Starting phenix.real_space_refine on Thu Jul 2 18:43:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.map" model { file = "/net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j3r_35965/07_2026/8j3r_35965.cif" } resolution = 2.95 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 ------------------------------------------------------------------------------- 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= 0.010 sd= 0.076 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 140 5.49 5 Mg 3 5.21 5 S 32 5.16 5 C 5481 2.51 5 N 1731 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9526 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3429 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 10, 'TRANS': 411} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2345 Classifications: {'RNA': 109} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 2, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 12, 'rna3p': 96} Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3116 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3055 SG CYS A 372 88.301 55.825 32.384 1.00103.10 S ATOM 3076 SG CYS A 375 91.722 54.642 33.836 1.00 97.25 S ATOM 3193 SG CYS A 391 90.472 58.181 34.340 1.00116.70 S ATOM 3215 SG CYS A 394 91.398 56.126 32.490 1.00100.31 S Time building chain proxies: 1.74, per 1000 atoms: 0.18 Number of scatterers: 9526 At special positions: 0 Unit cell: (102.3, 117.7, 113.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 140 15.00 Mg 3 11.99 O 2138 8.00 N 1731 7.00 C 5481 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: 0.84 Conformation dependent library (CDL) restraints added in 153.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 372 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 375 " Number of angles added : 6 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 49.3% alpha, 17.6% beta 46 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 16 through 57 Processing helix chain 'A' and resid 61 through 66 Processing helix chain 'A' and resid 70 through 80 removed outlier: 3.628A pdb=" N TYR A 74 " --> pdb=" O ASN A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 105 removed outlier: 3.638A pdb=" N ALA A 98 " --> pdb=" O THR A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 111 Processing helix chain 'A' and resid 150 through 157 Processing helix chain 'A' and resid 171 through 183 removed outlier: 4.060A pdb=" N THR A 175 " --> pdb=" O GLY A 171 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ILE A 176 " --> pdb=" O ALA A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 196 through 199 Processing helix chain 'A' and resid 247 through 268 removed outlier: 3.759A pdb=" N GLU A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ASN A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 271 No H-bonds generated for 'chain 'A' and resid 269 through 271' Processing helix chain 'A' and resid 272 through 276 Processing helix chain 'A' and resid 279 through 284 removed outlier: 3.632A pdb=" N ARG A 283 " --> pdb=" O GLY A 279 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 316 Processing helix chain 'A' and resid 341 through 356 removed outlier: 3.569A pdb=" N ALA A 356 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 409 Processing helix chain 'A' and resid 412 through 420 Processing helix chain 'B' and resid 16 through 46 Processing helix chain 'B' and resid 50 through 56 removed outlier: 4.153A pdb=" N ASP B 54 " --> pdb=" O SER B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 70 through 81 removed outlier: 3.547A pdb=" N HIS B 77 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 78 " --> pdb=" O TYR B 74 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N THR B 81 " --> pdb=" O HIS B 77 " (cutoff:3.500A) Processing helix chain 'B' and resid 87 through 105 Processing helix chain 'B' and resid 105 through 112 Processing helix chain 'B' and resid 150 through 157 Processing helix chain 'B' and resid 171 through 183 Processing helix chain 'B' and resid 247 through 265 Processing helix chain 'B' and resid 286 through 317 Processing helix chain 'B' and resid 341 through 356 removed outlier: 3.553A pdb=" N GLU B 355 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N ALA B 356 " --> pdb=" O LYS B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 410 removed outlier: 3.808A pdb=" N ILE B 410 " --> pdb=" O ARG B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.851A pdb=" N ALA B 418 " --> pdb=" O ASP B 414 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER B 420 " --> pdb=" O ILE B 416 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.507A pdb=" N GLN A 191 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 200 " --> pdb=" O LYS A 195 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N TRP A 201 " --> pdb=" O ILE A 9 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE A 166 " --> pdb=" O VAL A 10 " (cutoff:3.500A) removed outlier: 7.229A pdb=" N SER A 164 " --> pdb=" O PRO A 12 " (cutoff:3.500A) removed outlier: 4.682A pdb=" N TYR A 142 " --> pdb=" O ILE A 167 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 125 through 127 removed outlier: 3.507A pdb=" N GLN A 191 " --> pdb=" O ASN A 204 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LYS A 200 " --> pdb=" O LYS A 195 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 242 through 245 removed outlier: 3.521A pdb=" N ALA A 232 " --> pdb=" O LEU A 245 " (cutoff:3.500A) removed outlier: 6.129A pdb=" N MET A 222 " --> pdb=" O GLN A 322 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLU A 324 " --> pdb=" O MET A 222 " (cutoff:3.500A) removed outlier: 8.742A pdb=" N ILE A 224 " --> pdb=" O GLU A 324 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N ILE A 321 " --> pdb=" O ILE A 361 