569A pdb=" N ILE D 105 " --> pdb=" O VAL D 245 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 247 " --> pdb=" O ILE D 105 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N GLY D 107 " --> pdb=" O VAL D 247 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N ASN D 249 " --> pdb=" O GLY D 107 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N ASN D 131 " --> pdb=" O LYS D 201 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N VAL D 203 " --> pdb=" O ASN D 131 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N LEU D 133 " --> pdb=" O VAL D 203 " (cutoff:3.500A) removed outlier: 5.350A pdb=" N VAL D 205 " --> pdb=" O LEU D 133 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N VAL D 135 " --> pdb=" O VAL D 205 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 251 through 253 Processing sheet with id= E, first strand: chain 'X' and resid 276 through 279 removed outlier: 4.352A pdb=" N GLN X 252 " --> pdb=" O GLN X 244 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS X 237 " --> pdb=" O ILE X 43 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU X 191 " --> pdb=" O LEU X 44 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N PHE X 46 " --> pdb=" O LEU X 191 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ALA X 193 " --> pdb=" O PHE X 46 " (cutoff:3.500A) removed outlier: 8.191A pdb=" N GLY X 48 " --> pdb=" O ALA X 193 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR X 195 " --> pdb=" O GLY X 48 " (cutoff:3.500A) 332 hydrogen bonds defined for protein. 954 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: 2.15 Time building geometry restraints manager: 3.35 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: 2444 1.34 - 1.46: 1285 1.46 - 1.57: 3765 1.57 - 1.69: 25 1.69 - 1.81: 72 Bond restraints: 7591 Sorted by residual: bond pdb=" O3A ANP X 301 " pdb=" PB ANP X 301 " ideal model delta sigma weight residual 1.700 1.553 0.147 2.00e-02 2.50e+03 5.37e+01 bond pdb=" O3A ANP D 401 " pdb=" PB ANP D 401 " ideal model delta sigma weight residual 1.700 1.554 0.146 2.00e-02 2.50e+03 5.34e+01 bond pdb=" O3A ANP C 401 " pdb=" PB ANP C 401 " ideal model delta sigma weight residual 1.700 1.555 0.145 2.00e-02 2.50e+03 5.25e+01 bond pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 1.795 1.688 0.107 2.00e-02 2.50e+03 2.85e+01 bond pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 1.795 1.689 0.106 2.00e-02 2.50e+03 2.82e+01 ... (remaining 7586 not shown) Histogram of bond angle deviations from ideal: 99.71 - 106.57: 213 106.57 - 113.42: 4305 113.42 - 120.28: 2740 120.28 - 127.14: 2946 127.14 - 134.00: 73 Bond angle restraints: 10277 Sorted by residual: angle pdb=" PB ANP X 301 " pdb=" N3B ANP X 301 " pdb=" PG ANP X 301 " ideal model delta sigma weight residual 126.95 109.49 17.46 3.00e+00 1.11e-01 3.39e+01 angle pdb=" PB ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sigma weight residual 126.95 110.36 16.59 3.00e+00 1.11e-01 3.06e+01 angle pdb=" PB ANP D 401 " pdb=" N3B ANP D 401 " pdb=" PG ANP D 401 " ideal model delta sigma weight residual 126.95 110.60 16.35 3.00e+00 1.11e-01 2.97e+01 angle pdb=" C GLN D 220 " pdb=" N ARG D 221 " pdb=" CA ARG D 221 " ideal model delta sigma weight residual 122.49 116.55 5.94 1.55e+00 4.16e-01 1.47e+01 angle pdb=" O1B ANP D 401 " pdb=" PB ANP D 401 " pdb=" O2B ANP D 401 " ideal model delta sigma weight residual 120.08 108.86 11.22 3.00e+00 1.11e-01 1.40e+01 ... (remaining 10272 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.76: 4232 19.76 - 39.52: 288 39.52 - 59.28: 70 59.28 - 79.04: 31 79.04 - 98.80: 13 Dihedral angle restraints: 4634 sinusoidal: 1963 harmonic: 2671 Sorted by residual: dihedral pdb=" CA LEU C 278 " pdb=" C LEU C 278 " pdb=" N ALA C 279 " pdb=" CA ALA C 279 " ideal model delta harmonic sigma weight residual 180.00 162.27 17.73 0 5.00e+00 4.00e-02 1.26e+01 dihedral pdb=" CA THR B 42 " pdb=" C THR B 42 " pdb=" N GLY B 43 " pdb=" CA GLY B 43 " ideal model delta harmonic sigma weight residual 180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" O1B ANP C 401 " pdb=" N3B ANP C 401 " pdb=" PB ANP C 401 " pdb=" PG ANP C 401 " ideal model delta sinusoidal sigma weight residual 35.15 -63.65 98.80 1 3.00e+01 1.11e-03 1.23e+01 ... (remaining 4631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 998 0.057 - 0.113: 187 0.113 - 0.170: 16 0.170 - 0.227: 1 0.227 - 0.283: 3 Chirality restraints: 1205 Sorted by residual: chirality pdb=" C3' ANP D 401 " pdb=" C2' ANP D 401 " pdb=" C4' ANP D 401 " pdb=" O3' ANP D 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" C3' ANP X 301 " pdb=" C2' ANP X 301 " pdb=" C4' ANP X 301 " pdb=" O3' ANP X 301 " both_signs ideal model delta sigma weight residual