Starting phenix.real_space_refine on Fri May 16 01:15:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u8f_42023/05_2025/8u8f_42023_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u8f_42023/05_2025/8u8f_42023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u8f_42023/05_2025/8u8f_42023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u8f_42023/05_2025/8u8f_42023.map" model { file = "/net/cci-nas-00/data/ceres_data/8u8f_42023/05_2025/8u8f_42023_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u8f_42023/05_2025/8u8f_42023_trim.cif" } resolution = 3.49 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= -0.003 sd= 0.065 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 S 49 5.16 5 C 4433 2.51 5 N 1209 2.21 5 O 1275 1.98 5 H 6925 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 13891 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 231, 3800 Classifications: {'peptide': 231} Link IDs: {'PTRANS': 6, 'TRANS': 224} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 5094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 337, 5094 Classifications: {'peptide': 337} Link IDs: {'PTRANS': 5, 'TRANS': 331} Chain: "G" Number of atoms: 871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 871 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 4, 'TRANS': 51} Chain: "R" Number of atoms: 4094 Number of conformers: 1 Conformer: "" Number of residues, atoms: 265, 4094 Classifications: {'peptide': 265} Link IDs: {'PTRANS': 10, 'TRANS': 254} Chain breaks: 1 Chain: "R" Number of atoms: 32 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1, 16 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 2 Conformer: "B" Number of residues, atoms: 1, 16 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 2 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" CA APLM R 401 " occ=0.68 ... (30 atoms not shown) pdb=" CF BPLM R 401 " occ=0.32 Time building chain proxies: 6.70, per 1000 atoms: 0.48 Number of scatterers: 13891 At special positions: 0 Unit cell: (78.26, 100.62, 126.42, 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 49 16.00 O 1275 8.00 N 1209 7.00 C 4433 6.00 H 6925 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 177 " - pdb=" SG CYS R 184 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 3.74 Conformation dependent library (CDL) restraints added in 1.1 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1670 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 8 sheets defined 46.1% alpha, 16.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 14 through 38 removed outlier: 3.552A pdb=" N LYS A 28 " --> pdb=" O LYS A 24 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN A 29 " --> pdb=" O LYS A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 52 through 61 Processing helix chain 'A' and resid 233 through 239 Processing helix chain 'A' and resid 264 through 279 removed outlier: 4.130A pdb=" N ALA A 268 " --> pdb=" O ASN A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.533A pdb=" N GLY A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 307 through 312 removed outlier: 4.093A pdb=" N TYR A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 316 Processing helix chain 'A' and resid 331 through 350 removed outlier: 3.799A pdb=" N THR A 335 " --> pdb=" O ASP A 331 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N ILE A 348 " --> pdb=" O GLU A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 370 through 391 Processing helix chain 'B' and resid 5 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'B' and resid 35 through 37 No H-bonds generated for 'chain 'B' and resid 35 through 37' Processing helix chain 'G' and resid 8 through 24 Processing helix chain 'G' and resid 29 through 44 removed outlier: 3.565A pdb=" N ALA G 33 " --> pdb=" O LYS G 29 " (cutoff:3.500A) Processing helix chain 'R' and resid 44 through 68 removed outlier: 3.691A pdb=" N CYS R 48 " --> pdb=" O ASP R 44 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU R 60 " --> pdb=" O CYS R 56 " (cutoff:3.500A) Processing helix chain 'R' and resid 73 through 101 removed outlier: 3.649A pdb=" N PHE R 101 " --> pdb=" O PHE R 97 " (cutoff:3.500A) Processing helix chain 'R' and resid 105 through 140 removed outlier: 3.610A pdb=" N SER R 109 " --> pdb=" O SER R 105 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N LEU R 110 " --> pdb=" O ALA R 106 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N VAL R 111 " --> pdb=" O GLU R 107 " (cutoff:3.500A) Processing helix chain 'R' and resid 142 through 146 removed outlier: 4.059A pdb=" N TYR R 145 " --> pdb=" O LEU R 142 " (cutoff:3.500A) Processing helix chain 'R' and resid 147 through 170 removed outlier: 4.035A pdb=" N LEU R 170 " --> pdb=" O GLY R 166 " (cutoff:3.500A) Processing helix chain 'R' and resid 191 through 230 removed outlier: 3.549A pdb=" N LEU R 229 " --> pdb=" O GLN R 225 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N GLN R 230 " --> pdb=" O GLN R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 244 