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N ILE A 363 " --> pdb=" O ILE A 321 " (cutoff:3.500A) removed outlier: 6.209A pdb=" N MET A 323 " --> pdb=" O ILE A 363 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 388 through 390 removed outlier: 3.638A pdb=" N ALA A 398 " --> pdb=" O PHE A 389 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 2 through 5 removed outlier: 3.514A pdb=" N ALA B 189 " --> pdb=" O SER B 206 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N ARG B 208 " --> pdb=" O VAL B 187 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N VAL B 187 " --> pdb=" O ARG B 208 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 9 through 12 removed outlier: 6.756A pdb=" N ILE B 166 " --> pdb=" O VAL B 10 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N SER B 164 " --> pdb=" O PRO B 12 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N TYR B 142 " --> pdb=" O ILE B 167 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 242 through 245 removed outlier: 7.169A pdb=" N LEU B 218 " --> pdb=" O CYS B 318 " (cutoff:3.500A) removed outlier: 6.806A pdb=" N THR B 320 " --> pdb=" O LEU B 218 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS B 220 " --> pdb=" O THR B 320 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N GLN B 322 " --> pdb=" O LYS B 220 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N MET B 222 " --> pdb=" O GLN B 322 " (cutoff:3.500A) removed outlier: 8.324A pdb=" N GLU B 324 " --> pdb=" O MET B 222 " (cutoff:3.500A) removed outlier: 8.620A pdb=" N ILE B 224 " --> pdb=" O GLU B 324 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 388 through 390 356 hydrogen bonds defined for protein. 1026 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 114 hydrogen bonds 212 hydrogen bond angles 0 basepair planarities 46 basepair parallelities 86 stacking parallelities Total time for adding SS restraints: 1.32 Time building geometry restraints manager: 1.05 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: 2190 1.33 - 1.45: 2776 1.45 - 1.57: 4700 1.57 - 1.69: 277 1.69 - 1.81: 54 Bond restraints: 9997 Sorted by residual: bond pdb=" C1' DT E -7 " pdb=" N1 DT E -7 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C3' DG E 0 " pdb=" C2' DG E 0 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.68e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.55e+00 bond pdb=" C3' DT D 15 " pdb=" C2' DT D 15 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.52e+00 bond pdb=" C1' DC D 10 " pdb=" N1 DC D 10 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.47e+00 ... (remaining 9992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13787 1.53 - 3.06: 329 3.06 - 4.58: 21 4.58 - 6.11: 4 6.11 - 7.64: 2 Bond angle restraints: 14143 Sorted by residual: angle pdb=" N3 DT D 19 " pdb=" C4 DT D 19 " pdb=" O4 DT D 19 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E -7 " pdb=" C4 DT E -7 " pdb=" O4 DT E -7 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 23 " pdb=" C4 DT D 23 " pdb=" O4 DT D 23 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 14138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 4947 17.90 - 35.80: 481 35.80 - 53.71: 203 53.71 - 71.61: 66 71.61 - 89.51: 11 Dihedral angle restraints: 5708 sinusoidal: 3341 harmonic: 2367 Sorted by residual: dihedral pdb=" CA LYS A 11 " pdb=" C LYS A 11 " pdb=" N PRO A 12 " pdb=" CA PRO A 12 " ideal model delta harmonic sigma weight residual 180.00 162.90 17.10 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASN A 131 " pdb=" CB ASN A 131 " pdb=" CG ASN A 131 " pdb=" OD1 ASN A 131 " ideal model delta sinusoidal sigma weight residual 120.00 -168.80 -71.20 2 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA ASP B 364 " pdb=" CB ASP B 364 " pdb=" CG ASP B 364 " pdb=" OD1 ASP B 364 " ideal model delta sinusoidal sigma weight residual -30.00 -86.06 56.06 1 2.00e+01 2.50e-03 1.06e+01 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1205 0.035 - 0.069: 290 0.069 - 0.104: 103 0.104 - 0.138: 27 0.138 - 0.173: 3 Chirality restraints: 1628 Sorted by residual: chirality pdb=" C1' G C -83 " pdb=" O4' G C -83 " pdb=" C2' G C -83 " pdb=" N9 G C -83 " both_signs ideal model delta sigma weight residual False 2.46 2.28 0.17 2.00e-01 2.50e+01 7.47e-01 chirality pdb=" CA ILE A 116 " pdb=" N ILE A 116 " pdb=" C ILE A 116 " pdb=" CB ILE A 116 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.37e-01 chirality pdb=" C1' U C -49 " pdb=" O4' U C -49 " pdb=" C2' U C -49 " pdb=" N1 U C -49 " both_signs ideal model delta sigma weight residual False 2.47 2.32 0.14 2.00e-01 2.50e+01 5.13e-01 ... (remaining 1625 not shown) Planarity restraints: 1293 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U C 6 " -0.030 2.00e-02 2.50e+03 1.51e-02 5.12e+00 pdb=" N1 U C 6 " 0.032 2.00e-02 2.50e+03 pdb=" C2 U C 6 " 0.004 2.00e-02 2.50e+03 pdb=" O2 U C 6 " 0.002 2.00e-02 2.50e+03 pdb=" N3 U C 6 " -0.001 2.00e-02 2.50e+03 pdb=" C4 U C 6 " -0.003 2.00e-02 2.50e+03 pdb=" O4 U C 6 " -0.009 2.00e-02 2.50e+03 pdb=" C5 U C 6 " -0.001 2.00e-02 2.50e+03 pdb=" C6 U C 6 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G C -44 " -0.028 2.00e-02 2.50e+03 1.16e-02 4.04e+00 pdb=" N9 G C -44 " 0.026 2.00e-02 2.50e+03 pdb=" C8 G C -44 " 0.004 2.00e-02 2.50e+03 pdb=" N7 G C -44 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G C -44 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G C -44 " -0.003 2.00e-02 2.50e+03 pdb=" O6 G C -44 " -0.008 2.00e-02 2.50e+03 pdb=" N1 G C -44 " -0.003 2.00e-02 2.50e+03 pdb=" C2 G C -44 " 0.002 2.00e-02 2.50e+03 pdb=" N2 G C -44 " 0.001 2.00e-02 2.50e+03 pdb=" N3 G C -44 " 0.005 2.00e-02 2.50e+03 pdb=" C4 G C -44 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' A C 7 " -0.026 2.00e-02 2.50e+03 1.18e-02 3.86e+00 pdb=" N9 A C 7 " 