Starting phenix.real_space_refine on Tue Feb 3 18:08:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9op1_70677/02_2026/9op1_70677.cif Found real_map, /net/cci-nas-00/data/ceres_data/9op1_70677/02_2026/9op1_70677.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9op1_70677/02_2026/9op1_70677.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9op1_70677/02_2026/9op1_70677.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9op1_70677/02_2026/9op1_70677.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9op1_70677/02_2026/9op1_70677.map" } resolution = 4.05 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= 0.014 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 3768 2.51 5 N 965 2.21 5 O 1088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 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: 5843 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1766 Classifications: {'peptide': 232} Link IDs: {'PCIS': 3, 'PTRANS': 12, 'TRANS': 216} Chain: "B" Number of atoms: 1579 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1579 Classifications: {'peptide': 210} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 195} Chain: "C" Number of atoms: 2498 Number of conformers: 1 Conformer: "" Number of residues, atoms: 324, 2498 Classifications: {'peptide': 324} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 7, 'TRANS': 316} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 17 Planarities with less than four sites: {'ARG:plan': 1, 'TYR:plan': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 1.41, per 1000 atoms: 0.24 Number of scatterers: 5843 At special positions: 0 Unit cell: (66.72, 80.898, 138.444, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 1088 8.00 N 965 7.00 C 3768 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 92 " distance=2.03 Simple disulfide: pdb=" SG CYS A 140 " - pdb=" SG CYS A 196 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.03 Simple disulfide: pdb=" SG CYS B 135 " - pdb=" SG CYS B 194 " 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: 0.47 Conformation dependent library (CDL) restraints added in 320.8 milliseconds 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1378 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 13 sheets defined 36.3% alpha, 30.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing helix chain 'A' and resid 83 through 87 removed outlier: 3.828A pdb=" N THR A 87 " --> pdb=" O THR A 84 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 158 No H-bonds generated for 'chain 'A' and resid 156 through 158' Processing helix chain 'B' and resid 27 through 30 Processing helix chain 'B' and resid 79 through 83 removed outlier: 4.022A pdb=" N GLU B 83 " --> pdb=" O ALA B 80 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 182 through 187 removed outlier: 3.552A pdb=" N LYS B 187 " --> pdb=" O PRO B 183 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 95 removed outlier: 3.898A pdb=" N ASN C 67 " --> pdb=" O PHE C 63 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N LEU C 87 " --> pdb=" O ILE C 83 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL C 88 " --> pdb=" O TRP C 84 " (cutoff:3.500A) Processing helix chain 'C' and resid 106 through 125 removed outlier: 3.842A pdb=" N ASN C 110 " --> pdb=" O VAL C 106 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE C 111 " --> pdb=" O ILE C 107 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU C 119 " --> pdb=" O VAL C 115 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA C 120 " --> pdb=" O VAL C 116 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N ASP C 122 " --> pdb=" O GLY C 118 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N GLY C 123 " --> pdb=" O LEU C 119 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N VAL C 125 " --> pdb=" O ILE C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 125 through 131 Processing helix chain 'C' and resid 151 through 157 removed outlier: 3.867A pdb=" N SER C 157 " --> pdb=" O CYS C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 158 through 171 Processing helix chain 'C' and resid 180 through 218 removed outlier: 3.562A pdb=" N GLY C 184 " --> pdb=" O HIS C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 248 removed outlier: 3.900A pdb=" N VAL C 230 " --> pdb=" O ARG C 226 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N THR C 246 " --> pdb=" O LEU C 242 " (cutoff:3.500A) Processing helix chain 'C' and resid 258 through 282 removed outlier: 3.791A pdb=" N THR C 262 " --> pdb=" O TRP C 258 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N PHE C 263 " --> pdb=" O ARG C 259 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N SER C 264 " --> pdb=" O SER C 260 " (cutoff:3.500A) Proline residue: C 269 - end of helix Processing helix chain 'C' and resid 291 through 312 Processing helix chain 'C' and resid 318 through 323 Processing helix chain 'C' and resid 327 through 344 removed