through 253 removed outlier: 3.655A pdb=" N VAL R 251 " --> pdb=" O ALA R 247 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 270 Proline residue: R 262 - end of helix Processing helix chain 'R' and resid 275 through 282 removed outlier: 4.236A pdb=" N THR R 279 " --> pdb=" O PRO R 275 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR R 280 " --> pdb=" O PRO R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 282 through 298 removed outlier: 3.772A pdb=" N ALA R 286 " --> pdb=" O THR R 282 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ASN R 289 " --> pdb=" O PRO R 285 " (cutoff:3.500A) removed outlier: 4.101A pdb=" N SER R 290 " --> pdb=" O ALA R 286 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N MET R 291 " --> pdb=" O THR R 287 " (cutoff:3.500A) Proline residue: R 294 - end of helix Processing helix chain 'R' and resid 301 through 313 Processing sheet with id=AA1, first strand: chain 'A' and resid 208 through 214 removed outlier: 3.518A pdb=" N PHE A 208 " --> pdb=" O ASP A 223 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ASP A 223 " --> pdb=" O PHE A 208 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N LEU A 45 " --> pdb=" O PHE A 222 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ALA A 243 " --> pdb=" O ARG A 42 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 50 removed outlier: 3.790A pdb=" N LYS B 337 " --> pdb=" O THR B 329 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.901A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 5.273A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.442A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 102 through 105 removed outlier: 6.533A pdb=" N CYS B 121 " --> pdb=" O GLU B 138 " (cutoff:3.500A) removed outlier: 5.171A pdb=" N GLU B 138 " --> pdb=" O CYS B 121 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N ILE B 123 " --> pdb=" O SER B 136 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ARG B 134 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 146 through 153 removed outlier: 3.627A pdb=" N CYS B 148 " --> pdb=" O SER B 160 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLN B 156 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N THR B 165 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 6.857A pdb=" N GLY B 202 " --> pdb=" O MET B 188 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N LEU B 190 " --> pdb=" O VAL B 200 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N VAL B 200 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N LEU B 192 " --> pdb=" O LEU B 198 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU B 198 " --> pdb=" O LEU B 192 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU B 210 " --> pdb=" O GLN B 220 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.837A pdb=" N CYS B 233 " --> pdb=" O ALA B 242 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 273 through 278 removed outlier: 6.484A pdb=" N GLY B 288 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N VAL B 276 " --> pdb=" O LEU B 286 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU B 286 " --> pdb=" O VAL B 276 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N PHE B 278 " --> pdb=" O LEU B 284 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU B 284 " --> pdb=" O PHE B 278 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N CYS B 294 " --> pdb=" O LEU B 308 " (cutoff:3.500A) 363 hydrogen bonds defined for protein. 1053 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.93 Time building geometry restraints manager: 4.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 6897 1.04 - 1.23: 246 1.23 - 1.43: 2748 1.43 - 1.63: 4065 1.63 - 1.83: 68 Bond restraints: 14024 Sorted by residual: bond pdb=" N VAL R 132 " pdb=" CA VAL R 132 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.30e-02 5.92e+03 8.90e+00 bond pdb=" N LEU R 136 " pdb=" H LEU R 136 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.83e+00 bond pdb=" N ALA R 129 " pdb=" H ALA R 129 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.74e+00 bond pdb=" N VAL R 155 " pdb=" H VAL R 155 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.73e+00 bond pdb=" N LEU R 78 " pdb=" H LEU R 78 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.70e+00 ... (remaining 14019 not shown) Histogram of bond angle deviations from ideal: 0.00 - 7.09: 25239 7.09 - 14.18: 2 14.18 - 21.27: 0 21.27 - 28.36: 0 28.36 - 35.45: 3 Bond angle restraints: 25244 Sorted by residual: angle pdb=" C ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 109.00 73.55 35.45 3.00e+00 1.11e-01 1.40e+02 angle pdb=" N ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 110.00 74.70 35.30 3.00e+00 1.11e-01 1.38e+02 angle pdb=" CB ASN B 340 " pdb=" CA ASN B 340 " pdb=" HA ASN B 340 " ideal model delta sigma weight residual 109.00 79.73 29.27 3.00e+00 1.11e-01 9.52e+01 angle pdb=" CA PRO G 49 " pdb=" N PRO G 49 " pdb=" CD PRO G 49 " ideal model delta sigma weight residual 112.00 104.99 7.01 1.40e+00 5.10e-01 2.51e+01 angle