Starting phenix.real_space_refine on Wed Feb 4 00:57:44 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9n9o_49174/02_2026/9n9o_49174_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9n9o_49174/02_2026/9n9o_49174.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9n9o_49174/02_2026/9n9o_49174_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9n9o_49174/02_2026/9n9o_49174_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9n9o_49174/02_2026/9n9o_49174.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9n9o_49174/02_2026/9n9o_49174.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.030 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: 5 Type Number sf(0) Gaussians P 109 5.49 5 S 30 5.16 5 C 4823 2.51 5 N 1463 2.21 5 O 1760 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8185 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3016 Number of conformers: 1 Conformer: "" Number of residues, atoms: 365, 3016 Classifications: {'peptide': 365} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 357} Chain: "B" Number of atoms: 2860 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2860 Classifications: {'peptide': 346} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 338} Chain breaks: 1 Chain: "a" Number of atoms: 124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 124 Classifications: {'DNA': 6} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 5} Chain: "b" Number of atoms: 408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 408 Classifications: {'DNA': 20} Link IDs: {'rna3p': 19} Chain: "c" Number of atoms: 1777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 1777 Classifications: {'RNA': 83} Modifications used: {'rna2p_pur': 4, 'rna2p_pyr': 2, 'rna3p_pur': 44, 'rna3p_pyr': 33} Link IDs: {'rna2p': 6, 'rna3p': 76} Time building chain proxies: 2.12, per 1000 atoms: 0.26 Number of scatterers: 8185 At special positions: 0 Unit cell: (107.682, 103.572, 88.776, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 30 16.00 P 109 15.00 O 1760 8.00 N 1463 7.00 C 4823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 226.9 milliseconds 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1342 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 6 sheets defined 51.9% alpha, 21.4% beta 39 base pairs and 61 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 20 through 64 removed outlier: 4.060A pdb=" N GLN A 52 " --> pdb=" O HIS A 48 " (cutoff:3.500A) removed outlier: 4.136A pdb=" N GLU A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 97 Processing helix chain 'A' and resid 101 through 119 removed outlier: 4.156A pdb=" N LEU A 105 " --> pdb=" O PRO A 101 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N HIS A 110 " --> pdb=" O SER A 106 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLY A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS A 118 " --> pdb=" O SER A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 126 Processing helix chain 'A' and resid 142 through 146 Processing helix chain 'A' and resid 178 through 187 removed outlier: 3.546A pdb=" N LYS A 187 " --> pdb=" O GLU A 183 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 270 removed outlier: 3.637A pdb=" N TYR A 254 " --> pdb=" O GLU A 250 " (cutoff:3.500A) removed outlier: 4.199A pdb=" N ARG A 255 " --> pdb=" O GLU A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 271 through 273 No H-bonds generated for 'chain 'A' and resid 271 through 273' Processing helix chain 'A' and resid 278 through 283 removed outlier: 3.603A pdb=" N LYS A 282 " --> pdb=" O GLY A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 288 Processing helix chain 'A' and resid 291 through 315 Processing helix chain 'A' and resid 324 through 333 Processing helix chain 'A' and resid 335 through 342 removed outlier: 3.517A pdb=" N LEU A 339 " --> pdb=" O GLU A 335 " (cutoff:3.500A) Processing helix chain 'A' and resid 343 through 359 removed outlier: 3.565A pdb=" N LEU A 347 " --> pdb=" O SER A 343 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 54 Processing helix chain 'B' and resid 55 through 58 Processing helix chain 'B' and resid 84 through 97 removed outlier: 4.386A pdb=" N THR B 88 " --> pdb=" O ARG B 84 " (cutoff:3.500A) Processing helix chain 'B' and resid 101 through 125 removed outlier: 5.323A pdb=" N VAL B 121 " --> pdb=" O ASN B 117 " (cutoff:3.500A) removed outlier: 5.818A pdb=" N GLN B 122 " --> pdb=" O LYS B 118 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS B 125 " --> pdb=" O VAL B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 144 No H-bonds generated for 'chain 'B' and resid 142 through 144' Processing helix chain 'B' and resid 177 through 187 Processing helix chain 'B' and resid 248 through 272 removed outlier: 4.496A pdb=" N ARG B 255 " --> pdb=" O GLU B 251 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ARG B 256 " --> pdb=" O PHE B 252 " (cutoff:3.500A) Processing helix chain 'B' and resid 278 through 315 removed outlier: 5.812A pdb=" N ALA B 285 " --> pdb=" O ARG B 281 " (cutoff:3.500A) removed outlier: 5.313A pdb=" N VAL B 286 " --> pdb=" O LYS B 282 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N HIS B 315 " --> pdb=" O PHE B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 359 Processing sheet with id=AA1, first strand: chain 'A' and resid 139 through 140 removed outlier: 4.355A pdb=" N VAL A 209 " --> pdb=" O CYS A 193 " (cutoff:3.500A) removed outlier: 4.965A pdb=" N SER A 195 " --> pdb=" O LEU A 207 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU A 207 " --> pdb=" O SER A 195 