outlier: 3.535A pdb=" N LEU C 332 " --> pdb=" O ALA C 328 " (cutoff:3.500A) removed outlier: 4.639A pdb=" N CYS C 340 " --> pdb=" O ASP C 336 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N GLY C 341 " --> pdb=" O ASP C 337 " (cutoff:3.500A) Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 360 through 381 removed outlier: 3.552A pdb=" N LEU C 380 " --> pdb=" O VAL C 376 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 7 removed outlier: 4.359A pdb=" N ARG A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N SER A 25 " --> pdb=" O ARG A 3 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N THR A 77 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ASP A 72 " --> pdb=" O THR A 77 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N SER A 70 " --> pdb=" O TYR A 79 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.712A pdb=" N ILE A 110 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N TRP A 33 " --> pdb=" O THR A 95 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N MET A 34 " --> pdb=" O ARG A 50 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N ARG A 50 " --> pdb=" O MET A 34 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 10 through 12 removed outlier: 3.712A pdb=" N ILE A 110 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TYR A 98 " --> pdb=" O GLU A 100I" (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.664A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 123 through 124 removed outlier: 3.664A pdb=" N GLY A 139 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N ALA A 137 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 184 " --> pdb=" O ALA A 137 " (cutoff:3.500A) removed outlier: 5.993A pdb=" N GLY A 139 " --> pdb=" O VAL A 182 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL A 182 " --> pdb=" O GLY A 139 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU A 141 " --> pdb=" O SER A 180 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N SER A 180 " --> pdb=" O LEU A 141 " (cutoff:3.500A) removed outlier: 4.971A pdb=" N LYS A 143 " --> pdb=" O LEU A 178 " (cutoff:3.500A) removed outlier: 7.160A pdb=" N LEU A 178 " --> pdb=" O LYS A 143 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AA7, first strand: chain 'B' and resid 4 through 6 Processing sheet with id=AA8, first strand: chain 'B' and resid 9 through 13 Processing sheet with id=AA9, first strand: chain 'B' and resid 45 through 49 removed outlier: 6.564A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N SER B 89 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER B 90 " --> pdb=" O VAL B 97 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.503A pdb=" N SER B 138 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B 173 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 115 through 119 removed outlier: 3.503A pdb=" N SER B 138 " --> pdb=" O SER B 115 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N VAL B 134 " --> pdb=" O PHE B 119 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N TYR B 173 " --> pdb=" O ASP B 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 154 through 155 Processing sheet with id=AB4, first strand: chain 'B' and resid 154 through 155 313 hydrogen bonds defined for protein. 846 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: 0.90 Time building geometry restraints manager: 0.62 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: 1782 1.34 - 1.45: 1049 1.45 - 1.57: 3132 1.57 - 1.69: 0 1.69 - 1.81: 31 Bond restraints: 5994 Sorted by residual: bond pdb=" C THR C 96 " pdb=" N THR C 97 " ideal model delta sigma weight residual 1.328 1.342 -0.014 1.30e-02 5.92e+03 1.14e+00 bond pdb=" CG1 ILE C 107 " pdb=" CD1 ILE C 107 " ideal model delta sigma weight residual 1.513 1.472 0.041 3.90e-02 6.57e+02 1.12e+00 bond pdb=" C TYR C 181 " pdb=" N PRO C 182 " ideal model delta sigma weight residual 1.334 1.358 -0.024 2.34e-02 1.83e+03 1.05e+00 bond pdb=" CA THR C 97 " pdb=" CB THR C 97 " ideal model delta sigma weight residual 1.527 1.543 -0.016 1.61e-02 3.86e+03 1.03e+00 bond pdb=" CA LYS C 357 " pdb=" C LYS C 357 " ideal model delta sigma weight residual 1.532 1.523 0.009 9.60e-03 1.09e+04 9.50e-01 ... (remaining 5989 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 7886 1.60 - 3.21: 234 3.21 - 4.81: 31 4.81 - 6.41: 4 6.41 - 8.01: 5 Bond angle restraints: 8160 Sorted by residual: angle pdb=" N VAL A 63 " pdb=" CA VAL A 63 " pdb=" C VAL A 63 " ideal model delta sigma weight residual 113.71 109.87 3.84 9.50e-01 1.11e+00 1.64e+01 angle pdb=" C ASN C 283 " pdb=" N ASN C 284 " pdb=" CA ASN C 284 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 angle pdb=" N LYS B 157 " pdb=" CA LYS B 157 " pdb=" C LYS B 157 " ideal model delta sigma weight residual 114.09 109.56 4.53 1.55e+00 4.16e-01 8.52e+00 angle pdb=" C LEU B 126 " pdb=" N GLN B 127 " pdb=" CA GLN B 127 " ideal model delta sigma weight residual 120.72 116.19 4.53 1.67e+00 3.59e-01 7.35e+00 