Starting phenix.real_space_refine on Wed Feb 4 05:35:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ydu_72835/02_2026/9ydu_72835.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ydu_72835/02_2026/9ydu_72835.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9ydu_72835/02_2026/9ydu_72835.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ydu_72835/02_2026/9ydu_72835.map" model { file = "/net/cci-nas-00/data/ceres_data/9ydu_72835/02_2026/9ydu_72835.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ydu_72835/02_2026/9ydu_72835.cif" } resolution = 3.19 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.011 sd= 1.254 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 2 5.49 5 S 58 5.16 5 C 5673 2.51 5 N 1476 2.21 5 O 1650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 1 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8859 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 214, 1691 Classifications: {'peptide': 214} Incomplete info: {'truncation_to_alanine': 9} Link IDs: {'PTRANS': 2, 'TRANS': 211} Chain breaks: 3 Unresolved non-hydrogen bonds: 37 Unresolved non-hydrogen angles: 42 Unresolved non-hydrogen dihedrals: 32 Planarities with less than four sites: {'ASN:plan1': 1, 'ARG:plan': 2, 'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 20 Chain: "C" Number of atoms: 2593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2593 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 333} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'ASP:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 55, 399 Classifications: {'peptide': 55} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 50} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 29 Unresolved non-hydrogen dihedrals: 21 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 13 Chain: "E" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "A" Number of atoms: 2357 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2357 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 10, 'TRANS': 276} Chain: "A" Number of atoms: 36 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 36 Unusual residues: {'UPG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.17, per 1000 atoms: 0.24 Number of scatterers: 8859 At special positions: 0 Unit cell: (99.636, 117.116, 126.73, 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 58 16.00 P 2 15.00 O 1650 8.00 N 1476 7.00 C 5673 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 217 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 172 " distance=2.03 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: 0.45 Conformation dependent library (CDL) restraints added in 254.2 milliseconds 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2120 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 37.2% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'B' and resid 6 through 32 removed outlier: 3.959A pdb=" N ARG B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) Processing helix chain 'B' and resid 207 through 216 removed outlier: 3.558A pdb=" N LYS B 210 " --> pdb=" O GLU B 207 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE B 212 " --> pdb=" O LYS B 209 " (cutoff:3.500A) removed outlier: 5.756A pdb=" N HIS B 213 " --> pdb=" O LYS B 210 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N CYS B 214 " --> pdb=" O TRP B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 255 Processing helix chain 'B' and resid 270 through 279 removed outlier: 4.237A pdb=" N LYS B 279 " --> pdb=" O GLU B 275 " (cutoff:3.500A) Processing helix chain 'B' and resid 282 through 286 removed outlier: 3.690A pdb=" N ILE B 285 " --> pdb=" O PRO B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 309 Processing helix chain 'B' and resid 329 through 351 Processing helix chain 'C' and resid 3 through 26 Processing helix chain 'C' and resid 29 through 35 Processing helix chain 'D' and resid 9 through 24 Processing helix chain 'D' and resid 29 through 44 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.585A pdb=" N PHE E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) Processing helix chain 'E' and resid 53 through 56 removed outlier: 4.057A pdb=" N GLY E 56 " --> pdb=" O SER E 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 53 through 56' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.817A pdb=" N THR E 91 " --> pdb=" O SER E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 208 through 212 removed outlier: 3.587A pdb=" N VAL E 212 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 23 Processing helix chain 'A' and resid 23 through 44 Processing helix chain 'A' and resid 45 through 47 No H-bonds generated for 'chain 'A' and resid 45 through 47' Processing helix chain 'A' and resid 56 through 82 Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 86 through 96 removed outlier: 3.710A pdb=" N ASN A 90 " --> pdb=" O PRO A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 Processing helix chain 'A' and resid 137 through 160 Proline residue: A 155 - end of helix Processing helix chain 'A' and resid 180 through 216 removed outlier: 3.565A pdb=" N SER A 216 " --> pdb=" O LYS A 212 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 262 Proline residue: A 248 - end of helix removed outlier: 5.291A pdb=" N ILE A 254 " --> pdb=" O HIS A 250 " (cutoff:3.500A) Proline residue: A 255 - end of helix Processing helix chain 'A' and resid 266 through 296 removed outlier: 4.706A pdb=" N VAL A 288 " --> pdb=" O SER A 