Starting phenix.real_space_refine on Sun Apr 5 05:57:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9m2o_63587/04_2026/9m2o_63587.cif Found real_map, /net/cci-nas-00/data/ceres_data/9m2o_63587/04_2026/9m2o_63587.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9m2o_63587/04_2026/9m2o_63587.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9m2o_63587/04_2026/9m2o_63587.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9m2o_63587/04_2026/9m2o_63587.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9m2o_63587/04_2026/9m2o_63587.map" } resolution = 2.59 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= 0.001 sd= 0.023 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 62 5.16 5 C 5357 2.51 5 N 1445 2.21 5 O 1570 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8434 Number of models: 1 Model: "" Number of chains: 6 Chain: "R" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 317, 2526 Classifications: {'peptide': 317} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 304} Chain breaks: 1 Chain: "B" Number of atoms: 2600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 338, 2600 Classifications: {'peptide': 338} Link IDs: {'PTRANS': 5, 'TRANS': 332} Chain: "C" Number of atoms: 436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 436 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 4, 'TRANS': 52} Chain: "N" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 967 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 5, 'TRANS': 121} Chain: "A" Number of atoms: 1899 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1899 Classifications: {'peptide': 232} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 225} Chain breaks: 1 Chain: "R" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 6 Unusual residues: {'PUT': 1} Classifications: {'undetermined': 1} Time building chain proxies: 1.98, per 1000 atoms: 0.23 Number of scatterers: 8434 At special positions: 0 Unit cell: (77.376, 98.176, 138.944, 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 62 16.00 O 1570 8.00 N 1445 7.00 C 5357 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS R 14 " - pdb=" SG CYS R 97 " distance=2.06 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 186 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS N 99 " - pdb=" SG CYS N 107 " 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: 0.88 Conformation dependent library (CDL) restraints added in 352.7 milliseconds 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 43.4% alpha, 19.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.29 Creating SS restraints... Processing helix chain 'R' and resid 28 through 60 Processing helix chain 'R' and resid 61 through 64 Processing helix chain 'R' and resid 65 through 85 removed outlier: 3.584A pdb=" N LEU R 70 " --> pdb=" O THR R 66 " (cutoff:3.500A) Processing helix chain 'R' and resid 85 through 95 removed outlier: 3.639A pdb=" N ILE R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) Processing helix chain 'R' and resid 101 through 136 removed outlier: 3.533A pdb=" N SER R 117 " --> pdb=" O LEU R 113 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 168 Processing helix chain 'R' and resid 169 through 171 No H-bonds generated for 'chain 'R' and resid 169 through 171' Processing helix chain 'R' and resid 177 through 184 Processing helix chain 'R' and resid 195 through 207 Processing helix chain 'R' and resid 207 through 233 Processing helix chain 'R' and resid 251 through 279 removed outlier: 3.976A pdb=" N PHE R 265 " --> pdb=" O VAL R 261 " (cutoff:3.500A) Proline residue: R 271 - end of helix Processing helix chain 'R' and resid 280 through 283 removed outlier: 3.766A pdb=" N ASN R 283 " --> pdb=" O PRO R 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 280 through 283' Processing helix chain 'R' and resid 287 through 309 removed outlier: 3.782A pdb=" N SER R 302 " --> pdb=" O GLY R 298 " (cutoff:3.500A) Proline residue: R 306 - end of helix Processing helix chain 'R' and resid 313 through 325 Processing helix chain 'R' and resid 326 through 330 removed outlier: 3.509A pdb=" N PHE R 329 " --> pdb=" O ARG R 326 " (cutoff:3.500A) Processing helix chain 'R' and resid 332 through 336 removed outlier: 3.716A pdb=" N ASP R 335 " --> pdb=" O ASN R 332 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ILE R 336 " --> pdb=" O SER R 333 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 332 through 336' Processing helix chain 'B' and resid 4 through 26 Processing helix chain 'B' and resid 29 through 34 Processing helix chain 'C' and resid 7 through 24 Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'C' and resid 45 through 48 Processing helix chain 'N' and resid 28 through 32 Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.617A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 36 Processing helix chain 'A' and resid 52 through 60 Processing