angle pdb=" CA GLN B 109 " pdb=" CB GLN B 109 " pdb=" CG GLN B 109 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.29e+00 ... (remaining 8155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 3175 18.00 - 35.99: 250 35.99 - 53.99: 43 53.99 - 71.99: 6 71.99 - 89.99: 4 Dihedral angle restraints: 3478 sinusoidal: 1306 harmonic: 2172 Sorted by residual: dihedral pdb=" CB CYS A 140 " pdb=" SG CYS A 140 " pdb=" SG CYS A 196 " pdb=" CB CYS A 196 " ideal model delta sinusoidal sigma weight residual 93.00 175.14 -82.14 1 1.00e+01 1.00e-02 8.29e+01 dihedral pdb=" CA LEU C 353 " pdb=" C LEU C 353 " pdb=" N PHE C 354 " pdb=" CA PHE C 354 " ideal model delta harmonic sigma weight residual -180.00 -158.24 -21.76 0 5.00e+00 4.00e-02 1.89e+01 dihedral pdb=" CA THR C 97 " pdb=" C THR C 97 " pdb=" N TYR C 98 " pdb=" CA TYR C 98 " ideal model delta harmonic sigma weight residual -180.00 -159.23 -20.77 0 5.00e+00 4.00e-02 1.72e+01 ... (remaining 3475 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 595 0.035 - 0.069: 225 0.069 - 0.104: 73 0.104 - 0.139: 31 0.139 - 0.174: 1 Chirality restraints: 925 Sorted by residual: chirality pdb=" CB VAL C 106 " pdb=" CA VAL C 106 " pdb=" CG1 VAL C 106 " pdb=" CG2 VAL C 106 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.53e-01 chirality pdb=" CB VAL C 371 " pdb=" CA VAL C 371 " pdb=" CG1 VAL C 371 " pdb=" CG2 VAL C 371 " both_signs ideal model delta sigma weight residual False -2.63 -2.50 -0.13 2.00e-01 2.50e+01 4.43e-01 chirality pdb=" CG LEU C 356 " pdb=" CB LEU C 356 " pdb=" CD1 LEU C 356 " pdb=" CD2 LEU C 356 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 4.21e-01 ... (remaining 922 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN B 109 " 0.035 5.00e-02 4.00e+02 5.33e-02 4.55e+00 pdb=" N PRO B 110 " -0.092 5.00e-02 4.00e+02 pdb=" CA PRO B 110 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 110 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 125 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 126 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 126 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 126 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU A 148 " 0.026 5.00e-02 4.00e+02 3.89e-02 2.42e+00 pdb=" N PRO A 149 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 149 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 149 " 0.020 5.00e-02 4.00e+02 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 135 2.68 - 3.24: 5971 3.24 - 3.79: 9056 3.79 - 4.35: 11416 4.35 - 4.90: 18870 Nonbonded interactions: 45448 Sorted by model distance: nonbonded pdb=" OE2 GLU B 204 " pdb=" OG1 THR B 206 " model vdw 2.127 3.040 nonbonded pdb=" OG SER B 34 " pdb=" OG SER B 89 " model vdw 2.144 3.040 nonbonded pdb=" OG1 THR C 96 " pdb=" OG SER C 104 " model vdw 2.222 3.040 nonbonded pdb=" OE1 GLN B 185 " pdb=" OG SER B 188 " model vdw 2.268 3.040 nonbonded pdb=" OE1 GLN B 6 " pdb=" OG1 THR B 102 " model vdw 2.271 3.040 ... (remaining 45443 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 group one per residue 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: 2.800 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: 0.110 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 7.240 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:1.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 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 0.041 5998 Z= 0.158 Angle : 0.652 8.014 8168 Z= 0.347 Chirality : 0.043 0.174 925 Planarity : 0.005 0.053 1021 Dihedral : 13.322 89.985 2088 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 13.40 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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 (0.31), residues: 760 helix: 1.01 (0.33), residues: 240 sheet: 0.27 (0.43), residues: 160 loop : -1.88 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 29 TYR 0.015 0.001 TYR A 90 PHE 0.012 0.001 PHE C 159 TRP 0.012 0.001 TRP B 35 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 5994) covalent geometry : angle 0.65029 ( 8160) SS BOND : bond 0.00146 ( 4) SS BOND : angle 1.43976 ( 8) hydrogen bonds : bond 0.19802 ( 283) hydrogen bonds : angle 8.59084 ( 846) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 150 time to evaluate : 0.215 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 197 ASN cc_start: 0.7736 (m110) cc_final: 0.7457 (m110) REVERT: A 206 LYS cc_start: 0.8375 (tptt) cc_final: 0.7472 (mttt) REVERT: B 74 THR cc_start: 0.9324 (m) cc_final: 0.9088 (p) REVERT: B 125 GLU cc_start: 0.5848 (pt0) cc_final: 0.5559 (pt0) REVERT: B 167 LYS cc_start: 0.8551 (mmtp) cc_final: 0.7966 (tmtt) REVERT: B 171 ASN cc_start: 0.7292 (t0) cc_final: 0.6316 (t0) REVERT: C 204 MET cc_start: 0.8005 (mtp) cc_final: 0.7722 (mtt) REVERT: C 265 MET cc_start: 0.8568 (ttm) cc_final: 0.8202 (ttm) REVERT: C 352 GLU cc_start: 0.8548 (tt0) cc_final: 0.8197 (tt0) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.0831 time to fit residues: 16.2169 Evaluate side-chains 119 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.167855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.125385 restraints weight = 10152.