pdb=" N ASN B 313 " pdb=" CA ASN B 313 " pdb=" CB ASN B 313 " ideal model delta sigma weight residual 114.17 109.59 4.58 1.14e+00 7.69e-01 1.62e+01 ... (remaining 25239 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 5908 17.91 - 35.83: 502 35.83 - 53.74: 143 53.74 - 71.66: 36 71.66 - 89.57: 14 Dihedral angle restraints: 6603 sinusoidal: 3564 harmonic: 3039 Sorted by residual: dihedral pdb=" CB CYS R 177 " pdb=" SG CYS R 177 " pdb=" SG CYS R 184 " pdb=" CB CYS R 184 " ideal model delta sinusoidal sigma weight residual -86.00 -26.65 -59.35 1 1.00e+01 1.00e-02 4.71e+01 dihedral pdb=" CA ASN R 176 " pdb=" C ASN R 176 " pdb=" N CYS R 177 " pdb=" CA CYS R 177 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA VAL R 187 " pdb=" C VAL R 187 " pdb=" N TYR R 188 " pdb=" CA TYR R 188 " ideal model delta harmonic sigma weight residual -180.00 -161.61 -18.39 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 6600 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.091: 1050 0.091 - 0.182: 53 0.182 - 0.273: 0 0.273 - 0.364: 0 0.364 - 0.455: 1 Chirality restraints: 1104 Sorted by residual: chirality pdb=" CA ASN B 340 " pdb=" N ASN B 340 " pdb=" C ASN B 340 " pdb=" CB ASN B 340 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 5.17e+00 chirality pdb=" CA VAL R 155 " pdb=" N VAL R 155 " pdb=" C VAL R 155 " pdb=" CB VAL R 155 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA LEU R 159 " pdb=" N LEU R 159 " pdb=" C LEU R 159 " pdb=" CB LEU R 159 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.83e-01 ... (remaining 1101 not shown) Planarity restraints: 2076 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG R 152 " 0.447 9.50e-02 1.11e+02 1.51e-01 3.60e+01 pdb=" NE ARG R 152 " -0.006 2.00e-02 2.50e+03 pdb=" CZ ARG R 152 " -0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG R 152 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG R 152 " -0.005 2.00e-02 2.50e+03 pdb="HH11 ARG R 152 " -0.048 2.00e-02 2.50e+03 pdb="HH12 ARG R 152 " 0.051 2.00e-02 2.50e+03 pdb="HH21 ARG R 152 " 0.011 2.00e-02 2.50e+03 pdb="HH22 ARG R 152 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP G 48 " 0.085 5.00e-02 4.00e+02 1.25e-01 2.51e+01 pdb=" N PRO G 49 " -0.217 5.00e-02 4.00e+02 pdb=" CA PRO G 49 " 0.065 5.00e-02 4.00e+02 pdb=" CD PRO G 49 " 0.066 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 136 " 0.013 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" N SER R 137 " -0.042 2.00e-02 2.50e+03 pdb=" CA SER R 137 " 0.011 2.00e-02 2.50e+03 pdb=" H SER R 137 " 0.018 2.00e-02 2.50e+03 ... (remaining 2073 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 912 2.20 - 2.80: 28548 2.80 - 3.40: 38690 3.40 - 4.00: 49337 4.00 - 4.60: 76825 Nonbonded interactions: 194312 Sorted by model distance: nonbonded pdb=" OD1 ASN R 176 " pdb=" H SER R 191 " model vdw 1.600 2.450 nonbonded pdb=" O ASN R 140 " pdb=" H TYR R 144 " model vdw 1.634 2.450 nonbonded pdb=" OD1 ASP R 179 " pdb=" H LEU R 181 " model vdw 1.662 2.450 nonbonded pdb="HH21 ARG A 38 " pdb=" OE2 GLU R 147 " model vdw 1.666 2.450 nonbonded pdb=" H PHE B 235 " pdb=" O ALA B 240 " model vdw 1.666 2.450 ... (remaining 194307 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 0.950 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: 0.210 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 31.890 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6712 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 0.109 7100 Z= 0.172 Angle : 0.545 10.634 9618 Z= 0.326 Chirality : 0.042 0.455 1104 Planarity : 0.007 0.182 1219 Dihedral : 15.464 89.571 2563 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 2.51 % Favored : 97.37 % Rotamer: Outliers : 0.13 % Allowed : 19.46 % Favored : 80.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.30), residues: 875 helix: 2.63 (0.28), residues: 358 sheet: 0.14 (0.42), residues: 156 loop : -0.42 (0.35), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 63 HIS 0.002 0.000 HIS R 223 PHE 0.013 0.001 PHE R 299 TYR 0.024 0.001 TYR R 139 ARG 0.004 0.000 ARG B 42 Details of bonding type rmsd hydrogen bonds : bond 0.17459 ( 363) hydrogen bonds : angle 7.02043 ( 1053) SS BOND : bond 0.01154 ( 1) SS BOND : angle 1.38070 ( 2) covalent geometry : bond 0.00323 ( 7099) covalent geometry : angle 0.54445 ( 9616) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 139 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 138 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 139 average time/residue: 0.4581 time to fit residues: 82.6386 Evaluate side-chains 132 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 131 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 234 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 73 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 50 optimal weight: 3.9990 chunk 79 optimal weight: 0.9980 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 371 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 = 0.4252 r_free = 0.4252 target = 0.188514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.152702 