0.028 2.00e-02 2.50e+03 pdb=" C8 A C 7 " 0.004 2.00e-02 2.50e+03 pdb=" N7 A C 7 " -0.002 2.00e-02 2.50e+03 pdb=" C5 A C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C6 A C 7 " -0.003 2.00e-02 2.50e+03 pdb=" N6 A C 7 " -0.006 2.00e-02 2.50e+03 pdb=" N1 A C 7 " -0.001 2.00e-02 2.50e+03 pdb=" C2 A C 7 " 0.003 2.00e-02 2.50e+03 pdb=" N3 A C 7 " 0.004 2.00e-02 2.50e+03 pdb=" C4 A C 7 " -0.000 2.00e-02 2.50e+03 ... (remaining 1290 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 117 2.63 - 3.20: 7902 3.20 - 3.76: 16080 3.76 - 4.33: 22344 4.33 - 4.90: 33220 Nonbonded interactions: 79663 Sorted by model distance: nonbonded pdb=" OG SER A 334 " pdb="MG MG A 502 " model vdw 2.060 2.170 nonbonded pdb=" NE2 GLN B 322 " pdb=" O ILE B 408 " model vdw 2.229 3.120 nonbonded pdb=" O LEU B 337 " pdb=" OH TYR B 342 " model vdw 2.246 3.040 nonbonded pdb=" O2' U C -45 " pdb=" NZ LYS B 129 " model vdw 2.260 3.120 nonbonded pdb=" O2' A C -66 " pdb=" OE2 GLU B 108 " model vdw 2.266 3.040 ... (remaining 79658 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 58 or resid 65 through 81 or (resid 82 through 8 \ 3 and (name N or name CA or name C or name O or name CB )) or resid 84 through 1 \ 60 or (resid 161 and (name N or name CA or name C or name O or name CB )) or res \ id 162 through 219 or (resid 220 and (name N or name CA or name C or name O or n \ ame CB )) or resid 221 through 224 or (resid 225 and (name N or name CA or name \ C or name O or name CB )) or resid 226 through 243 or (resid 244 and (name N or \ name CA or name C or name O or name CB )) or resid 245 through 257 or (resid 258 \ and (name N or name CA or name C or name O or name CB )) or resid 259 through 2 \ 65 or resid 285 through 326 or resid 331 or (resid 332 and (name N or name CA or \ name C or name O or name CB )) or resid 333 through 365 or (resid 366 and (name \ N or name CA or name C or name O or name CB )) or resid 367 through 378 or (res \ id 379 and (name N or name CA or name C or name O or name CB )) or resid 385 thr \ ough 414 or (resid 415 and (name N or name CA or name C or name O or name CB )) \ or resid 416 through 421)) 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: 0.130 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: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.650 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 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 : 0.003 0.071 10001 Z= 0.227 Angle : 0.787 56.945 14149 Z= 0.385 Chirality : 0.037 0.173 1628 Planarity : 0.003 0.034 1293 Dihedral : 16.737 89.510 4192 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.46 % Allowed : 11.01 % Favored : 86.52 % 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: 0.87 (0.29), residues: 797 helix: 1.90 (0.26), residues: 361 sheet: 0.11 (0.39), residues: 162 loop : -0.90 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.011 0.001 TYR A 119 PHE 0.007 0.001 PHE B 102 TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.23 ( 9997) covalent geometry : angle 0.53419 / 0.37 (14143) hydrogen bonds : bond 0.22544 / 14.29 ( 462) hydrogen bonds : angle 6.19927 / 4.61 ( 1238) metal coordination : bond 0.03778 / 1.89 ( 4) metal coordination : angle 28.09070 / 11.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6447 (m110) REVERT: A 377 ASN cc_start: 0.6732 (t0) cc_final: 0.6497 (t0) REVERT: B 141 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6234 (m-30) REVERT: B 142 TYR cc_start: 0.2633 (m-80) cc_final: 0.1485 (m-80) REVERT: B 288 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4004 (tm-30) outliers start: 17 outliers final: 2 residues processed: 164 average time/residue: 0.4934 time to fit residues: 86.3316 Evaluate side-chains 113 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 108 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 204 ASN Chi-restraints excluded: chain B residue 141 ASP Chi-restraints excluded: chain B residue 236 PHE Chi-restraints excluded: chain B residue 288 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 49 optimal weight: 10.0000 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 6.9990 chunk 33 optimal weight: 6.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 131 ASN A 204 ASN B 72 HIS B 186 GLN B 322 GLN ** B 403 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142434 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.116606 restraints weight = 15123.825| |-----------------------------------------------------------------------------| r_work (start): 0.3539 rms_B_bonded: 1.90 r_work: 0.3410 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3264 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3264 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.101 10001 Z= 0.308 Angle : 0.937 28.647 14149 Z= 0.477 Chirality : 0.049 0.428 1628 Planarity : 0.007 0.055 1293 Dihedral : 17.519 88.065 2571 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 10.