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.129059 restraints weight = 6144.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131420 restraints weight = 4436.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.132799 restraints weight = 3622.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134122 restraints weight = 3199.451| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.1115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5998 Z= 0.167 Angle : 0.641 7.677 8168 Z= 0.335 Chirality : 0.043 0.188 925 Planarity : 0.005 0.055 1021 Dihedral : 4.567 18.726 817 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.03 % Favored : 91.84 % Rotamer: Outliers : 0.31 % Allowed : 6.13 % Favored : 93.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.59 (0.31), residues: 760 helix: 1.13 (0.33), residues: 248 sheet: 0.79 (0.45), residues: 155 loop : -2.16 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 259 TYR 0.016 0.001 TYR A 176 PHE 0.015 0.001 PHE C 159 TRP 0.010 0.001 TRP A 47 HIS 0.004 0.001 HIS B 198 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5994) covalent geometry : angle 0.63857 ( 8160) SS BOND : bond 0.00293 ( 4) SS BOND : angle 1.79033 ( 8) hydrogen bonds : bond 0.04306 ( 283) hydrogen bonds : angle 5.90403 ( 846) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 149 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7873 (m-10) cc_final: 0.7643 (m-10) REVERT: A 206 LYS cc_start: 0.8315 (tptt) cc_final: 0.7479 (mttt) REVERT: B 74 THR cc_start: 0.9193 (m) cc_final: 0.8852 (p) REVERT: B 167 LYS cc_start: 0.8714 (mmtp) cc_final: 0.8432 (mmtp) REVERT: B 171 ASN cc_start: 0.7419 (t0) cc_final: 0.6592 (t0) REVERT: B 185 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8136 (mm-40) REVERT: C 117 MET cc_start: 0.8704 (tpp) cc_final: 0.8127 (ttm) REVERT: C 204 MET cc_start: 0.7915 (mtp) cc_final: 0.7517 (mtp) REVERT: C 330 HIS cc_start: 0.8288 (m-70) cc_final: 0.8085 (m-70) REVERT: C 352 GLU cc_start: 0.8556 (tt0) cc_final: 0.8128 (tt0) outliers start: 2 outliers final: 0 residues processed: 151 average time/residue: 0.0800 time to fit residues: 16.0290 Evaluate side-chains 113 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 36 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 72 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 75 optimal weight: 0.7980 chunk 1 optimal weight: 0.0870 chunk 43 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 190 GLN C 255 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.169773 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.127096 restraints weight = 10316.350| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130773 restraints weight = 6324.449| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133393 restraints weight = 4612.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.134732 restraints weight = 3755.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.135844 restraints weight = 3315.469| |-----------------------------------------------------------------------------| r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.1475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5998 Z= 0.149 Angle : 0.627 8.211 8168 Z= 0.326 Chirality : 0.043 0.161 925 Planarity : 0.005 0.056 1021 Dihedral : 4.543 18.877 817 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 10.65 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.68 % Favored : 91.18 % Rotamer: Outliers : 0.31 % Allowed : 4.40 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.54 (0.31), residues: 760 helix: 1.13 (0.33), residues: 249 sheet: 0.80 (0.44), residues: 155 loop : -2.09 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 259 TYR 0.013 0.001 TYR B 36 PHE 0.020 0.001 PHE B 119 TRP 0.031 0.001 TRP A 47 HIS 0.008 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5994) covalent geometry : angle 0.62517 ( 8160) SS BOND : bond 0.00298 ( 4) SS BOND : angle 1.75248 ( 8) hydrogen bonds : bond 0.04055 ( 283) hydrogen bonds : angle 5.53382 ( 846) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 154 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 TYR cc_start: 0.7890 (m-10) cc_final: 0.7656 (m-10) REVERT: B 74 THR cc_start: 0.9158 (m) cc_final: 0.8888 (p) REVERT: B 185 GLN cc_start: 0.8568 (mm-40) cc_final: 0.8126 (mm-40) REVERT: C 117 MET cc_start: 0.8719 (tpp) cc_final: 0.7994 (ttm) REVERT: C 204 MET cc_start: 0.7914 (mtp) cc_final: 0.7500 (mtp) REVERT: C 352 GLU cc_start: 0.8506 (tt0) cc_final: 0.8073 (tt0) outliers start: 2 outliers final: 0 residues processed: 155 average time/residue: 0.0704 time to fit residues: 14.4734 Evaluate side-chains 110 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 110 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 73 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 74 optimal weight: 0.9980 chunk 13 optimal weight: 10.0000 chunk 69 optimal weight: 0.0060 chunk 70 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.170965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.128899 restraints weight = 10354.