Starting phenix.real_space_refine on Thu Mar 13 19:58:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6o_36925/03_2025/8k6o_36925.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6o_36925/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8k6o_36925/03_2025/8k6o_36925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6o_36925/03_2025/8k6o_36925.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6o_36925/03_2025/8k6o_36925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6o_36925/03_2025/8k6o_36925.cif" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 5.71, per 1000 atoms: 0.61 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: 2.60 Conformation dependent library (CDL) restraints added in 1.4 seconds 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: 0.99 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: 2.59 Time building geometry restraints manager: 3.08 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: 1.120 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: 0.420 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 24.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.040 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:2.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.170 ------------------------------------------------------------------------------- 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 9532 Z= 0.161 Angle : 0.584 7.839 12907 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.030 0.001 TRP B 82 HIS 0.003 0.001 HIS A 281 PHE 0.017 0.001 PHE B 199 TYR 0.022 0.001 TYR S 235 ARG 0.006 0.000 ARG E 19 *********************** 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 : 0.931 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: 0.7208 (m-80) REVERT: B 245 SER cc_start: 0.7354 (t) cc_final: 0.6379 (t) REVERT: B 246 ASP cc_start: 0.7126 (m-30) cc_final: 0.6728 (m-30) REVERT: B 312 ASP cc_start: 0.7160 (p0) cc_final: 0.6811 (p0) outliers start: 1 outliers final: 0 residues processed: 189 average time/residue: 0.2058 time to fit residues: 54.5262 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 : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 98 optimal weight: 0.6980 chunk 88 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 chunk 47 optimal weight: 0.2980 chunk 91 optimal weight: 0.0070 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 68 optimal weight: 3.9990 chunk 106 optimal weight: 1.9990 overall best weight: 0.4598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN A 256 ASN B 75 GLN B 110 ASN D 177 GLN ** E 7 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 = 0.4132 r_free = 0.4132 target = 0.165871 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.140909 restraints weight = 13769.844| |-----------------------------------------------------------------------------| r_work (start): 0.3830 rms_B_bonded: 2.37 r_work: 0.3723 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6749 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9532 Z= 0.176 Angle : 0.541 7.112 12907 Z= 0.289 Chirality : 0.041 0.160 1456 Planarity : 0.004 0.039 1637 Dihedral : 3.958 24.388 1281 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.80 % Favored : 98.20 % Rotamer: Outliers : 1.46 % Allowed : 8.10 % Favored : 90.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.24), residues: 1165 helix: 3.09 (0.24), residues: 435 sheet: 1.36 (0.31), residues: 287 loop : -0.58 (0.26), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 82 HIS 0.004 0.001 HIS B 54 PHE 0.020 0.001 PHE S 177 TYR 0.023 0.001 TYR S 235 ARG 0.003 0.000 ARG D 254 *********************** 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 186 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 171 time to evaluate : 0.976 Fit side-chains REVERT: A 191 THR cc_start: 0.8256 (m) cc_final: 0.8032 (p) REVERT: A 241 MET cc_start: 0.5664 (OUTLIER) cc_final: 0.5247 (pmm) REVERT: A 338 ASP cc_start: 0.7435 (m-30) cc_final: 0.7163 (m-30) REVERT: B 55 LEU cc_start: 0.7734 (mt) cc_final: 0.7492 (mp) REVERT: B 124 TYR cc_start: 0.8064 (m-80) cc_final: 0.7734 (m-80) REVERT: B 290 ASP cc_start: 0.7209 (m-30) cc_final: 0.6711 (m-30) REVERT: D 84 PHE cc_start: 0.7255 (t80) cc_final: 0.7035 (t80) REVERT: D 103 MET cc_start: 0.3202 (ptm) cc_final: 0.2975 (ttt) REVERT: S 23 SER cc_start: 0.6956 (m) cc_final: 0.6753 (p) outliers start: 15 outliers final: 6 residues processed: 174 average time/residue: 0.2218 time to fit residues: 53.4749 Evaluate side-chains 159 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 152 time to evaluate : 0.892 ------------------------------------------------------------------------------- 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 108 SER Chi-restraints excluded: chain B residue 278 PHE 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 103 optimal weight: 2.9990 chunk 106 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 87 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 88 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS A 256 ASN B 110 ASN D 306 HIS S 231 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.152483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.127084 restraints weight = 13496.016| |-----------------------------------------------------------------------------| r_work (start): 0.3632 rms_B_bonded: 2.38 r_work: 0.3518 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3357 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3357 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7325 moved from start: 0.4181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 9532 Z= 0.347 Angle : 0.673 8.266 12907 Z= 0.367 Chirality : 0.046 0.222 1456 Planarity : 0.005 0.060 1637 Dihedral : 4.705 20.236 1281 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.85 % Allowed : 12.78 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1165 helix: 2.74 (0.24), residues: 425 sheet: 1.12 (0.30), residues: 294 loop : -0.90 (0.26), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP D 163 HIS 0.011 0.002 HIS D 306 PHE 0.021 0.003 PHE D 118 TYR 0.032 0.003 TYR S 235 ARG 0.007 0.001 ARG D 208 *********************** 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 198 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 179 time to evaluate : 0.922 Fit side-chains REVERT: A 262 ASP cc_start: 0.7824 (p0) cc_final: 0.7342 (p0) REVERT: A 338 ASP cc_start: 0.7697 (m-30) cc_final: 0.7488 (m-30) REVERT: B 55 LEU cc_start: 0.8040 (mt) cc_final: 0.7790 (mp) REVERT: B 108 SER cc_start: 0.8782 (t) cc_final: 0.8571 (p) REVERT: B 110 ASN cc_start: 0.8439 (m-40) cc_final: 0.8214 (m110) REVERT: B 294 CYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7295 (m) REVERT: B 304 ARG cc_start: 0.8610 (OUTLIER) cc_final: 0.8396 (ttp-170) REVERT: B 312 ASP cc_start: 0.8245 (p0) cc_final: 0.8002 (p0) REVERT: C 50 LEU cc_start: 0.8372 (mm) cc_final: 0.8064 (mt) REVERT: D 226 PHE cc_start: 0.7510 (t80) cc_final: 0.7296 (t80) REVERT: D 310 MET cc_start: 0.7688 (tpp) cc_final: 0.7121 (mpp) REVERT: D 316 ASN cc_start: 0.7543 (t0) cc_final: 0.7342 (t0) REVERT: S 23 SER cc_start: 0.7359 (m) cc_final: 0.7067 (p) REVERT: S 230 MET cc_start: 0.8075 (ttp) cc_final: 0.7874 (ttt) outliers start: 19 outliers final: 6 residues processed: 186 average time/residue: 0.2188 time to fit residues: 55.7158 Evaluate side-chains 169 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 0.918 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 271 CYS Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain S residue 70 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 0.6980 chunk 113 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 45 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.151583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.126231 restraints weight = 13402.915| |-----------------------------------------------------------------------------| r_work (start): 0.3642 rms_B_bonded: 2.37 r_work: 0.3528 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3367 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3367 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7308 moved from start: 0.4480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9532 Z= 0.206 Angle : 0.555 7.143 12907 Z= 0.298 Chirality : 0.042 0.188 1456 Planarity : 0.004 0.048 1637 Dihedral : 4.374 22.688 1281 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 2.24 % Allowed : 15.90 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.24), residues: 1165 helix: 2.86 (0.24), residues: 431 sheet: 0.93 (0.30), residues: 296 loop : -0.95 (0.26), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 176 HIS 0.006 0.001 HIS B 54 PHE 0.022 0.002 PHE D 184 TYR 0.031 0.002 TYR S 235 ARG 0.005 0.000 ARG B 134 *********************** 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: 23 poor density : 157 time to evaluate : 1.003 Fit side-chains REVERT: A 220 THR cc_start: 0.8585 (OUTLIER) cc_final: 0.8346 (m) REVERT: A 338 ASP cc_start: 0.7667 (m-30) cc_final: 0.7447 (m-30) REVERT: B 55 LEU cc_start: 0.8044 (mt) cc_final: 0.7776 (mp) REVERT: B 98 SER cc_start: 0.8179 (m) cc_final: 0.7893 (p) REVERT: B 108 SER cc_start: 0.8794 (t) cc_final: 0.8520 (p) REVERT: B 110 ASN cc_start: 0.8428 (m-40) cc_final: 0.8140 (m110) REVERT: B 290 ASP cc_start: 0.7315 (m-30) cc_final: 0.6996 (m-30) REVERT: B 312 ASP cc_start: 0.8269 (p0) cc_final: 0.8056 (p0) REVERT: B 336 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8461 (mp) REVERT: D 233 LYS cc_start: 0.8219 (ttmm) cc_final: 0.7975 (mtpp) REVERT: S 23 SER cc_start: 0.7321 (m) cc_final: 0.7034 (p) REVERT: S 32 PHE cc_start: 0.8288 (m-80) cc_final: 0.8070 (m-10) outliers start: 23 outliers final: 16 residues processed: 169 average time/residue: 0.2156 time to fit residues: 50.3215 Evaluate side-chains 174 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 156 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 319 GLU Chi-restraints excluded: chain B residue 33 ILE 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 B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 143 ILE Chi-restraints excluded: chain D residue 236 ILE 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 113 optimal weight: 0.5980 chunk 104 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 115 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 56 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3928 r_free = 0.3928 target = 0.149078 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.123584 restraints weight = 13421.416| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 2.44 r_work: 0.3456 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.4915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9532 Z= 0.199 Angle : 0.539 8.385 12907 Z= 0.288 Chirality : 0.041 0.176 1456 Planarity : 0.004 0.046 1637 Dihedral : 4.259 22.634 1281 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.63 % Allowed : 16.59 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.24), residues: 1165 helix: 3.10 (0.24), residues: 426 sheet: 0.75 (0.30), residues: 298 loop : -1.01 (0.26), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP S 176 HIS 0.005 0.001 HIS B 225 PHE 0.023 0.002 PHE D 184 TYR 0.031 0.002 TYR S 235 ARG 0.006 0.000 ARG B 134 *********************** 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 206 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 179 time to evaluate : 0.898 Fit side-chains REVERT: A 35 LYS cc_start: 0.8138 (mtmm) cc_final: 0.7888 (mtmm) REVERT: A 220 THR cc_start: 0.8513 (OUTLIER) cc_final: 0.8297 (m) REVERT: A 241 MET cc_start: 0.5516 (pmm) cc_final: 0.4287 (pmm) REVERT: A 278 LYS cc_start: 0.6608 (mttt) cc_final: 0.6376 (mttt) REVERT: A 338 ASP cc_start: 0.7512 (m-30) cc_final: 0.7245 (m-30) REVERT: B 82 TRP cc_start: 0.8043 (OUTLIER) cc_final: 0.6920 (p90) REVERT: B 86 THR cc_start: 0.8436 (OUTLIER) cc_final: 0.8218 (p) REVERT: B 98 SER cc_start: 0.8142 (m) cc_final: 0.7842 (p) REVERT: B 108 SER cc_start: 0.8726 (t) cc_final: 0.8443 (p) REVERT: B 110 ASN cc_start: 0.8221 (m-40) cc_final: 0.7884 (m110) REVERT: B 130 GLU cc_start: 0.7840 (mp0) cc_final: 0.7551 (mp0) REVERT: B 171 ILE cc_start: 0.7726 (mm) cc_final: 0.7492 (mt) REVERT: B 312 ASP cc_start: 0.8061 (p0) cc_final: 0.7844 (p0) REVERT: B 336 LEU cc_start: 0.8773 (OUTLIER) cc_final: 0.8494 (mp) REVERT: D 88 LEU cc_start: 0.6758 (tp) cc_final: 0.6549 (tt) REVERT: D 103 MET cc_start: 0.4314 (ptm) cc_final: 0.3559 (ttt) REVERT: D 233 LYS cc_start: 0.8029 (ttmm) cc_final: 0.7800 (mtpp) REVERT: D 310 MET cc_start: 0.7265 (tpp) cc_final: 0.6808 (mmm) REVERT: D 316 ASN cc_start: 0.7475 (t0) cc_final: 0.7254 (t0) REVERT: S 23 SER cc_start: 0.7120 (m) cc_final: 0.6856 (p) outliers start: 27 outliers final: 17 residues processed: 197 average time/residue: 0.2280 time to fit residues: 62.7489 Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE 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 278 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU 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 236 ILE Chi-restraints excluded: chain D residue 298 HIS 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 223 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 22 optimal weight: 7.9990 chunk 75 optimal weight: 1.9990 chunk 115 optimal weight: 9.9990 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 96 optimal weight: 0.9990 chunk 45 optimal weight: 0.8980 chunk 110 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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 S 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.150791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126060 restraints weight = 13179.607| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.28 r_work: 0.3517 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3359 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7350 moved from start: 0.5340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9532 Z= 0.210 Angle : 0.549 7.281 12907 Z= 0.293 Chirality : 0.042 0.184 1456 Planarity : 0.004 0.042 1637 Dihedral : 4.294 24.382 1281 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.32 % Allowed : 17.95 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1165 helix: 2.99 (0.24), residues: 433 sheet: 0.76 (0.30), residues: 292 loop : -1.14 (0.26), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP D 148 HIS 0.005 0.001 HIS B 225 PHE 0.023 0.002 PHE D 184 TYR 0.032 0.002 TYR S 235 ARG 0.006 0.000 ARG B 134 *********************** 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 213 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 179 time to evaluate : 0.928 Fit side-chains REVERT: A 35 LYS cc_start: 0.8277 (mtmm) cc_final: 0.7979 (mtmm) REVERT: A 220 THR cc_start: 0.8564 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 241 MET cc_start: 0.5679 (pmm) cc_final: 0.4486 (pmm) REVERT: A 338 ASP cc_start: 0.7665 (m-30) cc_final: 0.7437 (m-30) REVERT: B 82 TRP cc_start: 0.8140 (OUTLIER) cc_final: 0.7118 (p90) REVERT: B 98 SER cc_start: 0.8292 (m) cc_final: 0.8048 (p) REVERT: B 171 ILE cc_start: 0.7952 (mm) cc_final: 0.7725 (mt) REVERT: B 336 LEU cc_start: 0.8831 (OUTLIER) cc_final: 0.8554 (mp) REVERT: D 88 LEU cc_start: 0.7181 (tp) cc_final: 0.6952 (tt) REVERT: D 103 MET cc_start: 0.4875 (ptm) cc_final: 0.4035 (ttt) REVERT: D 310 MET cc_start: 0.7571 (tpp) cc_final: 0.7173 (mmm) REVERT: S 23 SER cc_start: 0.7317 (m) cc_final: 0.7086 (p) outliers start: 34 outliers final: 26 residues processed: 200 average time/residue: 0.2090 time to fit residues: 58.0372 Evaluate side-chains 199 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 170 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER 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 B residue 304 ARG Chi-restraints excluded: chain B residue 336 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 143 ILE Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 236 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 298 HIS 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 223 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 43 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 77 optimal weight: 0.0770 chunk 85 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 81 optimal weight: 0.9980 chunk 110 optimal weight: 0.7980 overall best weight: 0.6738 ------------------------------------------------------------------------------- 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 = 0.3946 r_free = 0.3946 target = 0.150945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.126055 restraints weight = 13217.204| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 2.32 r_work: 0.3508 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3347 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.5473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9532 Z= 0.184 Angle : 0.553 8.086 12907 Z= 0.291 Chirality : 0.041 0.188 1456 Planarity : 0.004 0.043 1637 Dihedral : 4.248 27.096 1281 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 3.51 % Allowed : 18.93 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.25), residues: 1165 helix: 3.05 (0.24), residues: 433 sheet: 0.78 (0.31), residues: 