False -2.36 -2.64 0.28 2.00e-01 2.50e+01 2.00e+00 chirality pdb=" C3' ANP C 401 " pdb=" C2' ANP C 401 " pdb=" C4' ANP C 401 " pdb=" O3' ANP C 401 " both_signs ideal model delta sigma weight residual False -2.36 -2.63 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1202 not shown) Planarity restraints: 1267 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG D 300 " -0.127 9.50e-02 1.11e+02 5.70e-02 2.04e+00 pdb=" NE ARG D 300 " 0.006 2.00e-02 2.50e+03 pdb=" CZ ARG D 300 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 300 " 0.000 2.00e-02 2.50e+03 pdb=" NH2 ARG D 300 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP D 254 " -0.007 2.00e-02 2.50e+03 1.37e-02 1.89e+00 pdb=" C ASP D 254 " 0.024 2.00e-02 2.50e+03 pdb=" O ASP D 254 " -0.009 2.00e-02 2.50e+03 pdb=" N ARG D 255 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 46 " -0.013 2.00e-02 2.50e+03 9.55e-03 1.82e+00 pdb=" CG TYR B 46 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR B 46 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR B 46 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR B 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR B 46 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 46 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 46 " 0.000 2.00e-02 2.50e+03 ... (remaining 1264 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.64: 127 2.64 - 3.20: 7037 3.20 - 3.77: 12537 3.77 - 4.33: 17674 4.33 - 4.90: 28462 Nonbonded interactions: 65837 Sorted by model distance: nonbonded pdb=" OG1 THR X 83 " pdb=" O SER X 150 " model vdw 2.073 2.440 nonbonded pdb=" O1B ANP D 401 " pdb=" O2G ANP D 401 " model vdw 2.094 3.040 nonbonded pdb=" OG1 THR C 200 " pdb=" OD1 ASP C 202 " model vdw 2.156 2.440 nonbonded pdb=" O LEU D 58 " pdb=" OG SER D 62 " model vdw 2.179 2.440 nonbonded pdb=" OG SER B 45 " pdb=" O PRO C 18 " model vdw 2.192 2.440 ... (remaining 65832 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: 1.110 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: 4.070 Check model and map are aligned: 0.110 Set scattering table: 0.080 Process input model: 24.800 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 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 : 0.006 0.147 7591 Z= 0.416 Angle : 0.818 17.461 10277 Z= 0.372 Chirality : 0.045 0.283 1205 Planarity : 0.004 0.057 1267 Dihedral : 16.138 98.797 2899 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 0.37 % Allowed : 0.37 % Favored : 99.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.15 (0.28), residues: 908 helix: 0.91 (0.25), residues: 444 sheet: -0.48 (0.41), residues: 152 loop : -0.63 (0.36), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 317 HIS 0.006 0.001 HIS B 50 PHE 0.014 0.001 PHE X 80 TYR 0.023 0.002 TYR B 46 ARG 0.007 0.001 ARG X 224 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 115 time to evaluate : 0.853 Fit side-chains REVERT: B 28 GLN cc_start: 0.8375 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: B 29 ASP cc_start: 0.8695 (m-30) cc_final: 0.8413 (m-30) outliers start: 3 outliers final: 0 residues processed: 117 average time/residue: 0.2143 time to fit residues: 33.2532 Evaluate side-chains 105 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 104 time to evaluate : 0.815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 76 optimal weight: 0.7980 chunk 68 optimal weight: 4.9990 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 53 optimal weight: 3.9990 chunk 82 optimal weight: 2.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: X 252 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 7591 Z= 0.345 Angle : 0.611 9.316 10277 Z= 0.299 Chirality : 0.044 0.154 1205 Planarity : 0.004 0.047 1267 Dihedral : 11.927 71.968 1149 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.99 % Allowed : 7.69 % Favored : 91.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: -0.05 (0.28), residues: 908 helix: 0.77 (0.25), residues: 443 sheet: -0.72 (0.40), residues: 152 loop : -0.67 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 317 HIS 0.004 0.001 HIS D 250 PHE 0.012 0.002 PHE X 270 TYR 0.012 0.001 TYR B 46 ARG 0.005 0.001 ARG X 64 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 114 time to evaluate : 0.857 Fit side-chains revert: symmetry clash REVERT: B 29 ASP cc_start: 0.8738 (m-30) cc_final: 0.8440 (m-30) REVERT: D 16 MET cc_start: 0.4928 (mtp) cc_final: 0.4645 (mpp) outliers start: 8 outliers final: 5 residues processed: 118 average time/residue: 0.2090 time to fit residues: 32.7340 Evaluate side-chains 111 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 106 time to evaluate : 0.894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 45 