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.132689 restraints weight = 6389.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134993 restraints weight = 4648.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 53)----------------| | r_work = 0.3605 r_free = 0.3605 target = 0.136869 restraints weight = 3823.563| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.137748 restraints weight = 3336.369| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5998 Z= 0.146 Angle : 0.630 7.928 8168 Z= 0.322 Chirality : 0.044 0.164 925 Planarity : 0.005 0.058 1021 Dihedral : 4.466 19.361 817 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.13 % Allowed : 8.95 % Favored : 90.92 % Rotamer: Outliers : 0.31 % Allowed : 4.72 % Favored : 94.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.58 (0.31), residues: 760 helix: 1.04 (0.33), residues: 249 sheet: 0.84 (0.44), residues: 153 loop : -2.08 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 259 TYR 0.027 0.001 TYR C 228 PHE 0.036 0.002 PHE B 119 TRP 0.022 0.001 TRP A 100B HIS 0.009 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00328 ( 5994) covalent geometry : angle 0.62877 ( 8160) SS BOND : bond 0.00325 ( 4) SS BOND : angle 1.59106 ( 8) hydrogen bonds : bond 0.03637 ( 283) hydrogen bonds : angle 5.18508 ( 846) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 145 time to evaluate : 0.227 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8386 (t80) cc_final: 0.7886 (t80) REVERT: A 176 TYR cc_start: 0.7951 (m-10) cc_final: 0.7669 (m-10) REVERT: A 192 GLN cc_start: 0.8456 (mt0) cc_final: 0.8072 (mt0) REVERT: B 74 THR cc_start: 0.9111 (m) cc_final: 0.8866 (p) REVERT: B 170 ASN cc_start: 0.8667 (p0) cc_final: 0.8421 (p0) REVERT: C 117 MET cc_start: 0.8792 (tpp) cc_final: 0.8027 (ttm) REVERT: C 204 MET cc_start: 0.7872 (mtp) cc_final: 0.7467 (mtp) REVERT: C 352 GLU cc_start: 0.8542 (tt0) cc_final: 0.8123 (tt0) outliers start: 2 outliers final: 1 residues processed: 147 average time/residue: 0.0756 time to fit residues: 14.6359 Evaluate side-chains 114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 113 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 2.9990 chunk 43 optimal weight: 10.0000 chunk 61 optimal weight: 0.9990 chunk 56 optimal weight: 9.9990 chunk 23 optimal weight: 2.9990 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.166012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.123729 restraints weight = 10284.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.127352 restraints weight = 6238.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.129590 restraints weight = 4494.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.131406 restraints weight = 3663.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132165 restraints weight = 3181.478| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5998 Z= 0.195 Angle : 0.659 7.659 8168 Z= 0.342 Chirality : 0.044 0.189 925 Planarity : 0.005 0.059 1021 Dihedral : 4.562 19.592 817 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.74 % Favored : 90.13 % Rotamer: Outliers : 0.16 % Allowed : 2.67 % Favored : 97.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.63 (0.31), residues: 760 helix: 1.10 (0.33), residues: 248 sheet: 0.41 (0.43), residues: 165 loop : -2.05 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 259 TYR 0.011 0.001 TYR C 364 PHE 0.019 0.002 PHE C 212 TRP 0.014 0.001 TRP B 35 HIS 0.010 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00440 ( 5994) covalent geometry : angle 0.65729 ( 8160) SS BOND : bond 0.00273 ( 4) SS BOND : angle 1.56984 ( 8) hydrogen bonds : bond 0.03801 ( 283) hydrogen bonds : angle 5.10572 ( 846) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 141 time to evaluate : 0.273 Fit side-chains revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8521 (t80) cc_final: 0.8005 (t80) REVERT: A 99 TYR cc_start: 0.8924 (t80) cc_final: 0.8709 (t80) REVERT: A 176 TYR cc_start: 0.7996 (m-80) cc_final: 0.7726 (m-10) REVERT: A 192 GLN cc_start: 0.8501 (mt0) cc_final: 0.8142 (mt0) REVERT: A 206 LYS cc_start: 0.8468 (tptt) cc_final: 0.8070 (mttt) REVERT: B 74 THR cc_start: 0.9153 (m) cc_final: 0.8921 (p) REVERT: B 118 LEU cc_start: 0.8579 (tp) cc_final: 0.7972 (tp) REVERT: B 135 CYS cc_start: 0.6744 (t) cc_final: 0.5974 (t) REVERT: B 170 ASN cc_start: 0.8661 (p0) cc_final: 0.8425 (p0) REVERT: C 204 MET cc_start: 0.7912 (mtp) cc_final: 0.7493 (mtp) REVERT: C 330 HIS cc_start: 0.8516 (m-70) cc_final: 0.8224 (m-70) REVERT: C 352 GLU cc_start: 0.8574 (tt0) cc_final: 0.8160 (tt0) outliers start: 1 outliers final: 0 residues processed: 142 average time/residue: 0.0720 time to fit residues: 13.5856 Evaluate side-chains 116 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 29 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 58 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 13 optimal weight: 8.9990 chunk 47 optimal weight: 0.4980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.167377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.124640 restraints weight = 10391.