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.07 % Allowed : 17.39 % Favored : 77.54 % 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: -0.14 (0.28), residues: 797 helix: 0.91 (0.25), residues: 373 sheet: -0.57 (0.39), residues: 145 loop : -1.10 (0.35), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.002 ARG B 111 TYR 0.034 0.003 TYR A 402 PHE 0.041 0.005 PHE B 33 TRP 0.026 0.004 TRP B 201 HIS 0.008 0.002 HIS B 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.31 ( 9997) covalent geometry : angle 0.89013 / 0.47 (14143) hydrogen bonds : bond 0.07211 / 4.40 ( 462) hydrogen bonds : angle 4.68990 / 3.45 ( 1238) metal coordination : bond 0.01619 / 0.81 ( 4) metal coordination : angle 14.19525 / 5.66 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 149 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7537 (t0) cc_final: 0.7223 (t0) REVERT: A 79 ILE cc_start: 0.7151 (OUTLIER) cc_final: 0.6903 (pt) REVERT: A 130 GLU cc_start: 0.7663 (tm-30) cc_final: 0.7359 (tm-30) REVERT: A 318 CYS cc_start: 0.6130 (OUTLIER) cc_final: 0.5882 (m) REVERT: A 377 ASN cc_start: 0.7925 (t0) cc_final: 0.7655 (t0) REVERT: B 90 ASN cc_start: 0.7913 (m-40) cc_final: 0.7693 (m-40) REVERT: B 142 TYR cc_start: 0.3679 (m-80) cc_final: 0.3009 (m-80) REVERT: B 233 TYR cc_start: 0.4500 (OUTLIER) cc_final: 0.4103 (m-10) REVERT: B 242 ARG cc_start: 0.5490 (ptp90) cc_final: 0.5282 (ttp80) REVERT: B 312 MET cc_start: 0.5918 (mmm) cc_final: 0.4780 (mmm) outliers start: 35 outliers final: 8 residues processed: 170 average time/residue: 0.4530 time to fit residues: 82.6438 Evaluate side-chains 131 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 120 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 116 ILE Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 2.9990 chunk 28 optimal weight: 0.4980 chunk 17 optimal weight: 0.8980 chunk 10 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 60 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 302 ASN A 347 GLN B 87 ASN B 338 GLN B 403 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.142875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.116595 restraints weight = 15176.133| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.91 r_work: 0.3409 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3263 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3263 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6750 moved from start: 0.4843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 10001 Z= 0.148 Angle : 0.634 21.584 14149 Z= 0.328 Chirality : 0.039 0.159 1628 Planarity : 0.005 0.059 1293 Dihedral : 17.261 87.543 2562 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.48 % Allowed : 21.74 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 797 helix: 2.02 (0.25), residues: 372 sheet: 0.04 (0.40), residues: 155 loop : -1.21 (0.36), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 254 TYR 0.020 0.002 TYR A 396 PHE 0.014 0.002 PHE B 33 TRP 0.017 0.002 TRP B 43 HIS 0.010 0.002 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.15 ( 9997) covalent geometry : angle 0.60112 / 0.33 (14143) hydrogen bonds : bond 0.05520 / 3.36 ( 462) hydrogen bonds : angle 3.94316 / 2.93 ( 1238) metal coordination : bond 0.00938 / 0.46 ( 4) metal coordination : angle 9.75190 / 3.56 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 135 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7260 (OUTLIER) cc_final: 0.7034 (ttm) REVERT: A 130 GLU cc_start: 0.7804 (tm-30) cc_final: 0.7491 (tm-30) REVERT: A 169 VAL cc_start: 0.7662 (t) cc_final: 0.7197 (t) REVERT: A 177 MET cc_start: 0.8181 (tpt) cc_final: 0.6902 (tpt) REVERT: A 347 GLN cc_start: 0.8238 (tp40) cc_final: 0.8024 (tp-100) REVERT: A 360 VAL cc_start: 0.7735 (m) cc_final: 0.7477 (t) REVERT: A 377 ASN cc_start: 0.7895 (t0) cc_final: 0.7645 (t0) REVERT: B 90 ASN cc_start: 0.8145 (m-40) cc_final: 0.7939 (m-40) REVERT: B 126 ASP cc_start: 0.7011 (m-30) cc_final: 0.6280 (m-30) REVERT: B 137 MET cc_start: 0.6292 (mmm) cc_final: 0.6073 (mmm) REVERT: B 177 MET cc_start: 0.7509 (mmp) cc_final: 0.7284 (mmp) REVERT: B 233 TYR cc_start: 0.4910 (OUTLIER) cc_final: 0.4412 (m-10) REVERT: B 264 MET cc_start: 0.6028 (mmt) cc_final: 0.5641 (mmt) REVERT: B 323 MET cc_start: 0.3491 (OUTLIER) cc_final: 0.2673 (ptm) outliers start: 24 outliers final: 8 residues processed: 145 average time/residue: 0.5029 time to fit residues: 77.9242 Evaluate side-chains 135 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 124 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 0.9980 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 9.9990 chunk 70 optimal weight: 3.9990 chunk 87 optimal weight: 0.7980 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 0.0980 chunk 18 optimal weight: 0.0970 chunk 85 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 131 ASN A 139 HIS B 87 ASN B 303 HIS B 338 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3899 r_free = 0.3899 target = 0.143944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.117401 restraints weight = 15323.120| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 1.95 r_work: 0.3415 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3415 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 10001 Z= 0.135 Angle : 0.596 15.352 14149 Z= 0.313 Chirality : 0.040 0.167 1628 Planarity : 0.005 0.063 1293 Dihedral : 17.240 87.003 2562 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 4.06 % Allowed : 21.88 % Favored : 74.06 % 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: 1.13 (0.30), residues: 797 helix: 2.33 (0.26), residues: 372 sheet: 0.10 (0.40), residues: 153 loop : -1.12 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 254 TYR 0.034 0.002 TYR B 185 PHE 0.010 0.002 PHE A 336 TRP 0.011 0.001 TRP B 17 HIS 0.004 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.14 ( 9997) covalent geometry : angle 0.57809 / 0.31 (14143) hydrogen bonds : bond 0.04618 / 2.84 ( 462) hydrogen bonds : angle 3.72885 / 2.75 ( 1238) metal coordination : bond 0.00685 / 0.34 ( 4) metal coordination : angle 7.08535 / 2.68 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7304 (OUTLIER) cc_final: 0.7053 (ttm) REVERT: A 197 ARG cc_start: 0.8384 (tmt90) cc_final: 0.8081 (ppp80) REVERT: A 298 ARG cc_start: 0.7182 (mtp85) cc_final: 0.6952 (mtp85) REVERT: A 360 VAL cc_start: 0.7821 (m) cc_final: 0.7619 (t) REVERT: A 403 ASN cc_start: 0.7528 (t0) cc_final: 0.7213 (t0) REVERT: A 407 ASN cc_start: 0.6880 (m-40) cc_final: 0.6514 (m-40) REVERT: B 90 ASN cc_start: 0.8279 (m-40) cc_final: 0.8062 (m110) REVERT: B 126 ASP cc_start: 0.6889 (m-30) cc_final: 0.6222 (m-30) REVERT: B 