restraints weight = 24491.294| |-----------------------------------------------------------------------------| r_work (start): 0.3892 rms_B_bonded: 3.04 r_work: 0.3758 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.3758 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3760 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3760 r_free = 0.3760 target_work(ls_wunit_k1) = 0.140 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3760 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.1317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7100 Z= 0.170 Angle : 0.553 10.195 9618 Z= 0.299 Chirality : 0.042 0.444 1104 Planarity : 0.005 0.078 1219 Dihedral : 4.844 51.376 992 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.34 % Favored : 95.54 % Rotamer: Outliers : 2.42 % Allowed : 17.58 % Favored : 80.00 % 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: 0.91 (0.30), residues: 875 helix: 2.47 (0.27), residues: 368 sheet: -0.82 (0.42), residues: 167 loop : -0.73 (0.34), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 63 HIS 0.004 0.001 HIS B 54 PHE 0.021 0.002 PHE B 241 TYR 0.015 0.002 TYR B 124 ARG 0.008 0.001 ARG G 27 Details of bonding type rmsd hydrogen bonds : bond 0.04706 ( 363) hydrogen bonds : angle 4.87899 ( 1053) SS BOND : bond 0.01186 ( 1) SS BOND : angle 2.33893 ( 2) covalent geometry : bond 0.00369 ( 7099) covalent geometry : angle 0.55243 ( 9616) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 157 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 139 time to evaluate : 1.038 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7439 (m-10) cc_final: 0.7130 (m-10) REVERT: G 17 GLU cc_start: 0.8366 (mm-30) cc_final: 0.8153 (mm-30) REVERT: R 56 CYS cc_start: 0.7743 (OUTLIER) cc_final: 0.6995 (m) REVERT: R 145 TYR cc_start: 0.7456 (m-80) cc_final: 0.7052 (m-80) REVERT: R 179 ASP cc_start: 0.6881 (p0) cc_final: 0.6491 (t0) outliers start: 18 outliers final: 13 residues processed: 150 average time/residue: 0.4515 time to fit residues: 87.7169 Evaluate side-chains 145 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain B residue 55 LEU Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 228 ASP Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 45 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 58 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 64 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.186288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.150616 restraints weight = 24500.349| |-----------------------------------------------------------------------------| r_work (start): 0.3876 rms_B_bonded: 3.01 r_work: 0.3739 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3737 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3737 r_free = 0.3737 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3737 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.1735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 7100 Z= 0.150 Angle : 0.520 10.193 9618 Z= 0.280 Chirality : 0.041 0.440 1104 Planarity : 0.004 0.068 1219 Dihedral : 4.810 49.845 992 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.11 % Allowed : 3.89 % Favored : 96.00 % Rotamer: Outliers : 2.68 % Allowed : 18.66 % Favored : 78.66 % 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 (0.30), residues: 875 helix: 2.48 (0.27), residues: 366 sheet: -1.14 (0.42), residues: 165 loop : -0.77 (0.34), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 63 HIS 0.003 0.001 HIS R 223 PHE 0.016 0.002 PHE B 241 TYR 0.013 0.001 TYR A 311 ARG 0.010 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04434 ( 363) hydrogen bonds : angle 4.64780 ( 1053) SS BOND : bond 0.01146 ( 1) SS BOND : angle 2.13699 ( 2) covalent geometry : bond 0.00322 ( 7099) covalent geometry : angle 0.51964 ( 9616) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 154 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 134 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 TRP cc_start: 0.7441 (m-10) cc_final: 0.7047 (m-10) REVERT: B 258 ASP cc_start: 0.7165 (t70) cc_final: 0.6682 (t70) REVERT: G 13 ARG cc_start: 0.8398 (ttm110) cc_final: 0.8161 (ttm110) REVERT: G 17 GLU cc_start: 0.8444 (mm-30) cc_final: 0.8216 (mm-30) REVERT: R 56 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7026 (m) REVERT: R 179 ASP cc_start: 0.6865 (p0) cc_final: 0.6400 (t70) outliers start: 20 outliers final: 12 residues processed: 147 average time/residue: 0.4735 time to fit residues: 89.6784 Evaluate side-chains 143 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 130 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 24 optimal weight: 8.9990 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 74 optimal weight: 0.