Starting phenix.real_space_refine on Tue Feb 3 21:59:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9uyh_64610/02_2026/9uyh_64610.cif Found real_map, /net/cci-nas-00/data/ceres_data/9uyh_64610/02_2026/9uyh_64610.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9uyh_64610/02_2026/9uyh_64610.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9uyh_64610/02_2026/9uyh_64610.map" model { file = "/net/cci-nas-00/data/ceres_data/9uyh_64610/02_2026/9uyh_64610.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9uyh_64610/02_2026/9uyh_64610.cif" } resolution = 3.3 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= -0.000 sd= 0.032 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 5 5.49 5 S 22 5.16 5 C 4617 2.51 5 N 1206 2.21 5 O 1326 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model 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: 7176 Number of models: 1 Model: "" Number of chains: 5 Chain: "L" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 88 Classifications: {'peptide': 10} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 8} Chain: "A" Number of atoms: 2553 Number of conformers: 1 Conformer: "" Number of residues, atoms: 339, 2553 Classifications: {'peptide': 339} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 25, 'TRANS': 313} Chain breaks: 3 Unresolved non-hydrogen bonds: 157 Unresolved non-hydrogen angles: 188 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLU:plan': 10, 'PHE:plan': 1, 'ARG:plan': 5, 'GLN:plan1': 1, 'HIS:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 100 Chain: "B" Number of atoms: 789 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 789 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 18} Link IDs: {'PTRANS': 2, 'TRANS': 108} Unresolved non-hydrogen bonds: 62 Unresolved non-hydrogen angles: 75 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 4, 'PHE:plan': 1, 'ASP:plan': 3, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 34 Chain: "R" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 2066 Classifications: {'peptide': 283} Incomplete info: {'truncation_to_alanine': 64} Link IDs: {'PTRANS': 9, 'TRANS': 273} Chain breaks: 2 Unresolved non-hydrogen bonds: 310 Unresolved non-hydrogen angles: 408 Unresolved non-hydrogen dihedrals: 281 Unresolved non-hydrogen chiralities: 24 Planarities with less than four sites: {'TRP:plan': 5, 'PHE:plan': 10, 'ASN:plan1': 4, 'ASP:plan': 2, 'HIS:plan': 4, 'ARG:plan': 5, 'GLU:plan': 2, 'TYR:plan': 2, 'TPO:plan-1': 2} Unresolved non-hydrogen planarities: 192 Chain: "C" Number of atoms: 1680 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1680 Classifications: {'peptide': 222} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 8, 'TRANS': 213} Chain breaks: 1 Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 33 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'ARG:plan': 2, 'GLU:plan': 2, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Time building chain proxies: 1.88, per 1000 atoms: 0.26 Number of scatterers: 7176 At special positions: 0 Unit cell: (81.396, 112.455, 141.372, 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 22 16.00 P 5 15.00 O 1326 8.00 N 1206 7.00 C 4617 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 187 " distance=2.04 Simple disulfide: pdb=" SG CYS C 24 " - pdb=" SG CYS C 89 " distance=2.03 Simple disulfide: pdb=" SG CYS C 146 " - pdb=" SG CYS C 220 " 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: 0.83 Conformation dependent library (CDL) restraints added in 305.2 milliseconds 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1818 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 15 sheets defined 24.6% alpha, 25.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.28 Creating SS restraints... Processing helix chain 'A' and resid 64 through 68 removed outlier: 3.727A pdb=" N ASP A 67 " --> pdb=" O GLY A 64 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N LEU A 68 " --> pdb=" O ARG A 65 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 64 through 68' Processing helix chain 'A' and resid 98 through 109 Processing helix chain 'B' and resid 86 through 90 removed outlier: 3.594A pdb=" N THR B 90 " --> pdb=" O PRO B 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 37 through 66 Proline residue: R 54 - end of helix Processing helix chain 'R' and resid 70 through 89 removed outlier: 4.090A pdb=" N PHE R 89 " --> pdb=" O ILE R 85 " (cutoff:3.500A) Processing helix chain 'R' and resid 89 through 97 removed outlier: 3.569A pdb=" N SER R 95 " --> pdb=" O PRO R 91 " (cutoff:3.500A) Processing helix chain 'R' and resid 98 through 102 removed outlier: 3.879A pdb=" N HIS R 102 " --> pdb=" O MET R 99 " (cutoff:3.500A) Processing helix chain 'R' and resid 109 through 139 removed outlier: 4.381A pdb=" N ASN R 113 " --> pdb=" O LEU R 109 " (cutoff:3.500A) Processing helix chain 'R' and resid 150 through 169 Processing helix chain 'R' and resid 201 through 217 removed outlier: 3.577A pdb=" N PHE R 217 " --> pdb=" O ILE R 213 " (cutoff:3.500A) Processing helix chain 'R' and resid 217 through 226 removed outlier: 3.757A pdb=" N THR R 221 " --> pdb=" O PHE R 217 " (cutoff:3.500A) Processing helix chain 'R' and resid 226 through 231 Processing helix chain 'R' and resid 241 through 273 Proline residue: R 261 - end of helix Processing helix chain 'R' and resid 287 through 305 Proline residue: R 301 - end of helix Processing helix chain 'R' and resid 308 through 317 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.522A pdb=" N ASP C 214 " --> pdb=" O ARG C 211 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N THR C 215 " --> pdb=" O ALA C 212 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 