helix chain 'A' and resid 95 through 101 removed outlier: 3.836A pdb=" N ASN A 101 " --> pdb=" O GLN A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 131 Processing helix chain 'A' and resid 145 through 156 removed outlier: 3.576A pdb=" N GLY A 156 " --> pdb=" O LYS A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 159 through 164 removed outlier: 4.146A pdb=" N TYR A 163 " --> pdb=" O LYS A 159 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 removed outlier: 3.660A pdb=" N ALA A 168 " --> pdb=" O PRO A 165 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 165 through 168' Processing helix chain 'A' and resid 183 through 205 removed outlier: 3.822A pdb=" N ILE A 200 " --> pdb=" O GLU A 196 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N SER A 204 " --> pdb=" O ILE A 200 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 243 Processing sheet with id=AA1, first strand: chain 'B' and resid 47 through 52 removed outlier: 4.358A pdb=" N PHE B 335 " --> pdb=" O SER B 331 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N CYS B 317 " --> pdb=" O GLY B 330 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 63 removed outlier: 3.512A pdb=" N ALA B 60 " --> pdb=" O ALA B 73 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 100 through 105 removed outlier: 6.667A pdb=" N GLY B 115 " --> pdb=" O MET B 101 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N CYS B 103 " --> pdb=" O ALA B 113 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ALA B 113 " --> pdb=" O CYS B 103 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N TYR B 105 " --> pdb=" O TYR B 111 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N TYR B 111 " --> pdb=" O TYR B 105 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 146 through 151 removed outlier: 6.435A pdb=" N ASP B 170 " --> pdb=" O GLN B 176 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N GLN B 176 " --> pdb=" O ASP B 170 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.372A pdb=" N SER B 207 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 229 through 234 removed outlier: 5.988A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 273 through 278 removed outlier: 3.884A pdb=" N SER B 275 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N GLY B 306 " --> pdb=" O VAL B 296 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AA9, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.520A pdb=" N THR N 125 " --> pdb=" O GLY N 10 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG N 38 " --> pdb=" O TRP N 47 " (cutoff:3.500A) removed outlier: 5.522A pdb=" N TRP N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 69 through 75 removed outlier: 4.908A pdb=" N VAL A 86 " --> pdb=" O LEU A 45 " (cutoff:3.500A) removed outlier: 8.733A pdb=" N GLY A 47 " --> pdb=" O VAL A 86 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ALA A 105 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N ILE A 106 " --> pdb=" O ILE A 140 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N PHE A 142 " --> pdb=" O ILE A 106 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N PHE A 108 " --> pdb=" O PHE A 142 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ASN A 144 " --> pdb=" O PHE A 108 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N VAL A 110 " --> pdb=" O ASN A 144 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1293 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: 1.49 Time building geometry restraints manager: 1.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1389 1.32 - 1.44: 2392 1.44 - 1.57: 4742 1.57 - 1.69: 0 1.69 - 1.82: 92 Bond restraints: 8615 Sorted by residual: bond pdb=" CA SER B 147 " pdb=" CB SER B 147 " ideal model delta sigma weight residual 1.534 1.484 0.050 1.45e-02 4.76e+03 1.18e+01 bond pdb=" CA SER B 84 " pdb=" CB SER B 84 " ideal model delta sigma weight residual 1.529 1.474 0.054 1.64e-02 3.72e+03 1.10e+01 bond pdb=" N ILE B 270 " pdb=" CA ILE B 270 " ideal model delta sigma weight residual 1.457 1.487 -0.030 9.30e-03 1.16e+04 1.07e+01 bond pdb=" C PRO R 147 " pdb=" O PRO R 147 " ideal model delta sigma weight residual 1.238 1.195 0.042 1.35e-02 5.49e+03 9.80e+00 bond pdb=" N LEU N 79 " pdb=" CA LEU N 79 " ideal model delta sigma weight residual 1.456 1.492 -0.036 1.21e-02 6.83e+03 8.67e+00 ... (remaining 8610 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 11294 1.69 - 3.39: 317 3.39 - 5.08: 57 5.08 - 6.77: 7 6.77 - 8.46: 2 Bond angle restraints: 11677 Sorted by residual: angle pdb=" N ILE B 270 " pdb=" CA ILE B 270 " pdb=" C ILE B 270 " ideal model delta sigma weight residual 113.20 106.50 6.70 9.60e-01 1.09e+00 4.87e+01 angle pdb=" N GLN R 12 " pdb=" CA GLN R 12 " pdb=" C GLN R 12 " ideal model delta sigma weight residual 112.30 105.40 6.90 1.36e+00 5.41e-01 2.57e+01 angle pdb=" C CYS R 97 " pdb=" CA CYS R 97 " pdb=" CB CYS R 97 " ideal model delta sigma