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 68 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 89 optimal weight: 0.8980 chunk 73 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 81 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN C 181 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.1071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 7591 Z= 0.213 Angle : 0.504 7.645 10277 Z= 0.253 Chirality : 0.041 0.168 1205 Planarity : 0.004 0.034 1267 Dihedral : 11.133 75.013 1146 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.11 % Allowed : 9.93 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.16 (0.28), residues: 908 helix: 1.03 (0.25), residues: 442 sheet: -0.68 (0.41), residues: 151 loop : -0.67 (0.35), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 317 HIS 0.003 0.001 HIS D 250 PHE 0.009 0.001 PHE D 173 TYR 0.008 0.001 TYR B 46 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 115 time to evaluate : 0.897 Fit side-chains REVERT: B 29 ASP cc_start: 0.8714 (m-30) cc_final: 0.8427 (m-30) REVERT: X 64 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7350 (mmm160) outliers start: 17 outliers final: 9 residues processed: 123 average time/residue: 0.2025 time to fit residues: 33.5200 Evaluate side-chains 114 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 105 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 168 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.0870 chunk 39 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 83 optimal weight: 0.9990 chunk 87 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.7960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN C 276 HIS D 18 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7905 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7591 Z= 0.218 Angle : 0.503 8.232 10277 Z= 0.253 Chirality : 0.041 0.172 1205 Planarity : 0.003 0.035 1267 Dihedral : 10.515 76.159 1146 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 13.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 2.23 % Allowed : 11.41 % Favored : 86.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.28 (0.28), residues: 908 helix: 1.15 (0.25), residues: 440 sheet: -0.64 (0.41), residues: 152 loop : -0.64 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 317 HIS 0.003 0.001 HIS C 316 PHE 0.011 0.001 PHE X 80 TYR 0.007 0.001 TYR C 210 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 102 time to evaluate : 0.845 Fit side-chains REVERT: B 29 ASP cc_start: 0.8694 (m-30) cc_final: 0.8418 (m-30) REVERT: X 22 SER cc_start: 0.8681 (t) cc_final: 0.8433 (m) REVERT: X 64 ARG cc_start: 0.7893 (mtp85) cc_final: 0.7380 (mmm160) outliers start: 18 outliers final: 9 residues processed: 111 average time/residue: 0.1917 time to fit residues: 29.3055 Evaluate side-chains 106 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 97 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 49 optimal weight: 1.9990 chunk 1 optimal weight: 4.9990 chunk 65 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 75 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 44 optimal weight: 0.0570 chunk 78 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 29 optimal weight: 0.6980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN D 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 7591 Z= 0.157 Angle : 0.460 6.489 10277 Z= 0.236 Chirality : 0.039 0.177 1205 Planarity : 0.003 0.038 1267 Dihedral : 10.076 78.296 1146 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.86 % Allowed : 13.40 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.52 (0.29), residues: 908 helix: 1.37 (0.26), residues: 440 sheet: -0.45 (0.42), residues: 152 loop : -0.59 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 317 HIS 0.002 0.001 HIS X 86 PHE 0.013 0.001 PHE C 99 TYR 0.007 0.001 TYR B 46 ARG 0.003 0.000 ARG X 224 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 108 time to evaluate : 0.921 Fit side-chains REVERT: B 29 ASP cc_start: 0.8692 (m-30) cc_final: 0.8416 (m-30) REVERT: X 45 GLU cc_start: 0.8334 (tt0) cc_final: 0.8112 (tt0) REVERT: X 64 ARG cc_start: 0.7813 (mtp85) cc_final: 0.7337 (mmm160) outliers start: 15 outliers final: 9 residues processed: 117 average time/residue: 0.1845 time to fit residues: 29.7414 Evaluate side-chains 107 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.670 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 94 ASP Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 196 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 79 optimal weight: 3.9990 chunk 17 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 88 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 7.9990 chunk 7 optimal weight: 0.0970 chunk 29 optimal weight: 0.0570 chunk 46 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 overall best weight: 0.8310 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN D 131 ASN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 7591 Z= 0.220 Angle : 0.495 9.736 10277 Z= 0.249 Chirality : 0.040 0.144 1205 Planarity : 0.003 0.038 1267 Dihedral : 10.075 74.110 1146 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.74 % Allowed : 13.77 % Favored : 84.