Starting phenix.real_space_refine on Mon May 12 17:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k6o_36925/05_2025/8k6o_36925.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k6o_36925/05_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_36925/05_2025/8k6o_36925.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k6o_36925/05_2025/8k6o_36925.map" model { file = "/net/cci-nas-00/data/ceres_data/8k6o_36925/05_2025/8k6o_36925.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k6o_36925/05_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-5687/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: 5.22, per 1000 atoms: 0.56 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: 2.14 Conformation dependent library (CDL) restraints added in 1.0 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: 1.03 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: 2.79 Time building geometry restraints manager: 2.53 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: 0.870 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: 0.400 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 22.270 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.700 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.12534 ( 478) hydrogen bonds : angle 5.21493 ( 1362) SS BOND : bond 0.00420 ( 1) SS BOND : angle 0.04632 ( 2) covalent geometry : bond 0.00250 ( 9532) covalent geometry : angle 0.58374 (12907) *********************** 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 : 0.951 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: 0.2071 time to fit residues: 54.9107 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 : 1.037 ------------------------------------------------------------------------------- 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 = 37)----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.140871 restraints weight = 13769.844| |-----------------------------------------------------------------------------| r_work (start): 0.3829 rms_B_bonded: 2.37 r_work: 0.3719 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.3719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6766 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 9533 Z= 0.134 Angle : 0.541 7.112 12909 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 Details of bonding type rmsd hydrogen bonds : bond 0.04608 ( 478) hydrogen bonds : angle 4.11042 ( 1362) SS BOND : bond 0.00500 ( 1) SS BOND : angle 0.27429 ( 2) covalent geometry : bond 0.00270 ( 9532) covalent geometry : angle 0.54063 (12907) *********************** 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 : 0.925 Fit side-chains REVERT: A 191 THR cc_start: 0.8258 (m) cc_final: 0.8031 (p) REVERT: A 241 MET cc_start: 0.5691 (OUTLIER) cc_final: 0.5296 (pmm) REVERT: A 338 ASP cc_start: 0.7441 (m-30) cc_final: 0.7182 (m-30) REVERT: B 55 LEU cc_start: 0.7715 (mt) cc_final: 0.7467 (mp) REVERT: B 124 TYR cc_start: 0.8074 (m-80) cc_final: 0.7759 (m-80) REVERT: B 290 ASP cc_start: 0.7166 (m-30) cc_final: 0.6675 (m-30) REVERT: D 84 PHE cc_start: 0.7286 (t80) cc_final: 0.7068 (t80) REVERT: D 103 MET cc_start: 0.3283 (ptm) cc_final: 0.3041 (ttt) outliers start: 15 outliers final: 6 residues processed: 174 average time/residue: 0.2166 time to fit residues: 51.8373 Evaluate side-chains 158 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 151 time to evaluate : 1.021 ------------------------------------------------------------------------------- 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: 0.0270 chunk 11 optimal weight: 0.8980 chunk 84 optimal weight: 0.7980 chunk 98 optimal weight: 2.9990 chunk 87 optimal weight: 0.9980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 88 optimal weight: 0.6980 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN B 110 ASN D 306 HIS S 231 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.158384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.132877 restraints weight = 13664.036| |-----------------------------------------------------------------------------| r_work (start): 0.3730 rms_B_bonded: 2.40 r_work: 0.3617 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.3617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7011 