weight residual 110.30 101.84 8.46 1.98e+00 2.55e-01 1.83e+01 angle pdb=" CA HIS B 225 " pdb=" CB HIS B 225 " pdb=" CG HIS B 225 " ideal model delta sigma weight residual 113.80 117.85 -4.05 1.00e+00 1.00e+00 1.64e+01 angle pdb=" N MET B 61 " pdb=" CA MET B 61 " pdb=" C MET B 61 " ideal model delta sigma weight residual 108.55 102.27 6.28 1.62e+00 3.81e-01 1.50e+01 ... (remaining 11672 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.06: 4526 15.06 - 30.13: 458 30.13 - 45.19: 103 45.19 - 60.25: 19 60.25 - 75.32: 18 Dihedral angle restraints: 5124 sinusoidal: 2005 harmonic: 3119 Sorted by residual: dihedral pdb=" CA CYS R 22 " pdb=" CB CYS R 22 " pdb=" SG CYS R 22 " pdb=" SG CYS R 186 " ideal model delta sinusoidal sigma weight residual -73.00 -7.30 -65.70 1 2.00e+01 2.50e-03 1.41e+01 dihedral pdb=" CD ARG A 188 " pdb=" NE ARG A 188 " pdb=" CZ ARG A 188 " pdb=" NH1 ARG A 188 " ideal model delta sinusoidal sigma weight residual 0.00 30.91 -30.91 1 1.00e+01 1.00e-02 1.36e+01 dihedral pdb=" CA PHE N 108 " pdb=" C PHE N 108 " pdb=" N ASP N 109 " pdb=" CA ASP N 109 " ideal model delta harmonic sigma weight residual 180.00 -161.80 -18.20 0 5.00e+00 4.00e-02 1.33e+01 ... (remaining 5121 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 986 0.047 - 0.095: 243 0.095 - 0.142: 75 0.142 - 0.189: 8 0.189 - 0.237: 3 Chirality restraints: 1315 Sorted by residual: chirality pdb=" CA MET B 61 " pdb=" N MET B 61 " pdb=" C MET B 61 " pdb=" CB MET B 61 " both_signs ideal model delta sigma weight residual False 2.51 2.75 -0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA ILE C 28 " pdb=" N ILE C 28 " pdb=" C ILE C 28 " pdb=" CB ILE C 28 " both_signs ideal model delta sigma weight residual False 2.43 2.65 -0.22 2.00e-01 2.50e+01 1.17e+00 chirality pdb=" CA VAL B 327 " pdb=" N VAL B 327 " pdb=" C VAL B 327 " pdb=" CB VAL B 327 " both_signs ideal model delta sigma weight residual False 2.44 2.65 -0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 1312 not shown) Planarity restraints: 1487 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 188 " 0.561 9.50e-02 1.11e+02 2.52e-01 3.87e+01 pdb=" NE ARG A 188 " -0.033 2.00e-02 2.50e+03 pdb=" CZ ARG A 188 " -0.008 2.00e-02 2.50e+03 pdb=" NH1 ARG A 188 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG A 188 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU R 201 " 0.011 2.00e-02 2.50e+03 2.14e-02 4.60e+00 pdb=" C LEU R 201 " -0.037 2.00e-02 2.50e+03 pdb=" O LEU R 201 " 0.014 2.00e-02 2.50e+03 pdb=" N ASP R 202 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 58 " -0.010 2.00e-02 2.50e+03 2.09e-02 4.39e+00 pdb=" C ILE B 58 " 0.036 2.00e-02 2.50e+03 pdb=" O ILE B 58 " -0.014 2.00e-02 2.50e+03 pdb=" N TYR B 59 " -0.012 2.00e-02 2.50e+03 ... (remaining 1484 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 928 2.75 - 3.29: 8339 3.29 - 3.82: 15296 3.82 - 4.36: 18313 4.36 - 4.90: 31009 Nonbonded interactions: 73885 Sorted by model distance: nonbonded pdb=" O ILE B 58 " pdb=" OG SER B 316 " model vdw 2.211 3.040 nonbonded pdb=" O ARG B 68 " pdb=" OG SER B 84 " model vdw 2.261 3.040 nonbonded pdb=" OG1 THR R 46 " pdb=" OG1 THR R 303 " model vdw 2.264 3.040 nonbonded pdb=" O CYS N 107 " pdb=" OG SER A 127 " model vdw 2.273 3.040 nonbonded pdb=" OG1 THR B 65 " pdb=" O PRO B 107 " model vdw 2.325 3.040 ... (remaining 73880 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.680 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 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:8.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 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 : 0.004 0.065 8620 Z= 0.261 Angle : 0.651 11.119 11687 Z= 0.417 Chirality : 0.047 0.237 1315 Planarity : 0.008 0.252 1487 Dihedral : 13.356 75.315 3093 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 0.11 % Allowed : 1.09 % Favored : 98.80 % 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: 0.76 (0.26), residues: 1057 helix: 1.78 (0.26), residues: 412 sheet: -0.36 (0.32), residues: 229 loop : -0.17 (0.31), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 135 TYR 0.022 0.001 TYR B 59 PHE 0.012 0.001 PHE B 234 TRP 0.013 0.001 TRP A 96 HIS 0.013 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8615) covalent geometry : angle 0.64180 (11677) SS BOND : bond 0.01326 ( 5) SS BOND : angle 3.86180 ( 10) hydrogen bonds : bond 0.16907 ( 452) hydrogen bonds : angle 6.71592 ( 1293) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 207 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 254 ASP cc_start: 0.6541 (t70) cc_final: 0.6322 (t70) REVERT: N 32 TYR cc_start: 0.7889 (m-80) cc_final: 0.7458 (m-80) REVERT: A 15 ASP cc_start: 0.6859 (m-30) cc_final: 0.6569 (m-30) REVERT: A 174 GLU cc_start: 0.6724 (pm20) cc_final: 0.6504 (pm20) outliers start: 1 outliers final: 1 residues processed: 207 average time/residue: 0.5243 time to fit residues: 115.6953 Evaluate