284 " (cutoff:3.500A) removed outlier: 4.667A pdb=" N CYS A 289 " --> pdb=" O ALA A 285 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Proline residue: A 292 - end of helix Processing sheet with id=AA1, first strand: chain 'B' and resid 185 through 190 removed outlier: 3.556A pdb=" N ALA B 220 " --> pdb=" O LYS B 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.597A pdb=" N CYS C 317 " --> pdb=" O GLY C 330 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 58 through 63 removed outlier: 3.786A pdb=" N ALA C 60 " --> pdb=" O ALA C 73 " (cutoff:3.500A) removed outlier: 3.973A pdb=" N LYS C 78 " --> pdb=" O SER C 74 " (cutoff:3.500A) removed outlier: 6.025A pdb=" N LEU C 79 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.394A pdb=" N ALA C 92 " --> pdb=" O LEU C 79 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ILE C 81 " --> pdb=" O VAL C 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 100 through 105 removed outlier: 6.717A pdb=" N GLY C 115 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N CYS C 103 " --> pdb=" O ALA C 113 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ALA C 113 " --> pdb=" O CYS C 103 " (cutoff:3.500A) removed outlier: 5.003A pdb=" N TYR C 105 " --> pdb=" O TYR C 111 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N TYR C 111 " --> pdb=" O TYR C 105 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLY C 116 " --> pdb=" O ILE C 120 " (cutoff:3.500A) removed outlier: 5.040A pdb=" N ILE C 120 " --> pdb=" O GLY C 116 " (cutoff:3.500A) removed outlier: 6.164A pdb=" N CYS C 121 " --> pdb=" O GLU C 138 " (cutoff:3.500A) removed outlier: 4.957A pdb=" N GLU C 138 " --> pdb=" O CYS C 121 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE C 123 " --> pdb=" O SER C 136 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG C 134 " --> pdb=" O ASN C 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 146 through 151 removed outlier: 3.526A pdb=" N CYS C 148 " --> pdb=" O SER C 160 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ASP C 170 " --> pdb=" O GLN C 176 " (cutoff:3.500A) removed outlier: 6.127A pdb=" N GLN C 176 " --> pdb=" O ASP C 170 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 187 through 191 removed outlier: 6.675A pdb=" N GLY C 202 " --> pdb=" O MET C 188 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N LEU C 190 " --> pdb=" O VAL C 200 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N VAL C 200 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN C 220 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 229 through 234 removed outlier: 6.708A pdb=" N GLY C 244 " --> pdb=" O ASN C 230 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ILE C 232 " --> pdb=" O ALA C 242 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N ALA C 242 " --> pdb=" O ILE C 232 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N PHE C 234 " --> pdb=" O ALA C 240 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N ALA C 240 " --> pdb=" O PHE C 234 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N MET C 262 " --> pdb=" O LEU C 252 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N ASP C 254 " --> pdb=" O GLU C 260 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N GLU C 260 " --> pdb=" O ASP C 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 276 through 278 removed outlier: 3.558A pdb=" N GLY C 306 " --> pdb=" O VAL C 296 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N ASP C 298 " --> pdb=" O ARG C 304 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ARG C 304 " --> pdb=" O ASP C 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 3 through 7 Processing sheet with id=AB1, first strand: chain 'E' and resid 10 through 12 removed outlier: 6.731A pdb=" N MET E 34 " --> pdb=" O TYR E 50 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N TYR E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 10 through 12 removed outlier: 4.107A pdb=" N PHE E 110 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 128 through 129 Processing sheet with id=AB4, first strand: chain 'E' and resid 135 through 136 removed outlier: 6.680A pdb=" N VAL E 135 " --> pdb=" O GLU E 234 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N LEU E 166 " --> pdb=" O LEU E 175 " (cutoff:3.500A) removed outlier: 5.931A pdb=" N LEU E 175 " --> pdb=" O LEU E 166 " (cutoff:3.500A) 450 hydrogen bonds defined for protein. 1260 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: 1.24 Time building geometry restraints manager: 0.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1863 1.33 - 1.45: 2142 1.45 - 1.57: 4961 1.57 - 1.69: 4 1.69 - 1.81: 83 Bond restraints: 9053 Sorted by residual: bond pdb=" O5C UPG A 401 " pdb=" PA UPG A 401 " ideal model delta sigma weight residual 1.648 1.584 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" O3A UPG A 401 " pdb=" PA UPG A 401 " ideal model delta sigma weight residual 1.645 1.587 0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" O3B UPG A 401 " pdb=" PB UPG A 401 " ideal model delta sigma weight residual 1.652 1.595 0.057 2.00e-02 2.50e+03 8.24e+00 bond pdb=" O3A UPG A 401 " pdb=" PB UPG A 401 " ideal model delta sigma weight residual 1.648 1.598 0.050 2.00e-02 2.50e+03 6.28e+00 bond pdb=" C5C UPG A 401 " pdb=" O5C UPG A 401 " ideal model delta sigma weight residual 1.406 1.448 -0.042 2.00e-02 2.50e+03 4.38e+00 ... (remaining 9048 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.15: 12162 2.15 - 4.30: 79 4.30 - 6.45: 23 