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.183489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.148421 restraints weight = 24255.832| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 2.94 r_work: 0.3712 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3712 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3710 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3710 r_free = 0.3710 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3710 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7189 moved from start: 0.2140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 7100 Z= 0.170 Angle : 0.542 10.097 9618 Z= 0.292 Chirality : 0.042 0.437 1104 Planarity : 0.004 0.064 1219 Dihedral : 5.084 48.246 992 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 6.81 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.91 % Favored : 94.97 % Rotamer: Outliers : 3.49 % Allowed : 18.93 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.29), residues: 875 helix: 2.33 (0.27), residues: 366 sheet: -1.50 (0.41), residues: 165 loop : -0.90 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 63 HIS 0.004 0.001 HIS R 223 PHE 0.020 0.002 PHE B 241 TYR 0.009 0.001 TYR A 311 ARG 0.008 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04320 ( 363) hydrogen bonds : angle 4.58204 ( 1053) SS BOND : bond 0.01077 ( 1) SS BOND : angle 2.29597 ( 2) covalent geometry : bond 0.00371 ( 7099) covalent geometry : angle 0.54112 ( 9616) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 1.004 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7614 (tpp80) cc_final: 0.7349 (tpp80) REVERT: A 358 TYR cc_start: 0.8071 (m-80) cc_final: 0.7748 (m-80) REVERT: B 63 TRP cc_start: 0.7445 (m-10) cc_final: 0.6873 (m-10) REVERT: B 262 MET cc_start: 0.7618 (tpp) cc_final: 0.7302 (tpp) REVERT: G 17 GLU cc_start: 0.8499 (mm-30) cc_final: 0.8289 (mm-30) REVERT: R 56 CYS cc_start: 0.7783 (OUTLIER) cc_final: 0.7022 (m) REVERT: R 179 ASP cc_start: 0.6958 (p0) cc_final: 0.6431 (t70) REVERT: R 204 MET cc_start: 0.7394 (ttm) cc_final: 0.7175 (mtp) outliers start: 26 outliers final: 19 residues processed: 150 average time/residue: 0.4812 time to fit residues: 93.6234 Evaluate side-chains 151 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 SER Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 68 THR Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 63 optimal weight: 4.9990 chunk 23 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 71 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 27 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.178713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.142877 restraints weight = 24885.268| |-----------------------------------------------------------------------------| r_work (start): 0.3799 rms_B_bonded: 3.00 r_work: 0.3656 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.3656 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3660 r_free = 0.3660 target_work(ls_wunit_k1) = 0.131 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.2653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 7100 Z= 0.251 Angle : 0.624 10.056 9618 Z= 0.341 Chirality : 0.044 0.432 1104 Planarity : 0.005 0.064 1219 Dihedral : 5.711 47.045 992 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.94 % Favored : 93.94 % Rotamer: Outliers : 3.89 % Allowed : 19.73 % Favored : 76.38 % 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: -0.15 (0.29), residues: 875 helix: 1.82 (0.27), residues: 369 sheet: -1.95 (0.40), residues: 161 loop : -1.27 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 63 HIS 0.006 0.002 HIS R 223 PHE 0.029 0.002 PHE B 241 TYR 0.015 0.002 TYR A 311 ARG 0.012 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04856 ( 363) hydrogen bonds : angle 4.90907 ( 1053) SS BOND : bond 0.00981 ( 1) SS BOND : angle 2.80845 ( 2) covalent geometry : bond 0.00557 ( 7099) covalent geometry : angle 0.62250 ( 9616) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 161 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 132 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7642 (tpp80) cc_final: 0.7344 (tpp80) REVERT: A 358 TYR cc_start: 0.8100 (m-80) cc_final: 0.7818 (m-80) REVERT: G 13 ARG cc_start: 0.8401 (ttm110) cc_final: 0.8182 (ttm110) REVERT: R 56 CYS cc_start: 0.7802 (OUTLIER) cc_final: 0.7096 (m) outliers start: 29 outliers final: 24 residues processed: 149 average time/residue: 0.4772 time to fit residues: 91.0095 Evaluate side-chains 152 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 127 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 23 ASN Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 248 VAL Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 254 ASP Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 115 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 226 GLN Chi-restraints excluded: chain R residue 261 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 41 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 82 optimal weight: 0.6980 chunk 4 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 6 optimal weight: 0.0570 chunk 81 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 18 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 overall best weight: 