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.50 (0.29), residues: 908 helix: 1.29 (0.26), residues: 439 sheet: -0.53 (0.41), residues: 152 loop : -0.46 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 317 HIS 0.003 0.001 HIS X 98 PHE 0.014 0.001 PHE C 99 TYR 0.007 0.001 TYR B 46 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.934 Fit side-chains REVERT: B 29 ASP cc_start: 0.8720 (m-30) cc_final: 0.8435 (m-30) REVERT: X 22 SER cc_start: 0.8726 (t) cc_final: 0.8461 (m) REVERT: X 45 GLU cc_start: 0.8384 (tt0) cc_final: 0.8157 (tt0) REVERT: X 64 ARG cc_start: 0.7861 (mtp85) cc_final: 0.7372 (mmm160) outliers start: 14 outliers final: 12 residues processed: 108 average time/residue: 0.2094 time to fit residues: 30.7184 Evaluate side-chains 110 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 98 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 9 optimal weight: 4.9990 chunk 50 optimal weight: 0.1980 chunk 64 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 74 optimal weight: 0.8980 chunk 87 optimal weight: 0.9980 chunk 54 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN C 178 GLN D 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7591 Z= 0.198 Angle : 0.488 9.245 10277 Z= 0.245 Chirality : 0.040 0.191 1205 Planarity : 0.003 0.039 1267 Dihedral : 10.022 72.295 1146 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.74 % Allowed : 14.89 % Favored : 83.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.52 (0.29), residues: 908 helix: 1.31 (0.26), residues: 439 sheet: -0.52 (0.41), residues: 152 loop : -0.45 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 317 HIS 0.002 0.001 HIS X 98 PHE 0.013 0.001 PHE C 99 TYR 0.007 0.001 TYR B 46 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 101 time to evaluate : 0.886 Fit side-chains REVERT: B 28 GLN cc_start: 0.8274 (OUTLIER) cc_final: 0.8046 (tt0) REVERT: B 29 ASP cc_start: 0.8511 (m-30) cc_final: 0.8246 (m-30) REVERT: X 22 SER cc_start: 0.8725 (t) cc_final: 0.8448 (m) REVERT: X 45 GLU cc_start: 0.8373 (tt0) cc_final: 0.8148 (tt0) REVERT: X 64 ARG cc_start: 0.7825 (mtp85) cc_final: 0.7348 (mmm160) outliers start: 14 outliers final: 11 residues processed: 107 average time/residue: 0.2011 time to fit residues: 29.4322 Evaluate side-chains 111 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 99 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 196 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 79 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7930 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 7591 Z= 0.270 Angle : 0.528 8.811 10277 Z= 0.263 Chirality : 0.041 0.175 1205 Planarity : 0.004 0.038 1267 Dihedral : 10.084 70.095 1146 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.99 % Allowed : 14.89 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 908 helix: 1.12 (0.26), residues: 440 sheet: -0.66 (0.41), residues: 152 loop : -0.51 (0.35), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 317 HIS 0.003 0.001 HIS C 316 PHE 0.016 0.001 PHE C 99 TYR 0.007 0.001 TYR C 210 ARG 0.004 0.000 ARG D 300 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 96 time to evaluate : 0.864 Fit side-chains REVERT: X 22 SER cc_start: 0.8722 (t) cc_final: 0.8515 (m) REVERT: X 64 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7084 (mmm160) outliers start: 16 outliers final: 14 residues processed: 104 average time/residue: 0.1860 time to fit residues: 27.0599 Evaluate side-chains 108 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 94 time to evaluate : 0.884 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 81 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 25 optimal weight: 2.9990 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.7980 chunk 53 optimal weight: 0.0060 chunk 86 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 overall best weight: 0.