moved from start: 0.3231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 9533 Z= 0.147 Angle : 0.551 5.813 12909 Z= 0.298 Chirality : 0.042 0.171 1456 Planarity : 0.004 0.050 1637 Dihedral : 4.150 19.308 1281 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.37 % Allowed : 12.39 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.87 (0.24), residues: 1165 helix: 3.11 (0.24), residues: 427 sheet: 1.26 (0.30), residues: 296 loop : -0.72 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 297 HIS 0.013 0.002 HIS D 306 PHE 0.022 0.002 PHE D 184 TYR 0.024 0.002 TYR S 235 ARG 0.006 0.001 ARG D 208 Details of bonding type rmsd hydrogen bonds : bond 0.05191 ( 478) hydrogen bonds : angle 4.06090 ( 1362) SS BOND : bond 0.00962 ( 1) SS BOND : angle 1.02972 ( 2) covalent geometry : bond 0.00316 ( 9532) covalent geometry : angle 0.55111 (12907) *********************** 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 172 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.933 Fit side-chains REVERT: A 338 ASP cc_start: 0.7474 (m-30) cc_final: 0.7204 (m-30) REVERT: B 55 LEU cc_start: 0.7870 (mt) cc_final: 0.7626 (mp) REVERT: B 82 TRP cc_start: 0.7499 (OUTLIER) cc_final: 0.6910 (p90) REVERT: B 108 SER cc_start: 0.8628 (t) cc_final: 0.8358 (p) REVERT: B 110 ASN cc_start: 0.8207 (m-40) cc_final: 0.7878 (m-40) REVERT: B 130 GLU cc_start: 0.7692 (mp0) cc_final: 0.7476 (mp0) REVERT: B 188 MET cc_start: 0.8111 (mmm) cc_final: 0.7898 (mmm) REVERT: B 276 VAL cc_start: 0.8562 (OUTLIER) cc_final: 0.8356 (t) REVERT: B 312 ASP cc_start: 0.8021 (p0) cc_final: 0.7731 (p0) REVERT: C 58 GLU cc_start: 0.7336 (pm20) cc_final: 0.6914 (pm20) REVERT: D 233 LYS cc_start: 0.8189 (ttmm) cc_final: 0.7913 (mtpp) outliers start: 14 outliers final: 5 residues processed: 166 average time/residue: 0.2299 time to fit residues: 51.6115 Evaluate side-chains 154 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 278 PHE Chi-restraints excluded: chain B residue 304 ARG Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain S residue 23 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 90 optimal weight: 3.9990 chunk 113 optimal weight: 0.9980 chunk 67 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 89 optimal weight: 0.4980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 59 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4008 r_free = 0.4008 target = 0.155720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.130176 restraints weight = 13461.266| |-----------------------------------------------------------------------------| r_work (start): 0.3689 rms_B_bonded: 2.38 r_work: 0.3576 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7074 moved from start: 0.3829 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= 0.138 Angle : 0.537 6.944 12909 Z= 0.288 Chirality : 0.041 0.182 1456 Planarity : 0.004 0.044 1637 Dihedral : 4.120 22.423 1281 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.66 % Allowed : 14.54 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.74 (0.24), residues: 1165 helix: 3.03 (0.24), residues: 434 sheet: 1.11 (0.30), residues: 292 loop : -0.83 (0.26), residues: 439 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 82 HIS 0.006 0.001 HIS B 54 PHE 0.022 0.002 PHE D 184 TYR 0.024 0.002 TYR S 235 ARG 0.004 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05053 ( 478) hydrogen bonds : angle 3.99448 ( 1362) SS BOND : bond 0.00880 ( 1) SS BOND : angle 0.98794 ( 2) covalent geometry : bond 0.00296 ( 9532) covalent geometry : angle 0.53650 (12907) *********************** 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 173 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 156 time to evaluate : 0.989 Fit side-chains REVERT: A 191 THR cc_start: 0.8884 (p) cc_final: 0.8515 (m) REVERT: A 262 ASP cc_start: 0.7638 (p0) cc_final: 0.7127 (p0) REVERT: A 338 ASP cc_start: 0.7473 (m-30) cc_final: 0.7240 (m-30) REVERT: B 55 LEU cc_start: 0.7869 (mt) cc_final: 0.7617 (mp) REVERT: B 108 SER cc_start: 0.8689 (OUTLIER) cc_final: 0.8434 (p) REVERT: B 110 ASN cc_start: 0.8246 (m-40) cc_final: 0.7928 (m110) REVERT: B 188 MET