Starting phenix.real_space_refine on Sat Aug 23 02:34:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6o_36925/08_2025/8k6o_36925.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6o_36925/08_2025/8k6o_36925.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8k6o_36925/08_2025/8k6o_36925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6o_36925/08_2025/8k6o_36925.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8k6o_36925/08_2025/8k6o_36925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6o_36925/08_2025/8k6o_36925.map" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.033 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 68 5.16 5 C 5943 2.51 5 N 1588 2.21 5 O 1734 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9333 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1794 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 220} Chain breaks: 1 Chain: "B" Number of atoms: 2611 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2611 Classifications: {'peptide': 340} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 334} Chain: "C" Number of atoms: 445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 445 Classifications: {'peptide': 58} Link IDs: {'PTRANS': 4, 'TRANS': 53} Chain: "D" Number of atoms: 2444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2444 Classifications: {'peptide': 300} Link IDs: {'PTRANS': 11, 'TRANS': 288} Chain: "S" Number of atoms: 1783 Number of conformers: 1 Conformer: "" Number of residues, atoms: 232, 1783 Classifications: {'peptide': 232} Link IDs: {'PTRANS': 10, 'TRANS': 221} Chain breaks: 1 Chain: "E" Number of atoms: 256 Number of conformers: 1 Conformer: "" Number of residues, atoms: 30, 256 Classifications: {'peptide': 30} Link IDs: {'PTRANS': 4, 'TRANS': 25} Chain breaks: 1 Time building chain proxies: 2.55, per 1000 atoms: 0.27 Number of scatterers: 9333 At special positions: 0 Unit cell: (138.55, 121.55, 102.85, 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 68 16.00 O 1734 8.00 N 1588 7.00 C 5943 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS S 159 " - pdb=" SG CYS S 229 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 380.1 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2226 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 13 sheets defined 38.4% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 8 through 33 removed outlier: 3.794A pdb=" N GLU A 33 " --> pdb=" O LYS A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 208 through 214 removed outlier: 4.248A pdb=" N TRP A 212 " --> pdb=" O GLU A 208 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N HIS A 214 " --> pdb=" O LYS A 210 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 217 No H-bonds generated for 'chain 'A' and resid 215 through 217' Processing helix chain 'A' and resid 242 through 256 Processing helix chain 'A' and resid 271 through 282 Processing helix chain 'A' and resid 296 through 311 removed outlier: 3.947A pdb=" N ALA A 300 " --> pdb=" O LYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 353 Processing helix chain 'B' and resid 2 through 26 Processing helix chain 'B' and resid 29 through 35 Processing helix chain 'C' and resid 7 through 24 removed outlier: 3.724A pdb=" N ASN C 24 " --> pdb=" O LYS C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 29 through 44 Processing helix chain 'D' and resid 36 through 68 Processing helix chain 'D' and resid 73 through 103 removed outlier: 3.569A pdb=" N ILE D 77 " --> pdb=" O ASN D 73 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N LEU D 94 " --> pdb=" O ALA D 90 " (cutoff:3.500A) Proline residue: D 95 - end of helix Processing helix chain 'D' and resid 109 through 144 Proline residue: D 117 - end of helix Processing helix chain 'D' and resid 151 through 176 Proline residue: D 172 - end of helix Processing helix chain 'D' and resid 204 through 220 Processing helix chain 'D' and resid 220 through 249 removed outlier: 3.671A pdb=" N MET D 245 " --> pdb=" O ARG D 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS D 247 " --> pdb=" O ASN D 243 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N MET D 248 " --> pdb=" O MET D 244 " (cutoff:3.500A) Processing helix chain 'D' and resid 251 through 288 Proline residue: D 278 - end of helix Processing helix chain 'D' and resid 289 through 293 Processing helix chain 'D' and resid 297 through 321 removed outlier: 3.635A pdb=" N SER D 312 " --> pdb=" O THR D 308 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR D 313 " --> pdb=" O ALA D 309 " (cutoff:3.500A) Proline residue: D 317 - end of helix removed outlier: 3.873A pdb=" N TYR D 320 " --> pdb=" O ASN D 316 " (cutoff:3.500A) Processing helix chain 'D' and resid 324 through 333 Processing helix chain 'S' and resid 53 through 56 removed outlier: 3.895A pdb=" N GLY S 56 " --> pdb=" O SER S 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 53 through 56' Processing helix chain 'S' and resid 62 through 65 removed outlier: 3.525A pdb=" N LYS S 65 " --> pdb=" O ASP S 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 62 through 65' Processing helix chain 'E' and resid 17 through 32 Processing sheet with id=AA1, first strand: chain 'A' and resid 186 through 192 removed outlier: 3.929A pdb=" N ALA A 221 " --> pdb=" O LYS A 35 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 47 through 51 removed outlier: 6.806A pdb=" N ILE B 338 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N THR B 50 " --> pdb=" O LEU B 336 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N LEU B 336 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 58 through 63 removed outlier: 6.828A pdb=" N ALA B 73 " --> pdb=" O TYR B 59 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N MET B 61 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL B 71 " --> pdb=" O MET B 61 " (cutoff:3.500A) removed outlier: 5.363A pdb=" N TRP B 63 " --> pdb=" O LEU B 69 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU B 69 " --> pdb=" O TRP B 63 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N SER B 74 " --> pdb=" O LYS B 78 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N LYS B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N LEU B 79 " --> pdb=" O ALA B 92 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA B 92 " --> pdb=" O LEU B 79 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE B 81 " --> pdb=" O VAL B 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 104 through 105 removed outlier: 5.952A pdb=" N ASN B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 5.864A pdb=" N VAL B 135 " --> pdb=" O ASN B 125 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 150 through 151 removed outlier: 3.767A pdb=" N LEU B 168 " --> pdb=" O THR B 177 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 187 through 192 removed outlier: 4.067A pdb=" N GLN B 220 " --> pdb=" O LEU B 210 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP B 212 " --> pdb=" O CYS B 218 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N CYS B 218 " --> pdb=" O ASP B 212 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 232 through 234 removed outlier: 3.993A pdb=" N MET B 262 " --> pdb=" O LEU B 252 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N ASP B 254 " --> pdb=" O GLU B 260 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N GLU B 260 " --> pdb=" O ASP B 254 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 276 through 278 removed outlier: 6.367A pdb=" N ASP B 298 " --> pdb=" O ARG B 304 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG B 304 " --> pdb=" O ASP B 298 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 178 through 180 Processing sheet with id=AB1, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AB2, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.665A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TYR S 50 " --> pdb=" O MET S 34 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N MET S 34 " --> pdb=" O TYR S 50 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG S 98 " --> pdb=" O PHE S 110 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE S 110 " --> pdb=" O ARG S 98 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'S' and resid 140 through 142 Processing sheet with id=AB4, first strand: chain 'S' and resid 146 through 148 removed outlier: 7.096A pdb=" N VAL S 147 " --> pdb=" O GLU S 246 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N LEU S 178 " --> pdb=" O LEU S 187 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU S 187 " --> pdb=" O LEU S 178 " (cutoff:3.500A) 478 hydrogen bonds defined for protein. 1362 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: 1.26 Time building geometry restraints manager: 1.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3013 1.34 - 1.46: 2103 1.46 - 1.58: 4315 1.58 - 1.69: 0 1.69 - 1.81: 101 Bond restraints: 9532 Sorted by residual: bond pdb=" CA PHE A 288 " pdb=" CB PHE A 288 " ideal model delta sigma weight residual 1.522 1.530 -0.008 7.00e-03 2.04e+04 1.33e+00 bond pdb=" CA GLY B 330 " pdb=" C GLY B 330 " ideal model delta sigma weight residual 1.512 1.522 -0.010 8.70e-03 1.32e+04 1.32e+00 bond pdb=" CA VAL A 202 " pdb=" CB VAL A 202 " ideal model delta sigma weight residual 1.532 1.544 -0.012 1.08e-02 8.57e+03 1.26e+00 bond pdb=" CA ILE D 91 " pdb=" C ILE D 91 " ideal model delta sigma weight residual 1.522 1.535 -0.014 1.32e-02 5.74e+03 1.07e+00 bond pdb=" CG ARG E 19 " pdb=" CD ARG E 19 " ideal model delta sigma weight residual 1.520 1.551 -0.031 3.00e-02 1.11e+03 1.05e+00 ... (remaining 9527 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 12583 1.57 - 3.14: 257 3.14 - 4.70: 55 4.70 - 6.27: 8 6.27 - 7.84: 4 Bond angle restraints: 12907 Sorted by residual: angle pdb=" C ALA C 45 " pdb=" N LYS C 46 " pdb=" CA LYS C 46 " ideal model delta sigma weight residual 121.54 129.38 -7.84 1.91e+00 2.74e-01 1.68e+01 angle pdb=" CG ARG E 19 " pdb=" CD ARG E 19 " pdb=" NE ARG E 19 " ideal model delta sigma weight residual 112.00 118.91 -6.91 2.20e+00 2.07e-01 9.87e+00 angle pdb=" CA MET D 92 " pdb=" CB MET D 92 " pdb=" CG MET D 92 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" N VAL A 202 " pdb=" CA VAL A 202 " pdb=" C VAL A 202 " ideal model delta sigma weight residual 106.42 110.63 -4.21 1.51e+00 4.39e-01 7.78e+00 angle pdb=" CG ARG C 13 " pdb=" CD ARG C 13 " pdb=" NE ARG C 13 " ideal model delta sigma weight residual 112.00 117.80 -5.80 2.20e+00 2.07e-01 6.94e+00 ... (remaining 12902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.10: 