6.45 - 8.59: 4 8.59 - 10.74: 2 Bond angle restraints: 12270 Sorted by residual: angle pdb=" PA UPG A 401 " pdb=" O3A UPG A 401 " pdb=" PB UPG A 401 " ideal model delta sigma weight residual 128.28 139.02 -10.74 3.00e+00 1.11e-01 1.28e+01 angle pdb=" O1B UPG A 401 " pdb=" PB UPG A 401 " pdb=" O2B UPG A 401 " ideal model delta sigma weight residual 122.19 112.13 10.06 3.00e+00 1.11e-01 1.12e+01 angle pdb=" O3A UPG A 401 " pdb=" PB UPG A 401 " pdb=" O3B UPG A 401 " ideal model delta sigma weight residual 97.80 105.91 -8.11 3.00e+00 1.11e-01 7.31e+00 angle pdb=" C ASN B 47 " pdb=" N THR B 48 " pdb=" CA THR B 48 " ideal model delta sigma weight residual 121.54 126.65 -5.11 1.91e+00 2.74e-01 7.16e+00 angle pdb=" N GLU B 308 " pdb=" CA GLU B 308 " pdb=" CB GLU B 308 " ideal model delta sigma weight residual 110.41 114.90 -4.49 1.68e+00 3.54e-01 7.14e+00 ... (remaining 12265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.21: 4876 17.21 - 34.43: 419 34.43 - 51.64: 61 51.64 - 68.85: 15 68.85 - 86.07: 12 Dihedral angle restraints: 5383 sinusoidal: 2101 harmonic: 3282 Sorted by residual: dihedral pdb=" CA TYR E 223 " pdb=" C TYR E 223 " pdb=" N PRO E 224 " pdb=" CA PRO E 224 " ideal model delta harmonic sigma weight residual 180.00 125.30 54.70 0 5.00e+00 4.00e-02 1.20e+02 dihedral pdb=" CB CYS E 147 " pdb=" SG CYS E 147 " pdb=" SG CYS E 217 " pdb=" CB CYS E 217 " ideal model delta sinusoidal sigma weight residual 93.00 172.31 -79.31 1 1.00e+01 1.00e-02 7.82e+01 dihedral pdb=" CB CYS A 94 " pdb=" SG CYS A 94 " pdb=" SG CYS A 172 " pdb=" CB CYS A 172 " ideal model delta sinusoidal sigma weight residual -86.00 -146.09 60.09 1 1.00e+01 1.00e-02 4.81e+01 ... (remaining 5380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 867 0.031 - 0.061: 354 0.061 - 0.092: 103 0.092 - 0.122: 66 0.122 - 0.153: 10 Chirality restraints: 1400 Sorted by residual: chirality pdb=" C2C UPG A 401 " pdb=" C1C UPG A 401 " pdb=" C3C UPG A 401 " pdb=" O2C UPG A 401 " both_signs ideal model delta sigma weight residual False -2.53 -2.68 0.15 2.00e-01 2.50e+01 5.85e-01 chirality pdb=" CA GLU B 308 " pdb=" N GLU B 308 " pdb=" C GLU B 308 " pdb=" CB GLU B 308 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.66e-01 chirality pdb=" C1C UPG A 401 " pdb=" C2C UPG A 401 " pdb=" N1 UPG A 401 " pdb=" O4C UPG A 401 " both_signs ideal model delta sigma weight residual False 2.35 2.50 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 1397 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 223 " 0.043 5.00e-02 4.00e+02 6.50e-02 6.76e+00 pdb=" N PRO E 224 " -0.112 5.00e-02 4.00e+02 pdb=" CA PRO E 224 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 224 " 0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE C 235 " 0.028 5.00e-02 4.00e+02 4.29e-02 2.95e+00 pdb=" N PRO C 236 " -0.074 5.00e-02 4.00e+02 pdb=" CA PRO C 236 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO C 236 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 25 " -0.024 5.00e-02 4.00e+02 3.59e-02 2.06e+00 pdb=" N PRO A 26 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO A 26 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 26 " -0.020 5.00e-02 4.00e+02 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 205 2.70 - 3.25: 8511 3.25 - 3.80: 14196 3.80 - 4.35: 18149 4.35 - 4.90: 31620 Nonbonded interactions: 72681 Sorted by model distance: nonbonded pdb=" OG SER C 331 " pdb=" OD1 ASP C 333 " model vdw 2.149 3.040 nonbonded pdb=" OE1 GLU B 33 " pdb=" NZ LYS B 197 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP C 163 " pdb=" OG1 THR C 165 " model vdw 2.166 3.040 nonbonded pdb=" OE2 GLU B 308 " pdb=" OG1 THR B 321 " model vdw 2.171 3.040 nonbonded pdb=" OD1 ASP B 251 " pdb=" ND2 ASN B 255 " model vdw 2.183 3.120 ... (remaining 72676 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=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: 2.110 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 8.770 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6779 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 0.064 9055 Z= 0.157 Angle : 0.554 10.742 12274 Z= 0.277 Chirality : 0.041 0.153 1400 Planarity : 0.004 0.065 1531 Dihedral : 13.453 86.066 3257 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.26), residues: 1109 helix: 2.16 (0.27), residues: 389 sheet: 0.24 (0.31), residues: 275 loop : -0.82 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG C 214 TYR 0.018 0.001 TYR E 178 PHE 0.020 0.001 PHE E 32 TRP 0.010 0.001 TRP C 82 HIS 0.002 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9053) covalent geometry : angle 0.55342 (12270) SS BOND : bond 0.00169 ( 2) SS BOND : angle 0.93494 ( 4) hydrogen bonds : bond 0.15787 ( 443) hydrogen bonds : angle 6.53437 ( 1260) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 202 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 308 GLU cc_start: 0.7131 (mp0) cc_final: 0.6790 (mp0) REVERT: B 310 LEU cc_start: 0.8098 (mt) cc_final: 0.7777 (mt) REVERT: E 218 MET cc_start: 0.8183 (ttm) cc_final: 0.7920 (ttp) REVERT: A 146 TRP cc_start: 0.7267 (m100) cc_final: 0.6026 (m100) REVERT: A 282 LEU cc_start: 0.6930 (tp) cc_final: 0.6320 (tp) outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.1051 time to fit residues: 28.4378 Evaluate side-chains 191 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 191 time to evaluate : 0.