211 through 215' Processing sheet with id=AA1, first strand: chain 'A' and resid 112 through 114 Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 28 removed outlier: 5.893A pdb=" N PHE A 27 " --> pdb=" O VAL A 171 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 78 through 85 removed outlier: 6.580A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 78 through 85 removed outlier: 6.580A pdb=" N ALA A 59 " --> pdb=" O LEU A 79 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL A 81 " --> pdb=" O LEU A 57 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N LEU A 57 " --> pdb=" O VAL A 81 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N ASN A 83 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL A 55 " --> pdb=" O ASN A 83 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLN A 85 " --> pdb=" O VAL A 53 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N VAL A 53 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ARG A 62 " --> pdb=" O GLY A 141 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N ILE A 140 " --> pdb=" O LEU A 129 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N VAL A 127 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.550A pdb=" N ALA A 184 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 186 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 183 through 186 removed outlier: 3.550A pdb=" N ALA A 184 " --> pdb=" O ALA A 201 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 186 " --> pdb=" O LEU A 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 207 through 208 removed outlier: 3.596A pdb=" N VAL A 345 " --> pdb=" O VAL A 325 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR A 321 " --> pdb=" O PHE A 349 " (cutoff:3.500A) removed outlier: 7.295A pdb=" N LEU A 351 " --> pdb=" O VAL A 319 " (cutoff:3.500A) removed outlier: 9.457A pdb=" N VAL A 319 " --> pdb=" O LEU A 351 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 322 " --> pdb=" O ARG A 236 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS A 230 " --> pdb=" O VAL A 328 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N ILE A 231 " --> pdb=" O GLU A 257 " (cutoff:3.500A) removed outlier: 4.720A pdb=" N GLU A 257 " --> pdb=" O ILE A 231 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N ILE A 233 " --> pdb=" O MET A 255 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N MET A 255 " --> pdb=" O ILE A 233 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N VAL A 235 " --> pdb=" O VAL A 253 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 5 through 7 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.727A pdb=" N TRP B 36 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR B 108 " --> pdb=" O TYR B 93 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'R' and resid 176 through 181 removed outlier: 3.832A pdb=" N VAL R 179 " --> pdb=" O LEU R 186 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 5 through 6 Processing sheet with id=AB3, first strand: chain 'C' and resid 11 through 12 removed outlier: 6.554A pdb=" N TRP C 36 " --> pdb=" O LEU C 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 20 through 23 Processing sheet with id=AB5, first strand: chain 'C' and resid 127 through 131 removed outlier: 3.525A pdb=" N GLN C 127 " --> pdb=" O SER C 149 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 181 through 184 removed outlier: 5.170A pdb=" N TRP C 171 " --> pdb=" O ARG C 162 " (cutoff:3.500A) removed outlier: 6.170A pdb=" N ARG C 162 " --> pdb=" O TRP C 171 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N ARG C 224 " --> pdb=" O LEU C 231 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N LEU C 231 " --> pdb=" O ARG C 224 " (cutoff:3.500A) 311 hydrogen bonds defined for protein. 864 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: 1.02 Time building geometry restraints manager: 1.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2260 1.34 - 1.46: 1724 1.46 - 1.58: 3317 1.58 - 1.70: 12 1.70 - 1.82: 32 Bond restraints: 7345 Sorted by residual: bond pdb=" C PHE L 150 " pdb=" N PRO L 151 " ideal model delta sigma weight residual 1.334 1.372 -0.038 2.34e-02 1.83e+03 2.67e+00 bond pdb=" CA ASN A 122 " pdb=" CB ASN A 122 " ideal model delta sigma weight residual 1.527 1.546 -0.019 1.70e-02 3.46e+03 1.19e+00 bond pdb=" CA PHE R 101 " pdb=" CB PHE R 101 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.70e-02 3.46e+03 8.72e-01 bond pdb=" N PRO A 131 " pdb=" CA PRO A 131 " ideal model delta sigma weight residual 1.469 1.479 -0.010 1.28e-02 6.10e+03 6.07e-01 bond pdb=" CA LYS R 234 " pdb=" CB LYS R 234 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 5.87e-01 ... (remaining 7340 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 9730 1.40 - 2.80: 236 2.80 - 4.20: 63 4.20 - 5.60: 15 5.60 - 7.00: 3 Bond angle restraints: 10047 Sorted by residual: angle pdb=" C PRO A 121 " pdb=" N ASN A 122 " pdb=" CA ASN A 122 " ideal model delta sigma weight residual 122.46 128.09 -5.63 1.41e+00 5.03e-01 1.60e+01 angle pdb=" N VAL R 97 " pdb=" CA VAL R 97 " pdb=" C VAL R 97 " ideal model delta sigma weight residual 112.80 109.00 3.80 1.15e+00 7.56e-01 1.09e+01 angle pdb=" C ASN A 153 " pdb=" N LEU A 154 " pdb=" CA LEU A 154 " ideal model delta sigma weight residual 121.54 126.96 -5.42 1.91e+00 2.74e-01 8.05e+00 angle pdb=" C TYR L 149 " pdb=" N PHE L 150 " pdb=" CA PHE L 150 " ideal model delta sigma weight residual 120.06 123.40 -3.34 1.19e+00 7.06e-01 7.87e+00 angle pdb=" C GLY R 285 " pdb=" N ILE R 286 " pdb=" CA ILE R 286 " ideal model delta sigma weight residual 122.13 127.17 -5.04 1.85e+00 2.92e-01 7.41e+00 ... (remaining 10042 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.36: 