287 loop : -1.21 (0.26), residues: 445 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 148 HIS 0.004 0.001 HIS B 225 PHE 0.025 0.001 PHE D 184 TYR 0.031 0.001 TYR S 235 ARG 0.006 0.000 ARG B 134 *********************** 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 200 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 164 time to evaluate : 1.030 Fit side-chains REVERT: A 220 THR cc_start: 0.8557 (OUTLIER) cc_final: 0.8315 (m) REVERT: A 241 MET cc_start: 0.5675 (pmm) cc_final: 0.4543 (pmm) REVERT: A 338 ASP cc_start: 0.7692 (m-30) cc_final: 0.7462 (m-30) REVERT: B 82 TRP cc_start: 0.8139 (OUTLIER) cc_final: 0.7170 (p90) REVERT: B 98 SER cc_start: 0.8316 (m) cc_final: 0.8057 (p) REVERT: B 154 ASP cc_start: 0.6375 (OUTLIER) cc_final: 0.6103 (m-30) REVERT: B 336 LEU cc_start: 0.8850 (OUTLIER) cc_final: 0.8559 (mp) REVERT: D 88 LEU cc_start: 0.7136 (tp) cc_final: 0.6913 (tt) REVERT: D 103 MET cc_start: 0.4980 (ptm) cc_final: 0.4158 (ttt) REVERT: D 310 MET cc_start: 0.7560 (tpp) cc_final: 0.7189 (mmm) REVERT: S 23 SER cc_start: 0.7298 (m) cc_final: 0.7072 (p) outliers start: 36 outliers final: 24 residues processed: 187 average time/residue: 0.2045 time to fit residues: 53.9403 Evaluate side-chains 191 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 163 time to evaluate : 0.914 ------------------------------------------------------------------------------- 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 187 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE Chi-restraints excluded: chain B residue 67 SER 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 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS 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 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 Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.9990 chunk 14 optimal weight: 0.1980 chunk 104 optimal weight: 5.9990 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 89 optimal weight: 0.0770 chunk 98 optimal weight: 0.7980 overall best weight: 0.5338 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.151449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.126499 restraints weight = 13446.318| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.35 r_work: 0.3521 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9532 Z= 0.164 Angle : 0.544 9.112 12907 Z= 0.284 Chirality : 0.041 0.187 1456 Planarity : 0.004 0.043 1637 Dihedral : 4.207 28.657 1281 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 3.22 % Allowed : 20.29 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1165 helix: 3.19 (0.24), residues: 427 sheet: 0.77 (0.31), residues: 287 loop : -1.12 (0.27), residues: 451 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 148 HIS 0.003 0.001 HIS B 225 PHE 0.026 0.001 PHE D 184 TYR 0.029 0.001 TYR S 235 ARG 0.007 0.000 ARG B 134 *********************** 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 201 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 168 time to evaluate : 1.206 Fit side-chains revert: symmetry clash REVERT: A 220 THR cc_start: 0.8547 (OUTLIER) cc_final: 0.8309 (m) REVERT: A 241 MET cc_start: 0.5672 (pmm) cc_final: 0.4787 (pmm) REVERT: A 338 ASP cc_start: 0.7696 (m-30) cc_final: 0.7438 (m-30) REVERT: B 82 TRP cc_start: 0.8122 (OUTLIER) cc_final: 0.7139 (p90) REVERT: B 98 SER cc_start: 0.8319 (m) cc_final: 0.8052 (p) REVERT: B 130 GLU cc_start: 0.8051 (mp0) cc_final: 0.7805 (mp0) REVERT: B 154 ASP cc_start: 0.6341 (OUTLIER) cc_final: 0.6006 (m-30) REVERT: B 171 ILE cc_start: 0.7932 (mm) cc_final: 0.7705 (mt) REVERT: B 247 ASP cc_start: 0.7981 (p0) cc_final: 0.7714 (p0) REVERT: B 294 CYS cc_start: 0.8045 (OUTLIER) cc_final: 0.7429 (m) REVERT: B 336 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8523 (mp) REVERT: D 88 LEU cc_start: 0.7125 (tp) cc_final: 0.6885 (tt) REVERT: D 103 MET cc_start: 0.5034 (ptm) cc_final: 0.4289 (ttt) REVERT: D 310 MET cc_start: 0.7531 (tpp) cc_final: 0.7187 (mmm) REVERT: S 23 SER cc_start: 0.7291 (m) cc_final: 0.7057 (p) outliers start: 33 outliers final: 25 residues processed: 192 average time/residue: 0.2269 time to fit residues: 60.7269 Evaluate side-chains 198 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 168 time to evaluate : 1.233 ------------------------------------------------------------------------------- 