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 108 optimal weight: 0.7980 chunk 49 optimal weight: 0.0040 chunk 97 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 51 optimal weight: 0.7980 chunk 100 optimal weight: 0.2980 chunk 106 optimal weight: 1.9990 overall best weight: 0.4592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 255 ASN B 294 ASN C 110 ASN ** C 119 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 156 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3973 r_free = 0.3973 target = 0.165360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.144606 restraints weight = 11635.962| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 1.72 r_work: 0.3549 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7208 moved from start: 0.0879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9055 Z= 0.136 Angle : 0.526 7.633 12274 Z= 0.280 Chirality : 0.042 0.134 1400 Planarity : 0.004 0.066 1531 Dihedral : 5.349 58.803 1265 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 0.73 % Allowed : 6.54 % Favored : 92.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1109 helix: 2.28 (0.27), residues: 391 sheet: 0.26 (0.30), residues: 287 loop : -0.75 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 214 TYR 0.019 0.001 TYR E 178 PHE 0.012 0.001 PHE A 111 TRP 0.019 0.001 TRP C 169 HIS 0.002 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 9053) covalent geometry : angle 0.52602 (12270) SS BOND : bond 0.00241 ( 2) SS BOND : angle 0.71001 ( 4) hydrogen bonds : bond 0.04139 ( 443) hydrogen bonds : angle 4.82694 ( 1260) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 199 time to evaluate : 0.290 Fit side-chains revert: symmetry clash REVERT: B 308 GLU cc_start: 0.7570 (mp0) cc_final: 0.6917 (mp0) REVERT: B 310 LEU cc_start: 0.7850 (mt) cc_final: 0.7512 (mt) REVERT: C 59 TYR cc_start: 0.8542 (m-80) cc_final: 0.8284 (m-80) REVERT: C 111 TYR cc_start: 0.8437 (m-80) cc_final: 0.7828 (m-80) REVERT: C 220 GLN cc_start: 0.8514 (mt0) cc_final: 0.7923 (mt0) REVERT: C 276 VAL cc_start: 0.8458 (m) cc_final: 0.8243 (t) REVERT: C 285 LEU cc_start: 0.8680 (tp) cc_final: 0.8386 (tt) REVERT: A 146 TRP cc_start: 0.7579 (m100) cc_final: 0.6214 (m100) REVERT: A 147 MET cc_start: 0.7732 (mmm) cc_final: 0.7492 (mmm) REVERT: A 282 LEU cc_start: 0.7190 (tp) cc_final: 0.6566 (tp) outliers start: 7 outliers final: 6 residues processed: 200 average time/residue: 0.0932 time to fit residues: 25.5478 Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 192 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 127 VAL Chi-restraints excluded: chain E residue 225 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 13 optimal weight: 0.8980 chunk 79 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 89 optimal weight: 0.6980 chunk 81 optimal weight: 0.3980 chunk 83 optimal weight: 0.0970 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 80 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.162447 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.142014 restraints weight = 11807.797| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.70 r_work: 0.3526 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7240 moved from start: 0.1087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9055 Z= 0.145 Angle : 0.517 8.082 12274 Z= 0.273 Chirality : 0.042 0.137 1400 Planarity : 0.004 0.064 1531 Dihedral : 5.243 58.585 1265 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.35 % Allowed : 9.85 % Favored : 88.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1109 helix: 2.22 (0.27), residues: 390 sheet: 0.33 (0.30), residues: 285 loop : -0.73 (0.30), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 251 TYR 0.021 0.002 TYR E 178 PHE 0.020 0.001 PHE B 334 TRP 0.015 0.002 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 9053) covalent geometry : angle 0.51749 (12270) SS BOND : bond 0.00214 ( 2) SS BOND : angle 0.46407 ( 4) hydrogen bonds : bond 0.03909 ( 443) hydrogen bonds : angle 4.63833 ( 1260) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 191 time to evaluate : 0.335 Fit side-chains REVERT: B 294 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7648 (t0) REVERT: B 308 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6946 (mp0) REVERT: B 310 LEU cc_start: 0.7870 (mt) cc_final: 0.7539 (mt) REVERT: B 336 PHE cc_start: 0.8091 (t80) cc_final: 0.7795 (t80) REVERT: C 111 TYR cc_start: 0.8472 (m-80) cc_final: 0.7831 (m-80) REVERT: C 249 THR cc_start: 0.8131 (m) cc_final: 0.7818 (t) REVERT: C 276 VAL cc_start: 0.8440 (m) cc_final: 0.8224 (t) REVERT: C 285 LEU cc_start: 0.8707 (tp) cc_final: 0.8427 (tt) REVERT: A 46 ILE cc_start: 0.6898 (tp) cc_final: 0.6481 (mt) REVERT: A 146 TRP cc_start: 0.7588 (m100) cc_final: 0.6217 (m100) REVERT: A 147 MET cc_start: 0.7743 (mmm) cc_final: 0.7535 (mmm) REVERT: A 282 LEU cc_start: 0.7161 (tp) cc_final: 0.6751 (tp) outliers start: 13 outliers final: 8 residues processed: 194 average time/residue: 0.0828 time to fit residues: 22.3081 Evaluate side-chains 195 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 185 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 95 optimal weight: 0.6980 chunk 91 optimal weight: 0.8980 chunk 88 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 21 optimal weight: 20.0000 chunk 57 optimal weight: 0.0870 chunk 35 optimal weight: 1.9990 chunk 8 optimal weight: 0.4980 chunk 40 optimal weight: 2.9990 chunk 96 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 223 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.162999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.142651 