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N ILE A 197 " --> pdb=" O PHE A 205 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N PHE A 205 " --> pdb=" O ILE A 197 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ILE A 204 " --> pdb=" O ILE A 14 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE A 158 " --> pdb=" O THR A 169 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA A 157 " --> pdb=" O ASP A 152 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 152 " --> pdb=" O ALA A 157 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 68 through 71 removed outlier: 8.258A pdb=" N LYS A 68 " --> pdb=" O ILE A 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 246 removed outlier: 4.472A pdb=" N THR A 319 " --> pdb=" O PRO A 221 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 223 " --> pdb=" O THR A 319 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N ILE A 321 " --> pdb=" O VAL A 223 " (cutoff:3.500A) removed outlier: 6.117A pdb=" N ALA A 225 " --> pdb=" O ILE A 321 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.550A pdb=" N PHE B 141 " --> pdb=" O SER B 195 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N ILE B 204 " --> pdb=" O ILE B 14 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA B 208 " --> pdb=" O ARG B 10 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N GLN B 13 " --> pdb=" O TYR B 170 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N PHE B 158 " --> pdb=" O THR B 169 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ALA B 157 " --> pdb=" O TYR B 151 " (cutoff:3.500A) removed outlier: 5.209A pdb=" N TYR B 151 " --> pdb=" O ALA B 157 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N CYS B 159 " --> pdb=" O LEU B 149 " (cutoff:3.500A) removed outlier: 4.429A pdb=" N LEU B 149 " --> pdb=" O CYS B 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 139 through 141 removed outlier: 3.550A pdb=" N PHE B 141 " --> pdb=" O SER B 195 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 242 through 246 removed outlier: 3.639A pdb=" N LEU B 244 " --> pdb=" O VAL B 237 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N THR B 319 " --> pdb=" O PRO B 221 " (cutoff:3.500A) removed outlier: 5.817A pdb=" N VAL B 223 " --> pdb=" O THR B 319 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N ILE B 321 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 5.642A pdb=" N ALA B 225 " --> pdb=" O ILE B 321 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU B 322 " --> pdb=" O ILE B 363 " (cutoff:3.500A) 341 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 98 hydrogen bonds 184 hydrogen bond angles 0 basepair planarities 39 basepair parallelities 61 stacking parallelities Total time for adding SS restraints: 1.38 Time building geometry restraints manager: 0.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1944 1.33 - 1.45: 2293 1.45 - 1.57: 4069 1.57 - 1.69: 215 1.69 - 1.82: 52 Bond restraints: 8573 Sorted by residual: bond pdb=" CB MET A 31 " pdb=" CG MET A 31 " ideal model delta sigma weight residual 1.520 1.476 0.044 3.00e-02 1.11e+03 2.13e+00 bond pdb=" O4' DC b -5 " pdb=" C1' DC b -5 " ideal model delta sigma weight residual 1.414 1.388 0.026 2.00e-02 2.50e+03 1.69e+00 bond pdb=" CA ASN A 132 " pdb=" CB ASN A 132 " ideal model delta sigma weight residual 1.528 1.495 0.034 2.61e-02 1.47e+03 1.65e+00 bond pdb=" CB GLU B 250 " pdb=" CG GLU B 250 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" CG MET A 31 " pdb=" SD MET A 31 " ideal model delta sigma weight residual 1.803 1.773 0.030 2.50e-02 1.60e+03 1.44e+00 ... (remaining 8568 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.03: 11775 2.03 - 4.06: 218 4.06 - 6.08: 27 6.08 - 8.11: 5 8.11 - 10.14: 2 Bond angle restraints: 12027 Sorted by residual: angle pdb=" CA ARG A 265 " pdb=" CB ARG A 265 " pdb=" CG ARG A 265 " ideal model delta sigma weight residual 114.10 123.87 -9.77 2.00e+00 2.50e-01 2.39e+01 angle pdb=" N ILE B 331 " pdb=" CA ILE B 331 " pdb=" C ILE B 331 " ideal model delta sigma weight residual 113.39 108.01 5.38 1.47e+00 4.63e-01 1.34e+01 angle pdb=" CB GLU B 232 " pdb=" CG GLU B 232 " pdb=" CD GLU B 232 " ideal model delta sigma weight residual 112.60 118.82 -6.22 1.70e+00 3.46e-01 1.34e+01 angle pdb=" N SER B 343 " pdb=" CA SER B 343 " pdb=" C SER B 343 " ideal model delta sigma weight residual 113.19 107.60 5.59 1.58e+00 4.01e-01 1.25e+01 angle pdb=" CB MET A 323 " pdb=" CG MET A 323 " pdb=" SD MET A 323 " ideal model delta sigma weight residual 112.70 122.84 -10.14 3.00e+00 1.11e-01 1.14e+01 ... (remaining 12022 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.08: 4756 33.08 - 66.15: 425 66.15 - 99.23: 26 99.23 - 132.30: 0 132.30 - 165.38: 1 Dihedral angle restraints: 5208 sinusoidal: 3123 harmonic: 2085 Sorted by residual: dihedral pdb=" O4' C c 13 " pdb=" C1' C c 13 " pdb=" N1 C c 13 " pdb=" C2 C c 13 " ideal model delta sinusoidal sigma weight residual 200.00 34.62 165.38 1 1.50e+01 4.44e-03 8.40e+01 dihedral pdb=" O4' U c 25 " pdb=" C1' U c 25 " pdb=" N1 U c 25 " pdb=" C2 U c 25 " ideal model delta sinusoidal sigma weight residual -160.00 -110.09 -49.91 1 1.50e+01 4.44e-03 1.52e+01 dihedral pdb=" O4' U c 75 " pdb=" C1' U c 75 " pdb=" N1 U c 75 " pdb=" C2 U c 75 " ideal model delta sinusoidal sigma weight residual -128.00 -72.64 -55.36 1 1.70e+01 3.46e-03 1.43e+01 ... (remaining 5205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 1006 0.040 - 0.080: 279 0.080 - 0.120: 86 0.120 - 0.160: 11 0.160 - 0.200: 2 Chirality restraints: 1384 Sorted by residual: chirality pdb=" CA GLU B 232 " pdb=" N GLU B 