side-chains 178 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 177 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 61 MET Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 0.8980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.2980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 0.2980 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 36 ASN B 237 ASN B 268 ASN C 24 ASN A 146 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.117232 restraints weight = 11416.642| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 1.70 r_work: 0.3528 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3386 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8620 Z= 0.173 Angle : 0.546 8.463 11687 Z= 0.293 Chirality : 0.044 0.158 1315 Planarity : 0.004 0.044 1487 Dihedral : 4.349 28.206 1171 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.20 % Allowed : 11.76 % Favored : 87.04 % 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 (0.26), residues: 1057 helix: 2.00 (0.26), residues: 416 sheet: -0.25 (0.33), residues: 229 loop : -0.18 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 96 TYR 0.013 0.001 TYR A 191 PHE 0.016 0.001 PHE R 114 TRP 0.021 0.002 TRP B 169 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00392 ( 8615) covalent geometry : angle 0.54455 (11677) SS BOND : bond 0.00388 ( 5) SS BOND : angle 1.47708 ( 10) hydrogen bonds : bond 0.04533 ( 452) hydrogen bonds : angle 5.07736 ( 1293) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 184 time to evaluate : 0.257 Fit side-chains revert: symmetry clash REVERT: R 173 ASN cc_start: 0.7889 (p0) cc_final: 0.7673 (p0) REVERT: A 15 ASP cc_start: 0.7408 (m-30) cc_final: 0.6994 (m-30) REVERT: A 195 ASP cc_start: 0.7747 (m-30) cc_final: 0.7307 (m-30) outliers start: 11 outliers final: 6 residues processed: 185 average time/residue: 0.5130 time to fit residues: 101.4095 Evaluate side-chains 179 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 173 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain A residue 83 MET Chi-restraints excluded: chain A residue 233 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 72 optimal weight: 1.9990 chunk 17 optimal weight: 0.3980 chunk 95 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 75 optimal weight: 1.9990 chunk 99 optimal weight: 0.0000 chunk 33 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 overall best weight: 0.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN R 275 ASN R 305 ASN B 156 GLN B 230 ASN B 237 ASN B 268 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.129109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.117362 restraints weight = 11346.905| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.67 r_work: 0.3530 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.1920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 8620 Z= 0.155 Angle : 0.513 9.021 11687 Z= 0.274 Chirality : 0.042 0.147 1315 Planarity : 0.004 0.043 1487 Dihedral : 4.025 16.639 1168 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.51 % Allowed : 13.07 % Favored : 84.42 % 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: 0.96 (0.26), residues: 1057 helix: 2.01 (0.26), residues: 416 sheet: -0.21 (0.32), residues: 224 loop : -0.20 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.013 0.001 TYR A 191 PHE 0.014 0.001 PHE R 114 TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00352 ( 8615) covalent geometry : angle 0.51209 (11677) SS BOND : bond 0.00301 ( 5) SS BOND : angle 1.10926 ( 10) hydrogen bonds : bond 0.04186 ( 452) hydrogen bonds : angle 4.86196 ( 1293) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 189 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: R 50 ASN cc_start: 0.8322 (m-40) cc_final: 0.8110 (m110) REVERT: R 193 TYR cc_start: 0.8160 (m-80) cc_final: 0.7931 (m-80) REVERT: B 212 ASP cc_start: 0.7969 (t0) cc_final: 0.7654 (t0) REVERT: B 217 MET cc_start: 0.8267 (OUTLIER) cc_final: 0.8003 (pmm) REVERT: B 304 ARG cc_start: 0.8318 (OUTLIER) cc_final: 0.7799 (ttm170) REVERT: C 42 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.7320 (mt-10) REVERT: A 15 ASP cc_start: 0.7390 (m-30) cc_final: 0.7000 (m-30) REVERT: A 166 GLU cc_start: 0.7976 (mm-30) cc_final: 0.7542 (mm-30) REVERT: A 195 ASP cc_start: 0.7757 (m-30) cc_final: 0.7306 (m-30) outliers start: 23 outliers final: 14 residues processed: 193 average time/residue: 0.5012 time to fit residues: 103.3358 Evaluate side-chains 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 180 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 158 SER Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 61 MET Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 23 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 13 optimal weight: 0.4980 chunk 73 optimal weight: 0.9980 chunk 82 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 14 optimal weight: 0.4980 