restraints weight = 11908.935| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.68 r_work: 0.3530 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 9055 Z= 0.130 Angle : 0.508 8.451 12274 Z= 0.266 Chirality : 0.041 0.146 1400 Planarity : 0.004 0.063 1531 Dihedral : 5.109 56.329 1265 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.76 % Allowed : 11.31 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.26), residues: 1109 helix: 2.26 (0.27), residues: 390 sheet: 0.47 (0.30), residues: 281 loop : -0.70 (0.30), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG C 134 TYR 0.019 0.001 TYR E 178 PHE 0.014 0.001 PHE B 334 TRP 0.014 0.001 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 9053) covalent geometry : angle 0.50799 (12270) SS BOND : bond 0.00187 ( 2) SS BOND : angle 0.42583 ( 4) hydrogen bonds : bond 0.03667 ( 443) hydrogen bonds : angle 4.51361 ( 1260) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 202 time to evaluate : 0.332 Fit side-chains REVERT: B 196 PHE cc_start: 0.8266 (m-80) cc_final: 0.8014 (m-80) REVERT: B 294 ASN cc_start: 0.8247 (OUTLIER) cc_final: 0.7636 (t0) REVERT: B 308 GLU cc_start: 0.7563 (OUTLIER) cc_final: 0.6883 (mp0) REVERT: B 310 LEU cc_start: 0.7865 (mt) cc_final: 0.7533 (mt) REVERT: C 61 MET cc_start: 0.8130 (tmm) cc_final: 0.7843 (ppp) REVERT: C 72 SER cc_start: 0.8423 (m) cc_final: 0.8124 (p) REVERT: C 111 TYR cc_start: 0.8455 (m-80) cc_final: 0.7859 (m-80) REVERT: C 228 ASP cc_start: 0.7378 (m-30) cc_final: 0.6734 (p0) REVERT: E 162 LEU cc_start: 0.8386 (tp) cc_final: 0.8173 (tp) REVERT: A 46 ILE cc_start: 0.6916 (tp) cc_final: 0.6411 (mt) REVERT: A 146 TRP cc_start: 0.7603 (m100) cc_final: 0.6188 (m100) REVERT: A 273 LEU cc_start: 0.7628 (OUTLIER) cc_final: 0.7337 (mp) REVERT: A 282 LEU cc_start: 0.7238 (tp) cc_final: 0.6907 (tp) outliers start: 17 outliers final: 11 residues processed: 205 average time/residue: 0.0939 time to fit residues: 26.3392 Evaluate side-chains 205 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 191 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 21 SER Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 52 optimal weight: 2.9990 chunk 22 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 18 optimal weight: 4.9990 chunk 95 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 10 optimal weight: 3.9990 chunk 96 optimal weight: 0.0270 overall best weight: 1.0242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 340 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3896 r_free = 0.3896 target = 0.154874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.133999 restraints weight = 11889.181| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 1.72 r_work: 0.3480 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3334 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3334 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 9055 Z= 0.217 Angle : 0.575 9.150 12274 Z= 0.302 Chirality : 0.044 0.154 1400 Planarity : 0.005 0.062 1531 Dihedral : 5.510 59.183 1265 Min Nonbonded Distance : 2.596 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.80 % Allowed : 11.62 % Favored : 85.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.69 (0.26), residues: 1109 helix: 1.91 (0.27), residues: 389 sheet: 0.35 (0.30), residues: 283 loop : -0.77 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 251 TYR 0.029 0.002 TYR E 163 PHE 0.020 0.002 PHE B 334 TRP 0.015 0.002 TRP A 183 HIS 0.004 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00506 ( 9053) covalent geometry : angle 0.57476 (12270) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.78141 ( 4) hydrogen bonds : bond 0.04362 ( 443) hydrogen bonds : angle 4.72808 ( 1260) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 191 time to evaluate : 0.361 Fit side-chains REVERT: B 197 LYS cc_start: 0.8331 (mttp) cc_final: 0.8099 (mttp) REVERT: B 249 LEU cc_start: 0.7741 (tp) cc_final: 0.7535 (tt) REVERT: B 294 ASN cc_start: 0.8292 (OUTLIER) cc_final: 0.7820 (t0) REVERT: B 308 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.6997 (mp0) REVERT: B 310 LEU cc_start: 0.7989 (mt) cc_final: 0.7606 (mt) REVERT: C 72 SER cc_start: 0.8580 (m) cc_final: 0.8139 (p) REVERT: C 111 TYR cc_start: 0.8463 (m-80) cc_final: 0.7743 (m-80) REVERT: C 228 ASP cc_start: 0.7438 (m-30) cc_final: 0.6716 (p0) REVERT: A 46 ILE cc_start: 0.7048 (tp) cc_final: 0.6266 (mt) REVERT: A 146 TRP cc_start: 0.7721 (m100) cc_final: 0.6544 (m100) REVERT: A 273 LEU cc_start: 0.7729 (OUTLIER) cc_final: 0.7374 (mp) REVERT: A 282 LEU cc_start: 0.7191 (tp) cc_final: 0.6876 (tp) outliers start: 27 outliers final: 15 residues processed: 198 average time/residue: 0.0903 time to fit residues: 24.3433 Evaluate side-chains 206 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 188 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 21 THR Chi-restraints excluded: chain A residue 251 ILE Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 88 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 85 optimal weight: 0.6980 chunk 46 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 104 optimal weight: 0.5980 chunk 56 optimal weight: 0.8980 chunk 95 optimal weight: 0.3980 chunk 50 optimal weight: 1.