Starting phenix.real_space_refine on Fri Oct 10 23:10:56 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8j3r_35965/10_2025/8j3r_35965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j3r_35965/10_2025/8j3r_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_35965/10_2025/8j3r_35965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j3r_35965/10_2025/8j3r_35965.map" model { file = "/net/cci-nas-00/data/ceres_data/8j3r_35965/10_2025/8j3r_35965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j3r_35965/10_2025/8j3r_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/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: 2.21, per 1000 atoms: 0.23 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: 1.00 Conformation dependent library (CDL) restraints added in 245.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 1.29 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: 1.99 Time building geometry restraints manager: 1.26 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=" CA ILE A 163 " pdb=" CB ILE A 163 " ideal model delta sigma weight residual 1.530 1.542 -0.012 1.11e-02 8.12e+03 1.19e+00 bond pdb=" CA ILE A 410 " pdb=" CB ILE A 410 " ideal model delta sigma weight residual 1.537 1.525 0.013 1.29e-02 6.01e+03 9.67e-01 bond pdb=" CB PRO B 365 " pdb=" CG PRO B 365 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.95e-01 bond pdb=" C1' DT E -7 " pdb=" N1 DT E -7 " ideal model delta sigma weight residual 1.490 1.518 -0.028 3.00e-02 1.11e+03 8.74e-01 bond pdb=" CB VAL A 10 " pdb=" CG2 VAL A 10 " ideal model delta sigma weight residual 1.521 1.496 0.025 3.30e-02 9.18e+02 5.59e-01 ... (remaining 9992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13872 1.53 - 3.06: 248 3.06 - 4.58: 17 4.58 - 6.11: 4 6.11 - 7.64: 2 Bond angle restraints: 14143 Sorted by residual: angle pdb=" C ARG A 197 " pdb=" N LYS A 198 " pdb=" CA LYS A 198 " ideal model delta sigma weight residual 121.54 127.03 -5.49 1.91e+00 2.74e-01 8.27e+00 angle pdb=" C1' U C -45 " pdb=" N1 U C -45 " pdb=" C2 U C -45 " ideal model delta sigma weight residual 117.70 125.34 -7.64 3.00e+00 1.11e-01 6.48e+00 angle pdb=" C2' U C 6 " pdb=" C1' U C 6 " pdb=" N1 U C 6 " ideal model delta sigma weight residual 112.00 115.56 -3.56 1.50e+00 4.44e-01 5.64e+00 angle pdb=" N GLN A 338 " pdb=" CA GLN A 338 " pdb=" C GLN A 338 " ideal model delta sigma weight residual 112.93 110.33 2.60 1.12e+00 7.97e-01 5.37e+00 angle pdb=" N ASN A 158 " pdb=" CA ASN A 158 " pdb=" CB ASN A 158 " ideal model delta sigma weight residual 113.65 110.33 3.32 1.47e+00 4.63e-01 5.11e+00 ... (remaining 14138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 5076 17.90 - 35.80: 534 35.80 - 53.71: 264 53.71 - 71.61: 171 71.61 - 89.51: 33 Dihedral angle restraints: 6078 sinusoidal: 3711 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 6075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1234 0.035 - 0.069: 277 0.069 - 0.104: 87 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: 0.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 12.140 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:9.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.600 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4967 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= 0.131 Angle : 0.765 56.945 14149 Z= 0.307 Chirality : 0.036 0.173 1628 Planarity : 0.003 0.034 1293 Dihedral : 20.205 89.510 4562 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 aren 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 covalent geometry : bond 0.00262 ( 9997) covalent geometry : angle 0.50010 (14143) hydrogen bonds : bond 0.22544 ( 462) hydrogen bonds : angle 6.19927 ( 1238) metal coordination : bond 0.03778 ( 4) metal coordination : angle 28.09070 ( 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 : 0.322 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: 0.2634 (m-80) cc_final: 0.1486 (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: 0.6235 time to fit residues: 108.9366 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 : 0.297 ------------------------------------------------------------------------------- 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: 8.9990 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... Flipped N/Q/H residues before XYZ refinement: A 322 GLN B 29 GLN B 77 HIS B 322 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 = 0.4009 r_free = 0.4009 target = 0.153417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.127458 restraints weight = 15766.323| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 2.02 r_work: 0.3538 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.8341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.114 10001 Z= 0.273 Angle : 0.847 11.090 14149 Z= 0.453 Chirality : 0.047 0.206 1628 Planarity : 0.007 0.075 1293 Dihedral : 22.005 85.448 2941 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 4.35 % Allowed : 15.94 % Favored : 79.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.41 (0.27), residues: 797 helix: 0.75 (0.25), residues: 377 sheet: -0.53 (0.40), residues: 128 loop : -1.43 (0.33), residues: 292 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 111 TYR 0.022 0.003 TYR B 202 PHE 0.019 0.004 PHE A 336 TRP 0.033 0.004 TRP B 43 HIS 0.013 0.003 HIS A 139 Details of bonding type rmsd covalent geometry : bond 0.00575 ( 9997) covalent geometry : angle 0.84267 (14143) hydrogen bonds : bond 0.05952 ( 462) hydrogen bonds : angle 4.77006 ( 1238) metal coordination : bond 0.00888 ( 4) metal coordination : angle 4.31746 ( 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 249 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7492 (t0) cc_final: 0.7289 (t70) REVERT: A 28 GLN cc_start: 0.8175 (mt0) cc_final: 0.7759 (mt0) REVERT: A 120 LYS cc_start: 0.8147 (pttt) cc_final: 0.7901 (pttt) REVERT: A 157 MET cc_start: 0.7968 (mtm) cc_final: 0.7768 (mtm) REVERT: A 233 TYR cc_start: 0.8067 (OUTLIER) cc_final: 0.7749 (t80) REVERT: A 294 ILE cc_start: 0.8852 (mt) cc_final: 0.8509 (mp) REVERT: A 323 MET cc_start: 0.8637 (OUTLIER) cc_final: 0.8374 (mtm) REVERT: A 332 ILE cc_start: 0.6968 (OUTLIER) cc_final: 0.6721 (pp) REVERT: A 342 TYR cc_start: 0.7911 (m-80) cc_final: 0.7684 (m-80) REVERT: A 351 TYR cc_start: 0.7327 (OUTLIER) cc_final: 0.6739 (t80) REVERT: B 27 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7626 (mt) REVERT: B 145 SER cc_start: 0.7352 (m) cc_final: 0.7132 (p) REVERT: B 196 ASP cc_start: 0.5490 (OUTLIER) cc_final: 0.5129 (p0) REVERT: B 312 MET cc_start: 0.7108 (mmm) cc_final: 0.6336 (mmt) REVERT: B 323 MET cc_start: 0.4256 (ptm) cc_final: 0.3747 (ptm) outliers start: 30 outliers final: 4 residues processed: 233 average time/residue: 0.6827 time to fit residues: 168.2959 Evaluate side-chains 182 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 172 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 233 TYR Chi-restraints excluded: chain A residue 323 MET Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 108 GLU Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 245 LEU Chi-restraints excluded: chain B residue 246 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: 4.9990 chunk 89 optimal weight: 9.9990 chunk 15 optimal weight: 0.7980 chunk 84 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 60 optimal weight: 5.9990 chunk 44 optimal weight: 8.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 155 GLN A 186 GLN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 87 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.139065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.110322 restraints weight = 14910.200| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.99 r_work: 0.3294 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 1.0368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 10001 Z= 0.187 Angle : 0.640 11.420 14149 Z= 0.342 Chirality : 0.041 0.267 1628 Planarity : 0.005 0.050 1293 Dihedral : 21.790 89.205 2932 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 5.51 % Allowed : 22.17 % Favored : 72.