145 SER cc_start: 0.6839 (m) cc_final: 0.6609 (p) REVERT: B 177 MET cc_start: 0.7302 (mmp) cc_final: 0.7077 (mmp) REVERT: B 233 TYR cc_start: 0.4867 (OUTLIER) cc_final: 0.4442 (m-10) REVERT: B 264 MET cc_start: 0.5823 (mmt) cc_final: 0.5456 (mmt) REVERT: B 323 MET cc_start: 0.3818 (OUTLIER) cc_final: 0.3450 (ptm) outliers start: 28 outliers final: 12 residues processed: 151 average time/residue: 0.5000 time to fit residues: 80.9035 Evaluate side-chains 151 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 136 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 116 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 17 optimal weight: 4.9990 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 35 optimal weight: 0.0020 chunk 58 optimal weight: 4.9990 chunk 12 optimal weight: 0.6980 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 0.8980 overall best weight: 1.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 278 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 = 0.3905 r_free = 0.3905 target = 0.145960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.118666 restraints weight = 15447.919| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.01 r_work: 0.3389 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.8570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.107 10001 Z= 0.230 Angle : 0.791 14.771 14149 Z= 0.416 Chirality : 0.046 0.209 1628 Planarity : 0.010 0.209 1293 Dihedral : 17.189 88.572 2562 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 5.22 % Allowed : 21.88 % Favored : 72.90 % 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: 0.32 (0.29), residues: 797 helix: 1.46 (0.25), residues: 372 sheet: -0.19 (0.43), residues: 147 loop : -1.24 (0.34), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.054 0.002 ARG B 179 TYR 0.056 0.003 TYR B 202 PHE 0.025 0.003 PHE B 209 TRP 0.023 0.003 TRP B 45 HIS 0.016 0.003 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00512 / 0.23 ( 9997) covalent geometry : angle 0.78086 / 0.42 (14143) hydrogen bonds : bond 0.05863 / 3.56 ( 462) hydrogen bonds : angle 4.06059 / 3.01 ( 1238) metal coordination : bond 0.01124 / 0.55 ( 4) metal coordination : angle 6.14158 / 2.78 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 190 time to evaluate : 0.187 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7533 (t0) cc_final: 0.7210 (t70) REVERT: A 120 LYS cc_start: 0.8345 (pttt) cc_final: 0.8070 (pttt) REVERT: A 121 ARG cc_start: 0.7577 (ptm-80) cc_final: 0.7260 (ptm-80) REVERT: A 169 VAL cc_start: 0.8858 (t) cc_final: 0.8645 (t) REVERT: A 210 GLU cc_start: 0.8299 (mp0) cc_final: 0.8060 (mp0) REVERT: A 234 MET cc_start: 0.8002 (OUTLIER) cc_final: 0.7775 (mtt) REVERT: A 288 GLU cc_start: 0.7564 (tm-30) cc_final: 0.7259 (tm-30) REVERT: A 290 LEU cc_start: 0.8343 (tp) cc_final: 0.8010 (tm) REVERT: B 107 LYS cc_start: 0.8623 (OUTLIER) cc_final: 0.8366 (mttp) REVERT: B 145 SER cc_start: 0.7198 (m) cc_final: 0.6933 (p) REVERT: B 264 MET cc_start: 0.6327 (mmt) cc_final: 0.5899 (mmt) REVERT: B 312 MET cc_start: 0.6976 (mmm) cc_final: 0.6177 (mmt) REVERT: B 323 MET cc_start: 0.4389 (OUTLIER) cc_final: 0.4169 (ptm) REVERT: B 339 ASN cc_start: 0.7816 (p0) cc_final: 0.7583 (p0) REVERT: B 401 ASP cc_start: 0.5571 (m-30) cc_final: 0.5357 (m-30) outliers start: 36 outliers final: 13 residues processed: 205 average time/residue: 0.5514 time to fit residues: 120.4335 Evaluate side-chains 178 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 162 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 6.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 8 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 30 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 39 optimal weight: 10.0000 chunk 35 optimal weight: 0.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 106 GLN A 155 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3883 r_free = 0.3883 target = 0.142502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.114495 restraints weight = 15244.666| |-----------------------------------------------------------------------------| r_work (start): 0.3498 rms_B_bonded: 2.00 r_work: 0.3366 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.9118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10001 Z= 0.144 Angle : 0.616 10.432 14149 Z= 0.328 Chirality : 0.041 0.172 1628 Planarity : 0.005 0.062 1293 Dihedral : 17.081 85.090 2562 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.77 % Allowed : 27.54 % Favored : 68.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.89 (0.29), residues: 797 helix: 2.09 (0.25), residues: 377 sheet: -0.03 (0.39), residues: 159 loop : -1.27 (0.36), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 25 TYR 0.022 0.002 TYR B 207 PHE 0.012 0.002 PHE B 33 TRP 0.016 0.002 TRP B 201 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.14 ( 9997) covalent geometry : angle 0.60619 / 0.33 (14143) hydrogen bonds : bond 0.04530 / 2.78 ( 462) hydrogen bonds : angle 3.70254 / 2.75 ( 1238) metal coordination : bond 0.00636 / 0.30 ( 4) metal coordination : angle 5.40448 / 2.