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 295 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 = 0.3916 r_free = 0.3916 target = 0.156635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135794 restraints weight = 11934.256| |-----------------------------------------------------------------------------| r_work (start): 0.3636 rms_B_bonded: 1.73 r_work: 0.3497 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3353 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.3353 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7258 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9055 Z= 0.132 Angle : 0.523 9.271 12274 Z= 0.272 Chirality : 0.042 0.184 1400 Planarity : 0.004 0.060 1531 Dihedral : 5.216 54.409 1265 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 2.18 % Allowed : 13.49 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1109 helix: 2.18 (0.27), residues: 390 sheet: 0.42 (0.30), residues: 275 loop : -0.74 (0.30), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 134 TYR 0.026 0.002 TYR E 163 PHE 0.014 0.001 PHE B 189 TRP 0.015 0.002 TRP C 169 HIS 0.002 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9053) covalent geometry : angle 0.52289 (12270) SS BOND : bond 0.00197 ( 2) SS BOND : angle 0.53850 ( 4) hydrogen bonds : bond 0.03679 ( 443) hydrogen bonds : angle 4.51030 ( 1260) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 190 time to evaluate : 0.338 Fit side-chains revert: symmetry clash REVERT: B 197 LYS cc_start: 0.8301 (mttp) cc_final: 0.8081 (mttp) REVERT: B 261 ASP cc_start: 0.7483 (p0) cc_final: 0.7221 (p0) REVERT: B 294 ASN cc_start: 0.8269 (OUTLIER) cc_final: 0.7820 (t0) REVERT: B 308 GLU cc_start: 0.7567 (OUTLIER) cc_final: 0.6868 (mp0) REVERT: B 310 LEU cc_start: 0.7933 (mt) cc_final: 0.7562 (mt) REVERT: B 336 PHE cc_start: 0.7998 (t80) cc_final: 0.7656 (t80) REVERT: C 49 ARG cc_start: 0.8575 (mmt-90) cc_final: 0.8373 (mmt90) REVERT: C 72 SER cc_start: 0.8536 (m) cc_final: 0.8155 (p) REVERT: C 111 TYR cc_start: 0.8444 (m-80) cc_final: 0.7824 (m-80) REVERT: C 219 ARG cc_start: 0.8093 (mmt180) cc_final: 0.7892 (mmt-90) REVERT: C 220 GLN cc_start: 0.8534 (mt0) cc_final: 0.8327 (mt0) REVERT: C 258 ASP cc_start: 0.7796 (t0) cc_final: 0.7575 (t70) REVERT: C 335 PHE cc_start: 0.7467 (m-80) cc_final: 0.7245 (m-80) REVERT: A 46 ILE cc_start: 0.6941 (tp) cc_final: 0.6183 (mt) REVERT: A 146 TRP cc_start: 0.7655 (m100) cc_final: 0.6301 (m100) REVERT: A 282 LEU cc_start: 0.7196 (tp) cc_final: 0.6891 (tp) outliers start: 21 outliers final: 15 residues processed: 199 average time/residue: 0.1050 time to fit residues: 28.1730 Evaluate side-chains 198 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 181 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 83 MET Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 80 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 0.1980 chunk 76 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 31 optimal weight: 0.6980 chunk 53 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 35 optimal weight: 0.8980 chunk 82 optimal weight: 0.0020 overall best weight: 0.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3933 r_free = 0.3933 target = 0.158031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3693 r_free = 0.3693 target = 0.137219 restraints weight = 11952.220| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.72 r_work: 0.3524 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 9055 Z= 0.111 Angle : 0.494 9.003 12274 Z= 0.259 Chirality : 0.041 0.179 1400 Planarity : 0.004 0.060 1531 Dihedral : 4.979 51.861 1265 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.49 % Allowed : 13.38 % Favored : 84.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.97 (0.26), residues: 1109 helix: 2.33 (0.27), residues: 390 sheet: 0.37 (0.30), residues: 272 loop : -0.71 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG C 251 TYR 0.016 0.001 TYR E 178 PHE 0.015 0.001 PHE E 227 TRP 0.014 0.001 TRP C 82 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 9053) covalent geometry : angle 0.49367 (12270) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.46412 ( 4) hydrogen bonds : bond 0.03415 ( 443) hydrogen bonds : angle 4.34618 ( 1260) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 195 time to evaluate : 0.342 Fit side-chains revert: symmetry clash REVERT: B 196 PHE cc_start: 0.8288 (m-80) cc_final: 0.8043 (m-80) REVERT: B 257 LYS cc_start: 0.8605 (pttp) cc_final: 0.8243 (pttp) REVERT: B 261 ASP cc_start: 0.7490 (p0) cc_final: 0.7222 (p0) REVERT: B 294 ASN cc_start: 0.8249 (OUTLIER) cc_final: 0.7835 (t0) REVERT: B 308 GLU cc_start: 0.7573 (OUTLIER) cc_final: 0.6863 (mp0) REVERT: C 49 ARG cc_start: 0.8588 (mmt-90) cc_final: 0.8355 (mmt90) REVERT: C 59 TYR cc_start: 0.8519 (m-80) cc_final: 0.8284 (m-80) REVERT: C 61 MET cc_start: 0.8179 (tmm) cc_final: 0.7882 (ppp) REVERT: C 72 SER cc_start: 0.8536 (m) cc_final: 0.8178 (p) REVERT: C 111 TYR cc_start: 0.8432 (m-80) cc_final: 0.7770 (m-80) REVERT: A 37 ILE cc_start: 0.5888 (OUTLIER) cc_final: 0.5673 (tp) REVERT: A 46 ILE cc_start: 0.6930 (tp) cc_final: 0.6213 (mt) REVERT: A 146 TRP cc_start: 0.7640 (m100) cc_final: 0.7325 (m100) REVERT: A 273 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7348 (mp) REVERT: A 282 LEU cc_start: 0.7306 (tp) cc_final: 0.7036 (tp) outliers start: 24 outliers final: 16 residues processed: 205 average time/residue: 0.0957 time to fit residues: 26.6135 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 37 ILE Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 41 optimal weight: 3.9990 chunk 95 optimal weight: 0.9980 chunk 103 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 52 optimal weight: 0.4980 chunk 64 