5108 16.10 - 32.19: 435 32.19 - 48.29: 102 48.29 - 64.38: 19 64.38 - 80.48: 6 Dihedral angle restraints: 5670 sinusoidal: 2225 harmonic: 3445 Sorted by residual: dihedral pdb=" CA MET D 92 " pdb=" C MET D 92 " pdb=" N CYS D 93 " pdb=" CA CYS D 93 " ideal model delta harmonic sigma weight residual -180.00 -154.26 -25.74 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CA ASP D 86 " pdb=" CB ASP D 86 " pdb=" CG ASP D 86 " pdb=" OD1 ASP D 86 " ideal model delta sinusoidal sigma weight residual -30.00 -89.46 59.46 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ILE D 91 " pdb=" C ILE D 91 " pdb=" N MET D 92 " pdb=" CA MET D 92 " ideal model delta harmonic sigma weight residual 180.00 162.85 17.15 0 5.00e+00 4.00e-02 1.18e+01 ... (remaining 5667 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 1242 0.056 - 0.112: 184 0.112 - 0.168: 29 0.168 - 0.224: 0 0.224 - 0.279: 1 Chirality restraints: 1456 Sorted by residual: chirality pdb=" CB ILE D 91 " pdb=" CA ILE D 91 " pdb=" CG1 ILE D 91 " pdb=" CG2 ILE D 91 " both_signs ideal model delta sigma weight residual False 2.64 2.37 0.28 2.00e-01 2.50e+01 1.95e+00 chirality pdb=" CA ILE S 58 " pdb=" N ILE S 58 " pdb=" C ILE S 58 " pdb=" CB ILE S 58 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.50e-01 chirality pdb=" CA TYR S 235 " pdb=" N TYR S 235 " pdb=" C TYR S 235 " pdb=" CB TYR S 235 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.30e-01 ... (remaining 1453 not shown) Planarity restraints: 1637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 82 " 0.010 2.00e-02 2.50e+03 1.13e-02 3.19e+00 pdb=" CG TRP B 82 " -0.030 2.00e-02 2.50e+03 pdb=" CD1 TRP B 82 " 0.017 2.00e-02 2.50e+03 pdb=" CD2 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP B 82 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP B 82 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 82 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 82 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 82 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP B 82 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR S 235 " -0.014 2.00e-02 2.50e+03 9.37e-03 1.76e+00 pdb=" CG TYR S 235 " 0.022 2.00e-02 2.50e+03 pdb=" CD1 TYR S 235 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR S 235 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR S 235 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR S 235 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR S 235 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY D 222 " -0.022 5.00e-02 4.00e+02 3.31e-02 1.76e+00 pdb=" N PRO D 223 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 223 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 223 " -0.019 5.00e-02 4.00e+02 ... (remaining 1634 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1936 2.78 - 3.31: 8779 3.31 - 3.84: 14846 3.84 - 4.37: 16179 4.37 - 4.90: 29558 Nonbonded interactions: 71298 Sorted by model distance: nonbonded pdb=" NH2 ARG S 87 " pdb=" OE2 GLU S 89 " model vdw 2.255 3.120 nonbonded pdb=" O CYS D 305 " pdb=" OG1 THR D 308 " model vdw 2.278 3.040 nonbonded pdb=" ND2 ASN D 58 " pdb=" OD1 ASP D 86 " model vdw 2.304 3.120 nonbonded pdb=" OD1 ASP B 5 " pdb=" NH2 ARG B 8 " model vdw 2.309 3.120 nonbonded pdb=" O ARG B 314 " pdb=" OG SER B 331 " model vdw 2.326 3.040 ... (remaining 71293 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.810 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: 0.240 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.390 Find NCS groups from input model: 0.060 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:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.010 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6199 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 : 0.002 0.039 9533 Z= 0.131 Angle : 0.584 7.839 12909 Z= 0.324 Chirality : 0.040 0.279 1456 Planarity : 0.003 0.033 1637 Dihedral : 12.870 80.479 3441 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 0.10 % Allowed : 0.39 % Favored : 99.51 % 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 aren not related in a simple way. whole: 2.01 (0.24), residues: 1165 helix: 3.10 (0.25), residues: 421 sheet: 1.50 (0.31), residues: 280 loop : -0.50 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 19 TYR 0.022 0.001 TYR S 235 PHE 0.017 0.001 PHE B 199 TRP 0.030 0.001 TRP B 82 HIS 0.003 0.001 HIS A 281 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9532) covalent geometry : angle 0.58374 (12907) SS BOND : bond 0.00420 ( 1) SS BOND : angle 0.04632 ( 2) hydrogen bonds : bond 0.12534 ( 478) hydrogen bonds : angle 5.21493 ( 1362) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 188 time to evaluate : 0.308 Fit side-chains REVERT: A 53 MET cc_start: 0.4794 (mmm) cc_final: 0.4445 (mmm) REVERT: B 124 TYR cc_start: 0.7444 (m-80) cc_final: 0.7207 (m-80) REVERT: B 245 SER cc_start: 0.7354 (t) cc_final: 0.6380 (t) REVERT: B 246 ASP cc_start: 0.7126 (m-30) cc_final: 0.6730 (m-30) REVERT: B 312 ASP cc_start: 0.7160 (p0) cc_final: 0.6812 (p0) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.0883 time to fit residues: 23.6390 Evaluate side-chains 155 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.262 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 113 optimal weight: 3.