cc_start: 0.8100 (mmm) cc_final: 0.7880 (mmm) REVERT: B 276 VAL cc_start: 0.8614 (p) cc_final: 0.8407 (t) REVERT: B 296 VAL cc_start: 0.7896 (t) cc_final: 0.7690 (m) REVERT: C 58 GLU cc_start: 0.7287 (pm20) cc_final: 0.6901 (pm20) REVERT: D 103 MET cc_start: 0.3873 (ptm) cc_final: 0.3353 (ttt) REVERT: D 233 LYS cc_start: 0.8171 (ttmm) cc_final: 0.7832 (mtpp) outliers start: 17 outliers final: 12 residues processed: 163 average time/residue: 0.2264 time to fit residues: 50.6065 Evaluate side-chains 161 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 148 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 ILE 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 108 SER 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 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: 4.9990 chunk 104 optimal weight: 8.9990 chunk 111 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 115 optimal weight: 9.9990 chunk 15 optimal weight: 0.8980 chunk 93 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 81 optimal weight: 0.5980 chunk 59 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 245 HIS ** A 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 59 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.155143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.129528 restraints weight = 13374.450| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.38 r_work: 0.3572 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.4338 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= 0.128 Angle : 0.526 7.958 12909 Z= 0.281 Chirality : 0.041 0.164 1456 Planarity : 0.004 0.046 1637 Dihedral : 4.084 23.628 1281 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.85 % Allowed : 16.20 % Favored : 81.95 % 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: 1.72 (0.25), residues: 1165 helix: 3.18 (0.24), residues: 427 sheet: 0.93 (0.30), residues: 304 loop : -0.87 (0.27), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 148 HIS 0.004 0.001 HIS B 225 PHE 0.022 0.002 PHE D 184 TYR 0.026 0.001 TYR S 235 ARG 0.006 0.000 ARG E 33 Details of bonding type rmsd hydrogen bonds : bond 0.04819 ( 478) hydrogen bonds : angle 3.90928 ( 1362) SS BOND : bond 0.00863 ( 1) SS BOND : angle 1.01911 ( 2) covalent geometry : bond 0.00272 ( 9532) covalent geometry : angle 0.52602 (12907) *********************** 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 181 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 162 time to evaluate : 1.008 Fit side-chains REVERT: A 191 THR cc_start: 0.8982 (p) cc_final: 0.8717 (t) REVERT: A 241 MET cc_start: 0.5720 (pmm) cc_final: 0.4524 (pmm) REVERT: A 338 ASP cc_start: 0.7678 (m-30) cc_final: 0.7432 (m-30) REVERT: B 55 LEU cc_start: 0.8014 (mt) cc_final: 0.7773 (mp) REVERT: B 86 THR cc_start: 0.8496 (OUTLIER) cc_final: 0.8274 (p) REVERT: B 296 VAL cc_start: 0.7998 (t) cc_final: 0.7790 (m) REVERT: B 314 ARG cc_start: 0.7883 (ptm160) cc_final: 0.7588 (ptm-80) REVERT: C 58 GLU cc_start: 0.7374 (pm20) cc_final: 0.6933 (pm20) REVERT: D 88 LEU cc_start: 0.6756 (tp) cc_final: 0.6500 (tt) REVERT: D 103 MET cc_start: 0.4442 (ptm) cc_final: 0.3749 (ttt) REVERT: D 233 LYS cc_start: 0.8246 (ttmm) cc_final: 0.7957 (mtpp) REVERT: D 310 MET cc_start: 0.7404 (tpp) cc_final: 0.7157 (mpp) REVERT: S 98 ARG cc_start: 0.8592 (ptt180) cc_final: 0.8363 (ptt90) outliers start: 19 outliers final: 14 residues processed: 172 average time/residue: 0.2195 time to fit residues: 51.9175 Evaluate side-chains 169 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 154 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU Chi-restraints excluded: chain B residue 82 TRP Chi-restraints excluded: chain B residue 86 THR 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 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 143 ILE Chi-restraints excluded: chain D residue 270 VAL Chi-restraints excluded: chain D residue 326 ASN Chi-restraints excluded: chain S residue 93 MET 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: 8.9990 chunk 75 optimal weight: 0.8980 chunk 115 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 96 optimal weight: 0.5980 chunk 45 optimal weight: 0.5980 chunk 110 