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN ** D 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.1703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7591 Z= 0.208 Angle : 0.495 8.635 10277 Z= 0.249 Chirality : 0.040 0.198 1205 Planarity : 0.003 0.039 1267 Dihedral : 9.989 69.914 1146 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 2.11 % Allowed : 14.89 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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: 0.42 (0.28), residues: 908 helix: 1.21 (0.26), residues: 439 sheet: -0.59 (0.41), residues: 152 loop : -0.46 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 317 HIS 0.003 0.001 HIS X 98 PHE 0.015 0.001 PHE C 99 TYR 0.007 0.001 TYR B 46 ARG 0.004 0.000 ARG D 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.801 Fit side-chains REVERT: X 22 SER cc_start: 0.8770 (t) cc_final: 0.8524 (m) REVERT: X 45 GLU cc_start: 0.8377 (tt0) cc_final: 0.8160 (tt0) REVERT: X 64 ARG cc_start: 0.7792 (mtp85) cc_final: 0.7268 (mmm160) outliers start: 17 outliers final: 15 residues processed: 110 average time/residue: 0.1784 time to fit residues: 27.5844 Evaluate side-chains 114 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 99 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain B residue 55 MET Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 88 SER Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 41 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 83 optimal weight: 0.5980 chunk 72 optimal weight: 0.0870 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 57 optimal weight: 0.8980 chunk 76 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN D 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7591 Z= 0.186 Angle : 0.486 8.521 10277 Z= 0.246 Chirality : 0.040 0.206 1205 Planarity : 0.003 0.039 1267 Dihedral : 9.976 72.189 1146 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.99 % Allowed : 14.89 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 908 helix: 1.28 (0.26), residues: 439 sheet: -0.54 (0.41), residues: 152 loop : -0.46 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 317 HIS 0.002 0.001 HIS X 98 PHE 0.014 0.001 PHE C 99 TYR 0.007 0.001 TYR B 46 ARG 0.003 0.000 ARG D 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1816 Ramachandran restraints generated. 908 Oldfield, 0 Emsley, 908 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.839 Fit side-chains REVERT: D 26 LYS cc_start: 0.6084 (mtmt) cc_final: 0.5355 (mptt) REVERT: X 22 SER cc_start: 0.8784 (t) cc_final: 0.8529 (m) REVERT: X 45 GLU cc_start: 0.8345 (tt0) cc_final: 0.8129 (tt0) REVERT: X 64 ARG cc_start: 0.7797 (mtp85) cc_final: 0.7308 (mmm160) outliers start: 16 outliers final: 13 residues processed: 109 average time/residue: 0.1783 time to fit residues: 27.2364 Evaluate side-chains 111 residues out of total 806 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 98 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 GLN Chi-restraints excluded: chain C residue 10 MET Chi-restraints excluded: chain C residue 13 ASP Chi-restraints excluded: chain C residue 196 LEU Chi-restraints excluded: chain D residue 78 SER Chi-restraints excluded: chain D residue 279 ASP Chi-restraints excluded: chain X residue 55 THR Chi-restraints excluded: chain X residue 118 VAL Chi-restraints excluded: chain X residue 135 SER Chi-restraints excluded: chain X residue 144 CYS Chi-restraints excluded: chain X residue 173 LEU Chi-restraints excluded: chain X residue 196 GLN Chi-restraints excluded: chain X residue 254 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 91 random chunks: chunk 66 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 72 optimal weight: 0.0870 chunk 30 optimal weight: 0.9980 chunk 74 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 52 optimal weight: 0.0980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 28 GLN D 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.194607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.162790 restraints weight = 8038.902| |-----------------------------------------------------------------------------| r_work (start): 0.3812 rms_B_bonded: 2.28 r_work: 0.3636 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3636 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7886 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7591 Z= 0.189 Angle : 0.492 9.952 10277 Z= 0.247 Chirality : 0.040 0.195 1205 Planarity : 0.003 0.039 1267 Dihedral : 9.975 74.184 1146 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.86 % Allowed : 15.26 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.22 % 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 (0.28), residues: 908 helix: 1.28 (0.26), residues: 440 sheet: -0.52 (0.41), residues: 152 loop : -0.54 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 317 HIS 0.002 0.001 HIS X 98 PHE 0.016 0.001 PHE C 99 TYR 0.007 0.001 TYR B 46 ARG 0.003 0.000 ARG D 275 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1788.54 seconds wall clock time: 39 minutes 49.67 seconds (2389.67 seconds total)