232 " pdb=" C GLU B 232 " pdb=" CB GLU B 232 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 9.97e-01 chirality pdb=" CB THR A 349 " pdb=" CA THR A 349 " pdb=" OG1 THR A 349 " pdb=" CG2 THR A 349 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.20 2.00e-01 2.50e+01 9.59e-01 chirality pdb=" CG LEU A 18 " pdb=" CB LEU A 18 " pdb=" CD1 LEU A 18 " pdb=" CD2 LEU A 18 " both_signs ideal model delta sigma weight residual False -2.59 -2.43 -0.16 2.00e-01 2.50e+01 6.22e-01 ... (remaining 1381 not shown) Planarity restraints: 1106 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' G c 28 " 0.046 2.00e-02 2.50e+03 1.92e-02 1.11e+01 pdb=" N9 G c 28 " -0.044 2.00e-02 2.50e+03 pdb=" C8 G c 28 " -0.004 2.00e-02 2.50e+03 pdb=" N7 G c 28 " 0.001 2.00e-02 2.50e+03 pdb=" C5 G c 28 " -0.001 2.00e-02 2.50e+03 pdb=" C6 G c 28 " 0.010 2.00e-02 2.50e+03 pdb=" O6 G c 28 " 0.009 2.00e-02 2.50e+03 pdb=" N1 G c 28 " 0.006 2.00e-02 2.50e+03 pdb=" C2 G c 28 " -0.000 2.00e-02 2.50e+03 pdb=" N2 G c 28 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G c 28 " -0.008 2.00e-02 2.50e+03 pdb=" C4 G c 28 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR B 233 " -0.034 5.00e-02 4.00e+02 5.19e-02 4.30e+00 pdb=" N PRO B 234 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO B 234 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO B 234 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 254 " 0.015 2.00e-02 2.50e+03 1.40e-02 3.89e+00 pdb=" CG TYR B 254 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR B 254 " 0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 254 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 254 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 254 " 0.004 2.00e-02 2.50e+03 pdb=" CZ TYR B 254 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR B 254 " 0.001 2.00e-02 2.50e+03 ... (remaining 1103 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 309 2.68 - 3.24: 7582 3.24 - 3.79: 14419 3.79 - 4.35: 18343 4.35 - 4.90: 27737 Nonbonded interactions: 68390 Sorted by model distance: nonbonded pdb=" O ARG A 84 " pdb=" OG1 THR A 87 " model vdw 2.129 3.040 nonbonded pdb=" OE2 GLU A 336 " pdb=" O2' U c 83 " model vdw 2.137 3.040 nonbonded pdb=" OD1 ASN B 341 " pdb=" N TRP B 342 " model vdw 2.184 3.120 nonbonded pdb=" O ARG A 340 " pdb=" NH1 ARG A 340 " model vdw 2.237 3.120 nonbonded pdb=" OG1 THR A 88 " pdb=" OD1 ASN A 109 " model vdw 2.257 3.040 ... (remaining 68385 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 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 63 or resid 83 through 365)) selection = chain 'B' } 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: 1.100 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.440 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 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 : 0.005 0.045 8573 Z= 0.239 Angle : 0.689 10.139 12027 Z= 0.380 Chirality : 0.041 0.200 1384 Planarity : 0.004 0.052 1106 Dihedral : 20.636 165.379 3866 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.55 % Favored : 96.31 % Rotamer: Outliers : 3.31 % Allowed : 31.07 % Favored : 65.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.11 (0.32), residues: 705 helix: 1.23 (0.28), residues: 333 sheet: -0.58 (0.48), residues: 114 loop : -1.08 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 265 TYR 0.034 0.002 TYR B 254 PHE 0.022 0.002 PHE A 39 TRP 0.019 0.002 TRP B 342 HIS 0.003 0.001 HIS A 302 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 8573) covalent geometry : angle 0.68906 (12027) hydrogen bonds : bond 0.15175 ( 430) hydrogen bonds : angle 5.86515 ( 1153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 134 time to evaluate : 0.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 GLU cc_start: 0.5703 (mm-30) cc_final: 0.5392 (mm-30) REVERT: A 123 TYR cc_start: 0.5870 (m-80) cc_final: 0.5406 (m-80) REVERT: A 193 CYS cc_start: 0.7892 (m) cc_final: 0.7570 (m) REVERT: B 15 LEU cc_start: 0.6175 (OUTLIER) cc_final: 0.5952 (mt) REVERT: B 25 LYS cc_start: 0.7754 (OUTLIER) cc_final: 0.7541 (mmmm) REVERT: B 30 MET cc_start: 0.6624 (ttt) cc_final: 0.6353 (ttt) REVERT: B 57 ASP cc_start: 0.7232 (t0) cc_final: 0.6841 (t0) REVERT: B 124 TRP cc_start: 0.5602 (OUTLIER) cc_final: 0.5226 (m100) REVERT: B 187 LYS cc_start: 0.8317 (mttt) cc_final: 0.7967 (mttt) outliers start: 21 outliers final: 6 residues processed: 150 average time/residue: 0.1151 time to fit residues: 22.0939 Evaluate side-chains 129 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 120 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 48 HIS Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 25 LYS Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 49 optimal weight: 20.0000 chunk 53 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 40.0000 chunk 45 optimal weight: 3.9990 chunk 74 optimal weight: 2.