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 256 ASN B 75 GLN B 110 ASN C 18 GLN D 306 HIS S 231 GLN E 7 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.154892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.129701 restraints weight = 13515.893| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 2.37 r_work: 0.3570 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7082 moved from start: 0.3313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.100 9533 Z= 0.241 Angle : 0.699 8.365 12909 Z= 0.377 Chirality : 0.046 0.216 1456 Planarity : 0.005 0.043 1637 Dihedral : 4.633 21.557 1281 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.95 % Allowed : 9.27 % Favored : 88.78 % 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 aren not related in a simple way. whole: 1.55 (0.24), residues: 1165 helix: 2.68 (0.24), residues: 434 sheet: 1.24 (0.30), residues: 291 loop : -0.87 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 254 TYR 0.032 0.003 TYR S 235 PHE 0.022 0.003 PHE A 190 TRP 0.024 0.002 TRP B 82 HIS 0.011 0.002 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00549 ( 9532) covalent geometry : angle 0.69882 (12907) SS BOND : bond 0.01152 ( 1) SS BOND : angle 1.06088 ( 2) hydrogen bonds : bond 0.06814 ( 478) hydrogen bonds : angle 4.42483 ( 1362) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 165 time to evaluate : 0.355 Fit side-chains REVERT: A 191 THR cc_start: 0.8739 (m) cc_final: 0.8518 (p) REVERT: A 196 HIS cc_start: 0.7509 (m-70) cc_final: 0.7207 (m90) REVERT: A 241 MET cc_start: 0.5738 (OUTLIER) cc_final: 0.5399 (pmm) REVERT: A 244 MET cc_start: 0.8162 (tpp) cc_final: 0.7391 (tpp) REVERT: A 338 ASP cc_start: 0.7531 (m-30) cc_final: 0.7268 (m-30) REVERT: B 45 MET cc_start: 0.6870 (mmt) cc_final: 0.6605 (mmt) REVERT: B 55 LEU cc_start: 0.7896 (mt) cc_final: 0.7682 (mp) REVERT: B 108 SER cc_start: 0.8739 (OUTLIER) cc_final: 0.8513 (p) REVERT: B 110 ASN cc_start: 0.8250 (m-40) cc_final: 0.7961 (m-40) REVERT: B 124 TYR cc_start: 0.8426 (m-80) cc_final: 0.8202 (m-80) REVERT: B 130 GLU cc_start: 0.7853 (mp0) cc_final: 0.7527 (mp0) REVERT: B 192 LEU cc_start: 0.8230 (OUTLIER) cc_final: 0.7958 (tp) REVERT: B 245 SER cc_start: 0.7549 (t) cc_final: 0.7331 (t) REVERT: B 276 VAL cc_start: 0.8599 (OUTLIER) cc_final: 0.8390 (t) REVERT: B 290 ASP cc_start: 0.7171 (m-30) cc_final: 0.6743 (m-30) REVERT: B 296 VAL cc_start: 0.7992 (t) cc_final: 0.7662 (m) REVERT: B 314 ARG cc_start: 0.7881 (ptm160) cc_final: 0.7586 (ptm160) REVERT: D 226 PHE cc_start: 0.7214 (t80) cc_final: 0.7002 (t80) outliers start: 20 outliers final: 6 residues processed: 172 average time/residue: 0.1076 time to fit residues: 25.2655 Evaluate side-chains 157 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 29 LYS Chi-restraints excluded: chain A residue 241 MET Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 108 SER Chi-restraints excluded: chain B residue 192 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 114 optimal weight: 0.0000 chunk 21 optimal weight: 0.5980 chunk 49 optimal weight: 3.9990 chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 25 optimal weight: 0.3980 chunk 91 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4015 r_free = 0.4015 target = 0.156035 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.130472 restraints weight = 13467.352| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 2.39 r_work: 0.3554 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7057 moved from start: 0.3672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9533 Z= 0.131 Angle : 0.531 6.167 12909 Z= 0.286 Chirality : 0.041 0.182 1456 Planarity : 0.004 0.046 1637 Dihedral : 4.229 21.191 1281 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 1.07 % Allowed : 13.46 % Favored : 85.46 % 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 aren not related in a simple way. whole: 1.73 (0.24), residues: 1165 helix: 3.12 (0.24), residues: 428 sheet: 1.09 (0.30), residues: 294 loop : -0.88 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 134 TYR 0.028 0.002 TYR S 235 PHE 0.022 0.002 PHE D 184 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 9532) covalent geometry : angle 0.53109 (12907) SS BOND : bond 0.00859 ( 1) SS BOND : angle 0.96358 ( 2) hydrogen bonds : bond 0.05167 ( 478) hydrogen bonds : angle 4.08551 ( 1362) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 159 time to evaluate : 0.362 Fit side-chains REVERT: A 196 HIS cc_start: 0.7509 (m-70) cc_final: 0.7303 (m90) REVERT: A 338 ASP cc_start: 0.7490 (m-30) cc_final: 0.7219 (m-30) REVERT: B 55 LEU cc_start: 0.7889 (mt) cc_final: 0.7637 (mp) REVERT: B 108 SER cc_start: 0.8716 (t) cc_final: 0.8500 (p) REVERT: B 124 TYR cc_start: 0.8403 (m-80) cc_final: 0.8190 (m-80) REVERT: B 130 GLU cc_start: 0.7780 (mp0) cc_final: 0.7510 (mp0) REVERT: B 188 MET cc_start: 0.8092 (mmm) cc_final: 0.7827 (mmm) REVERT: B 245 SER cc_start: 0.7559 (t) cc_final: 0.7280 (t) REVERT: B 276 VAL cc_start: 0.8605 (p) cc_final: 0.8397 (t) REVERT: B 296 VAL cc_start: 0.7926 (t) cc_final: 0.7680 (m) REVERT: C 21 MET cc_start: 0.6690 (tmm) cc_final: 0.6259 (tmm) REVERT: D 233 LYS cc_start: 0.8174 (ttmm) cc_final: 0.7927 (mtpp) REVERT: S 23 SER cc_start: 0.7071 (m) cc_final: 0.6816 (p) outliers