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.152980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.127295 restraints weight = 13311.206| |-----------------------------------------------------------------------------| r_work (start): 0.3625 rms_B_bonded: 2.38 r_work: 0.3516 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 9533 Z= 0.139 Angle : 0.537 8.928 12909 Z= 0.287 Chirality : 0.041 0.177 1456 Planarity : 0.004 0.048 1637 Dihedral : 4.147 24.838 1281 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.34 % Allowed : 17.07 % Favored : 80.59 % 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: 1.70 (0.25), residues: 1165 helix: 3.19 (0.24), residues: 426 sheet: 0.97 (0.30), residues: 295 loop : -0.91 (0.27), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP D 148 HIS 0.005 0.001 HIS B 225 PHE 0.023 0.002 PHE D 184 TYR 0.027 0.002 TYR S 235 ARG 0.005 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.05066 ( 478) hydrogen bonds : angle 3.93164 ( 1362) SS BOND : bond 0.01022 ( 1) SS BOND : angle 1.31528 ( 2) covalent geometry : bond 0.00302 ( 9532) covalent geometry : angle 0.53689 (12907) *********************** 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 173 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 149 time to evaluate : 0.901 Fit side-chains REVERT: A 241 MET cc_start: 0.5725 (pmm) cc_final: 0.4513 (pmm) REVERT: A 338 ASP cc_start: 0.7660 (m-30) cc_final: 0.7417 (m-30) REVERT: B 55 LEU cc_start: 0.8033 (mt) cc_final: 0.7779 (mp) REVERT: B 86 THR cc_start: 0.8502 (OUTLIER) cc_final: 0.8296 (p) REVERT: B 154 ASP cc_start: 0.6195 (OUTLIER) cc_final: 0.5904 (m-30) REVERT: B 290 ASP cc_start: 0.7241 (m-30) cc_final: 0.6579 (m-30) REVERT: C 58 GLU cc_start: 0.7328 (pm20) cc_final: 0.6793 (pm20) REVERT: D 88 LEU cc_start: 0.6842 (tp) cc_final: 0.6574 (tt) REVERT: D 103 MET cc_start: 0.4581 (ptm) cc_final: 0.3900 (ttt) REVERT: D 233 LYS cc_start: 0.8198 (ttmm) cc_final: 0.7951 (mtpp) REVERT: D 310 MET cc_start: 0.7336 (tpp) cc_final: 0.6894 (mmm) outliers start: 24 outliers final: 18 residues processed: 164 average time/residue: 0.2199 time to fit residues: 49.6408 Evaluate side-chains 171 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 151 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU 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 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 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 143 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 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: 0.0970 chunk 45 optimal weight: 0.8980 chunk 57 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 85 optimal weight: 0.0970 chunk 17 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 81 optimal weight: 0.6980 chunk 110 optimal weight: 4.9990 overall best weight: 0.5576 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** 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 = 0.3976 r_free = 0.3976 target = 0.152998 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.127615 restraints weight = 13342.313| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 2.37 r_work: 0.3488 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3330 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 moved from start: 0.4856 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= 0.121 Angle : 0.527 9.950 12909 Z= 0.278 Chirality : 0.040 0.166 1456 Planarity : 0.003 0.046 1637 Dihedral : 4.088 26.604 1281 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 2.05 % Allowed : 17.76 % Favored : 80.20 % 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: 1.72 (0.25), residues: 1165 helix: 3.26 (0.24), residues: 427 sheet: 0.97 (0.30), residues: 288 loop : -0.92 (0.27), residues: 450 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP D 148 HIS 0.003 0.001 HIS B 54 PHE 0.024 0.001 PHE D 184 TYR 0.027 0.001 TYR S 235 ARG 0.006 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 478) hydrogen bonds : angle 3.86487 ( 1362) SS BOND : bond 0.00867 ( 1) SS BOND : angle 1.23126 ( 2) covalent geometry : bond 0.00256 ( 9532) covalent geometry : angle 0.52655 (12907) *********************** 