chunk 93 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN B 230 ASN B 237 ASN B 268 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.128499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.116868 restraints weight = 11653.321| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 1.68 r_work: 0.3523 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3381 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7838 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8620 Z= 0.173 Angle : 0.514 6.841 11687 Z= 0.276 Chirality : 0.043 0.148 1315 Planarity : 0.004 0.042 1487 Dihedral : 4.049 16.578 1168 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.51 % Allowed : 15.25 % Favored : 82.24 % 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: 0.95 (0.26), residues: 1057 helix: 2.02 (0.26), residues: 415 sheet: -0.15 (0.32), residues: 221 loop : -0.27 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 169 TYR 0.013 0.001 TYR A 191 PHE 0.013 0.001 PHE R 114 TRP 0.020 0.002 TRP B 169 HIS 0.007 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 8615) covalent geometry : angle 0.51350 (11677) SS BOND : bond 0.00307 ( 5) SS BOND : angle 1.02139 ( 10) hydrogen bonds : bond 0.04161 ( 452) hydrogen bonds : angle 4.82188 ( 1293) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 185 time to evaluate : 0.305 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8258 (OUTLIER) cc_final: 0.7772 (m-80) REVERT: B 217 MET cc_start: 0.8279 (OUTLIER) cc_final: 0.7898 (pmm) REVERT: B 304 ARG cc_start: 0.8341 (OUTLIER) cc_final: 0.7751 (ttm170) REVERT: N 35 ASN cc_start: 0.8515 (OUTLIER) cc_final: 0.8306 (m110) REVERT: A 15 ASP cc_start: 0.7425 (m-30) cc_final: 0.7033 (m-30) REVERT: A 126 LYS cc_start: 0.8377 (ttmm) cc_final: 0.8129 (ttmm) REVERT: A 195 ASP cc_start: 0.7783 (m-30) cc_final: 0.7366 (m-30) outliers start: 23 outliers final: 12 residues processed: 193 average time/residue: 0.4878 time to fit residues: 100.9123 Evaluate side-chains 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 181 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 35 ASN Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 79 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 64 optimal weight: 0.8980 chunk 69 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 81 optimal weight: 7.9990 chunk 60 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 95 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 275 ASN B 230 ASN B 268 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3759 r_free = 0.3759 target = 0.126810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.114841 restraints weight = 11406.152| |-----------------------------------------------------------------------------| r_work (start): 0.3595 rms_B_bonded: 1.69 r_work: 0.3490 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 8620 Z= 0.295 Angle : 0.582 8.084 11687 Z= 0.312 Chirality : 0.047 0.157 1315 Planarity : 0.004 0.041 1487 Dihedral : 4.356 17.300 1168 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.72 % Allowed : 15.90 % Favored : 81.37 % 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: 0.64 (0.26), residues: 1057 helix: 1.68 (0.26), residues: 422 sheet: -0.34 (0.32), residues: 228 loop : -0.36 (0.31), residues: 407 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 169 TYR 0.017 0.002 TYR A 191 PHE 0.017 0.002 PHE A 81 TRP 0.018 0.003 TRP B 169 HIS 0.008 0.002 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00683 ( 8615) covalent geometry : angle 0.58165 (11677) SS BOND : bond 0.00408 ( 5) SS BOND : angle 1.03046 ( 10) hydrogen bonds : bond 0.04792 ( 452) hydrogen bonds : angle 5.02031 ( 1293) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 187 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8276 (OUTLIER) cc_final: 0.7629 (m-80) REVERT: B 217 MET cc_start: 0.8286 (OUTLIER) cc_final: 0.7895 (pmm) REVERT: B 280 LYS cc_start: 0.8658 (OUTLIER) cc_final: 0.8204 (tmtt) REVERT: B 304 ARG cc_start: 0.8364 (OUTLIER) cc_final: 0.7759 (ttm170) REVERT: A 15 ASP cc_start: 0.7481 (m-30) cc_final: 0.7124 (m-30) REVERT: A 126 LYS cc_start: 0.8361 (ttmm) cc_final: 0.8081 (ttmm) REVERT: A 195 ASP cc_start: 0.7815 (m-30) cc_final: 0.7453 (m-30) REVERT: A 217 CYS cc_start: 0.7477 (m) cc_final: 0.7251 (m) outliers start: 25 outliers final: 15 residues processed: 195 average time/residue: 0.5003 time to fit residues: 104.3866 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 181 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 280 LYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain N residue 11 LEU Chi-restraints excluded: chain N residue 83 MET Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 40 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 68 optimal weight: 0.0970 chunk 21 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 86 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 84 