0.9502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 371 ASN B 155 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.183655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.147854 restraints weight = 24530.440| |-----------------------------------------------------------------------------| r_work (start): 0.3852 rms_B_bonded: 2.98 r_work: 0.3713 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.3713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3713 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3713 r_free = 0.3713 target_work(ls_wunit_k1) = 0.135 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3713 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7100 Z= 0.128 Angle : 0.521 9.944 9618 Z= 0.280 Chirality : 0.041 0.439 1104 Planarity : 0.004 0.059 1219 Dihedral : 5.131 46.501 992 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 3.09 % Allowed : 21.48 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.29), residues: 875 helix: 2.17 (0.27), residues: 367 sheet: -1.90 (0.40), residues: 165 loop : -1.18 (0.33), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 169 HIS 0.003 0.001 HIS R 223 PHE 0.013 0.001 PHE B 241 TYR 0.010 0.001 TYR A 311 ARG 0.008 0.000 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04100 ( 363) hydrogen bonds : angle 4.54807 ( 1053) SS BOND : bond 0.00925 ( 1) SS BOND : angle 1.79503 ( 2) covalent geometry : bond 0.00276 ( 7099) covalent geometry : angle 0.52091 ( 9616) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 155 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 132 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7574 (tpp80) cc_final: 0.7281 (tpp80) REVERT: A 358 TYR cc_start: 0.8064 (m-80) cc_final: 0.7789 (m-80) REVERT: B 63 TRP cc_start: 0.7520 (m-10) cc_final: 0.6801 (m-10) REVERT: R 56 CYS cc_start: 0.7778 (OUTLIER) cc_final: 0.7038 (m) REVERT: R 179 ASP cc_start: 0.7006 (p0) cc_final: 0.6418 (t70) REVERT: R 204 MET cc_start: 0.7374 (ttm) cc_final: 0.7149 (mtp) outliers start: 23 outliers final: 19 residues processed: 146 average time/residue: 0.4899 time to fit residues: 92.3742 Evaluate side-chains 147 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 127 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 100 VAL Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 60 optimal weight: 0.6980 chunk 16 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 86 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.181534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.145728 restraints weight = 24721.669| |-----------------------------------------------------------------------------| r_work (start): 0.3828 rms_B_bonded: 3.00 r_work: 0.3689 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.3689 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3688 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3688 r_free = 0.3688 target_work(ls_wunit_k1) = 0.133 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3688 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.2749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 7100 Z= 0.172 Angle : 0.550 9.963 9618 Z= 0.297 Chirality : 0.042 0.435 1104 Planarity : 0.005 0.066 1219 Dihedral : 5.227 46.223 992 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 8.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.37 % Favored : 94.51 % Rotamer: Outliers : 2.68 % Allowed : 22.42 % Favored : 74.90 % 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: 0.09 (0.29), residues: 875 helix: 2.14 (0.27), residues: 367 sheet: -1.86 (0.41), residues: 161 loop : -1.25 (0.32), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 281 HIS 0.004 0.001 HIS R 223 PHE 0.021 0.002 PHE B 241 TYR 0.013 0.001 TYR A 311 ARG 0.009 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.04255 ( 363) hydrogen bonds : angle 4.59550 ( 1053) SS BOND : bond 0.00956 ( 1) SS BOND : angle 2.12413 ( 2) covalent geometry : bond 0.00379 ( 7099) covalent geometry : angle 0.54928 ( 9616) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 145 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.965 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7624 (tpp80) cc_final: 0.7325 (tpp80) REVERT: A 358 TYR cc_start: 0.8097 (m-80) cc_final: 0.7833 (m-80) REVERT: B 63 TRP cc_start: 0.7496 (m-10) cc_final: 0.6711 (m-10) REVERT: R 56 CYS cc_start: 0.7810 (OUTLIER) cc_final: 0.7095 (m) REVERT: R 139 TYR cc_start: 0.8216 (t80) cc_final: 0.7846 (t80) REVERT: R 179 ASP cc_start: 0.6952 (p0) cc_final: 0.6268 (t70) REVERT: R 204 MET cc_start: 0.7418 (ttm) cc_final: 0.7196 (mtp) outliers start: 20 outliers final: 18 residues processed: 137 average time/residue: 0.5146 time to fit residues: 90.3239 Evaluate side-chains 142 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain A residue 357 HIS Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 90 VAL Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 191 SER Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 71 optimal weight: 0.1980 chunk 69 