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.128476 restraints weight = 6310.097| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.131110 restraints weight = 4561.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.132496 restraints weight = 3695.898| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133803 restraints weight = 3248.495| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5998 Z= 0.157 Angle : 0.643 8.929 8168 Z= 0.326 Chirality : 0.044 0.217 925 Planarity : 0.004 0.060 1021 Dihedral : 4.499 20.333 817 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.34 % Favored : 90.53 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.52 (0.31), residues: 760 helix: 1.15 (0.33), residues: 247 sheet: 0.73 (0.44), residues: 148 loop : -1.97 (0.32), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 259 TYR 0.010 0.001 TYR B 86 PHE 0.041 0.002 PHE B 119 TRP 0.012 0.001 TRP A 47 HIS 0.007 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 5994) covalent geometry : angle 0.64187 ( 8160) SS BOND : bond 0.00251 ( 4) SS BOND : angle 1.53506 ( 8) hydrogen bonds : bond 0.03632 ( 283) hydrogen bonds : angle 4.98548 ( 846) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 138 time to evaluate : 0.139 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8481 (t80) cc_final: 0.8005 (t80) REVERT: A 192 GLN cc_start: 0.8481 (mt0) cc_final: 0.8125 (mt0) REVERT: A 206 LYS cc_start: 0.8556 (tptt) cc_final: 0.8038 (mttt) REVERT: B 74 THR cc_start: 0.9108 (m) cc_final: 0.8881 (p) REVERT: B 170 ASN cc_start: 0.8593 (p0) cc_final: 0.8353 (p0) REVERT: B 185 GLN cc_start: 0.8521 (mm-40) cc_final: 0.7948 (tp-100) REVERT: C 117 MET cc_start: 0.8778 (tpp) cc_final: 0.7955 (ttm) REVERT: C 204 MET cc_start: 0.7897 (mtp) cc_final: 0.7496 (mtp) REVERT: C 352 GLU cc_start: 0.8605 (tt0) cc_final: 0.8226 (tt0) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.0631 time to fit residues: 11.5390 Evaluate side-chains 114 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 114 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 47 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 53 optimal weight: 0.7980 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 0.9990 chunk 42 optimal weight: 9.9990 chunk 63 optimal weight: 0.0980 chunk 39 optimal weight: 3.9990 chunk 23 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 69 optimal weight: 0.9980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 168 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.168597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.125911 restraints weight = 10379.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.129801 restraints weight = 6361.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.132428 restraints weight = 4613.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.133846 restraints weight = 3730.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.135000 restraints weight = 3288.057| |-----------------------------------------------------------------------------| r_work (final): 0.3584 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5998 Z= 0.143 Angle : 0.633 8.514 8168 Z= 0.323 Chirality : 0.044 0.191 925 Planarity : 0.005 0.060 1021 Dihedral : 4.455 20.009 817 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.21 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.44 (0.31), residues: 760 helix: 1.23 (0.33), residues: 248 sheet: 0.53 (0.43), residues: 157 loop : -1.87 (0.33), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 259 TYR 0.016 0.001 TYR A 176 PHE 0.023 0.001 PHE C 354 TRP 0.012 0.001 TRP A 47 HIS 0.005 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 5994) covalent geometry : angle 0.63161 ( 8160) SS BOND : bond 0.00265 ( 4) SS BOND : angle 1.39129 ( 8) hydrogen bonds : bond 0.03523 ( 283) hydrogen bonds : angle 4.84243 ( 846) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 141 time to evaluate : 0.138 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 98 TYR cc_start: 0.8428 (t80) cc_final: 0.7957 (t80) REVERT: A 192 GLN cc_start: 0.8429 (mt0) cc_final: 0.8087 (mt0) REVERT: A 206 LYS cc_start: 0.8558 (tptt) cc_final: 0.8039 (mttp) REVERT: B 74 THR cc_start: 0.9070 (m) cc_final: 0.8861 (p) REVERT: B 81 GLU cc_start: 0.7794 (pm20) cc_final: 0.7578 (pt0) REVERT: B 170 ASN cc_start: 0.8571 (p0) cc_final: 0.8340 (p0) REVERT: B 205 LYS cc_start: 0.8381 (tptt) cc_final: 0.8177 (tptt) REVERT: C 117 MET cc_start: 0.8791 (tpp) cc_final: 0.7515 (ttt) REVERT: C 204 MET cc_start: 0.7893 (mtp) cc_final: 0.7489 (mtp) REVERT: C 330 HIS cc_start: 0.8436 (m-70) cc_final: 0.8216 (m-70) REVERT: C 352 GLU cc_start: 0.8547 (tt0) cc_final: 0.7870 (tt0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.0531 time to fit residues: 10.0170 Evaluate side-chains 115 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 44 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 59 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 70 optimal weight: 0.9980 chunk 37 optimal weight: 4.9990 chunk 11 optimal weight: 0.0870 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.169160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.126408 restraints weight = 10390.