start: 11 outliers final: 9 residues processed: 162 average time/residue: 0.1005 time to fit residues: 22.7253 Evaluate side-chains 161 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 152 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 249 LYS Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 326 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 101 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 5 optimal weight: 0.4980 chunk 85 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 67 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 3 optimal weight: 0.0980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 18 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.155160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.129523 restraints weight = 13594.050| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.41 r_work: 0.3571 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3571 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7099 moved from start: 0.4133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9533 Z= 0.127 Angle : 0.527 6.744 12909 Z= 0.281 Chirality : 0.041 0.170 1456 Planarity : 0.004 0.048 1637 Dihedral : 4.151 23.737 1281 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.76 % Allowed : 14.93 % Favored : 83.32 % 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 aren not related in a simple way. whole: 1.73 (0.24), residues: 1165 helix: 3.17 (0.24), residues: 427 sheet: 0.96 (0.30), residues: 301 loop : -0.85 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 134 TYR 0.027 0.001 TYR S 235 PHE 0.022 0.001 PHE D 184 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 9532) covalent geometry : angle 0.52727 (12907) SS BOND : bond 0.00925 ( 1) SS BOND : angle 1.14912 ( 2) hydrogen bonds : bond 0.04922 ( 478) hydrogen bonds : angle 3.96356 ( 1362) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.273 Fit side-chains REVERT: A 262 ASP cc_start: 0.7667 (p0) cc_final: 0.7135 (p0) REVERT: A 278 LYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6491 (tttt) REVERT: A 338 ASP cc_start: 0.7479 (m-30) cc_final: 0.7215 (m-30) REVERT: B 55 LEU cc_start: 0.7857 (mt) cc_final: 0.7631 (mp) REVERT: B 86 THR cc_start: 0.8480 (OUTLIER) cc_final: 0.8230 (p) REVERT: B 103 CYS cc_start: 0.8082 (t) cc_final: 0.7878 (p) REVERT: B 129 ARG cc_start: 0.7757 (ttm-80) cc_final: 0.7536 (ttm-80) REVERT: B 130 GLU cc_start: 0.7774 (mp0) cc_final: 0.7537 (mp0) REVERT: C 21 MET cc_start: 0.6608 (tmm) cc_final: 0.6217 (tmm) REVERT: D 103 MET cc_start: 0.4004 (ptm) cc_final: 0.3448 (ttt) REVERT: D 233 LYS cc_start: 0.8133 (ttmm) cc_final: 0.7828 (mtpp) REVERT: S 23 SER cc_start: 0.7141 (m) cc_final: 0.6921 (p) outliers start: 18 outliers final: 9 residues processed: 171 average time/residue: 0.0945 time to fit residues: 22.6739 Evaluate side-chains 164 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 278 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 93 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 73 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 25 optimal weight: 0.0870 chunk 53 optimal weight: 0.6980 chunk 94 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 66 optimal weight: 1.9990 chunk 59 optimal weight: 0.7980 chunk 106 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 overall best weight: 0.6960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.152971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.127658 restraints weight = 13421.333| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 2.38 r_work: 0.3541 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3380 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7310 moved from start: 0.4613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9533 Z= 0.134 Angle : 0.530 6.903 12909 Z= 0.283 Chirality : 0.041 0.175 1456 Planarity : 0.004 0.050 1637 Dihedral : 4.155 23.096 1281 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.05 % Allowed : 17.46 % Favored : 80.49 % 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 aren not related in a simple way. whole: 1.65 (0.25), residues: 1165 helix: 3.16 (0.24), residues: 427 sheet: 0.86 (0.30), residues: 303 loop : -0.92 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 134 TYR 0.029 0.001 TYR S 235 PHE 0.023 0.002 PHE D 184 TRP 0.017 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00288 ( 9532) covalent geometry : angle 0.52976 (12907) SS BOND : bond 0.01010 ( 1) SS BOND : angle 1.27143 ( 2) hydrogen bonds : bond 0.05151 ( 478) hydrogen bonds : angle 3.94251 ( 1362) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 156 time to evaluate : 0.335 Fit side-chains REVERT: A 199 MET cc_start: 0.8365 (ttm) cc_final: 0.8082 (ttm) REVERT: A 338 ASP cc_start: 0.7702 (m-30) cc_final: 0.7455 (m-30) REVERT: B 55 LEU cc_start: 0.8004 (mt) cc_final: 0.7762 (mp) REVERT: B 103 CYS cc_start: 0.8312 (t) cc_final: 0.8078 (p) REVERT: B 130 GLU cc_start: 0.8024 (mp0) cc_final: 0.7755 (mp0) REVERT: B 262 MET cc_start: 0.8118 (mmt) cc_final: 0.7908 (mmt) REVERT: B 314 ARG cc_start: 0.7786 (ptm160) cc_final: 0.7554 (ptm160) REVERT: D 103 MET cc_start: 0.4649 (ptm) cc_final: 0.3898 (ttt) REVERT: D 233 LYS cc_start: 0.8240 (ttmm) cc_final: 0.7989 (mtpp) REVERT: S 23 SER