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 GLN ** A 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 260 GLN A 302 HIS B 103 ASN B 242 ASN B 299 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.205243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.167814 restraints weight = 12585.445| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.29 r_work: 0.3798 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.3798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6620 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.070 8573 Z= 0.338 Angle : 0.788 8.370 12027 Z= 0.423 Chirality : 0.047 0.191 1384 Planarity : 0.007 0.087 1106 Dihedral : 20.569 172.146 2352 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 14.03 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 5.52 % Allowed : 27.60 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.34 (0.31), residues: 705 helix: 0.65 (0.27), residues: 340 sheet: -0.65 (0.49), residues: 123 loop : -1.13 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 40 TYR 0.030 0.003 TYR B 254 PHE 0.022 0.003 PHE A 39 TRP 0.017 0.003 TRP B 34 HIS 0.010 0.002 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00721 ( 8573) covalent geometry : angle 0.78811 (12027) hydrogen bonds : bond 0.05999 ( 430) hydrogen bonds : angle 4.90553 ( 1153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8285 (OUTLIER) cc_final: 0.7950 (mmm-85) REVERT: A 65 ILE cc_start: 0.8377 (OUTLIER) cc_final: 0.7996 (pt) REVERT: A 92 VAL cc_start: 0.7515 (p) cc_final: 0.7091 (m) REVERT: A 141 PHE cc_start: 0.7223 (p90) cc_final: 0.6981 (p90) REVERT: A 212 ILE cc_start: 0.7847 (OUTLIER) cc_final: 0.7551 (mm) REVERT: A 277 LYS cc_start: 0.7921 (tptt) cc_final: 0.7394 (mmmm) REVERT: B 40 ARG cc_start: 0.7684 (mtm180) cc_final: 0.7457 (mtm180) REVERT: B 54 MET cc_start: 0.7116 (mmm) cc_final: 0.6845 (mmt) REVERT: B 119 ASN cc_start: 0.6657 (m110) cc_final: 0.6229 (m-40) REVERT: B 125 LYS cc_start: 0.7910 (OUTLIER) cc_final: 0.7664 (mttt) REVERT: B 136 ASP cc_start: 0.7832 (p0) cc_final: 0.7455 (p0) REVERT: B 168 LYS cc_start: 0.7172 (pttt) cc_final: 0.6508 (mtmt) REVERT: B 303 VAL cc_start: 0.6381 (OUTLIER) cc_final: 0.6146 (p) REVERT: B 313 ILE cc_start: 0.7360 (mp) cc_final: 0.7105 (mp) outliers start: 35 outliers final: 15 residues processed: 168 average time/residue: 0.1211 time to fit residues: 25.9597 Evaluate side-chains 156 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 136 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 155 LYS Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 212 ILE Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain B residue 20 THR Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 125 LYS Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 303 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 74 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 29 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 chunk 75 optimal weight: 10.0000 chunk 79 optimal weight: 1.9990 chunk 36 optimal weight: 20.0000 chunk 22 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 ASN ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 315 HIS B 316 GLN B 324 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.204742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.165880 restraints weight = 12355.214| |-----------------------------------------------------------------------------| r_work (start): 0.3925 rms_B_bonded: 2.30 r_work: 0.3771 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.3771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 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 : 0.005 0.045 8573 Z= 0.223 Angle : 0.620 6.911 12027 Z= 0.333 Chirality : 0.041 0.143 1384 Planarity : 0.005 0.048 1106 Dihedral : 20.442 169.305 2344 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.83 % Favored : 96.03 % Rotamer: Outliers : 5.68 % Allowed : 26.66 % Favored : 67.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.32), residues: 705 helix: 1.03 (0.27), residues: 343 sheet: -0.79 (0.48), residues: 123 loop : -1.11 (0.41), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 274 TYR 0.013 0.002 TYR A 60 PHE 0.020 0.002 PHE A 39 TRP 0.022 0.003 TRP A 124 HIS 0.006 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00477 ( 8573) covalent geometry : angle 0.61995 (12027) hydrogen bonds : bond 0.04890 ( 430) hydrogen bonds : angle 4.40456 ( 1153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 137 time to evaluate : 0.261 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 30 MET cc_start: 0.7021 (ttm) cc_final: 0.6820 (ttm) REVERT: A 248 THR cc_start: 0.7103 (OUTLIER) cc_final: 0.6813 (m) REVERT: A 255 ARG cc_start: 0.6671 (tpt170) cc_final: 0.6374 (tpt170) REVERT: A 277 LYS cc_start: 0.8055 (tptt) cc_final: 0.7753 (mptt) REVERT: B 15 LEU cc_start: 0.5818 (OUTLIER) cc_final: 0.5605 (tt) REVERT: B 54 MET cc_start: 0.6771 (mmm) cc_final: 0.6375 (mmm) REVERT: B 57 ASP cc_start: 0.7825 (t0) cc_final: 0.7524 (t0) REVERT: B 125 LYS cc_start: 0.7891 (mttt) cc_final: 0.7645 (mttt) REVERT: B 168 LYS cc_start: 0.6963 (pttt) cc_final: 0.6516 (mtmt) REVERT: B 184 ARG cc_start: 0.8468 (mtm110) cc_final: 0.8174 (mtm110) REVERT: B 187 LYS cc_start: 0.8150 (mttt) cc_final: 0.7642 (mttt) REVERT: B 220 LYS cc_start: 0.7791 (mttt) cc_final: 0.7488 (mttt) outliers start: 36 outliers final: 20 residues processed: 154 average time/residue: 0.1199 time to fit residues: 23.4985 Evaluate side-chains 155 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 67 TYR Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 245 THR Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 11 optimal weight: 0.7980 chunk 14 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 33 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 63 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 51 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 295 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.205303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.166693 restraints weight = 12510.382| |-----------------------------------------------------------------------------| r_work (start): 0.3944 rms_B_bonded: 2.28 r_work: 0.3796 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6627 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8573 Z= 0.158 Angle : 0.545 6.593 12027 Z= 0.293 Chirality : 0.037 0.143 1384 Planarity : 0.004 0.050 1106 Dihedral : 20.347 166.825 2339 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 11.