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 72 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 35 optimal weight: 0.4980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.186111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.150456 restraints weight = 24174.964| |-----------------------------------------------------------------------------| r_work (start): 0.3881 rms_B_bonded: 2.98 r_work: 0.3742 rms_B_bonded: 3.33 restraints_weight: 0.5000 r_work (final): 0.3742 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3738 r_free = 0.3738 target_work(ls_wunit_k1) = 0.137 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 7100 Z= 0.107 Angle : 0.498 9.980 9618 Z= 0.266 Chirality : 0.041 0.443 1104 Planarity : 0.004 0.069 1219 Dihedral : 4.769 48.013 992 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 2.55 % Allowed : 22.15 % Favored : 75.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.30), residues: 875 helix: 2.48 (0.27), residues: 367 sheet: -1.65 (0.42), residues: 161 loop : -1.10 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 281 HIS 0.002 0.001 HIS B 311 PHE 0.012 0.001 PHE A 290 TYR 0.012 0.001 TYR A 311 ARG 0.009 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.03747 ( 363) hydrogen bonds : angle 4.33788 ( 1053) SS BOND : bond 0.00915 ( 1) SS BOND : angle 1.43657 ( 2) covalent geometry : bond 0.00231 ( 7099) covalent geometry : angle 0.49750 ( 9616) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 153 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 134 time to evaluate : 1.031 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 35 GLN cc_start: 0.7925 (mt0) cc_final: 0.7676 (mt0) REVERT: A 38 ARG cc_start: 0.7532 (tpp80) cc_final: 0.7225 (tpp80) REVERT: A 358 TYR cc_start: 0.8021 (m-80) cc_final: 0.7752 (m-80) REVERT: B 63 TRP cc_start: 0.7503 (m-10) cc_final: 0.6742 (m-10) REVERT: B 258 ASP cc_start: 0.7169 (t70) cc_final: 0.6642 (t0) REVERT: R 56 CYS cc_start: 0.7790 (OUTLIER) cc_final: 0.7105 (m) REVERT: R 147 GLU cc_start: 0.7566 (mm-30) cc_final: 0.7301 (tp30) REVERT: R 179 ASP cc_start: 0.7039 (p0) cc_final: 0.6460 (t70) REVERT: R 204 MET cc_start: 0.7346 (ttm) cc_final: 0.7140 (mtp) outliers start: 19 outliers final: 17 residues processed: 144 average time/residue: 0.4890 time to fit residues: 92.2059 Evaluate side-chains 147 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 129 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain A residue 325 THR Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Chi-restraints excluded: chain R residue 309 TRP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 0.9980 chunk 85 optimal weight: 0.9990 chunk 83 optimal weight: 0.3980 chunk 1 optimal weight: 0.7980 chunk 38 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 54 optimal weight: 0.2980 chunk 45 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.185203 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150784 restraints weight = 24011.586| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.91 r_work: 0.3746 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.3746 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3743 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3743 r_free = 0.3743 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3743 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.2672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 7100 Z= 0.109 Angle : 0.504 10.008 9618 Z= 0.269 Chirality : 0.041 0.441 1104 Planarity : 0.004 0.062 1219 Dihedral : 4.725 50.189 992 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.15 % Allowed : 22.82 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.30), residues: 875 helix: 2.60 (0.27), residues: 367 sheet: -1.60 (0.42), residues: 161 loop : -1.03 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 281 HIS 0.002 0.001 HIS B 311 PHE 0.014 0.001 PHE A 212 TYR 0.011 0.001 TYR A 311 ARG 0.009 0.000 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.03667 ( 363) hydrogen bonds : angle 4.28268 ( 1053) SS BOND : bond 0.01674 ( 1) SS BOND : angle 1.60723 ( 2) covalent geometry : bond 0.00237 ( 7099) covalent geometry : angle 0.50349 ( 9616) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 140 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 ARG cc_start: 0.7492 (tpp80) cc_final: 0.7255 (tpp80) REVERT: A 358 TYR cc_start: 0.8024 (m-80) cc_final: 0.7735 (m-80) REVERT: B 63 TRP cc_start: 0.7453 (m-10) cc_final: 0.6701 (m-10) REVERT: B 258 ASP cc_start: 0.7147 (t70) cc_final: 0.6597 (t0) REVERT: R 56 CYS cc_start: 0.7735 (OUTLIER) cc_final: 0.7069 (m) REVERT: R 139 TYR cc_start: 0.8212 (t80) cc_final: 0.7839 (t80) REVERT: R 147 GLU cc_start: 0.7575 (mm-30) cc_final: 0.7364 (tp30) REVERT: R 179 ASP cc_start: 0.7046 (p0) cc_final: 0.6406 (t70) outliers start: 16 outliers final: 15 residues processed: 133 average time/residue: 0.4591 time to fit residues: 79.0561 Evaluate side-chains 138 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 27 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 