cc_start: 0.7309 (m) cc_final: 0.7088 (p) REVERT: S 139 VAL cc_start: 0.7837 (p) cc_final: 0.7610 (p) outliers start: 21 outliers final: 13 residues processed: 170 average time/residue: 0.0994 time to fit residues: 23.5664 Evaluate side-chains 164 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 5 optimal weight: 0.6980 chunk 16 optimal weight: 0.0670 chunk 7 optimal weight: 0.0060 chunk 12 optimal weight: 0.0770 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 102 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.3694 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3992 r_free = 0.3992 target = 0.154274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.128935 restraints weight = 13439.535| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 2.39 r_work: 0.3561 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3403 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.4749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9533 Z= 0.109 Angle : 0.516 7.229 12909 Z= 0.270 Chirality : 0.040 0.166 1456 Planarity : 0.003 0.046 1637 Dihedral : 4.046 27.433 1281 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 2.24 % Allowed : 17.66 % Favored : 80.10 % 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 aren not related in a simple way. whole: 1.71 (0.25), residues: 1165 helix: 3.27 (0.24), residues: 426 sheet: 0.83 (0.30), residues: 301 loop : -0.88 (0.27), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.026 0.001 TYR S 235 PHE 0.023 0.001 PHE D 184 TRP 0.018 0.001 TRP B 82 HIS 0.003 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00218 ( 9532) covalent geometry : angle 0.51575 (12907) SS BOND : bond 0.00772 ( 1) SS BOND : angle 1.08514 ( 2) hydrogen bonds : bond 0.04511 ( 478) hydrogen bonds : angle 3.81894 ( 1362) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 178 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 155 time to evaluate : 0.278 Fit side-chains REVERT: A 241 MET cc_start: 0.5905 (pmm) cc_final: 0.4696 (pmm) REVERT: A 278 LYS cc_start: 0.6642 (mttt) cc_final: 0.6403 (tttt) REVERT: A 338 ASP cc_start: 0.7641 (m-30) cc_final: 0.7405 (m-30) REVERT: B 55 LEU cc_start: 0.8001 (mt) cc_final: 0.7764 (mp) REVERT: B 86 THR cc_start: 0.8488 (OUTLIER) cc_final: 0.8282 (p) REVERT: B 110 ASN cc_start: 0.8305 (m-40) cc_final: 0.8008 (m110) REVERT: B 154 ASP cc_start: 0.6280 (OUTLIER) cc_final: 0.6011 (m-30) REVERT: D 103 MET cc_start: 0.4664 (ptm) cc_final: 0.4022 (ttt) REVERT: D 148 TRP cc_start: 0.7666 (t60) cc_final: 0.7421 (t60) REVERT: D 233 LYS cc_start: 0.8216 (ttmm) cc_final: 0.7983 (mtpp) outliers start: 23 outliers final: 17 residues processed: 166 average time/residue: 0.0944 time to fit residues: 21.9474 Evaluate side-chains 169 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 150 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 198 LEU Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 26 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 108 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 54 optimal weight: 5.9990 chunk 85 optimal weight: 0.7980 chunk 2 optimal weight: 0.6980 chunk 17 optimal weight: 0.4980 chunk 23 optimal weight: 7.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.152407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127012 restraints weight = 13374.568| |-----------------------------------------------------------------------------| r_work (start): 0.3643 rms_B_bonded: 2.38 r_work: 0.3531 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3369 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7321 moved from start: 0.4975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9533 Z= 0.135 Angle : 0.537 7.960 12909 Z= 0.283 Chirality : 0.041 0.183 1456 Planarity : 0.004 0.043 1637 Dihedral : 4.106 26.362 1281 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.83 % Allowed : 17.95 % Favored : 79.22 % 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 aren not related in a simple way. whole: 1.68 (0.25), residues: 1165 helix: 3.25 (0.24), residues: 427 sheet: 0.84 (0.30), residues: 292 loop : -0.90 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.030 0.001 TYR S 235 PHE 0.025 0.002 PHE D 184 TRP 0.019 0.001 TRP B 82 HIS 0.003 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9532) covalent geometry : angle 0.53700 (12907) SS BOND : bond 0.00966 ( 1) SS BOND : angle 1.36214 ( 2) hydrogen bonds : bond 0.04954 ( 478) hydrogen bonds : angle 3.87816 ( 1362) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 157 time to evaluate : 0.286 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.5862 (pmm) cc_final: 0.4651 (pmm) REVERT: A 307 LYS cc_start: 0.6839 (mtpt) cc_final: 0.6493 (ttpt) REVERT: A 338 ASP cc_start: 0.7676 (m-30) cc_final: 0.7441 (m-30) REVERT: B 55 LEU cc_start: 0.8016 (mt) cc_final: 0.7775 (mp) REVERT: B 86 THR cc_start: 0.8500 (OUTLIER) cc_final: 0.8295 (p) REVERT: B 110 ASN cc_start: 0.8308 (m-40) cc_final: 0.8018 (m110) REVERT: B 154 ASP cc_start: 0.6227 (OUTLIER) cc_final: 0.5967 (m-30) REVERT: D 103 MET cc_start: 0.4777 (ptm) cc_final: 0.4159 (ttt) outliers start: 29 outliers final: 26 residues processed: 176 average time/residue: 0.1008 time to fit residues: 24.6641 Evaluate side-chains 183 