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 39 optimal weight: 0.5980 chunk 20 optimal weight: 0.5980 chunk 26 optimal weight: 0.5980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 237 ASN B 268 ASN B 340 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.129080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.117323 restraints weight = 11311.634| |-----------------------------------------------------------------------------| r_work (start): 0.3638 rms_B_bonded: 1.68 r_work: 0.3528 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3388 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8620 Z= 0.144 Angle : 0.505 7.218 11687 Z= 0.273 Chirality : 0.042 0.157 1315 Planarity : 0.004 0.042 1487 Dihedral : 4.119 16.830 1168 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.83 % Allowed : 16.34 % Favored : 80.83 % 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: 0.81 (0.26), residues: 1057 helix: 1.95 (0.26), residues: 416 sheet: -0.28 (0.32), residues: 219 loop : -0.37 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 169 TYR 0.012 0.001 TYR R 36 PHE 0.012 0.001 PHE B 151 TRP 0.019 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 8615) covalent geometry : angle 0.50501 (11677) SS BOND : bond 0.00241 ( 5) SS BOND : angle 0.79033 ( 10) hydrogen bonds : bond 0.04016 ( 452) hydrogen bonds : angle 4.80386 ( 1293) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8255 (OUTLIER) cc_final: 0.7761 (m-80) REVERT: B 189 SER cc_start: 0.7836 (OUTLIER) cc_final: 0.7574 (p) REVERT: B 304 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7666 (ttm170) REVERT: A 15 ASP cc_start: 0.7419 (m-30) cc_final: 0.7077 (m-30) REVERT: A 126 LYS cc_start: 0.8349 (ttmm) cc_final: 0.8080 (ttmm) REVERT: A 195 ASP cc_start: 0.7757 (m-30) cc_final: 0.7381 (m-30) REVERT: A 217 CYS cc_start: 0.7446 (m) cc_final: 0.7231 (m) outliers start: 26 outliers final: 17 residues processed: 186 average time/residue: 0.5003 time to fit residues: 99.5927 Evaluate side-chains 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 176 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 47 ILE Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 25 optimal weight: 0.3980 chunk 92 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 chunk 100 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 50 ASN ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 259 GLN B 268 ASN B 340 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.117532 restraints weight = 11412.477| |-----------------------------------------------------------------------------| r_work (start): 0.3641 rms_B_bonded: 1.68 r_work: 0.3531 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8620 Z= 0.147 Angle : 0.501 6.739 11687 Z= 0.270 Chirality : 0.042 0.171 1315 Planarity : 0.004 0.046 1487 Dihedral : 4.087 17.180 1168 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.83 % Allowed : 16.78 % Favored : 80.39 % 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 (0.26), residues: 1057 helix: 2.01 (0.26), residues: 416 sheet: -0.30 (0.32), residues: 219 loop : -0.39 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG A 169 TYR 0.012 0.001 TYR A 191 PHE 0.015 0.001 PHE R 136 TRP 0.018 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8615) covalent geometry : angle 0.50032 (11677) SS BOND : bond 0.00263 ( 5) SS BOND : angle 0.79351 ( 10) hydrogen bonds : bond 0.03980 ( 452) hydrogen bonds : angle 4.76931 ( 1293) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 177 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7756 (m-80) REVERT: B 189 SER cc_start: 0.7834 (OUTLIER) cc_final: 0.7578 (p) REVERT: B 217 MET cc_start: 0.8316 (OUTLIER) cc_final: 0.7906 (pmm) REVERT: B 304 ARG cc_start: 0.8294 (OUTLIER) cc_final: 0.7650 (ttm170) REVERT: N 20 LEU cc_start: 0.8729 (mt) cc_final: 0.8524 (mt) REVERT: A 15 ASP cc_start: 0.7416 (m-30) cc_final: 0.7079 (m-30) REVERT: A 126 LYS cc_start: 0.8354 (ttmm) cc_final: 0.8081 (ttmm) REVERT: A 195 ASP cc_start: 0.7761 (OUTLIER) cc_final: 0.7357 (m-30) REVERT: A 217 CYS cc_start: 0.7454 (m) cc_final: 0.7196 (m) outliers start: 26 outliers final: 17 residues processed: 186 average time/residue: 0.4901 time to fit residues: 97.7882 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 178 time to evaluate : 0.