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 185 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 164 time to evaluate : 1.059 Fit side-chains REVERT: A 241 MET cc_start: 0.5681 (pmm) cc_final: 0.4541 (pmm) REVERT: A 338 ASP cc_start: 0.7645 (m-30) cc_final: 0.7366 (m-30) REVERT: B 55 LEU cc_start: 0.8038 (mt) cc_final: 0.7788 (mp) REVERT: B 86 THR cc_start: 0.8429 (OUTLIER) cc_final: 0.8170 (p) REVERT: B 154 ASP cc_start: 0.6164 (OUTLIER) cc_final: 0.5860 (m-30) REVERT: B 217 MET cc_start: 0.8025 (ptt) cc_final: 0.7580 (pmm) REVERT: C 58 GLU cc_start: 0.7288 (pm20) cc_final: 0.6700 (pm20) REVERT: D 88 LEU cc_start: 0.6734 (tp) cc_final: 0.6453 (tt) REVERT: D 103 MET cc_start: 0.4510 (ptm) cc_final: 0.3936 (ttt) REVERT: D 233 LYS cc_start: 0.8126 (ttmm) cc_final: 0.7893 (mtpp) REVERT: D 310 MET cc_start: 0.7308 (tpp) cc_final: 0.6903 (mmm) outliers start: 21 outliers final: 17 residues processed: 179 average time/residue: 0.2267 time to fit residues: 55.8181 Evaluate side-chains 179 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 160 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 LEU 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 119 ASN 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 C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 112 MET Chi-restraints excluded: chain D residue 298 HIS Chi-restraints excluded: chain S residue 23 SER 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.4980 chunk 104 optimal weight: 0.0070 chunk 41 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 93 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 99 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 89 optimal weight: 0.0870 chunk 98 optimal weight: 0.9980 overall best weight: 0.4376 ------------------------------------------------------------------------------- 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 = 0.3981 r_free = 0.3981 target = 0.153641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.128217 restraints weight = 13568.062| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.38 r_work: 0.3547 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.5026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9533 Z= 0.113 Angle : 0.531 9.958 12909 Z= 0.276 Chirality : 0.040 0.209 1456 Planarity : 0.003 0.045 1637 Dihedral : 4.037 29.249 1281 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.95 % Allowed : 19.12 % Favored : 78.93 % 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: 1.72 (0.25), residues: 1165 helix: 3.34 (0.24), residues: 427 sheet: 0.95 (0.31), residues: 282 loop : -0.97 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP D 148 HIS 0.002 0.001 HIS B 225 PHE 0.025 0.001 PHE D 184 TYR 0.025 0.001 TYR S 235 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04414 ( 478) hydrogen bonds : angle 3.78773 ( 1362) SS BOND : bond 0.00791 ( 1) SS BOND : angle 1.11504 ( 2) covalent geometry : bond 0.00235 ( 9532) covalent geometry : angle 0.53126 (12907) *********************** 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 177 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 157 time to evaluate : 0.918 Fit side-chains REVERT: A 199 MET cc_start: 0.8216 (ttm) cc_final: 0.8008 (ttm) REVERT: A 241 MET cc_start: 0.5717 (pmm) cc_final: 0.4661 (pmm) REVERT: A 338 ASP cc_start: 0.7644 (m-30) cc_final: 0.7411 (m-30) REVERT: B 154 ASP cc_start: 0.6177 (OUTLIER) cc_final: 0.5959 (m-30) REVERT: B 171 ILE cc_start: 0.7842 (mm) cc_final: 0.7526 (mt) REVERT: B 290 ASP cc_start: 0.7136 (m-30) cc_final: 0.6523 (m-30) REVERT: B 294 CYS cc_start: 0.8065 (t) cc_final: 0.7336 (m) REVERT: C 58 GLU cc_start: 0.7279 (pm20) cc_final: 0.6686 (pm20) REVERT: D 88 LEU cc_start: 0.6935 (tp) cc_final: 0.6632 (tt) REVERT: D 103 MET cc_start: 0.4795 (ptm) cc_final: 0.4254 (ttt) REVERT: D 233 LYS cc_start: 0.8163 (ttmm) cc_final: 0.7954 (mtpp) REVERT: D 310 MET cc_start: 0.7380 (tpp) cc_final: 0.6995 (mmm) outliers start: 20 outliers final: 18 residues processed: 171 average time/residue: 0.2182 time to fit residues: 51.3387 Evaluate side-chains 170 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 151 time to evaluate : 1.