3918 17.36 - 34.72: 319 34.72 - 52.08: 55 52.08 - 69.44: 4 69.44 - 86.80: 5 Dihedral angle restraints: 4301 sinusoidal: 1483 harmonic: 2818 Sorted by residual: dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 187 " pdb=" CB CYS R 187 " ideal model delta sinusoidal sigma weight residual -86.00 -136.97 50.97 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA ASN A 122 " pdb=" C ASN A 122 " pdb=" N LEU A 123 " pdb=" CA LEU A 123 " ideal model delta harmonic sigma weight residual 180.00 159.79 20.21 0 5.00e+00 4.00e-02 1.63e+01 dihedral pdb=" CA ILE R 286 " pdb=" C ILE R 286 " pdb=" N PRO R 287 " pdb=" CA PRO R 287 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 ... (remaining 4298 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 825 0.039 - 0.077: 248 0.077 - 0.116: 92 0.116 - 0.154: 20 0.154 - 0.193: 2 Chirality restraints: 1187 Sorted by residual: chirality pdb=" CB ILE R 107 " pdb=" CA ILE R 107 " pdb=" CG1 ILE R 107 " pdb=" CG2 ILE R 107 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ASN A 122 " pdb=" N ASN A 122 " pdb=" C ASN A 122 " pdb=" CB ASN A 122 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.88e-01 chirality pdb=" CA ILE R 140 " pdb=" N ILE R 140 " pdb=" C ILE R 140 " pdb=" CB ILE R 140 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.68e-01 ... (remaining 1184 not shown) Planarity restraints: 1259 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 300 " 0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO R 301 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO R 301 " 0.037 5.00e-02 4.00e+02 pdb=" CD PRO R 301 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 150 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO L 151 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO L 151 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO L 151 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 132 " 0.027 5.00e-02 4.00e+02 4.14e-02 2.74e+00 pdb=" N PRO A 133 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 133 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 133 " 0.023 5.00e-02 4.00e+02 ... (remaining 1256 not shown) Histogram of nonbonded interaction distances: 2.46 - 2.95: 3231 2.95 - 3.43: 7066 3.43 - 3.92: 11155 3.92 - 4.41: 12181 4.41 - 4.90: 21178 Nonbonded interactions: 54811 Sorted by model distance: nonbonded pdb=" O PRO A 121 " pdb=" OD1 ASN A 122 " model vdw 2.458 3.040 nonbonded pdb=" OD1 ASP A 32 " pdb=" N LEU A 33 " model vdw 2.549 3.120 nonbonded pdb=" O ASN R 100 " pdb=" OD1 ASN R 100 " model vdw 2.553 3.040 nonbonded pdb=" O THR C 70 " pdb=" OG1 THR C 70 " model vdw 2.574 3.040 nonbonded pdb=" O ASN C 201 " pdb=" OD1 ASN C 201 " model vdw 2.595 3.040 ... (remaining 54806 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: 1.230 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: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 8.820 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:1.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 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 0.038 7349 Z= 0.122 Angle : 0.583 6.999 10055 Z= 0.303 Chirality : 0.043 0.193 1187 Planarity : 0.005 0.071 1259 Dihedral : 12.925 86.798 2471 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.83 (0.28), residues: 936 helix: 1.17 (0.35), residues: 204 sheet: -0.21 (0.34), residues: 259 loop : -1.55 (0.30), residues: 473 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 76 TYR 0.013 0.001 TYR A 272 PHE 0.022 0.001 PHE R 101 TRP 0.011 0.001 TRP R 259 HIS 0.005 0.001 HIS A 353 Details of bonding type rmsd covalent geometry : bond 0.00266 ( 7345) covalent geometry : angle 0.58326 (10047) SS BOND : bond 0.00410 ( 4) SS BOND : angle 0.55700 ( 8) hydrogen bonds : bond 0.19247 ( 299) hydrogen bonds : angle 7.81016 ( 864) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 218 time to evaluate : 0.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7640 (tp30) cc_final: 0.7131 (pp20) REVERT: A 122 ASN cc_start: 0.8089 (p0) cc_final: 0.7529 (m-40) REVERT: A 367 GLU cc_start: 0.7624 (pm20) cc_final: 0.6973 (pm20) REVERT: B 56 THR cc_start: 0.6372 (p) cc_final: 0.6117 (p) REVERT: B 66 ARG cc_start: 0.7258 (ttt180) cc_final: 0.6884 (ttt180) REVERT: B 72 ASP cc_start: 0.6409 (t0) cc_final: 0.6119 (t0) REVERT: R 45 TYR cc_start: 0.7943 (m-10) cc_final: 0.7661 (m-10) REVERT: R 93 TYR cc_start: 0.7775 (t80) cc_final: 0.7466 (t80) REVERT: R 100 ASN cc_start: 0.6557 (t0) cc_final: 0.5636 (m110) REVERT: R 118 GLN cc_start: 0.8195 (tt0) cc_final: 0.7641 (tt0) REVERT: R 136 TYR cc_start: 0.8540 (t80) cc_final: 0.8195 (t80) REVERT: R 222 MET cc_start: 0.7566 (mtt) cc_final: 0.7215 (mtt) REVERT: R 232 LYS cc_start: 0.6841 (mmtt) cc_final: 0.5607 (ttpp) REVERT: C 5 MET cc_start: 0.7683 (mmm) cc_final: 0.7432 (tpp) REVERT: C 104 LYS cc_start: 0.9004 (mmmt) cc_final: 0.8636 (ttmt) REVERT: C 149 SER cc_start: 0.8719 (t) cc_final: 0.8457 (p) REVERT: C 238 THR cc_start: 0.8662 (p) cc_final: 0.8416 (p) outliers start: 0 outliers final: 0 residues processed: 218 average time/residue: 0.1073 time to fit residues: 29.7088 Evaluate side-chains 133 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 49 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 45 optimal weight: 20.0000 chunk 74 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 ASN ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.152111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.117285 restraints weight = 12129.715| |-----------------------------------------------------------------------------| r_work (start): 0.3623 rms_B_bonded: 2.89 r_work: 0.3434 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.3434 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.2634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 7349 Z= 0.258 Angle : 0.694 6.338 10055 Z= 0.365 Chirality : 0.047 0.277 1187 Planarity : 0.005 0.072 1259 Dihedral : 5.459 71.778 1044 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.44 % Favored : 91.56 % Rotamer: Outliers : 2.52 % Allowed : 13.31 % Favored : 84.