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.74 (0.29), residues: 797 helix: 1.99 (0.25), residues: 371 sheet: -0.13 (0.39), residues: 153 loop : -1.26 (0.35), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 121 TYR 0.020 0.002 TYR B 185 PHE 0.010 0.002 PHE A 253 TRP 0.013 0.002 TRP A 43 HIS 0.011 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00410 ( 9997) covalent geometry : angle 0.62901 (14143) hydrogen bonds : bond 0.05446 ( 462) hydrogen bonds : angle 4.08864 ( 1238) metal coordination : bond 0.00785 ( 4) metal coordination : angle 5.63691 ( 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 235 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 197 time to evaluate : 0.302 Fit side-chains revert: symmetry clash REVERT: A 1 MET cc_start: 0.6408 (pmm) cc_final: 0.6136 (mpp) REVERT: A 14 ASP cc_start: 0.7710 (t0) cc_final: 0.7482 (t70) REVERT: A 121 ARG cc_start: 0.7817 (ptm-80) cc_final: 0.7589 (ptm-80) REVERT: A 137 MET cc_start: 0.7664 (mmm) cc_final: 0.7162 (mmm) REVERT: A 197 ARG cc_start: 0.8684 (tmt90) cc_final: 0.8412 (ttp-170) REVERT: A 220 LYS cc_start: 0.8065 (OUTLIER) cc_final: 0.6851 (mmtp) REVERT: A 261 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7630 (ttp80) REVERT: A 262 ILE cc_start: 0.8250 (mt) cc_final: 0.7852 (mm) REVERT: A 351 TYR cc_start: 0.7306 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 377 ASN cc_start: 0.8392 (t0) cc_final: 0.8173 (t0) REVERT: A 415 LYS cc_start: 0.7797 (mmmm) cc_final: 0.7563 (mmmm) REVERT: B 118 SER cc_start: 0.8455 (t) cc_final: 0.8208 (p) REVERT: B 120 LYS cc_start: 0.8880 (mmmm) cc_final: 0.8666 (mmtp) REVERT: B 121 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7912 (mtm110) REVERT: B 193 ILE cc_start: 0.8416 (OUTLIER) cc_final: 0.8181 (pt) REVERT: B 312 MET cc_start: 0.7286 (mmm) cc_final: 0.6728 (mmt) outliers start: 38 outliers final: 9 residues processed: 221 average time/residue: 0.6877 time to fit residues: 160.7860 Evaluate side-chains 196 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 182 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 220 LYS Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 121 ARG Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 193 ILE Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 6.9990 chunk 46 optimal weight: 10.0000 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 87 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 88 optimal weight: 0.0970 chunk 18 optimal weight: 0.9990 chunk 85 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 GLN A 93 GLN A 155 GLN A 186 GLN A 347 GLN B 252 ASN B 256 GLN B 289 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3823 r_free = 0.3823 target = 0.137675 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.108572 restraints weight = 14964.491| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 2.00 r_work: 0.3276 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3122 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3122 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 1.1281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10001 Z= 0.150 Angle : 0.567 7.925 14149 Z= 0.302 Chirality : 0.039 0.158 1628 Planarity : 0.005 0.059 1293 Dihedral : 21.589 85.646 2932 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 4.93 % Allowed : 25.94 % Favored : 69.