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Rotamer: Outliers : 4.89 % Allowed : 28.08 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.32), residues: 705 helix: 1.48 (0.27), residues: 343 sheet: -0.89 (0.48), residues: 123 loop : -1.16 (0.40), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 40 TYR 0.012 0.001 TYR B 254 PHE 0.017 0.001 PHE A 139 TRP 0.018 0.002 TRP B 34 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 8573) covalent geometry : angle 0.54454 (12027) hydrogen bonds : bond 0.04292 ( 430) hydrogen bonds : angle 4.14552 ( 1153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 171 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 248 THR cc_start: 0.7173 (OUTLIER) cc_final: 0.6938 (m) REVERT: A 277 LYS cc_start: 0.8171 (tptt) cc_final: 0.7950 (mptt) REVERT: A 293 GLU cc_start: 0.6307 (OUTLIER) cc_final: 0.6079 (mm-30) REVERT: B 54 MET cc_start: 0.6716 (mmm) cc_final: 0.6382 (mmm) REVERT: B 119 ASN cc_start: 0.6672 (m110) cc_final: 0.6220 (m110) REVERT: B 125 LYS cc_start: 0.8075 (mttt) cc_final: 0.7853 (mttt) REVERT: B 168 LYS cc_start: 0.6868 (pttt) cc_final: 0.6403 (mtmt) REVERT: B 181 LEU cc_start: 0.8207 (mt) cc_final: 0.7930 (mt) REVERT: B 184 ARG cc_start: 0.8448 (mtm110) cc_final: 0.8191 (mtm110) REVERT: B 203 LYS cc_start: 0.5912 (mttt) cc_final: 0.5626 (mttt) REVERT: B 231 LEU cc_start: 0.5798 (OUTLIER) cc_final: 0.5346 (pt) REVERT: B 264 ARG cc_start: 0.6290 (mtm110) cc_final: 0.5899 (mtm110) REVERT: B 344 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.4891 (m-80) outliers start: 31 outliers final: 16 residues processed: 156 average time/residue: 0.1257 time to fit residues: 24.9853 Evaluate side-chains 159 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 139 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 124 TRP Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 344 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 1 optimal weight: 0.9980 chunk 37 optimal weight: 10.0000 chunk 67 optimal weight: 0.0070 chunk 4 optimal weight: 0.3980 chunk 3 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 43 optimal weight: 7.9990 overall best weight: 0.8600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 33 GLN ** B 242 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 = 0.4421 r_free = 0.4421 target = 0.204492 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.165068 restraints weight = 12457.790| |-----------------------------------------------------------------------------| r_work (start): 0.3932 rms_B_bonded: 2.28 r_work: 0.3784 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.6265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 8573 Z= 0.163 Angle : 0.544 7.191 12027 Z= 0.292 Chirality : 0.038 0.143 1384 Planarity : 0.004 0.050 1106 Dihedral : 20.380 166.038 2339 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Rotamer: Outliers : 5.52 % Allowed : 27.13 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.23 (0.32), residues: 705 helix: 1.54 (0.28), residues: 344 sheet: -0.97 (0.46), residues: 125 loop : -1.23 (0.40), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 40 TYR 0.012 0.001 TYR A 353 PHE 0.017 0.001 PHE A 139 TRP 0.019 0.002 TRP B 34 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 8573) covalent geometry : angle 0.54365 (12027) hydrogen bonds : bond 0.04230 ( 430) hydrogen bonds : angle 4.10949 ( 1153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 128 time to evaluate : 0.256 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8348 (OUTLIER) cc_final: 0.7735 (mmt180) REVERT: A 28 MET cc_start: 0.8153 (mmm) cc_final: 0.7869 (mmt) REVERT: A 68 LYS cc_start: 0.7656 (OUTLIER) cc_final: 0.7399 (mmmt) REVERT: A 277 LYS cc_start: 0.8169 (tptt) cc_final: 0.7690 (mtpp) REVERT: B 11 LYS cc_start: 0.6566 (OUTLIER) cc_final: 0.6318 (tptp) REVERT: B 54 MET cc_start: 0.6600 (mmm) cc_final: 0.6270 (mmm) REVERT: B 125 LYS cc_start: 0.8112 (mttt) cc_final: 0.7859 (mttt) REVERT: B 203 LYS cc_start: 0.6043 (mttt) cc_final: 0.5782 (mttt) REVERT: B 264 ARG cc_start: 0.6305 (mtm110) cc_final: 0.5805 (mtm110) REVERT: B 314 LYS cc_start: 0.7890 (tptp) cc_final: 0.7678 (tptp) REVERT: B 315 HIS cc_start: 0.7443 (m-70) cc_final: 0.6897 (m90) REVERT: B 339 LEU cc_start: 0.4754 (OUTLIER) cc_final: 0.3735 (mt) REVERT: B 344 TYR cc_start: 0.6387 (OUTLIER) cc_final: 0.5065 (m-80) REVERT: B 350 LYS cc_start: 0.6496 (mttt) cc_final: 0.6107 (mttt) outliers start: 35 outliers final: 22 residues processed: 149 average time/residue: 0.1275 time to fit residues: 24.1014 Evaluate side-chains 153 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 126 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 33 GLN Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 64 optimal weight: 0.6980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 30.0000 chunk 3 optimal weight: 0.8980 chunk 66 optimal weight: 9.9990 chunk 63 optimal weight: 0.9990 chunk 33 optimal weight: 0.0370 chunk 11 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 69 optimal weight: 4.9990 overall best weight: 0.7262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** B 242 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 = 0.4438 r_free = 0.4438 target = 0.204314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.168640 restraints weight = 12344.822| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.24 