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.92 (0.29), residues: 936 helix: 1.35 (0.37), residues: 205 sheet: -0.35 (0.31), residues: 289 loop : -1.76 (0.31), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 143 TYR 0.034 0.002 TYR A 47 PHE 0.021 0.002 PHE A 61 TRP 0.012 0.002 TRP R 75 HIS 0.006 0.002 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00595 ( 7345) covalent geometry : angle 0.69329 (10047) SS BOND : bond 0.00774 ( 4) SS BOND : angle 0.92389 ( 8) hydrogen bonds : bond 0.04411 ( 299) hydrogen bonds : angle 5.54660 ( 864) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 140 time to evaluate : 0.250 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7489 (tp30) cc_final: 0.6896 (pp20) REVERT: A 122 ASN cc_start: 0.8263 (p0) cc_final: 0.7793 (m-40) REVERT: A 305 LEU cc_start: 0.8732 (OUTLIER) cc_final: 0.8446 (pp) REVERT: B 38 ARG cc_start: 0.8885 (ptt180) cc_final: 0.8679 (ptt-90) REVERT: R 100 ASN cc_start: 0.6852 (t0) cc_final: 0.5748 (m110) REVERT: R 118 GLN cc_start: 0.8895 (tt0) cc_final: 0.8408 (tt0) REVERT: R 122 PHE cc_start: 0.8825 (m-80) cc_final: 0.8292 (m-80) REVERT: R 126 PHE cc_start: 0.9188 (m-10) cc_final: 0.8982 (m-10) REVERT: R 232 LYS cc_start: 0.7910 (mmtt) cc_final: 0.6550 (ttpp) REVERT: C 66 SER cc_start: 0.8636 (m) cc_final: 0.8424 (m) REVERT: C 238 THR cc_start: 0.8698 (p) cc_final: 0.8333 (p) outliers start: 18 outliers final: 12 residues processed: 152 average time/residue: 0.0885 time to fit residues: 17.8804 Evaluate side-chains 138 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 125 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 222 ASN Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 7 optimal weight: 4.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 12 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 61 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 38 optimal weight: 0.6980 overall best weight: 1.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 273 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.150861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116567 restraints weight = 12106.683| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.91 r_work: 0.3409 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 7349 Z= 0.227 Angle : 0.662 7.201 10055 Z= 0.346 Chirality : 0.046 0.264 1187 Planarity : 0.005 0.075 1259 Dihedral : 5.545 70.952 1044 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 3.78 % Allowed : 17.65 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.90 (0.29), residues: 936 helix: 1.45 (0.37), residues: 205 sheet: -0.34 (0.32), residues: 284 loop : -1.79 (0.30), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 143 TYR 0.038 0.002 TYR A 47 PHE 0.021 0.002 PHE R 101 TRP 0.010 0.001 TRP R 75 HIS 0.006 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 7345) covalent geometry : angle 0.66182 (10047) SS BOND : bond 0.00998 ( 4) SS BOND : angle 0.78609 ( 8) hydrogen bonds : bond 0.03941 ( 299) hydrogen bonds : angle 5.18513 ( 864) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 132 time to evaluate : 0.279 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7483 (tp30) cc_final: 0.6901 (pp20) REVERT: A 122 ASN cc_start: 0.8289 (p0) cc_final: 0.7877 (m-40) REVERT: A 305 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8488 (pp) REVERT: B 82 MET cc_start: 0.7793 (mpp) cc_final: 0.7377 (mpp) REVERT: R 118 GLN cc_start: 0.8763 (tt0) cc_final: 0.8184 (tt0) REVERT: R 122 PHE cc_start: 0.8823 (m-80) cc_final: 0.8267 (m-80) REVERT: R 126 PHE cc_start: 0.9185 (m-10) cc_final: 0.8977 (m-10) REVERT: R 150 THR cc_start: 0.8049 (p) cc_final: 0.7677 (p) REVERT: R 153 ASN cc_start: 0.7285 (m-40) cc_final: 0.7040 (m-40) REVERT: R 168 ILE cc_start: 0.6488 (mt) cc_final: 0.6252 (mt) REVERT: R 232 LYS cc_start: 0.7966 (mmtt) cc_final: 0.6637 (ttpp) REVERT: C 238 THR cc_start: 0.8689 (p) cc_final: 0.8277 (p) outliers start: 27 outliers final: 20 residues processed: 153 average time/residue: 0.0695 time to fit residues: 14.3838 Evaluate side-chains 141 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 120 time to evaluate : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 70 SER Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 81 GLN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 3 optimal weight: 0.5980 chunk 75 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 chunk 83 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 6 optimal weight: 4.9990 chunk 2 optimal weight: 0.5980 overall best weight: 2.2386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 283 GLN R 296 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.144921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.106275 restraints weight = 12276.866| |-----------------------------------------------------------------------------| r_work (start): 0.3427 rms_B_bonded: 3.01 r_work: 0.3283 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.3748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 7349 Z= 0.258 Angle : 0.686 8.442 10055 Z= 0.360 Chirality : 0.047 0.259 1187 Planarity : 0.005 0.076 1259 Dihedral : 5.634 68.954 1044 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.97 % Favored : 91.03 % Rotamer: Outliers : 5.32 % Allowed : 19.33 % Favored : 75.