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 179 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7607 (t0) cc_final: 0.7317 (t70) REVERT: A 86 LEU cc_start: 0.8683 (mm) cc_final: 0.8310 (mp) REVERT: A 120 LYS cc_start: 0.8311 (pttt) cc_final: 0.8074 (pttt) REVERT: A 150 SER cc_start: 0.8524 (t) cc_final: 0.8306 (p) REVERT: A 234 MET cc_start: 0.8154 (OUTLIER) cc_final: 0.7761 (mtt) REVERT: A 261 ARG cc_start: 0.7647 (OUTLIER) cc_final: 0.7130 (ttp-110) REVERT: A 264 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6556 (mtt) REVERT: A 288 GLU cc_start: 0.7513 (tm-30) cc_final: 0.7197 (tm-30) REVERT: A 293 LYS cc_start: 0.8153 (OUTLIER) cc_final: 0.7836 (tttm) REVERT: A 348 LYS cc_start: 0.8526 (OUTLIER) cc_final: 0.8243 (mptm) REVERT: B 1 MET cc_start: 0.5679 (mmm) cc_final: 0.5344 (mmt) REVERT: B 107 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8231 (mttm) REVERT: B 177 MET cc_start: 0.7434 (mmp) cc_final: 0.7053 (mmp) REVERT: B 202 TYR cc_start: 0.7852 (m-80) cc_final: 0.7472 (m-80) REVERT: B 264 MET cc_start: 0.6481 (mmt) cc_final: 0.6269 (mmt) REVERT: B 312 MET cc_start: 0.6991 (mmm) cc_final: 0.6349 (mmt) REVERT: B 339 ASN cc_start: 0.7991 (p0) cc_final: 0.7763 (p0) REVERT: B 401 ASP cc_start: 0.5625 (m-30) cc_final: 0.5422 (m-30) outliers start: 26 outliers final: 8 residues processed: 194 average time/residue: 0.5760 time to fit residues: 118.1918 Evaluate side-chains 183 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 169 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 146 LEU Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 264 MET Chi-restraints excluded: chain A residue 293 LYS Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 1.9990 chunk 49 optimal weight: 10.0000 chunk 8 optimal weight: 7.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 30.0000 chunk 15 optimal weight: 0.9980 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 155 GLN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN B 194 HIS B 252 ASN B 303 HIS B 322 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.136021 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.107560 restraints weight = 15050.965| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 2.02 r_work: 0.3203 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3050 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 1.1347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10001 Z= 0.285 Angle : 0.865 12.250 14149 Z= 0.450 Chirality : 0.050 0.217 1628 Planarity : 0.008 0.118 1293 Dihedral : 17.098 80.079 2561 Min Nonbonded Distance : 2.013 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 6.67 % Allowed : 26.52 % Favored : 66.81 % 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: 0.09 (0.28), residues: 797 helix: 1.30 (0.25), residues: 375 sheet: -0.36 (0.39), residues: 152 loop : -1.43 (0.34), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.002 ARG A 161 TYR 0.027 0.003 TYR B 308 PHE 0.015 0.002 PHE B 33 TRP 0.022 0.003 TRP B 201 HIS 0.020 0.003 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00643 / 0.29 ( 9997) covalent geometry : angle 0.85094 / 0.45 (14143) hydrogen bonds : bond 0.06073 / 3.75 ( 462) hydrogen bonds : angle 4.16767 / 3.07 ( 1238) metal coordination : bond 0.00719 / 0.35 ( 4) metal coordination : angle 7.59099 / 3.33 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 202 time to evaluate : 0.245 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8226 (t0) cc_final: 0.7828 (t70) REVERT: A 86 LEU cc_start: 0.8736 (mm) cc_final: 0.8360 (mp) REVERT: A 120 LYS cc_start: 0.8386 (pttt) cc_final: 0.8121 (pttt) REVERT: A 121 ARG cc_start: 0.8110 (ptm-80) cc_final: 0.7812 (ptm-80) REVERT: A 137 MET cc_start: 0.8342 (mmm) cc_final: 0.8062 (mmm) REVERT: A 197 ARG cc_start: 0.8937 (tmt90) cc_final: 0.8669 (ttp-170) REVERT: A 210 GLU cc_start: 0.8383 (mp0) cc_final: 0.8071 (mp0) REVERT: A 230 VAL cc_start: 0.8426 (t) cc_final: 0.8216 (m) REVERT: A 261 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7844 (ttp80) REVERT: A 288 GLU cc_start: 0.7919 (tm-30) cc_final: 0.7606 (tm-30) REVERT: A 312 MET cc_start: 0.8753 (mmp) cc_final: 0.8523 (mmp) REVERT: A 348 LYS cc_start: 0.8914 (OUTLIER) cc_final: 0.8678 (mptm) REVERT: A 403 ASN cc_start: 0.8499 (t0) cc_final: 0.8259 (t0) REVERT: B 118 SER cc_start: 0.8729 (OUTLIER) cc_final: 0.8525 (p) REVERT: B 120 LYS cc_start: 0.8825 (mmmm) cc_final: 0.8573 (mmtm) REVERT: B 126 ASP cc_start: 0.8091 (OUTLIER) cc_final: 0.7824 (m-30) REVERT: B 134 VAL cc_start: 0.7928 (OUTLIER) cc_final: 0.7707 (t) REVERT: B 150 SER cc_start: 0.8011 (t) cc_final: 0.7732 (p) REVERT: B 157 MET cc_start: 0.7951 (mmp) cc_final: 0.7422 (mpp) REVERT: B 167 ILE cc_start: 0.6644 (OUTLIER) cc_final: 0.6402 (tp) REVERT: B 233 TYR cc_start: 0.7719 (OUTLIER) cc_final: 0.7230 (m-80) REVERT: B 264 MET cc_start: 0.7536 (mmt) cc_final: 0.7290 (mmt) REVERT: B 312 MET cc_start: 0.7572 (mmm) cc_final: 0.6948 (mmt) REVERT: B 323 MET cc_start: 0.6533 (OUTLIER) cc_final: 0.6207 (ptm) REVERT: B 346 GLN cc_start: 0.7898 (tt0) cc_final: 0.7365 (mp10) REVERT: B 401 ASP cc_start: 0.6880 (m-30) cc_final: 0.6621 (m-30) outliers start: 46 outliers final: 11 residues processed: 225 average time/residue: 0.5637 time to fit residues: 134.4444 Evaluate side-chains 206 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 187 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 126 ASP Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 84 optimal weight: 5.9990 chunk 38 optimal weight: 0.0470 chunk 42 optimal weight: 50.0000 chunk 79 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 10.0000 chunk 17 optimal weight: 1.9990 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 overall best weight: 1.2682 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 155 GLN A 186 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN B 135 ASN B 296 ASN B 303 HIS B 322 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.135002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3376 r_free = 0.3376 target = 0.106287 restraints weight = 15028.893| |-----------------------------------------------------------------------------| r_work (start): 0.3379 rms_B_bonded: 1.98 r_work: 0.3238 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3084 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 1.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 10001 Z= 0.151 Angle : 0.680 10.836 14149 Z= 0.354 Chirality : 0.042 0.258 1628 Planarity : 0.005 0.052 1293 Dihedral : 17.021 80.582 2561 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.48 % Allowed : 31.74 % Favored : 64.