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 TYR Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 128 THR Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 195 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 65 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 16 optimal weight: 0.0050 chunk 99 optimal weight: 0.5980 chunk 68 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 8 optimal weight: 0.8980 chunk 71 optimal weight: 0.7980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 275 ASN ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 259 GLN B 268 ASN ** N 35 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.129224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.117525 restraints weight = 11354.543| |-----------------------------------------------------------------------------| r_work (start): 0.3640 rms_B_bonded: 1.67 r_work: 0.3530 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3390 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3390 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7827 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 8620 Z= 0.158 Angle : 0.519 7.833 11687 Z= 0.277 Chirality : 0.043 0.186 1315 Planarity : 0.004 0.042 1487 Dihedral : 4.111 18.418 1168 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.51 % Allowed : 17.32 % Favored : 80.17 % 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: 0.82 (0.26), residues: 1057 helix: 1.99 (0.26), residues: 416 sheet: -0.26 (0.33), residues: 219 loop : -0.41 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG A 169 TYR 0.012 0.001 TYR A 191 PHE 0.014 0.001 PHE R 114 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 8615) covalent geometry : angle 0.51871 (11677) SS BOND : bond 0.00279 ( 5) SS BOND : angle 0.76917 ( 10) hydrogen bonds : bond 0.04035 ( 452) hydrogen bonds : angle 4.77096 ( 1293) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.358 Fit side-chains revert: symmetry clash REVERT: B 59 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: B 189 SER cc_start: 0.7833 (OUTLIER) cc_final: 0.7581 (p) REVERT: B 217 MET cc_start: 0.8309 (OUTLIER) cc_final: 0.7896 (pmm) REVERT: A 15 ASP cc_start: 0.7411 (m-30) cc_final: 0.7094 (m-30) REVERT: A 195 ASP cc_start: 0.7766 (OUTLIER) cc_final: 0.7361 (m-30) REVERT: A 217 CYS cc_start: 0.7447 (m) cc_final: 0.7214 (m) outliers start: 23 outliers final: 17 residues processed: 190 average time/residue: 0.4843 time to fit residues: 98.6143 Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 TYR Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 195 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 43 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 34 optimal weight: 0.0270 chunk 58 optimal weight: 0.9980 chunk 46 optimal weight: 0.7980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 17 optimal weight: 0.2980 chunk 18 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 16 optimal weight: 0.7980 overall best weight: 0.4638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 259 GLN B 268 ASN ** N 35 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 = 0.3798 r_free = 0.3798 target = 0.129858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.118155 restraints weight = 11402.123| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.68 r_work: 0.3539 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7815 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 8620 Z= 0.136 Angle : 0.498 6.823 11687 Z= 0.269 Chirality : 0.043 0.199 1315 Planarity : 0.004 0.044 1487 Dihedral : 4.053 17.175 1168 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.61 % Allowed : 16.78 % Favored : 80.61 % 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: 0.85 (0.26), residues: 1057 helix: 2.03 (0.26), residues: 416 sheet: -0.26 (0.33), residues: 219 loop : -0.40 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 169 TYR 0.012 0.001 TYR R 36 PHE 0.018 0.001 PHE R 136 TRP 0.017 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 8615) covalent geometry : angle 0.49758 (11677) SS BOND : bond 0.00253 ( 5) SS BOND : angle 0.74309 ( 10) hydrogen bonds : bond 0.03882 ( 452) hydrogen bonds : angle 4.72660 ( 1293) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.317 Fit side-chains revert: symmetry clash REVERT: B 50 THR cc_start: 0.8039 (m) cc_final: 0.7767 (m) REVERT: B 59 TYR cc_start: 0.8231 (OUTLIER) cc_final: 0.7785 (m-80) REVERT: B 155 ASN cc_start: 0.8006 (t0) cc_final: 0.7750 (t0) REVERT: B 189 SER cc_start: 0.7835 (OUTLIER) cc_final: 0.7576 (p) REVERT: B 217 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.7874 (pmm) REVERT: A 15 ASP cc_start: 0.7413 (m-30) cc_final: 0.7126 (m-30) REVERT: A 85 ASP cc_start: 0.8003 (t0) cc_final: 0.7691 (t0) REVERT: A 195 ASP cc_start: 0.7752 (OUTLIER) cc_final: 0.7345 (m-30) REVERT: A 217 CYS cc_start: 0.7462 (m) cc_final: 0.7239 (m) outliers start: 24 outliers final: 18 residues processed: 195 average time/residue: 0.4905 time to fit residues: 102.2461 Evaluate side-chains 205 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.232 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 TYR Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 91 ASP Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 80 optimal weight: 0.0670 chunk 69 optimal weight: 1.9990 chunk 103 optimal weight: 0.9980 chunk 1 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 96 optimal weight: 0.0870 chunk 44 optimal weight: 0.9980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 