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 65 optimal weight: 0.5980 chunk 104 optimal weight: 0.7980 chunk 63 optimal weight: 0.6980 chunk 109 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 125 ASN C 156 GLN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3916 r_free = 0.3916 target = 0.156684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.135745 restraints weight = 11826.730| |-----------------------------------------------------------------------------| r_work (start): 0.3633 rms_B_bonded: 1.71 r_work: 0.3497 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3354 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7257 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 9055 Z= 0.151 Angle : 0.521 9.031 12274 Z= 0.276 Chirality : 0.042 0.183 1400 Planarity : 0.004 0.061 1531 Dihedral : 5.143 52.744 1265 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.59 % Allowed : 14.11 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.26), residues: 1109 helix: 2.19 (0.27), residues: 391 sheet: 0.40 (0.30), residues: 272 loop : -0.73 (0.30), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 134 TYR 0.017 0.002 TYR E 178 PHE 0.025 0.002 PHE B 334 TRP 0.012 0.001 TRP C 169 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00351 ( 9053) covalent geometry : angle 0.52101 (12270) SS BOND : bond 0.00245 ( 2) SS BOND : angle 0.45267 ( 4) hydrogen bonds : bond 0.03730 ( 443) hydrogen bonds : angle 4.41750 ( 1260) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.356 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8580 (pttp) cc_final: 0.8220 (pttp) REVERT: B 261 ASP cc_start: 0.7490 (p0) cc_final: 0.7229 (p0) REVERT: B 294 ASN cc_start: 0.8267 (OUTLIER) cc_final: 0.7845 (t0) REVERT: B 308 GLU cc_start: 0.7593 (OUTLIER) cc_final: 0.6942 (mp0) REVERT: B 336 PHE cc_start: 0.7969 (t80) cc_final: 0.7649 (t80) REVERT: C 59 TYR cc_start: 0.8537 (m-80) cc_final: 0.8303 (m-80) REVERT: C 72 SER cc_start: 0.8552 (m) cc_final: 0.8200 (p) REVERT: C 111 TYR cc_start: 0.8459 (m-80) cc_final: 0.7792 (m-80) REVERT: C 308 LEU cc_start: 0.8314 (mt) cc_final: 0.8088 (mt) REVERT: A 146 TRP cc_start: 0.7666 (m100) cc_final: 0.7331 (m100) REVERT: A 273 LEU cc_start: 0.7699 (OUTLIER) cc_final: 0.7359 (mp) REVERT: A 282 LEU cc_start: 0.7315 (tp) cc_final: 0.7047 (tp) outliers start: 25 outliers final: 19 residues processed: 200 average time/residue: 0.0945 time to fit residues: 25.9389 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 185 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 33 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 69 optimal weight: 0.5980 chunk 103 optimal weight: 1.9990 chunk 68 optimal weight: 1.9990 chunk 54 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 46 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 101 optimal weight: 0.6980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 125 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3908 r_free = 0.3908 target = 0.156062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135238 restraints weight = 11867.949| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.69 r_work: 0.3508 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7278 moved from start: 0.1681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 9055 Z= 0.172 Angle : 0.544 9.525 12274 Z= 0.287 Chirality : 0.043 0.192 1400 Planarity : 0.004 0.059 1531 Dihedral : 5.273 52.627 1265 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.49 % Allowed : 14.83 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.26), residues: 1109 helix: 1.98 (0.27), residues: 396 sheet: 0.37 (0.30), residues: 273 loop : -0.69 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 134 TYR 0.018 0.002 TYR E 178 PHE 0.021 0.002 PHE B 334 TRP 0.012 0.002 TRP A 183 HIS 0.003 0.001 HIS E 35 Details of bonding type rmsd covalent geometry : bond 0.00402 ( 9053) covalent geometry : angle 0.54364 (12270) SS BOND : bond 0.00299 ( 2) SS BOND : angle 0.52004 ( 4) hydrogen bonds : bond 0.03869 ( 443) hydrogen bonds : angle 4.48995 ( 1260) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.321 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8592 (pttp) cc_final: 0.8241 (pttp) REVERT: B 261 ASP cc_start: 0.7493 (p0) cc_final: 0.7235 (p0) REVERT: B 294 ASN cc_start: 0.8275 (OUTLIER) cc_final: 0.7862 (t0) REVERT: B 308 GLU cc_start: 0.7610 (OUTLIER) cc_final: 0.6965 (mp0) REVERT: C 49 ARG cc_start: 0.8608 (mmt-90) cc_final: 0.8390 (mmt90) REVERT: C 61 MET cc_start: 0.8088 (tmm) cc_final: 0.7864 (ppp) REVERT: C 72 SER cc_start: 0.8577 (m) cc_final: 0.8169 (p) REVERT: C 111 TYR cc_start: 0.8459 (m-80) cc_final: 0.7805 (m-80) REVERT: E 20 LEU cc_start: 0.7942 (mp) cc_final: 0.7714 (mt) REVERT: E 69 THR cc_start: 0.7986 (m) cc_final: 0.7751 (t) REVERT: A 146 TRP cc_start: 0.7686 (m100) cc_final: 0.6303 (m100) REVERT: A 273 LEU cc_start: 0.7727 (OUTLIER) cc_final: 0.7388 (mp) REVERT: A 282 LEU cc_start: 0.7254 (tp) cc_final: 0.6963 (tp) outliers start: 24 outliers final: 20 residues processed: 205 average time/residue: 0.0963 time to fit residues: 26.7213 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 184 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain B residue 350 ASP Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain C residue 318 LEU Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 207 LEU Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 1 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 