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU Chi-restraints excluded: chain A residue 233 LEU 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 119 ASN 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 C residue 19 LEU Chi-restraints excluded: chain C residue 59 ASN 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 S residue 23 SER 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 117 random chunks: chunk 99 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 52 optimal weight: 0.0270 chunk 73 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 chunk 79 optimal weight: 0.8980 chunk 42 optimal weight: 6.9990 chunk 22 optimal weight: 9.9990 chunk 70 optimal weight: 0.9980 chunk 76 optimal weight: 0.0970 chunk 15 optimal weight: 0.0770 overall best weight: 0.3994 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.153931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.128725 restraints weight = 13273.562| |-----------------------------------------------------------------------------| r_work (start): 0.3669 rms_B_bonded: 2.34 r_work: 0.3560 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3404 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3404 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7270 moved from start: 0.5154 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= 0.111 Angle : 0.540 10.048 12909 Z= 0.279 Chirality : 0.040 0.214 1456 Planarity : 0.004 0.045 1637 Dihedral : 4.017 30.015 1281 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.15 % Allowed : 20.00 % Favored : 77.85 % 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: 1.75 (0.25), residues: 1165 helix: 3.43 (0.24), residues: 421 sheet: 0.96 (0.31), residues: 283 loop : -0.97 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP D 148 HIS 0.003 0.001 HIS A 189 PHE 0.026 0.001 PHE D 184 TYR 0.024 0.001 TYR S 235 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 478) hydrogen bonds : angle 3.75019 ( 1362) SS BOND : bond 0.00774 ( 1) SS BOND : angle 1.08131 ( 2) covalent geometry : bond 0.00230 ( 9532) covalent geometry : angle 0.53941 (12907) *********************** 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 182 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 160 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.5682 (pmm) cc_final: 0.4825 (pmm) REVERT: A 338 ASP cc_start: 0.7633 (m-30) cc_final: 0.7385 (m-30) REVERT: B 110 ASN cc_start: 0.8289 (m-40) cc_final: 0.8046 (m110) REVERT: B 154 ASP cc_start: 0.6221 (OUTLIER) cc_final: 0.5966 (m-30) REVERT: B 171 ILE cc_start: 0.7816 (mm) cc_final: 0.7498 (mt) REVERT: B 290 ASP cc_start: 0.7118 (m-30) cc_final: 0.6359 (m-30) REVERT: D 88 LEU cc_start: 0.6944 (tp) cc_final: 0.6627 (tt) REVERT: D 103 MET cc_start: 0.4884 (ptm) cc_final: 0.4368 (ttt) REVERT: D 129 PHE cc_start: 0.8084 (m-80) cc_final: 0.7871 (m-80) REVERT: D 233 LYS cc_start: 0.8139 (ttmm) cc_final: 0.7923 (mtpp) REVERT: D 310 MET cc_start: 0.7400 (tpp) cc_final: 0.7027 (mmm) outliers start: 22 outliers final: 19 residues processed: 172 average time/residue: 0.2252 time to fit residues: 52.8415 Evaluate side-chains 175 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 187 GLU 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 119 ASN 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 C residue 19 LEU Chi-restraints excluded: chain C residue 41 CYS 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 S residue 23 SER 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 49 optimal weight: 0.5980 chunk 2 optimal weight: 0.8980 chunk 94 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 54 optimal weight: 0.0980 chunk 33 optimal weight: 0.0770 chunk 48 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 63 optimal weight: 1.