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 155 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 89 optimal weight: 0.0870 chunk 0 optimal weight: 7.9990 chunk 84 optimal weight: 0.7980 chunk 104 optimal weight: 7.9990 chunk 115 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 105 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3965 r_free = 0.3965 target = 0.152264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.126909 restraints weight = 13257.553| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.35 r_work: 0.3529 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.5173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 9533 Z= 0.128 Angle : 0.547 9.348 12909 Z= 0.285 Chirality : 0.041 0.181 1456 Planarity : 0.004 0.043 1637 Dihedral : 4.154 27.088 1281 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.12 % Allowed : 18.15 % Favored : 78.73 % 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 aren not related in a simple way. whole: 1.70 (0.25), residues: 1165 helix: 3.27 (0.24), residues: 427 sheet: 0.86 (0.30), residues: 291 loop : -0.90 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.029 0.001 TYR S 235 PHE 0.025 0.001 PHE D 184 TRP 0.019 0.002 TRP B 82 HIS 0.004 0.001 HIS A 189 Details of bonding type rmsd covalent geometry : bond 0.00278 ( 9532) covalent geometry : angle 0.54656 (12907) SS BOND : bond 0.00974 ( 1) SS BOND : angle 1.32250 ( 2) hydrogen bonds : bond 0.04924 ( 478) hydrogen bonds : angle 3.88109 ( 1362) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 0.381 Fit side-chains revert: symmetry clash REVERT: A 191 THR cc_start: 0.9024 (p) cc_final: 0.8761 (t) REVERT: A 241 MET cc_start: 0.5885 (pmm) cc_final: 0.4767 (pmm) REVERT: A 278 LYS cc_start: 0.6736 (mttt) cc_final: 0.6534 (mttt) REVERT: A 307 LYS cc_start: 0.6941 (mtpt) cc_final: 0.6480 (mtpt) REVERT: A 338 ASP cc_start: 0.7655 (m-30) cc_final: 0.7418 (m-30) REVERT: B 55 LEU cc_start: 0.7973 (mt) cc_final: 0.7755 (mp) REVERT: B 110 ASN cc_start: 0.8317 (m-40) cc_final: 0.8031 (m110) REVERT: B 129 ARG cc_start: 0.8004 (ttm-80) cc_final: 0.7757 (ttm-80) REVERT: B 154 ASP cc_start: 0.6281 (OUTLIER) cc_final: 0.6012 (m-30) REVERT: B 290 ASP cc_start: 0.7107 (m-30) cc_final: 0.6588 (m-30) REVERT: D 103 MET cc_start: 0.4845 (ptm) cc_final: 0.4241 (ttt) outliers start: 32 outliers final: 28 residues processed: 169 average time/residue: 0.0985 time to fit residues: 23.4819 Evaluate side-chains 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 146 time to evaluate : 0.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 258 LYS Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 93 ILE Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 12 VAL Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 82 optimal weight: 3.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 chunk 40 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 49 optimal weight: 0.8980 chunk 105 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 196 HIS C 59 ASN S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3924 r_free = 0.3924 target = 0.149041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.123904 restraints weight = 13199.627| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 2.35 r_work: 0.3426 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3266 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.5671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 9533 Z= 0.157 Angle : 0.586 8.277 12909 Z= 0.309 Chirality : 0.043 0.233 1456 Planarity : 0.004 0.044 1637 Dihedral : 4.358 26.606 1281 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.02 % Allowed : 18.54 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.50 (0.25), residues: 1165 helix: 3.06 (0.24), residues: 433 sheet: 0.86 (0.30), residues: 297 loop : -1.15 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 134 TYR 0.036 0.002 TYR S 235 PHE 0.027 0.002 PHE D 184 TRP 0.021 0.002 TRP B 82 HIS 0.004 0.001 HIS B 54 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 9532) covalent geometry : angle 0.58521 (12907) SS BOND : bond 0.01251 ( 1) SS BOND : angle 1.71854 ( 2) hydrogen bonds : bond 0.05803 ( 478) hydrogen bonds : angle 4.06757 ( 1362) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.262 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8282 (mtmm) cc_final: 0.7999 (mtmm) REVERT: A 191 THR cc_start: 0.8982 (p) cc_final: 0.8694 (t) REVERT: A 196 HIS cc_start: 0.7906 (m-70) cc_final: 0.7700 (m-70) REVERT: A 233 LEU cc_start: 0.7437 (OUTLIER) cc_final: 0.7070 (mp) REVERT: A 241 MET cc_start: 0.5842 (pmm) cc_final: 0.4708 (pmm) REVERT: A 307 LYS cc_start: 0.6842 (mtpt) cc_final: 0.6317 (mtpt) REVERT: A 338 ASP cc_start: 0.7645 (m-30) cc_final: 0.7405 (m-30) REVERT: B 129 ARG cc_start: 0.7909 (ttm-80) cc_final: 0.7640 (ttm-80) REVERT: B 154 ASP cc_start: 0.6262 (OUTLIER) cc_final: 0.5978 (m-30) REVERT: B 290 ASP cc_start: 0.7053 (m-30) cc_final: 0.6517 (m-30) REVERT: B 294 CYS cc_start: 0.8037 (OUTLIER) cc_final: 0.7316 (m) REVERT: D 103 MET cc_start: 0.4974 (ptm) cc_final: 0.4343 (ttt) REVERT: S 118 THR cc_start: 0.7713 (m) cc_final: 0.7416 (p) outliers start: 31 outliers final: 23 residues processed: 183 average time/residue: 0.0969 time to fit residues: 24.7653 Evaluate side-chains 