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -1.14 (0.28), residues: 936 helix: 1.41 (0.36), residues: 205 sheet: -0.65 (0.32), residues: 273 loop : -1.88 (0.29), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 211 TYR 0.039 0.002 TYR A 47 PHE 0.027 0.002 PHE L 150 TRP 0.010 0.002 TRP R 75 HIS 0.006 0.001 HIS R 204 Details of bonding type rmsd covalent geometry : bond 0.00598 ( 7345) covalent geometry : angle 0.68626 (10047) SS BOND : bond 0.00638 ( 4) SS BOND : angle 0.77352 ( 8) hydrogen bonds : bond 0.03867 ( 299) hydrogen bonds : angle 5.20264 ( 864) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 123 time to evaluate : 0.224 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7601 (tp30) cc_final: 0.6986 (pp20) REVERT: A 122 ASN cc_start: 0.8392 (p0) cc_final: 0.8009 (m-40) REVERT: A 305 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8501 (pp) REVERT: B 82 MET cc_start: 0.7838 (mpp) cc_final: 0.7545 (mpp) REVERT: R 118 GLN cc_start: 0.8754 (tt0) cc_final: 0.8257 (tt0) REVERT: R 122 PHE cc_start: 0.8974 (m-80) cc_final: 0.8449 (m-80) REVERT: R 150 THR cc_start: 0.8113 (p) cc_final: 0.7638 (p) REVERT: R 153 ASN cc_start: 0.7371 (m-40) cc_final: 0.7103 (m-40) REVERT: R 168 ILE cc_start: 0.6800 (mt) cc_final: 0.6540 (mt) REVERT: R 221 THR cc_start: 0.8628 (p) cc_final: 0.8353 (t) REVERT: R 232 LYS cc_start: 0.8184 (mmtt) cc_final: 0.6770 (ttpp) REVERT: R 283 GLN cc_start: 0.6949 (tt0) cc_final: 0.6236 (tt0) REVERT: R 286 ILE cc_start: 0.6622 (OUTLIER) cc_final: 0.6247 (mm) REVERT: C 211 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7775 (mtm-85) REVERT: C 238 THR cc_start: 0.8788 (OUTLIER) cc_final: 0.8274 (p) outliers start: 38 outliers final: 30 residues processed: 154 average time/residue: 0.0760 time to fit residues: 16.0252 Evaluate side-chains 149 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 116 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain R residue 56 ASN Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 207 THR Chi-restraints excluded: chain R residue 286 ILE Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 97 VAL Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 193 THR Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 88 optimal weight: 0.9980 chunk 78 optimal weight: 3.9990 chunk 48 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 11 optimal weight: 0.6980 chunk 74 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 22 optimal weight: 0.9980 chunk 57 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.147629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111284 restraints weight = 12016.384| |-----------------------------------------------------------------------------| r_work (start): 0.3500 rms_B_bonded: 3.08 r_work: 0.3326 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.3825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 7349 Z= 0.148 Angle : 0.618 8.553 10055 Z= 0.321 Chirality : 0.045 0.238 1187 Planarity : 0.005 0.075 1259 Dihedral : 5.454 74.382 1044 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 3.64 % Allowed : 21.99 % Favored : 74.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.94 (0.28), residues: 936 helix: 1.49 (0.36), residues: 207 sheet: -0.51 (0.31), residues: 289 loop : -1.77 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 76 TYR 0.041 0.001 TYR A 47 PHE 0.017 0.002 PHE R 101 TRP 0.011 0.001 TRP R 75 HIS 0.008 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 7345) covalent geometry : angle 0.61819 (10047) SS BOND : bond 0.00349 ( 4) SS BOND : angle 0.84264 ( 8) hydrogen bonds : bond 0.03437 ( 299) hydrogen bonds : angle 4.94750 ( 864) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 134 time to evaluate : 0.282 Fit side-chains revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7593 (tp30) cc_final: 0.6952 (pp20) REVERT: A 122 ASN cc_start: 0.8330 (p0) cc_final: 0.7972 (m-40) REVERT: A 305 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8525 (pp) REVERT: B 78 VAL cc_start: 0.9253 (OUTLIER) cc_final: 0.9001 (m) REVERT: R 100 ASN cc_start: 0.6668 (t0) cc_final: 0.5565 (m110) REVERT: R 118 GLN cc_start: 0.8766 (tt0) cc_final: 0.8324 (tt0) REVERT: R 122 PHE cc_start: 0.8951 (m-80) cc_final: 0.8414 (m-80) REVERT: R 150 THR cc_start: 0.8073 (p) cc_final: 0.7596 (p) REVERT: R 153 ASN cc_start: 0.7296 (m-40) cc_final: 0.7007 (m-40) REVERT: R 168 ILE cc_start: 0.6894 (mt) cc_final: 0.6661 (mt) REVERT: R 232 LYS cc_start: 0.8130 (mmtt) cc_final: 0.6716 (ttpp) REVERT: C 211 ARG cc_start: 0.8182 (mtt-85) cc_final: 0.7819 (mtm-85) REVERT: C 238 THR cc_start: 0.8708 (OUTLIER) cc_final: 0.8198 (p) outliers start: 26 outliers final: 21 residues processed: 151 average time/residue: 0.0855 time to fit residues: 17.4966 Evaluate side-chains 145 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 121 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain R residue 38 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 35 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 80 optimal weight: 0.6980 chunk 60 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 48 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.145762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.107746 restraints weight = 12114.823| |-----------------------------------------------------------------------------| r_work (start): 0.3450 rms_B_bonded: 2.99 r_work: 0.3300 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.4049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 7349 Z= 0.192 Angle : 0.648 8.856 10055 Z= 0.335 Chirality : 0.045 0.262 1187 Planarity : 0.005 0.074 1259 Dihedral : 5.397 74.183 1044 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.06 % Allowed : 23.95 % Favored : 71.