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 187 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 33 ILE 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 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASN 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 189 ILE Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 3.9990 chunk 2 optimal weight: 0.0980 chunk 52 optimal weight: 0.5980 chunk 73 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 0.6980 chunk 42 optimal weight: 7.9990 chunk 22 optimal weight: 8.9990 chunk 70 optimal weight: 0.8980 chunk 76 optimal weight: 0.2980 chunk 15 optimal weight: 0.0770 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.152217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.127376 restraints weight = 13260.091| |-----------------------------------------------------------------------------| r_work (start): 0.3598 rms_B_bonded: 2.33 r_work: 0.3487 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3329 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 9532 Z= 0.144 Angle : 0.550 8.796 12907 Z= 0.282 Chirality : 0.040 0.186 1456 Planarity : 0.003 0.043 1637 Dihedral : 4.090 29.635 1281 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.34 % Allowed : 21.27 % Favored : 76.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.25), residues: 1165 helix: 3.30 (0.24), residues: 427 sheet: 0.79 (0.31), residues: 286 loop : -1.09 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 148 HIS 0.002 0.001 HIS D 139 PHE 0.027 0.001 PHE D 184 TYR 0.024 0.001 TYR S 235 ARG 0.009 0.000 ARG B 134 *********************** 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 199 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.933 Fit side-chains revert: symmetry clash REVERT: A 191 THR cc_start: 0.8950 (p) cc_final: 0.8654 (t) REVERT: A 220 THR cc_start: 0.8522 (OUTLIER) cc_final: 0.8301 (m) REVERT: A 233 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6979 (mp) REVERT: A 241 MET cc_start: 0.5586 (OUTLIER) cc_final: 0.4612 (pmm) REVERT: A 338 ASP cc_start: 0.7624 (m-30) cc_final: 0.7369 (m-30) REVERT: B 98 SER cc_start: 0.8315 (m) cc_final: 0.8027 (p) REVERT: B 130 GLU cc_start: 0.7997 (mp0) cc_final: 0.7701 (mp0) REVERT: B 154 ASP cc_start: 0.6218 (OUTLIER) cc_final: 0.5881 (m-30) REVERT: B 201 SER cc_start: 0.8758 (m) cc_final: 0.8461 (t) REVERT: B 290 ASP cc_start: 0.6982 (m-30) cc_final: 0.6574 (m-30) REVERT: B 294 CYS cc_start: 0.8017 (OUTLIER) cc_final: 0.7342 (m) REVERT: B 336 LEU cc_start: 0.8726 (OUTLIER) cc_final: 0.8417 (mp) REVERT: C 27 ARG cc_start: 0.7451 (mmt-90) cc_final: 0.7231 (mmt-90) REVERT: D 88 LEU cc_start: 0.6881 (tp) cc_final: 0.6645 (tt) REVERT: D 103 MET cc_start: 0.4990 (ptm) cc_final: 0.4396 (ttt) REVERT: D 310 MET cc_start: 0.7432 (tpp) cc_final: 0.7098 (mmm) REVERT: S 23 SER cc_start: 0.7169 (m) cc_final: 0.6945 (p) REVERT: S 98 ARG cc_start: 0.8541 (ptt180) cc_final: 0.8276 (ptt90) outliers start: 24 outliers final: 16 residues processed: 192 average time/residue: 0.2254 time to fit residues: 60.2133 Evaluate side-chains 195 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 173 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 241 MET 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 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain C residue 44 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 297 ASN Chi-restraints excluded: chain D residue 313 THR Chi-restraints excluded: chain S residue 189 ILE Chi-restraints excluded: chain S residue 220 GLU Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 49 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 37 optimal weight: 2.9990 chunk 54 optimal weight: 0.0020 chunk 33 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 chunk 104 optimal weight: 5.9990 chunk 115 optimal weight: 0.9990 chunk 63 optimal weight: 0.6980 chunk 96 optimal weight: 0.7980 overall best weight: 0.6188 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3939 r_free = 0.3939 target = 0.150191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.125210 restraints weight = 13365.456| |-----------------------------------------------------------------------------| r_work (start): 0.3621 rms_B_bonded: 2.35 r_work: 0.3510 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.5803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9532 Z= 0.178 Angle : 0.554 10.095 12907 Z= 0.288 Chirality : 0.041 0.209 1456 Planarity : 0.004 0.041 1637 Dihedral : 4.103 28.614 1281 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.44 % Allowed : 22.05 % Favored : 75.