8 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.185384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3881 r_free = 0.3881 target = 0.150836 restraints weight = 24116.059| |-----------------------------------------------------------------------------| r_work (start): 0.3888 rms_B_bonded: 2.92 r_work: 0.3747 rms_B_bonded: 3.29 restraints_weight: 0.5000 r_work (final): 0.3747 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3744 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3744 r_free = 0.3744 target_work(ls_wunit_k1) = 0.138 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3744 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.2731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 7100 Z= 0.112 Angle : 0.502 10.040 9618 Z= 0.267 Chirality : 0.041 0.441 1104 Planarity : 0.004 0.079 1219 Dihedral : 4.729 52.552 992 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 2.15 % Allowed : 22.95 % Favored : 74.90 % 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 (0.30), residues: 875 helix: 2.64 (0.27), residues: 368 sheet: -1.56 (0.42), residues: 161 loop : -1.07 (0.33), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 281 HIS 0.002 0.001 HIS R 223 PHE 0.015 0.001 PHE A 212 TYR 0.011 0.001 TYR A 311 ARG 0.011 0.000 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.03626 ( 363) hydrogen bonds : angle 4.24550 ( 1053) SS BOND : bond 0.01614 ( 1) SS BOND : angle 1.53304 ( 2) covalent geometry : bond 0.00242 ( 7099) covalent geometry : angle 0.50120 ( 9616) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 58 is missing expected H atoms. Skipping. Residue SER 366 is missing expected H atoms. Skipping. Evaluate side-chains 142 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 358 TYR cc_start: 0.8046 (m-80) cc_final: 0.7755 (m-80) REVERT: B 63 TRP cc_start: 0.7442 (m-10) cc_final: 0.6647 (m-10) REVERT: B 258 ASP cc_start: 0.7167 (t70) cc_final: 0.6589 (t0) REVERT: R 56 CYS cc_start: 0.7697 (OUTLIER) cc_final: 0.7028 (m) REVERT: R 139 TYR cc_start: 0.8202 (t80) cc_final: 0.7838 (t80) REVERT: R 179 ASP cc_start: 0.7027 (p0) cc_final: 0.6338 (t70) outliers start: 16 outliers final: 15 residues processed: 135 average time/residue: 0.4894 time to fit residues: 84.3783 Evaluate side-chains 142 residues out of total 746 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 237 CYS Chi-restraints excluded: chain A residue 299 GLU Chi-restraints excluded: chain B residue 69 LEU Chi-restraints excluded: chain B residue 114 CYS Chi-restraints excluded: chain B residue 142 HIS Chi-restraints excluded: chain B residue 232 ILE Chi-restraints excluded: chain B residue 234 PHE Chi-restraints excluded: chain B residue 292 PHE Chi-restraints excluded: chain B residue 321 THR Chi-restraints excluded: chain G residue 51 LEU Chi-restraints excluded: chain R residue 56 CYS Chi-restraints excluded: chain R residue 150 VAL Chi-restraints excluded: chain R residue 170 LEU Chi-restraints excluded: chain R residue 281 LEU Chi-restraints excluded: chain R residue 284 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 15 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 54 optimal weight: 0.5980 chunk 72 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 74 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 43 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 overall best weight: 1.1242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.184348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.148617 restraints weight = 24461.274| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 3.00 r_work: 0.3723 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3714 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3714 r_free = 0.3714 target_work(ls_wunit_k1) = 0.136 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 5 | |-----------------------------------------------------------------------------| r_final: 0.3714 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 moved from start: 0.2776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7100 Z= 0.133 Angle : 0.518 10.053 9618 Z= 0.277 Chirality : 0.041 0.438 1104 Planarity : 0.004 0.077 1219 Dihedral : 4.893 54.486 992 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 2.28 % Allowed : 23.09 % Favored : 74.63 % 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: 0.55 (0.30), residues: 875 helix: 2.58 (0.27), residues: 368 sheet: -1.57 (0.43), residues: 159 loop : -1.13 (0.33), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 281 HIS 0.003 0.001 HIS R 223 PHE 0.017 0.002 PHE B 241 TYR 0.011 0.001 TYR A 311 ARG 0.011 0.001 ARG R 218 Details of bonding type rmsd hydrogen bonds : bond 0.03807 ( 363) hydrogen bonds : angle 4.32623 ( 1053) SS BOND : bond 0.01398 ( 1) SS BOND : angle 1.76673 ( 2) covalent geometry : bond 0.00292 ( 7099) covalent geometry : angle 0.51707 ( 9616) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6952.63 seconds wall clock time: 120 minutes 3.35 seconds (7203.35 seconds total)