r_work: 0.3796 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3796 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6710 moved from start: 0.6571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 8573 Z= 0.144 Angle : 0.523 11.114 12027 Z= 0.279 Chirality : 0.037 0.162 1384 Planarity : 0.004 0.049 1106 Dihedral : 20.314 165.345 2337 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.98 % Favored : 96.88 % Rotamer: Outliers : 5.21 % Allowed : 28.55 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.38 (0.32), residues: 705 helix: 1.66 (0.27), residues: 344 sheet: -0.95 (0.48), residues: 119 loop : -1.13 (0.40), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 184 TYR 0.015 0.001 TYR B 60 PHE 0.016 0.001 PHE A 139 TRP 0.017 0.002 TRP A 124 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00302 ( 8573) covalent geometry : angle 0.52337 (12027) hydrogen bonds : bond 0.03983 ( 430) hydrogen bonds : angle 3.99523 ( 1153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 126 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.8101 (mmm) cc_final: 0.7869 (mmt) REVERT: A 68 LYS cc_start: 0.7623 (OUTLIER) cc_final: 0.7423 (mmmt) REVERT: A 277 LYS cc_start: 0.8205 (tptt) cc_final: 0.7763 (mmmm) REVERT: B 10 ARG cc_start: 0.7308 (mmt-90) cc_final: 0.6839 (mmt-90) REVERT: B 35 ARG cc_start: 0.6717 (OUTLIER) cc_final: 0.6229 (ptm160) REVERT: B 54 MET cc_start: 0.6648 (mmm) cc_final: 0.6188 (mmm) REVERT: B 119 ASN cc_start: 0.6819 (m110) cc_final: 0.6345 (m110) REVERT: B 168 LYS cc_start: 0.6792 (pttt) cc_final: 0.6298 (mtmt) REVERT: B 203 LYS cc_start: 0.6092 (mttt) cc_final: 0.5847 (mttt) REVERT: B 220 LYS cc_start: 0.7883 (mttt) cc_final: 0.7582 (mttt) REVERT: B 264 ARG cc_start: 0.6439 (mtm110) cc_final: 0.5990 (mtm110) REVERT: B 313 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7212 (mp) REVERT: B 323 MET cc_start: 0.7242 (mmm) cc_final: 0.6697 (tmm) REVERT: B 339 LEU cc_start: 0.4918 (OUTLIER) cc_final: 0.3943 (mt) REVERT: B 344 TYR cc_start: 0.6425 (OUTLIER) cc_final: 0.5210 (m-80) REVERT: B 350 LYS cc_start: 0.6522 (mttt) cc_final: 0.6123 (mttt) outliers start: 33 outliers final: 24 residues processed: 148 average time/residue: 0.1348 time to fit residues: 24.8949 Evaluate side-chains 154 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 125 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 68 LYS Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 312 CYS Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 35 ARG Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 61 LEU Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 65 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 34 optimal weight: 0.9990 chunk 70 optimal weight: 2.9990 chunk 61 optimal weight: 30.0000 chunk 24 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 55 optimal weight: 20.0000 chunk 15 optimal weight: 0.9980 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4379 r_free = 0.4379 target = 0.199176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3971 r_free = 0.3971 target = 0.163115 restraints weight = 12438.680| |-----------------------------------------------------------------------------| r_work (start): 0.3924 rms_B_bonded: 2.38 r_work: 0.3723 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 moved from start: 0.7138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 8573 Z= 0.277 Angle : 0.659 10.363 12027 Z= 0.352 Chirality : 0.043 0.192 1384 Planarity : 0.005 0.049 1106 Dihedral : 20.621 172.524 2337 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.14 % Allowed : 4.82 % Favored : 95.04 % Rotamer: Outliers : 5.84 % Allowed : 28.71 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.02 (0.32), residues: 705 helix: 1.29 (0.27), residues: 344 sheet: -1.07 (0.46), residues: 125 loop : -1.27 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 40 TYR 0.020 0.002 TYR B 60 PHE 0.024 0.002 PHE A 39 TRP 0.021 0.003 TRP A 124 HIS 0.006 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 8573) covalent geometry : angle 0.65921 (12027) hydrogen bonds : bond 0.05165 ( 430) hydrogen bonds : angle 4.42490 ( 1153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 125 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.8094 (mtp180) REVERT: A 28 MET cc_start: 0.8227 (mmm) cc_final: 0.7808 (mmt) REVERT: A 62 SER cc_start: 0.8058 (OUTLIER) cc_final: 0.7673 (m) REVERT: A 277 LYS cc_start: 0.8153 (tptt) cc_final: 0.7773 (mmmm) REVERT: B 203 LYS cc_start: 0.6135 (mttt) cc_final: 0.5880 (mttt) REVERT: B 220 LYS cc_start: 0.7854 (mttt) cc_final: 0.7568 (mttt) REVERT: B 256 ARG cc_start: 0.7949 (ttt-90) cc_final: 0.7653 (ttm-80) REVERT: B 264 ARG cc_start: 0.6334 (mtm110) cc_final: 0.5919 (mtm110) REVERT: B 315 HIS cc_start: 0.7388 (m-70) cc_final: 0.7090 (m90) REVERT: B 323 MET cc_start: 0.7418 (mmm) cc_final: 0.6941 (tmm) REVERT: B 324 ASN cc_start: 0.6316 (t0) cc_final: 0.6051 (t0) REVERT: B 339 LEU cc_start: 0.5611 (OUTLIER) cc_final: 0.4272 (mt) REVERT: B 344 TYR cc_start: 0.6503 (OUTLIER) cc_final: 0.5431 (m-80) REVERT: B 350 LYS cc_start: 0.6472 (mttt) cc_final: 0.6049 (mttt) outliers start: 37 outliers final: 25 residues processed: 147 average time/residue: 0.1260 time to fit residues: 23.7845 Evaluate side-chains 152 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 123 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ARG Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 100 MET Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 8 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 chunk 49 optimal weight: 30.0000 chunk 74 optimal weight: 2.9990 chunk 47 optimal weight: 0.6980 chunk 53 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 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 = 0.4407 r_free = 0.4407 target = 0.201785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.166707 restraints weight = 12414.030| |-----------------------------------------------------------------------------| r_work (start): 0.3958 rms_B_bonded: 2.24 r_work: 0.3756 rms_B_bonded: 3.91 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8573 Z= 0.203 Angle : 0.582 10.268 12027 Z= 0.312 Chirality : 0.039 0.149 1384 Planarity : 0.004 0.048 1106 Dihedral : 20.471 171.301 2337 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Rotamer: Outliers : 5.36 % Allowed : 29.18 % Favored : 65.