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.93 (0.29), residues: 936 helix: 1.57 (0.36), residues: 207 sheet: -0.55 (0.31), residues: 286 loop : -1.75 (0.30), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 76 TYR 0.038 0.002 TYR A 47 PHE 0.020 0.002 PHE R 101 TRP 0.010 0.001 TRP R 75 HIS 0.007 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00442 ( 7345) covalent geometry : angle 0.64776 (10047) SS BOND : bond 0.00455 ( 4) SS BOND : angle 0.88581 ( 8) hydrogen bonds : bond 0.03522 ( 299) hydrogen bonds : angle 4.93531 ( 864) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 134 time to evaluate : 0.269 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7607 (tp30) cc_final: 0.7024 (pp20) REVERT: A 122 ASN cc_start: 0.8315 (p0) cc_final: 0.8031 (m-40) REVERT: A 268 PHE cc_start: 0.7421 (t80) cc_final: 0.7217 (t80) REVERT: A 305 LEU cc_start: 0.8782 (OUTLIER) cc_final: 0.8438 (pp) REVERT: B 78 VAL cc_start: 0.9286 (OUTLIER) cc_final: 0.9056 (m) REVERT: R 38 HIS cc_start: 0.5111 (OUTLIER) cc_final: 0.4649 (m170) REVERT: R 100 ASN cc_start: 0.6596 (t0) cc_final: 0.5728 (m110) REVERT: R 118 GLN cc_start: 0.8774 (tt0) cc_final: 0.8359 (tt0) REVERT: R 122 PHE cc_start: 0.8932 (m-80) cc_final: 0.8372 (m-80) REVERT: R 150 THR cc_start: 0.8054 (p) cc_final: 0.7484 (p) REVERT: R 153 ASN cc_start: 0.7219 (m-40) cc_final: 0.6908 (m-40) REVERT: R 168 ILE cc_start: 0.7088 (mt) cc_final: 0.6857 (mt) REVERT: R 221 THR cc_start: 0.8660 (p) cc_final: 0.8364 (t) REVERT: R 232 LYS cc_start: 0.8256 (mmtt) cc_final: 0.6780 (ttpp) REVERT: R 283 GLN cc_start: 0.6584 (tt0) cc_final: 0.5899 (tm-30) REVERT: C 142 LEU cc_start: 0.8129 (OUTLIER) cc_final: 0.7906 (tt) REVERT: C 211 ARG cc_start: 0.8270 (mtt-85) cc_final: 0.7929 (mtm-85) REVERT: C 238 THR cc_start: 0.8720 (OUTLIER) cc_final: 0.8203 (p) outliers start: 29 outliers final: 21 residues processed: 153 average time/residue: 0.0831 time to fit residues: 17.2563 Evaluate side-chains 151 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain R residue 38 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 275 ASN Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 25 optimal weight: 8.9990 chunk 71 optimal weight: 2.9990 chunk 39 optimal weight: 5.9990 chunk 82 optimal weight: 0.0060 chunk 76 optimal weight: 0.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 70 optimal weight: 0.8980 chunk 46 optimal weight: 0.5980 overall best weight: 0.9000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 56 ASN ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 275 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.147516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.111826 restraints weight = 11987.865| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.18 r_work: 0.3327 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.3327 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 7349 Z= 0.148 Angle : 0.634 9.082 10055 Z= 0.324 Chirality : 0.045 0.262 1187 Planarity : 0.005 0.081 1259 Dihedral : 5.210 76.599 1044 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 5.46 % Allowed : 22.69 % Favored : 71.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.82 (0.29), residues: 936 helix: 1.66 (0.37), residues: 207 sheet: -0.36 (0.32), residues: 278 loop : -1.76 (0.30), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 76 TYR 0.039 0.001 TYR A 47 PHE 0.022 0.001 PHE R 101 TRP 0.011 0.001 TRP R 75 HIS 0.010 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00335 ( 7345) covalent geometry : angle 0.63345 (10047) SS BOND : bond 0.00406 ( 4) SS BOND : angle 0.90028 ( 8) hydrogen bonds : bond 0.03310 ( 299) hydrogen bonds : angle 4.75227 ( 864) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 133 time to evaluate : 0.198 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7617 (tp30) cc_final: 0.6961 (pp20) REVERT: A 122 ASN cc_start: 0.8222 (p0) cc_final: 0.7889 (m-40) REVERT: A 305 LEU cc_start: 0.8699 (OUTLIER) cc_final: 0.8402 (pp) REVERT: B 78 VAL cc_start: 0.9331 (OUTLIER) cc_final: 0.9098 (m) REVERT: R 38 HIS cc_start: 0.5087 (OUTLIER) cc_final: 0.4610 (m170) REVERT: R 100 ASN cc_start: 0.6725 (t0) cc_final: 0.5839 (m110) REVERT: R 118 GLN cc_start: 0.8818 (tt0) cc_final: 0.8440 (tt0) REVERT: R 122 PHE cc_start: 0.8917 (m-80) cc_final: 0.8226 (m-80) REVERT: R 126 PHE cc_start: 0.9218 (m-10) cc_final: 0.8944 (m-10) REVERT: R 150 THR cc_start: 0.8032 (p) cc_final: 0.7453 (p) REVERT: R 153 ASN cc_start: 0.7206 (m-40) cc_final: 0.6884 (m-40) REVERT: R 188 TYR cc_start: 0.7527 (p90) cc_final: 0.7189 (p90) REVERT: R 221 THR cc_start: 0.8640 (p) cc_final: 0.8357 (t) REVERT: R 232 LYS cc_start: 0.8267 (mmtt) cc_final: 0.6755 (ttpp) REVERT: R 258 CYS cc_start: 0.8209 (m) cc_final: 0.8007 (p) REVERT: R 283 GLN cc_start: 0.6512 (OUTLIER) cc_final: 0.5884 (tm-30) REVERT: C 142 LEU cc_start: 0.8167 (OUTLIER) cc_final: 0.7903 (tt) REVERT: C 211 ARG cc_start: 0.8292 (mtt-85) cc_final: 0.7867 (mtm-85) REVERT: C 238 THR cc_start: 0.8707 (OUTLIER) cc_final: 0.8203 (p) outliers start: 39 outliers final: 30 residues processed: 159 average time/residue: 0.0714 time to fit residues: 15.6151 Evaluate side-chains 163 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 127 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 305 LEU Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain R residue 38 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 107 ILE Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 158 ILE Chi-restraints excluded: chain R residue 161 ILE Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 275 ASN Chi-restraints excluded: chain R residue 283 GLN Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 