96 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 4 optimal weight: 0.0170 chunk 6 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 21 optimal weight: 30.0000 chunk 14 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 82 optimal weight: 0.0570 overall best weight: 0.3736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.164276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.143579 restraints weight = 11829.857| |-----------------------------------------------------------------------------| r_work (start): 0.3657 rms_B_bonded: 1.75 r_work: 0.3524 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7241 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 9055 Z= 0.115 Angle : 0.506 9.254 12274 Z= 0.267 Chirality : 0.041 0.203 1400 Planarity : 0.004 0.057 1531 Dihedral : 5.038 49.397 1265 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 2.18 % Allowed : 15.15 % Favored : 82.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.96 (0.26), residues: 1109 helix: 2.28 (0.27), residues: 391 sheet: 0.39 (0.30), residues: 273 loop : -0.69 (0.30), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 134 TYR 0.015 0.001 TYR E 178 PHE 0.027 0.001 PHE B 336 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00258 ( 9053) covalent geometry : angle 0.50636 (12270) SS BOND : bond 0.00257 ( 2) SS BOND : angle 0.34206 ( 4) hydrogen bonds : bond 0.03438 ( 443) hydrogen bonds : angle 4.34100 ( 1260) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2218 Ramachandran restraints generated. 1109 Oldfield, 0 Emsley, 1109 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 187 time to evaluate : 0.335 Fit side-chains revert: symmetry clash REVERT: B 257 LYS cc_start: 0.8604 (pttp) cc_final: 0.8247 (pttp) REVERT: B 261 ASP cc_start: 0.7485 (p0) cc_final: 0.7219 (p0) REVERT: B 294 ASN cc_start: 0.8253 (OUTLIER) cc_final: 0.7853 (t0) REVERT: B 308 GLU cc_start: 0.7564 (OUTLIER) cc_final: 0.6842 (mp0) REVERT: B 336 PHE cc_start: 0.7900 (t80) cc_final: 0.7588 (t80) REVERT: C 49 ARG cc_start: 0.8540 (mmt-90) cc_final: 0.8329 (mmt90) REVERT: C 59 TYR cc_start: 0.8463 (m-80) cc_final: 0.8029 (m-80) REVERT: C 72 SER cc_start: 0.8558 (m) cc_final: 0.8252 (p) REVERT: C 111 TYR cc_start: 0.8447 (m-80) cc_final: 0.7866 (m-80) REVERT: E 20 LEU cc_start: 0.7858 (mp) cc_final: 0.7641 (mt) REVERT: E 69 THR cc_start: 0.7959 (m) cc_final: 0.7722 (t) REVERT: A 146 TRP cc_start: 0.7655 (m100) cc_final: 0.7335 (m100) REVERT: A 273 LEU cc_start: 0.7676 (OUTLIER) cc_final: 0.7344 (mp) REVERT: A 282 LEU cc_start: 0.7314 (tp) cc_final: 0.7047 (tp) outliers start: 21 outliers final: 17 residues processed: 198 average time/residue: 0.1004 time to fit residues: 27.0698 Evaluate side-chains 207 residues out of total 983 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 187 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 MET Chi-restraints excluded: chain B residue 185 VAL Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 308 GLU Chi-restraints excluded: chain B residue 312 LYS Chi-restraints excluded: chain B residue 339 VAL Chi-restraints excluded: chain C residue 114 CYS Chi-restraints excluded: chain C residue 135 VAL Chi-restraints excluded: chain C residue 143 THR Chi-restraints excluded: chain C residue 146 LEU Chi-restraints excluded: chain C residue 165 THR Chi-restraints excluded: chain E residue 91 THR Chi-restraints excluded: chain E residue 225 LEU Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 154 VAL Chi-restraints excluded: chain A residue 188 ASN Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain A residue 241 VAL Chi-restraints excluded: chain A residue 273 LEU Chi-restraints excluded: chain A residue 289 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 110 random chunks: chunk 20 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 65 optimal weight: 0.2980 chunk 77 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 93 optimal weight: 0.0020 chunk 1 optimal weight: 0.9980 chunk 98 optimal weight: 0.6980 chunk 82 optimal weight: 0.0980 chunk 16 optimal weight: 0.9980 overall best weight: 0.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN C 239 ASN ** C 295 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.166269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.144972 restraints weight = 11469.616| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.75 r_work: 0.3546 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.1815 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9055 Z= 0.107 Angle : 0.504 8.574 12274 Z= 0.263 Chirality : 0.041 0.190 1400 Planarity : 0.004 0.055 1531 Dihedral : 4.910 47.920 1265 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 2.90 % Allowed : 14.94 % Favored : 82.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 3.23 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.03 (0.26), residues: 1109 helix: 2.35 (0.27), residues: 391 sheet: 0.51 (0.30), residues: 271 loop : -0.71 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 134 TYR 0.017 0.001 TYR E 163 PHE 0.029 0.001 PHE B 334 TRP 0.014 0.001 TRP C 169 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9053) covalent geometry : angle 0.50374 (12270) SS BOND : bond 0.00222 ( 2) SS BOND : angle 0.48804 ( 4) hydrogen bonds : bond 0.03280 ( 443) hydrogen bonds : angle 4.24306 ( 1260) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2522.15 seconds wall clock time: 43 minutes 55.75 seconds (2635.75 seconds total)