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.32), residues: 705 helix: 1.41 (0.27), residues: 344 sheet: -1.09 (0.45), residues: 125 loop : -1.22 (0.41), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 40 TYR 0.018 0.001 TYR B 60 PHE 0.019 0.002 PHE A 139 TRP 0.020 0.002 TRP A 124 HIS 0.008 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00438 ( 8573) covalent geometry : angle 0.58153 (12027) hydrogen bonds : bond 0.04529 ( 430) hydrogen bonds : angle 4.20479 ( 1153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 126 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8285 (ptpp) cc_final: 0.8001 (mtmm) REVERT: A 277 LYS cc_start: 0.8208 (tptt) cc_final: 0.7888 (mmtp) REVERT: B 119 ASN cc_start: 0.6759 (m110) cc_final: 0.6330 (m-40) REVERT: B 203 LYS cc_start: 0.6105 (mttt) cc_final: 0.5849 (mttt) REVERT: B 220 LYS cc_start: 0.7905 (mttt) cc_final: 0.7620 (mttt) REVERT: B 256 ARG cc_start: 0.7987 (ttt-90) cc_final: 0.7671 (ttm-80) REVERT: B 264 ARG cc_start: 0.6345 (mtm110) cc_final: 0.5921 (mtm110) REVERT: B 313 ILE cc_start: 0.7606 (OUTLIER) cc_final: 0.7334 (mp) REVERT: B 323 MET cc_start: 0.7471 (mmm) cc_final: 0.7097 (tmm) REVERT: B 324 ASN cc_start: 0.6488 (t0) cc_final: 0.6228 (t0) REVERT: B 339 LEU cc_start: 0.5539 (OUTLIER) cc_final: 0.4532 (mt) REVERT: B 344 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5364 (m-80) REVERT: B 350 LYS cc_start: 0.6632 (mttt) cc_final: 0.6207 (mttt) outliers start: 34 outliers final: 26 residues processed: 143 average time/residue: 0.1227 time to fit residues: 22.5028 Evaluate side-chains 155 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 126 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 190 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 313 ILE Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 0 optimal weight: 4.9990 chunk 47 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 13 optimal weight: 0.7980 chunk 22 optimal weight: 4.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 74 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 103 ASN ** B 242 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 = 0.4408 r_free = 0.4408 target = 0.201497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.165713 restraints weight = 12374.924| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 2.31 r_work: 0.3756 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3756 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6775 moved from start: 0.7555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 8573 Z= 0.182 Angle : 0.584 10.075 12027 Z= 0.311 Chirality : 0.039 0.183 1384 Planarity : 0.004 0.045 1106 Dihedral : 20.432 170.066 2337 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.69 % Favored : 96.17 % Rotamer: Outliers : 4.73 % Allowed : 30.28 % Favored : 64.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.16 (0.32), residues: 705 helix: 1.46 (0.27), residues: 345 sheet: -1.14 (0.45), residues: 125 loop : -1.15 (0.41), residues: 235 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 40 TYR 0.019 0.001 TYR B 60 PHE 0.019 0.002 PHE A 139 TRP 0.019 0.002 TRP A 124 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 8573) covalent geometry : angle 0.58409 (12027) hydrogen bonds : bond 0.04393 ( 430) hydrogen bonds : angle 4.15576 ( 1153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 130 time to evaluate : 0.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 155 LYS cc_start: 0.8299 (ptpp) cc_final: 0.7969 (mtmm) REVERT: A 277 LYS cc_start: 0.8244 (tptt) cc_final: 0.7927 (mmtp) REVERT: B 119 ASN cc_start: 0.6774 (m110) cc_final: 0.6338 (m-40) REVERT: B 135 LYS cc_start: 0.7596 (mmmt) cc_final: 0.7232 (mmmt) REVERT: B 184 ARG cc_start: 0.8365 (ptp-110) cc_final: 0.8073 (ptt-90) REVERT: B 203 LYS cc_start: 0.6114 (mttt) cc_final: 0.5875 (mttt) REVERT: B 220 LYS cc_start: 0.7901 (mttt) cc_final: 0.7662 (mttt) REVERT: B 237 VAL cc_start: 0.6492 (m) cc_final: 0.6133 (p) REVERT: B 256 ARG cc_start: 0.7996 (ttt-90) cc_final: 0.7668 (ttm-80) REVERT: B 264 ARG cc_start: 0.6357 (mtm110) cc_final: 0.5945 (mtm110) REVERT: B 323 MET cc_start: 0.7420 (mmm) cc_final: 0.7100 (tmm) REVERT: B 324 ASN cc_start: 0.6686 (t0) cc_final: 0.6456 (t0) REVERT: B 339 LEU cc_start: 0.5572 (OUTLIER) cc_final: 0.4650 (mt) REVERT: B 344 TYR cc_start: 0.6368 (OUTLIER) cc_final: 0.5453 (m-80) REVERT: B 350 LYS cc_start: 0.6543 (mttt) cc_final: 0.6107 (mttt) outliers start: 30 outliers final: 26 residues processed: 145 average time/residue: 0.0997 time to fit residues: 18.4972 Evaluate side-chains 156 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 128 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 259 ILE Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 23 optimal weight: 0.3980 