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.29), residues: 797 helix: 1.93 (0.26), residues: 372 sheet: -0.04 (0.40), residues: 159 loop : -1.38 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 254 TYR 0.036 0.002 TYR B 402 PHE 0.009 0.001 PHE B 33 TRP 0.016 0.002 TRP B 201 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 ( 9997) covalent geometry : angle 0.66845 / 0.35 (14143) hydrogen bonds : bond 0.04744 / 2.93 ( 462) hydrogen bonds : angle 3.85129 / 2.83 ( 1238) metal coordination : bond 0.00699 / 0.33 ( 4) metal coordination : angle 6.07038 / 2.57 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 188 time to evaluate : 0.277 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8294 (t0) cc_final: 0.8002 (t0) REVERT: A 120 LYS cc_start: 0.8379 (pttt) cc_final: 0.8112 (pttt) REVERT: A 121 ARG cc_start: 0.8009 (ptm-80) cc_final: 0.7717 (ptm-80) REVERT: A 137 MET cc_start: 0.8326 (mmm) cc_final: 0.8041 (mmm) REVERT: A 178 ASP cc_start: 0.8727 (m-30) cc_final: 0.8357 (m-30) REVERT: A 197 ARG cc_start: 0.8923 (tmt90) cc_final: 0.8658 (ttp-170) REVERT: A 210 GLU cc_start: 0.8310 (mp0) cc_final: 0.8053 (mp0) REVERT: A 261 ARG cc_start: 0.8158 (OUTLIER) cc_final: 0.7907 (ttp80) REVERT: A 288 GLU cc_start: 0.7887 (tm-30) cc_final: 0.7538 (tm-30) REVERT: A 342 TYR cc_start: 0.8681 (m-80) cc_final: 0.8373 (m-80) REVERT: A 347 GLN cc_start: 0.8550 (tp40) cc_final: 0.8310 (tp40) REVERT: A 355 GLU cc_start: 0.8343 (tp30) cc_final: 0.7917 (tt0) REVERT: A 403 ASN cc_start: 0.8433 (t0) cc_final: 0.8192 (t0) REVERT: B 9 ILE cc_start: 0.7827 (pt) cc_final: 0.7415 (mt) REVERT: B 167 ILE cc_start: 0.6482 (OUTLIER) cc_final: 0.6208 (tp) REVERT: B 200 LYS cc_start: 0.8196 (mttt) cc_final: 0.7715 (mttt) REVERT: B 264 MET cc_start: 0.7569 (mmt) cc_final: 0.7345 (mmt) REVERT: B 323 MET cc_start: 0.6512 (ptp) cc_final: 0.6209 (ptm) REVERT: B 346 GLN cc_start: 0.7761 (tt0) cc_final: 0.7343 (mp10) outliers start: 24 outliers final: 10 residues processed: 199 average time/residue: 0.5689 time to fit residues: 119.9232 Evaluate side-chains 190 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 178 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 10.0000 chunk 87 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 8.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 chunk 53 optimal weight: 8.9990 chunk 82 optimal weight: 2.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 186 GLN A 237 GLN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN ** A 407 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 135 ASN B 252 ASN B 303 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.133830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105266 restraints weight = 15043.023| |-----------------------------------------------------------------------------| r_work (start): 0.3311 rms_B_bonded: 2.01 r_work: 0.3170 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3012 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 1.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.069 10001 Z= 0.262 Angle : 0.739 10.484 14149 Z= 0.384 Chirality : 0.047 0.329 1628 Planarity : 0.006 0.078 1293 Dihedral : 16.980 88.568 2561 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.75 % Allowed : 32.61 % Favored : 64.64 % 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: 0.58 (0.29), residues: 797 helix: 1.72 (0.25), residues: 377 sheet: 0.07 (0.40), residues: 159 loop : -1.39 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 6 TYR 0.022 0.002 TYR B 185 PHE 0.012 0.002 PHE A 336 TRP 0.014 0.002 TRP B 43 HIS 0.013 0.002 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00589 / 0.26 ( 9997) covalent geometry : angle 0.72749 / 0.38 (14143) hydrogen bonds : bond 0.05227 / 3.20 ( 462) hydrogen bonds : angle 3.88440 / 2.86 ( 1238) metal coordination : bond 0.00970 / 0.47 ( 4) metal coordination : angle 6.34512 / 2.83 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 196 time to evaluate : 0.196 Fit side-chains revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8298 (t0) cc_final: 0.8010 (t0) REVERT: A 121 ARG cc_start: 0.8107 (ptm-80) cc_final: 0.7817 (ptm-80) REVERT: A 137 MET cc_start: 0.8485 (mmm) cc_final: 0.8234 (mmm) REVERT: A 197 ARG cc_start: 0.8956 (tmt90) cc_final: 0.8695 (ttp-170) REVERT: A 210 GLU cc_start: 0.8346 (mp0) cc_final: 0.8092 (mp0) REVERT: A 261 ARG cc_start: 0.8219 (OUTLIER) cc_final: 0.8014 (ttp80) REVERT: A 291 ARG cc_start: 0.8211 (ttp-170) cc_final: 0.7887 (ttm170) REVERT: A 355 GLU cc_start: 0.8420 (tp30) cc_final: 0.8128 (tt0) REVERT: A 403 ASN cc_start: 0.8466 (t0) cc_final: 0.8257 (t0) REVERT: A 420 SER cc_start: 0.7844 (m) cc_final: 0.7598 (p) REVERT: B 9 ILE cc_start: 0.8245 (pt) cc_final: 0.7757 (mt) REVERT: B 39 THR cc_start: 0.9000 (t) cc_final: 0.8636 (m) REVERT: B 46 MET cc_start: 0.9014 (tpp) cc_final: 0.8700 (mmt) REVERT: B 69 THR cc_start: 0.9219 (OUTLIER) cc_final: 0.8963 (p) REVERT: B 118 SER cc_start: 0.8551 (m) cc_final: 0.8245 (p) REVERT: B 150 SER cc_start: 0.8111 (t) cc_final: 0.7712 (p) REVERT: B 157 MET cc_start: 0.8244 (mmp) cc_final: 0.7659 (mpp) REVERT: B 167 ILE cc_start: 0.7024 (OUTLIER) cc_final: 0.6769 (tp) REVERT: B 200 LYS cc_start: 0.8126 (mttt) cc_final: 0.7866 (mttt) REVERT: B 249 GLU cc_start: 0.7374 (tp30) cc_final: 0.7166 (tp30) REVERT: B 315 LYS cc_start: 0.8528 (ttpt) cc_final: 0.8086 (tttt) REVERT: B 346 GLN cc_start: 0.7904 (tt0) cc_final: 0.7335 (mp10) outliers start: 19 outliers final: 8 residues processed: 203 average time/residue: 0.5749 time to fit residues: 123.4617 Evaluate side-chains 202 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 339 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 1.9990 chunk 78 optimal weight: 4.