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.130164 restraints weight = 6397.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.132786 restraints weight = 4661.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.134123 restraints weight = 3788.193| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.135223 restraints weight = 3348.868| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5998 Z= 0.151 Angle : 0.647 8.383 8168 Z= 0.331 Chirality : 0.045 0.249 925 Planarity : 0.005 0.057 1021 Dihedral : 4.464 19.899 817 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.21 % Favored : 90.66 % Rotamer: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.57 (0.31), residues: 760 helix: 1.04 (0.33), residues: 256 sheet: 0.49 (0.43), residues: 157 loop : -1.96 (0.33), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 259 TYR 0.020 0.001 TYR A 176 PHE 0.013 0.001 PHE C 159 TRP 0.012 0.001 TRP A 47 HIS 0.004 0.001 HIS C 80 Details of bonding type rmsd covalent geometry : bond 0.00344 ( 5994) covalent geometry : angle 0.64543 ( 8160) SS BOND : bond 0.00161 ( 4) SS BOND : angle 1.40949 ( 8) hydrogen bonds : bond 0.03599 ( 283) hydrogen bonds : angle 4.84005 ( 846) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 147 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 85 GLU cc_start: 0.8192 (tp30) cc_final: 0.7880 (tp30) REVERT: A 98 TYR cc_start: 0.8424 (t80) cc_final: 0.7941 (t80) REVERT: A 192 GLN cc_start: 0.8407 (mt0) cc_final: 0.8142 (mt0) REVERT: A 206 LYS cc_start: 0.8571 (tptt) cc_final: 0.8016 (mttp) REVERT: B 81 GLU cc_start: 0.7943 (pm20) cc_final: 0.7719 (pm20) REVERT: B 170 ASN cc_start: 0.8597 (p0) cc_final: 0.8389 (p0) REVERT: B 171 ASN cc_start: 0.7270 (t0) cc_final: 0.6893 (t0) REVERT: B 185 GLN cc_start: 0.8510 (mm-40) cc_final: 0.8162 (tp-100) REVERT: B 205 LYS cc_start: 0.8399 (tptt) cc_final: 0.8117 (tptt) REVERT: C 117 MET cc_start: 0.8809 (tpp) cc_final: 0.7581 (ttt) REVERT: C 204 MET cc_start: 0.7908 (mtp) cc_final: 0.7510 (mtp) REVERT: C 352 GLU cc_start: 0.8577 (tt0) cc_final: 0.7575 (tt0) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.0588 time to fit residues: 11.4321 Evaluate side-chains 116 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 116 time to evaluate : 0.130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 34 optimal weight: 2.9990 chunk 70 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 56 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 chunk 19 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 63 optimal weight: 7.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3932 r_free = 0.3932 target = 0.164586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.122673 restraints weight = 10176.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.126207 restraints weight = 6300.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.128468 restraints weight = 4581.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.129985 restraints weight = 3733.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.130923 restraints weight = 3272.282| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5998 Z= 0.252 Angle : 0.721 8.251 8168 Z= 0.372 Chirality : 0.047 0.260 925 Planarity : 0.005 0.050 1021 Dihedral : 4.737 21.781 817 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.26 % Allowed : 9.47 % Favored : 90.26 % Rotamer: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.60 (0.31), residues: 760 helix: 1.01 (0.33), residues: 248 sheet: 0.40 (0.43), residues: 159 loop : -1.88 (0.33), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 91 TYR 0.014 0.002 TYR A 100K PHE 0.016 0.002 PHE B 119 TRP 0.017 0.002 TRP B 35 HIS 0.003 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 5994) covalent geometry : angle 0.71913 ( 8160) SS BOND : bond 0.00255 ( 4) SS BOND : angle 1.62963 ( 8) hydrogen bonds : bond 0.03914 ( 283) hydrogen bonds : angle 5.08089 ( 846) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 192 GLN cc_start: 0.8338 (mt0) cc_final: 0.8106 (mt0) REVERT: A 206 LYS cc_start: 0.8569 (tptt) cc_final: 0.8014 (mttp) REVERT: B 118 LEU cc_start: 0.8651 (tp) cc_final: 0.8095 (tp) REVERT: B 185 GLN cc_start: 0.8499 (mm-40) cc_final: 0.8052 (tp-100) REVERT: B 192 TYR cc_start: 0.7670 (m-80) cc_final: 0.7359 (m-80) REVERT: B 205 LYS cc_start: 0.8440 (tptt) cc_final: 0.8153 (tptt) REVERT: C 204 MET cc_start: 0.7922 (mtp) cc_final: 0.7628 (mtt) outliers start: 0 outliers final: 0 residues processed: 137 average time/residue: 0.0563 time to fit residues: 10.3422 Evaluate side-chains 115 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 115 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 56 optimal weight: 6.9990 chunk 58 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 17 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 45 optimal weight: 0.6980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3951 r_free = 0.3951 target = 0.165607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.123735 restraints weight = 10342.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.127542 restraints weight = 6044.160| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.130117 restraints weight = 4276.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.131770 restraints weight = 3428.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.132902 restraints weight = 2971.748| |-----------------------------------------------------------------------------| r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5998 Z= 0.169 Angle : 0.693 8.271 8168 Z= 0.355 Chirality : 0.046 0.218 925 Planarity : 0.005 0.056 1021 Dihedral : 4.613 21.463 817 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.47 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.51 (0.31), residues: 760 helix: 1.03 (0.32), residues: 249 sheet: 0.62 (0.45), residues: 146 loop : -1.80 (0.33), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 94 TYR 0.024 0.002 TYR A 99 PHE 0.020 0.002 PHE B 119 TRP 0.013 0.001 TRP A 154 HIS 0.002 0.001 HIS A 200 Details of bonding type rmsd covalent geometry : bond 0.00388 ( 5994) covalent geometry : angle 0.69147 ( 8160) SS BOND : bond 0.00314 ( 4) SS BOND : angle 1.43010 ( 8) hydrogen bonds : bond 0.03820 ( 283) hydrogen bonds : angle 5.00730 ( 846) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1520 Ramachandran restraints generated. 760 Oldfield, 0 Emsley, 760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 145 time to evaluate : 0.133 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 ASP cc_start: 0.8946 (t0) cc_final: 0.8716 (t0) REVERT: A 206 LYS cc_start: 0.8500 (tptt) cc_final: 0.7927 (mttp) REVERT: B 185 GLN cc_start: 0.8459 (mm-40) cc_final: 0.8070 (tp-100) REVERT: B 205 LYS cc_start: 0.8349 (tptt) cc_final: 0.8127 (tptt) REVERT: C 117 MET cc_start: 0.8880 (tpp) cc_final: 0.7811 (ttt) REVERT: C 204 MET cc_start: 0.7927 (mtp) cc_final: 0.7502 (mtp) REVERT: C 352 GLU cc_start: 0.8935 (tt0) cc_final: 0.8584 (tt0) outliers start: 0 outliers final: 0 residues processed: 145 average time/residue: 0.0579 time to fit residues: 11.2440 Evaluate side-chains 119 residues out of total 639 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 119 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 76 random chunks: chunk 49 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 72 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 26 optimal weight: 0.3980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 189 HIS ** C 110 ASN ** 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 = 0.3987 r_free = 0.3987 target = 0.168743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.126675 restraints weight = 10527.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130434 restraints weight = 6312.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133064 restraints weight = 4549.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.134687 restraints weight = 3685.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.135810 restraints weight = 3220.150| |-----------------------------------------------------------------------------| r_work (final): 0.3586 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.2808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 5998 Z= 0.163 Angle : 0.698 11.022 8168 Z= 0.353 Chirality : 0.045 0.202 925 Planarity : 0.005 0.059 1021 Dihedral : 4.582 21.177 817 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.13 % Allowed : 9.47 % Favored : 90.39 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: -0.52 (0.31), residues: 760 helix: 0.97 (0.32), residues: 249 sheet: 0.61 (0.44), residues: 153 loop : -1.80 (0.33), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 89 TYR 0.012 0.001 TYR A 90 PHE 0.021 0.001 PHE C 349 TRP 0.044 0.002 TRP B 186 HIS 0.002 0.001 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 5994) covalent geometry : angle 0.69632 ( 8160) SS BOND : bond 0.00222 ( 4) SS BOND : angle 1.61918 ( 8) hydrogen bonds : bond 0.03732 ( 283) hydrogen bonds : angle 4.99515 ( 846) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1042.21 seconds wall clock time: 18 minutes 46.62 seconds (1126.62 seconds total)