chunk 54 optimal weight: 4.9990 chunk 38 optimal weight: 10.0000 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 55 optimal weight: 4.9990 chunk 77 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4421 r_free = 0.4421 target = 0.202666 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.166029 restraints weight = 12342.683| |-----------------------------------------------------------------------------| r_work (start): 0.3969 rms_B_bonded: 2.13 r_work: 0.3824 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6662 moved from start: 0.7664 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8573 Z= 0.147 Angle : 0.557 10.348 12027 Z= 0.294 Chirality : 0.037 0.157 1384 Planarity : 0.004 0.042 1106 Dihedral : 20.360 168.240 2337 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.40 % Favored : 96.45 % Rotamer: Outliers : 4.10 % Allowed : 31.39 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.28 (0.32), residues: 705 helix: 1.54 (0.27), residues: 346 sheet: -0.97 (0.49), residues: 114 loop : -1.15 (0.41), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 40 TYR 0.018 0.001 TYR B 60 PHE 0.019 0.001 PHE A 139 TRP 0.019 0.002 TRP A 124 HIS 0.005 0.001 HIS B 315 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 8573) covalent geometry : angle 0.55737 (12027) hydrogen bonds : bond 0.04106 ( 430) hydrogen bonds : angle 3.96448 ( 1153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1410 Ramachandran restraints generated. 705 Oldfield, 0 Emsley, 705 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 126 time to evaluate : 0.162 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 28 MET cc_start: 0.7798 (tpp) cc_final: 0.7250 (mmt) REVERT: A 277 LYS cc_start: 0.8280 (tptt) cc_final: 0.7862 (mmmm) REVERT: A 280 LYS cc_start: 0.5444 (mttp) cc_final: 0.4852 (pttt) REVERT: B 100 MET cc_start: 0.6313 (tpt) cc_final: 0.6112 (tpt) REVERT: B 119 ASN cc_start: 0.6789 (m110) cc_final: 0.6359 (m110) REVERT: B 203 LYS cc_start: 0.6172 (mttt) cc_final: 0.5935 (mttt) REVERT: B 220 LYS cc_start: 0.7902 (mttt) cc_final: 0.7605 (mttt) REVERT: B 256 ARG cc_start: 0.7958 (ttt-90) cc_final: 0.7611 (ttm-80) REVERT: B 264 ARG cc_start: 0.6376 (mtm110) cc_final: 0.5960 (mtm110) REVERT: B 323 MET cc_start: 0.7324 (mmm) cc_final: 0.7049 (tmm) REVERT: B 324 ASN cc_start: 0.6662 (t0) cc_final: 0.6435 (t0) REVERT: B 339 LEU cc_start: 0.5509 (OUTLIER) cc_final: 0.4646 (mt) REVERT: B 344 TYR cc_start: 0.6194 (OUTLIER) cc_final: 0.5433 (m-80) REVERT: B 350 LYS cc_start: 0.6357 (mttt) cc_final: 0.5920 (mttt) outliers start: 26 outliers final: 24 residues processed: 139 average time/residue: 0.1125 time to fit residues: 19.7824 Evaluate side-chains 151 residues out of total 634 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 125 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 7 LYS Chi-restraints excluded: chain A residue 39 PHE Chi-restraints excluded: chain A residue 54 MET Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 62 SER Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 93 SER Chi-restraints excluded: chain A residue 124 TRP Chi-restraints excluded: chain A residue 150 VAL Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 213 GLU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 319 THR Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 11 LYS Chi-restraints excluded: chain B residue 15 LEU Chi-restraints excluded: chain B residue 16 ILE Chi-restraints excluded: chain B residue 47 THR Chi-restraints excluded: chain B residue 51 VAL Chi-restraints excluded: chain B residue 114 SER Chi-restraints excluded: chain B residue 236 VAL Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 339 LEU Chi-restraints excluded: chain B residue 344 TYR Chi-restraints excluded: chain B residue 364 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 29 optimal weight: 0.4980 chunk 79 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.0000 chunk 66 optimal weight: 9.9990 chunk 51 optimal weight: 7.9990 chunk 18 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 overall best weight: 0.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 242 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 315 HIS ** 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 = 0.4432 r_free = 0.4432 target = 0.204070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.169937 restraints weight = 12600.227| |-----------------------------------------------------------------------------| r_work (start): 0.3997 rms_B_bonded: 2.24 r_work: 0.3795 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.7773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8573 Z= 0.136 Angle : 0.559 12.350 12027 Z= 0.291 Chirality : 0.036 0.174 1384 Planarity : 0.004 0.043 1106 Dihedral : 20.277 166.088 2337 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 10.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.26 % Favored : 96.60 % Rotamer: Outliers : 4.57 % Allowed : 30.91 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.32), residues: 705 helix: 1.63 (0.27), residues: 346 sheet: -1.02 (0.47), residues: 125 loop : -1.08 (0.42), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG A 40 TYR 0.018 0.001 TYR B 60 PHE 0.018 0.001 PHE A 139 TRP 0.016 0.002 TRP A 124 HIS 0.003 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 8573) covalent geometry : angle 0.55928 (12027) hydrogen bonds : bond 0.03966 ( 430) hydrogen bonds : angle 3.88635 ( 1153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1915.58 seconds wall clock time: 33 minutes 36.20 seconds (2016.20 seconds total)