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 186 GLN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 407 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.134830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.106149 restraints weight = 14927.292| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.97 r_work: 0.3189 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work: 0.3033 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3033 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 1.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10001 Z= 0.183 Angle : 0.688 10.387 14149 Z= 0.359 Chirality : 0.043 0.175 1628 Planarity : 0.006 0.073 1293 Dihedral : 16.968 86.621 2561 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 2.61 % Allowed : 34.35 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.29), residues: 797 helix: 1.81 (0.26), residues: 372 sheet: 0.17 (0.40), residues: 159 loop : -1.34 (0.34), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 6 TYR 0.027 0.002 TYR B 243 PHE 0.009 0.001 PHE B 33 TRP 0.013 0.002 TRP B 43 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00402 / 0.18 ( 9997) covalent geometry : angle 0.67750 / 0.36 (14143) hydrogen bonds : bond 0.04773 / 2.95 ( 462) hydrogen bonds : angle 3.83309 / 2.84 ( 1238) metal coordination : bond 0.00820 / 0.40 ( 4) metal coordination : angle 5.80765 / 2.49 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 194 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8302 (t0) cc_final: 0.8006 (t0) REVERT: A 50 SER cc_start: 0.8329 (m) cc_final: 0.8013 (t) REVERT: A 120 LYS cc_start: 0.8302 (pttt) cc_final: 0.8079 (pttt) REVERT: A 121 ARG cc_start: 0.8080 (ptm-80) cc_final: 0.7777 (ptm-80) REVERT: A 137 MET cc_start: 0.8492 (mmm) cc_final: 0.8210 (mmm) REVERT: A 178 ASP cc_start: 0.8684 (m-30) cc_final: 0.8369 (m-30) REVERT: A 197 ARG cc_start: 0.8956 (tmt90) cc_final: 0.8692 (ttp-170) REVERT: A 210 GLU cc_start: 0.8329 (mp0) cc_final: 0.8064 (mp0) REVERT: A 261 ARG cc_start: 0.8291 (OUTLIER) cc_final: 0.7901 (ttp80) REVERT: A 291 ARG cc_start: 0.8195 (ttp-170) cc_final: 0.7812 (ttm170) REVERT: A 355 GLU cc_start: 0.8434 (tp30) cc_final: 0.8203 (tt0) REVERT: A 403 ASN cc_start: 0.8423 (t0) cc_final: 0.8200 (t0) REVERT: A 420 SER cc_start: 0.7905 (m) cc_final: 0.7617 (p) REVERT: B 9 ILE cc_start: 0.8369 (pt) cc_final: 0.7952 (mt) REVERT: B 22 THR cc_start: 0.8969 (m) cc_final: 0.8507 (p) REVERT: B 39 THR cc_start: 0.8961 (OUTLIER) cc_final: 0.8617 (m) REVERT: B 46 MET cc_start: 0.8947 (tpp) cc_final: 0.8644 (mmt) REVERT: B 69 THR cc_start: 0.9210 (OUTLIER) cc_final: 0.8995 (p) REVERT: B 118 SER cc_start: 0.8442 (m) cc_final: 0.8072 (p) REVERT: B 120 LYS cc_start: 0.8854 (mmmm) cc_final: 0.8421 (tppp) REVERT: B 150 SER cc_start: 0.8172 (t) cc_final: 0.7737 (p) REVERT: B 157 MET cc_start: 0.8274 (mmp) cc_final: 0.7804 (mpp) REVERT: B 167 ILE cc_start: 0.7146 (OUTLIER) cc_final: 0.6880 (tp) REVERT: B 233 TYR cc_start: 0.8077 (OUTLIER) cc_final: 0.7668 (m-80) REVERT: B 243 TYR cc_start: 0.7845 (m-80) cc_final: 0.7499 (m-10) REVERT: B 249 GLU cc_start: 0.7407 (tp30) cc_final: 0.7161 (tp30) REVERT: B 315 LYS cc_start: 0.8462 (ttpt) cc_final: 0.8161 (tttt) REVERT: B 346 GLN cc_start: 0.7829 (tt0) cc_final: 0.7305 (mp10) REVERT: B 413 ILE cc_start: 0.6995 (tp) cc_final: 0.6698 (mm) outliers start: 18 outliers final: 8 residues processed: 204 average time/residue: 0.5533 time to fit residues: 119.8075 Evaluate side-chains 207 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 194 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 54 ASP Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 320 THR Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 167 ILE Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 6.9990 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 37 optimal weight: 5.9990 chunk 55 optimal weight: 1.9990 chunk 57 optimal weight: 0.7980 chunk 73 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 0.0770 overall best weight: 1.3142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 186 GLN ** A 237 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 377 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.133038 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.104501 restraints weight = 14956.289| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 1.95 r_work: 0.3215 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3060 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3060 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8329 moved from start: 1.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 10001 Z= 0.148 Angle : 0.652 10.092 14149 Z= 0.342 Chirality : 0.041 0.163 1628 Planarity : 0.006 0.071 1293 Dihedral : 16.929 88.857 2561 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.88 % Allowed : 35.36 % Favored : 62.75 % 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: 0.93 (0.29), residues: 797 helix: 2.10 (0.26), residues: 373 sheet: 0.14 (0.40), residues: 156 loop : -1.25 (0.34), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 6 TYR 0.023 0.002 TYR B 243 PHE 0.008 0.001 PHE A 236 TRP 0.011 0.001 TRP B 201 HIS 0.006 0.001 HIS A 278 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 ( 9997) covalent geometry : angle 0.64294 / 0.34 (14143) hydrogen bonds : bond 0.04492 / 2.77 ( 462) hydrogen bonds : angle 3.78415 / 2.80 ( 1238) metal coordination : bond 0.00666 / 0.32 ( 4) metal coordination : angle 5.37413 / 2.31 ( 6) =============================================================================== Job complete usr+sys time: 3104.61 seconds wall clock time: 53 minutes 33.89 seconds (3213.89 seconds total)