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.3138 ------------------------------------------------------------------------------- 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 = 0.3993 r_free = 0.3993 target = 0.154626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.129489 restraints weight = 13434.230| |-----------------------------------------------------------------------------| r_work (start): 0.3677 rms_B_bonded: 2.36 r_work: 0.3567 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3408 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7260 moved from start: 0.5251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9533 Z= 0.106 Angle : 0.542 9.791 12909 Z= 0.278 Chirality : 0.040 0.219 1456 Planarity : 0.003 0.045 1637 Dihedral : 3.983 31.207 1281 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 1.76 % Allowed : 20.88 % Favored : 77.37 % 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: 1.78 (0.25), residues: 1165 helix: 3.46 (0.24), residues: 421 sheet: 0.95 (0.31), residues: 283 loop : -0.92 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP D 148 HIS 0.002 0.001 HIS D 139 PHE 0.026 0.001 PHE D 184 TYR 0.023 0.001 TYR S 235 ARG 0.008 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 478) hydrogen bonds : angle 3.69920 ( 1362) SS BOND : bond 0.00691 ( 1) SS BOND : angle 0.96888 ( 2) covalent geometry : bond 0.00217 ( 9532) covalent geometry : angle 0.54209 (12907) ********************** 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: 18 poor density : 158 time to evaluate : 0.931 Fit side-chains revert: symmetry clash REVERT: A 241 MET cc_start: 0.5615 (pmm) cc_final: 0.4593 (pmm) REVERT: A 338 ASP cc_start: 0.7624 (m-30) cc_final: 0.7389 (m-30) REVERT: B 154 ASP cc_start: 0.6225 (OUTLIER) cc_final: 0.5967 (m-30) REVERT: B 171 ILE cc_start: 0.7834 (mm) cc_final: 0.7504 (mt) REVERT: B 290 ASP cc_start: 0.7098 (m-30) cc_final: 0.6620 (m-30) REVERT: D 88 LEU cc_start: 0.6917 (tp) cc_final: 0.6610 (tt) REVERT: D 103 MET cc_start: 0.4914 (ptm) cc_final: 0.4425 (ttt) REVERT: D 129 PHE cc_start: 0.8053 (m-80) cc_final: 0.7849 (m-80) REVERT: D 233 LYS cc_start: 0.8135 (ttmm) cc_final: 0.7915 (mtpp) REVERT: D 310 MET cc_start: 0.7380 (tpp) cc_final: 0.7015 (mmm) outliers start: 18 outliers final: 15 residues processed: 169 average time/residue: 0.2326 time to fit residues: 53.6082 Evaluate side-chains 171 residues out of total 1025 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 155 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 MET Chi-restraints excluded: chain A residue 187 GLU 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 119 ASN 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 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 298 HIS Chi-restraints excluded: chain S residue 189 ILE 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: 0.6980 chunk 12 optimal weight: 0.6980 chunk 66 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 107 optimal weight: 0.8980 chunk 94 optimal weight: 0.0970 chunk 92 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 114 optimal weight: 0.0270 chunk 82 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.4236 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.153958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.128944 restraints weight = 13282.117| |-----------------------------------------------------------------------------| r_work (start): 0.3673 rms_B_bonded: 2.34 r_work: 0.3564 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3406 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3406 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 9533 Z= 0.112 Angle : 0.555 9.568 12909 Z= 0.284 Chirality : 0.040 0.220 1456 Planarity : 0.003 0.044 1637 Dihedral : 3.976 30.768 1281 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.24 % Allowed : 20.68 % Favored : 77.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.79 (0.25), residues: 1165 helix: 3.46 (0.24), residues: 421 sheet: 0.96 (0.31), residues: 283 loop : -0.93 (0.26), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP D 148 HIS 0.003 0.001 HIS A 189 PHE 0.027 0.001 PHE D 184 TYR 0.024 0.001 TYR S 235 ARG 0.007 0.000 ARG B 134 Details of bonding type rmsd hydrogen bonds : bond 0.04145 ( 478) hydrogen bonds : angle 3.71951 ( 1362) SS BOND : bond 0.00794 ( 1) SS BOND : angle 1.06415 ( 2) covalent geometry : bond 0.00237 ( 9532) covalent geometry : angle 0.55488 (12907) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5227.73 seconds wall clock time: 91 minutes 9.01 seconds (5469.01 seconds total)