259 GLN B 268 ASN ** N 35 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 = 0.3794 r_free = 0.3794 target = 0.129581 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117868 restraints weight = 11319.304| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.68 r_work: 0.3535 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3395 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8620 Z= 0.144 Angle : 0.507 7.136 11687 Z= 0.273 Chirality : 0.042 0.164 1315 Planarity : 0.004 0.047 1487 Dihedral : 4.012 17.163 1168 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.61 % Allowed : 16.99 % Favored : 80.39 % 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: 0.85 (0.26), residues: 1057 helix: 2.04 (0.26), residues: 416 sheet: -0.20 (0.33), residues: 213 loop : -0.46 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 169 TYR 0.012 0.001 TYR R 36 PHE 0.014 0.001 PHE R 114 TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8615) covalent geometry : angle 0.50716 (11677) SS BOND : bond 0.00251 ( 5) SS BOND : angle 0.72822 ( 10) hydrogen bonds : bond 0.03902 ( 452) hydrogen bonds : angle 4.72476 ( 1293) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.285 Fit side-chains revert: symmetry clash REVERT: B 50 THR cc_start: 0.8037 (m) cc_final: 0.7696 (m) REVERT: B 59 TYR cc_start: 0.8245 (OUTLIER) cc_final: 0.7833 (m-80) REVERT: B 155 ASN cc_start: 0.8007 (t0) cc_final: 0.7768 (t0) REVERT: B 186 ASP cc_start: 0.7365 (m-30) cc_final: 0.7159 (m-30) REVERT: B 189 SER cc_start: 0.7851 (OUTLIER) cc_final: 0.7588 (p) REVERT: B 217 MET cc_start: 0.8314 (OUTLIER) cc_final: 0.7883 (pmm) REVERT: A 15 ASP cc_start: 0.7426 (m-30) cc_final: 0.7153 (m-30) REVERT: A 60 MET cc_start: 0.6988 (ptp) cc_final: 0.6761 (ptp) REVERT: A 85 ASP cc_start: 0.8000 (t0) cc_final: 0.7700 (t0) REVERT: A 195 ASP cc_start: 0.7750 (OUTLIER) cc_final: 0.7354 (m-30) REVERT: A 217 CYS cc_start: 0.7455 (m) cc_final: 0.7231 (m) outliers start: 24 outliers final: 17 residues processed: 196 average time/residue: 0.5036 time to fit residues: 105.5452 Evaluate side-chains 206 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 20 ASN Chi-restraints excluded: chain R residue 23 LEU Chi-restraints excluded: chain R residue 36 TYR Chi-restraints excluded: chain R residue 154 MET Chi-restraints excluded: chain R residue 181 ILE Chi-restraints excluded: chain B residue 29 THR Chi-restraints excluded: chain B residue 59 TYR Chi-restraints excluded: chain B residue 122 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 189 SER Chi-restraints excluded: chain B residue 217 MET Chi-restraints excluded: chain B residue 275 SER Chi-restraints excluded: chain B residue 334 SER Chi-restraints excluded: chain C residue 21 MET Chi-restraints excluded: chain N residue 114 THR Chi-restraints excluded: chain N residue 125 THR Chi-restraints excluded: chain A residue 24 MET Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 40 THR Chi-restraints excluded: chain A residue 195 ASP Chi-restraints excluded: chain A residue 233 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 97 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 98 optimal weight: 0.7980 chunk 87 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 61 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 22 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 overall best weight: 0.3738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 50 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 275 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN B 259 GLN B 268 ASN ** N 35 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 = 0.3812 r_free = 0.3812 target = 0.131112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.119397 restraints weight = 11277.951| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.68 r_work: 0.3553 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3414 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8620 Z= 0.123 Angle : 0.492 7.202 11687 Z= 0.265 Chirality : 0.042 0.167 1315 Planarity : 0.004 0.047 1487 Dihedral : 3.938 17.138 1168 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 2.61 % Allowed : 17.32 % Favored : 80.07 % 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: 0.89 (0.26), residues: 1057 helix: 2.09 (0.26), residues: 416 sheet: -0.20 (0.33), residues: 213 loop : -0.44 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 169 TYR 0.012 0.001 TYR R 36 PHE 0.017 0.001 PHE R 136 TRP 0.016 0.002 TRP B 169 HIS 0.006 0.001 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 8615) covalent geometry : angle 0.49168 (11677) SS BOND : bond 0.00212 ( 5) SS BOND : angle 0.70223 ( 10) hydrogen bonds : bond 0.03748 ( 452) hydrogen bonds : angle 4.68272 ( 1293) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3498.84 seconds wall clock time: 60 minutes 11.21 seconds (3611.21 seconds total)