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.25), residues: 1165 helix: 3.26 (0.24), residues: 427 sheet: 0.82 (0.31), residues: 288 loop : -1.12 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP D 148 HIS 0.004 0.001 HIS B 225 PHE 0.028 0.001 PHE D 184 TYR 0.028 0.001 TYR S 235 ARG 0.008 0.000 ARG B 134 ********************** 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 203 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 178 time to evaluate : 0.909 Fit side-chains revert: symmetry clash REVERT: A 233 LEU cc_start: 0.7461 (OUTLIER) cc_final: 0.7076 (mp) REVERT: A 241 MET cc_start: 0.5634 (OUTLIER) cc_final: 0.4511 (pmm) REVERT: A 338 ASP cc_start: 0.7669 (m-30) cc_final: 0.7425 (m-30) REVERT: B 82 TRP cc_start: 0.8159 (OUTLIER) cc_final: 0.7231 (p90) REVERT: B 98 SER cc_start: 0.8353 (m) cc_final: 0.8065 (p) REVERT: B 130 GLU cc_start: 0.7994 (mp0) cc_final: 0.7725 (mp0) REVERT: B 154 ASP cc_start: 0.6198 (OUTLIER) cc_final: 0.5862 (m-30) REVERT: B 171 ILE cc_start: 0.7910 (mm) cc_final: 0.7672 (mt) REVERT: B 201 SER cc_start: 0.8781 (m) cc_final: 0.8505 (t) REVERT: B 294 CYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7438 (m) REVERT: B 336 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8503 (mp) REVERT: D 88 LEU cc_start: 0.7095 (tp) cc_final: 0.6860 (tt) REVERT: D 103 MET cc_start: 0.5086 (ptm) cc_final: 0.4475 (ttt) REVERT: D 310 MET cc_start: 0.7516 (tpp) cc_final: 0.7141 (mmm) REVERT: S 23 SER cc_start: 0.7261 (m) cc_final: 0.7048 (p) outliers start: 25 outliers final: 17 residues processed: 194 average time/residue: 0.2325 time to fit residues: 63.6856 Evaluate side-chains 199 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 176 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 202 VAL Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain A residue 241 MET 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 234 PHE Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 294 CYS Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain B residue 336 LEU Chi-restraints excluded: chain C residue 19 LEU Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 229 ILE Chi-restraints excluded: chain D residue 293 ILE Chi-restraints excluded: chain D residue 297 ASN 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 Chi-restraints excluded: chain S residue 223 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 23 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 66 optimal weight: 0.0060 chunk 41 optimal weight: 0.7980 chunk 107 optimal weight: 2.9990 chunk 94 optimal weight: 0.1980 chunk 92 optimal weight: 0.0170 chunk 53 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 chunk 82 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.3634 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 189 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 82 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.151928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.127240 restraints weight = 13288.550| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.33 r_work: 0.3533 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3374 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7304 moved from start: 0.5878 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 9532 Z= 0.149 Angle : 0.544 8.920 12907 Z= 0.282 Chirality : 0.040 0.225 1456 Planarity : 0.003 0.041 1637 Dihedral : 4.052 30.115 1281 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.34 % Allowed : 22.73 % Favored : 74.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.25), residues: 1165 helix: 3.26 (0.24), residues: 427 sheet: 0.91 (0.31), residues: 290 loop : -1.11 (0.27), residues: 448 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 148 HIS 0.002 0.000 HIS B 225 PHE 0.028 0.001 PHE D 184 TYR 0.022 0.001 TYR S 235 ARG 0.008 0.000 ARG B 134 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5604.59 seconds wall clock time: 99 minutes 0.33 seconds (5940.33 seconds total)