0.1980 chunk 76 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 46 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 4.9990 chunk 81 optimal weight: 0.7980 chunk 7 optimal weight: 3.9990 chunk 77 optimal weight: 1.9990 chunk 78 optimal weight: 0.4980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 210 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 120 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 = 0.3995 r_free = 0.3995 target = 0.148901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.113626 restraints weight = 12068.760| |-----------------------------------------------------------------------------| r_work (start): 0.3532 rms_B_bonded: 3.18 r_work: 0.3350 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 7349 Z= 0.126 Angle : 0.627 9.081 10055 Z= 0.317 Chirality : 0.044 0.263 1187 Planarity : 0.005 0.084 1259 Dihedral : 5.084 79.303 1044 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.01 % Favored : 91.99 % Rotamer: Outliers : 4.48 % Allowed : 23.39 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.74 (0.29), residues: 936 helix: 1.66 (0.37), residues: 208 sheet: -0.22 (0.32), residues: 275 loop : -1.75 (0.30), residues: 453 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 211 TYR 0.035 0.001 TYR A 47 PHE 0.022 0.001 PHE R 101 TRP 0.012 0.001 TRP R 75 HIS 0.021 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 7345) covalent geometry : angle 0.62640 (10047) SS BOND : bond 0.00362 ( 4) SS BOND : angle 0.93328 ( 8) hydrogen bonds : bond 0.03228 ( 299) hydrogen bonds : angle 4.66737 ( 864) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7598 (tp30) cc_final: 0.6943 (pp20) REVERT: A 122 ASN cc_start: 0.8195 (p0) cc_final: 0.7878 (m-40) REVERT: R 38 HIS cc_start: 0.5134 (OUTLIER) cc_final: 0.4707 (m170) REVERT: R 100 ASN cc_start: 0.6647 (t0) cc_final: 0.5876 (m110) REVERT: R 118 GLN cc_start: 0.8793 (tt0) cc_final: 0.8339 (tt0) REVERT: R 122 PHE cc_start: 0.8919 (m-80) cc_final: 0.8437 (m-80) REVERT: R 150 THR cc_start: 0.8016 (p) cc_final: 0.7524 (p) REVERT: R 153 ASN cc_start: 0.7182 (m-40) cc_final: 0.6892 (m-40) REVERT: R 221 THR cc_start: 0.8637 (p) cc_final: 0.8358 (t) REVERT: R 222 MET cc_start: 0.7580 (mmm) cc_final: 0.7263 (mtt) REVERT: R 232 LYS cc_start: 0.8241 (mmtt) cc_final: 0.6711 (ttpp) REVERT: C 142 LEU cc_start: 0.8138 (OUTLIER) cc_final: 0.7856 (tt) REVERT: C 211 ARG cc_start: 0.8227 (mtt-85) cc_final: 0.7817 (mtm-85) REVERT: C 238 THR cc_start: 0.8685 (OUTLIER) cc_final: 0.8390 (p) outliers start: 32 outliers final: 25 residues processed: 155 average time/residue: 0.0767 time to fit residues: 15.9600 Evaluate side-chains 156 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain R residue 38 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 207 MET Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 73 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 49 optimal weight: 0.8980 chunk 45 optimal weight: 9.9990 chunk 92 optimal weight: 4.9990 chunk 84 optimal weight: 0.0980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 210 HIS A 353 HIS R 56 ASN ** R 120 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 = 0.3998 r_free = 0.3998 target = 0.149298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.112923 restraints weight = 11986.914| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 3.17 r_work: 0.3355 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.4280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 7349 Z= 0.132 Angle : 0.639 8.690 10055 Z= 0.323 Chirality : 0.044 0.301 1187 Planarity : 0.005 0.088 1259 Dihedral : 5.030 80.387 1044 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.59 % Favored : 92.41 % Rotamer: Outliers : 3.50 % Allowed : 25.07 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.29), residues: 936 helix: 1.74 (0.37), residues: 208 sheet: -0.04 (0.34), residues: 257 loop : -1.68 (0.29), residues: 471 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 211 TYR 0.032 0.001 TYR A 47 PHE 0.019 0.001 PHE R 101 TRP 0.011 0.001 TRP R 75 HIS 0.009 0.001 HIS R 274 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 7345) covalent geometry : angle 0.63847 (10047) SS BOND : bond 0.00377 ( 4) SS BOND : angle 0.98901 ( 8) hydrogen bonds : bond 0.03365 ( 299) hydrogen bonds : angle 4.64251 ( 864) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 134 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 118 GLU cc_start: 0.7616 (tp30) cc_final: 0.6944 (pp20) REVERT: A 122 ASN cc_start: 0.8266 (p0) cc_final: 0.7930 (m-40) REVERT: B 36 TRP cc_start: 0.8583 (m100) cc_final: 0.8331 (m100) REVERT: R 38 HIS cc_start: 0.5163 (OUTLIER) cc_final: 0.4810 (m170) REVERT: R 100 ASN cc_start: 0.6724 (t0) cc_final: 0.5984 (m110) REVERT: R 118 GLN cc_start: 0.8770 (tt0) cc_final: 0.8392 (tt0) REVERT: R 122 PHE cc_start: 0.8906 (m-80) cc_final: 0.8310 (m-80) REVERT: R 126 PHE cc_start: 0.9160 (m-10) cc_final: 0.8898 (m-80) REVERT: R 221 THR cc_start: 0.8640 (p) cc_final: 0.8376 (t) REVERT: R 232 LYS cc_start: 0.8250 (mmtt) cc_final: 0.6699 (ttpp) REVERT: C 142 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7772 (tt) REVERT: C 211 ARG cc_start: 0.8172 (mtt-85) cc_final: 0.7722 (mtm-85) REVERT: C 238 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.8434 (p) outliers start: 25 outliers final: 21 residues processed: 148 average time/residue: 0.0770 time to fit residues: 15.4233 Evaluate side-chains 149 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 125 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain R residue 38 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 142 LEU Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 46 