190 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 164 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 67 SER Chi-restraints excluded: chain B residue 78 LYS Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 154 ASP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 70 ILE Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 63 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 25 optimal weight: 0.0970 chunk 6 optimal weight: 0.4980 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 61 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 94 optimal weight: 0.0000 overall best weight: 0.2960 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 HIS C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3961 r_free = 0.3961 target = 0.152282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.127287 restraints weight = 13284.915| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 2.35 r_work: 0.3505 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7306 moved from start: 0.5729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 9533 Z= 0.113 Angle : 0.558 11.254 12909 Z= 0.288 Chirality : 0.041 0.257 1456 Planarity : 0.004 0.044 1637 Dihedral : 4.196 31.366 1281 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 2.15 % Allowed : 20.68 % Favored : 77.17 % 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 aren not related in a simple way. whole: 1.69 (0.25), residues: 1165 helix: 3.39 (0.24), residues: 421 sheet: 0.87 (0.31), residues: 285 loop : -0.97 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 134 TYR 0.023 0.001 TYR S 235 PHE 0.027 0.001 PHE D 184 TRP 0.017 0.001 TRP B 82 HIS 0.002 0.001 HIS D 139 Details of bonding type rmsd covalent geometry : bond 0.00226 ( 9532) covalent geometry : angle 0.55781 (12907) SS BOND : bond 0.00682 ( 1) SS BOND : angle 1.06150 ( 2) hydrogen bonds : bond 0.04466 ( 478) hydrogen bonds : angle 3.82458 ( 1362) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2330 Ramachandran restraints generated. 1165 Oldfield, 0 Emsley, 1165 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 154 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 35 LYS cc_start: 0.8233 (mtmm) cc_final: 0.7972 (mtmm) REVERT: A 191 THR cc_start: 0.8991 (p) cc_final: 0.8720 (t) REVERT: A 241 MET cc_start: 0.5778 (pmm) cc_final: 0.4729 (pmm) REVERT: A 307 LYS cc_start: 0.6991 (mtpt) cc_final: 0.6472 (mtpt) REVERT: A 338 ASP cc_start: 0.7639 (m-30) cc_final: 0.7401 (m-30) REVERT: B 129 ARG cc_start: 0.7974 (ttm-80) cc_final: 0.7717 (ttm-80) REVERT: B 201 SER cc_start: 0.8744 (m) cc_final: 0.8488 (t) REVERT: B 290 ASP cc_start: 0.7062 (m-30) cc_final: 0.6528 (m-30) REVERT: B 294 CYS cc_start: 0.7941 (OUTLIER) cc_final: 0.7275 (m) REVERT: C 27 ARG cc_start: 0.7597 (mmt-90) cc_final: 0.7342 (mmt-90) REVERT: D 103 MET cc_start: 0.5012 (ptm) cc_final: 0.4458 (ttt) REVERT: D 129 PHE cc_start: 0.8089 (m-80) cc_final: 0.7815 (m-80) outliers start: 22 outliers final: 17 residues processed: 165 average time/residue: 0.0985 time to fit residues: 22.5629 Evaluate side-chains 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 154 time to evaluate : 0.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 159 THR Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain C residue 50 LEU Chi-restraints excluded: chain C residue 59 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 248 MET Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain S residue 93 MET Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 220 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 34 optimal weight: 0.4980 chunk 106 optimal weight: 0.8980 chunk 27 optimal weight: 0.0060 chunk 99 optimal weight: 0.3980 chunk 105 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 72 optimal weight: 0.8980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 230 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.151745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.127024 restraints weight = 13191.925| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 2.32 r_work: 0.3480 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 4.82 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.5711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 9533 Z= 0.194 Angle : 0.893 59.190 12909 Z= 0.527 Chirality : 0.041 0.282 1456 Planarity : 0.004 0.044 1637 Dihedral : 4.250 31.531 1281 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.85 % Allowed : 20.98 % Favored : 77.17 % Cbeta Deviations : 0.09 % 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 aren not related in a simple way. whole: 1.69 (0.25), residues: 1165 helix: 3.38 (0.24), residues: 421 sheet: 0.86 (0.31), residues: 285 loop : -0.97 (0.27), residues: 459 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 134 TYR 0.022 0.001 TYR S 235 PHE 0.027 0.001 PHE D 184 TRP 0.017 0.002 TRP B 82 HIS 0.002 0.001 HIS S 35 Details of bonding type rmsd covalent geometry : bond 0.00358 ( 9532) covalent geometry : angle 0.89340 (12907) SS BOND : bond 0.00711 ( 1) SS BOND : angle 1.08156 ( 2) hydrogen bonds : bond 0.04490 ( 478) hydrogen bonds : angle 3.82583 ( 1362) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2492.81 seconds wall clock time: 43 minutes 20.82 seconds (2600.82 seconds total)