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 19 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 64 optimal weight: 9.9990 chunk 23 optimal weight: 0.0770 overall best weight: 0.8944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 198 HIS ** R 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 296 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.151694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.117220 restraints weight = 12034.072| |-----------------------------------------------------------------------------| r_work (start): 0.3610 rms_B_bonded: 3.26 r_work: 0.3428 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7950 moved from start: 0.4365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7349 Z= 0.148 Angle : 0.655 9.159 10055 Z= 0.333 Chirality : 0.045 0.315 1187 Planarity : 0.005 0.090 1259 Dihedral : 5.005 79.219 1044 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.12 % Favored : 91.88 % Rotamer: Outliers : 4.48 % Allowed : 24.65 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.68 (0.29), residues: 936 helix: 1.73 (0.37), residues: 209 sheet: -0.23 (0.34), residues: 252 loop : -1.63 (0.29), residues: 475 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 162 TYR 0.031 0.001 TYR A 47 PHE 0.021 0.001 PHE R 101 TRP 0.010 0.001 TRP R 75 HIS 0.009 0.001 HIS R 204 Details of bonding type rmsd covalent geometry : bond 0.00341 ( 7345) covalent geometry : angle 0.65431 (10047) SS BOND : bond 0.00405 ( 4) SS BOND : angle 1.01530 ( 8) hydrogen bonds : bond 0.03336 ( 299) hydrogen bonds : angle 4.67682 ( 864) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1872 Ramachandran restraints generated. 936 Oldfield, 0 Emsley, 936 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 130 time to evaluate : 0.284 Fit side-chains REVERT: A 118 GLU cc_start: 0.7563 (tp30) cc_final: 0.7020 (pp20) REVERT: A 122 ASN cc_start: 0.8139 (p0) cc_final: 0.7926 (m-40) REVERT: R 38 HIS cc_start: 0.5084 (OUTLIER) cc_final: 0.4829 (m170) REVERT: R 100 ASN cc_start: 0.6566 (t0) cc_final: 0.5846 (m110) REVERT: R 118 GLN cc_start: 0.8738 (tt0) cc_final: 0.8442 (tt0) REVERT: R 122 PHE cc_start: 0.8921 (m-80) cc_final: 0.8255 (m-80) REVERT: R 126 PHE cc_start: 0.9183 (m-10) cc_final: 0.8933 (m-80) REVERT: R 221 THR cc_start: 0.8593 (p) cc_final: 0.8343 (t) REVERT: R 232 LYS cc_start: 0.8219 (mmtt) cc_final: 0.6713 (ttpp) REVERT: C 211 ARG cc_start: 0.8245 (mtt-85) cc_final: 0.7964 (mtm-85) REVERT: C 238 THR cc_start: 0.8682 (OUTLIER) cc_final: 0.8411 (p) outliers start: 32 outliers final: 27 residues processed: 149 average time/residue: 0.0651 time to fit residues: 13.6221 Evaluate side-chains 150 residues out of total 840 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 121 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 150 PHE Chi-restraints excluded: chain A residue 34 VAL Chi-restraints excluded: chain A residue 70 VAL Chi-restraints excluded: chain A residue 167 VAL Chi-restraints excluded: chain A residue 220 VAL Chi-restraints excluded: chain A residue 221 THR Chi-restraints excluded: chain A residue 241 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 365 VAL Chi-restraints excluded: chain B residue 38 ARG Chi-restraints excluded: chain B residue 56 THR Chi-restraints excluded: chain B residue 58 THR Chi-restraints excluded: chain B residue 76 ASN Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 108 THR Chi-restraints excluded: chain R residue 38 HIS Chi-restraints excluded: chain R residue 70 THR Chi-restraints excluded: chain R residue 113 ASN Chi-restraints excluded: chain R residue 119 LEU Chi-restraints excluded: chain R residue 139 LEU Chi-restraints excluded: chain R residue 155 LEU Chi-restraints excluded: chain R residue 249 LEU Chi-restraints excluded: chain R residue 298 CYS Chi-restraints excluded: chain R residue 302 ILE Chi-restraints excluded: chain C residue 152 ASN Chi-restraints excluded: chain C residue 174 SER Chi-restraints excluded: chain C residue 238 THR Chi-restraints excluded: chain C residue 241 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 9 optimal weight: 0.0000 chunk 83 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 78 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 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 = 0.4004 r_free = 0.4004 target = 0.149366 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.113830 restraints weight = 11998.964| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.23 r_work: 0.3356 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.4449 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 7349 Z= 0.135 Angle : 0.653 9.380 10055 Z= 0.328 Chirality : 0.044 0.294 1187 Planarity : 0.005 0.088 1259 Dihedral : 4.974 80.387 1044 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.11 % Allowed : 7.91 % Favored : 91.99 % Rotamer: Outliers : 4.06 % Allowed : 25.07 % Favored : 70.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % 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: -0.66 (0.29), residues: 936 helix: 1.68 (0.37), residues: 209 sheet: -0.15 (0.34), residues: 248 loop : -1.62 (0.29), residues: 479 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 162 TYR 0.031 0.001 TYR A 47 PHE 0.018 0.001 PHE R 101 TRP 0.012 0.001 TRP R 259 HIS 0.008 0.001 HIS R 273 Details of bonding type rmsd covalent geometry : bond 0.00305 ( 7345) covalent geometry : angle 0.65220 (10047) SS BOND : bond 0.00521 ( 4) SS BOND : angle 1.12499 ( 8) hydrogen bonds : bond 0.03204 ( 299) hydrogen bonds : angle 4.62740 ( 864) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1733.24 seconds wall clock time: 30 minutes 21.13 seconds (1821.13 seconds total)