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.13 (0.29), residues: 797 helix: 2.33 (0.26), residues: 371 sheet: -0.02 (0.38), residues: 159 loop : -1.06 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 111 TYR 0.019 0.001 TYR B 185 PHE 0.008 0.001 PHE A 253 TRP 0.014 0.002 TRP B 45 HIS 0.008 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 9997) covalent geometry : angle 0.56035 (14143) hydrogen bonds : bond 0.04288 ( 462) hydrogen bonds : angle 3.72301 ( 1238) metal coordination : bond 0.00707 ( 4) metal coordination : angle 4.09490 ( 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 228 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 194 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8195 (t0) cc_final: 0.7920 (t0) REVERT: A 120 LYS cc_start: 0.8359 (pttt) cc_final: 0.8113 (pttt) REVERT: A 137 MET cc_start: 0.8213 (mmm) cc_final: 0.7948 (mmm) REVERT: A 178 ASP cc_start: 0.8737 (m-30) cc_final: 0.8398 (m-30) REVERT: A 182 SER cc_start: 0.8904 (OUTLIER) cc_final: 0.8669 (p) REVERT: A 197 ARG cc_start: 0.8896 (tmt90) cc_final: 0.8651 (ttp-170) REVERT: A 261 ARG cc_start: 0.8342 (OUTLIER) cc_final: 0.7889 (ttp80) REVERT: A 262 ILE cc_start: 0.8547 (mt) cc_final: 0.8281 (mm) REVERT: A 291 ARG cc_start: 0.8045 (ttp-110) cc_final: 0.7583 (ttm170) REVERT: A 299 ASP cc_start: 0.8704 (t0) cc_final: 0.8433 (t0) REVERT: A 351 TYR cc_start: 0.7610 (OUTLIER) cc_final: 0.7160 (t80) REVERT: A 355 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7656 (tt0) REVERT: A 403 ASN cc_start: 0.8324 (t0) cc_final: 0.8008 (t0) REVERT: A 415 LYS cc_start: 0.8006 (mmmm) cc_final: 0.7709 (mmmm) REVERT: B 111 ARG cc_start: 0.8497 (mtm110) cc_final: 0.8271 (mtm110) REVERT: B 118 SER cc_start: 0.8591 (t) cc_final: 0.8308 (p) REVERT: B 120 LYS cc_start: 0.8863 (mmmm) cc_final: 0.8442 (tppp) REVERT: B 129 LYS cc_start: 0.7957 (ptmt) cc_final: 0.7557 (pttt) REVERT: B 134 VAL cc_start: 0.7704 (m) cc_final: 0.7499 (t) REVERT: B 135 ASN cc_start: 0.8566 (m110) cc_final: 0.8357 (m110) REVERT: B 157 MET cc_start: 0.8428 (mpp) cc_final: 0.7777 (mpp) REVERT: B 346 GLN cc_start: 0.7861 (tt0) cc_final: 0.7071 (mm110) REVERT: B 360 VAL cc_start: 0.8309 (m) cc_final: 0.8075 (t) outliers start: 34 outliers final: 9 residues processed: 211 average time/residue: 0.6591 time to fit residues: 147.4205 Evaluate side-chains 188 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 175 time to evaluate : 0.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 355 GLU Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 75 optimal weight: 7.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 chunk 21 optimal weight: 0.4980 chunk 54 optimal weight: 6.9990 chunk 56 optimal weight: 6.9990 chunk 80 optimal weight: 4.9990 overall best weight: 4.0988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 93 GLN A 131 ASN A 155 GLN A 186 GLN A 204 ASN ** A 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 346 GLN A 377 ASN B 72 HIS B 252 ASN B 256 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.127537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.098627 restraints weight = 14929.660| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.99 r_work: 0.3110 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.2948 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 1.3236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.051 10001 Z= 0.302 Angle : 0.722 12.031 14149 Z= 0.379 Chirality : 0.046 0.180 1628 Planarity : 0.006 0.062 1293 Dihedral : 21.683 88.761 2931 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.81 % Allowed : 25.07 % Favored : 68.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.43 (0.29), residues: 797 helix: 1.62 (0.26), residues: 381 sheet: -0.31 (0.39), residues: 159 loop : -1.33 (0.34), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 111 TYR 0.021 0.002 TYR B 185 PHE 0.014 0.002 PHE A 253 TRP 0.016 0.003 TRP B 201 HIS 0.012 0.002 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00676 ( 9997) covalent geometry : angle 0.70911 (14143) hydrogen bonds : bond 0.05802 ( 462) hydrogen bonds : angle 4.09080 ( 1238) metal coordination : bond 0.01393 ( 4) metal coordination : angle 6.59037 ( 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 247 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 200 time to evaluate : 0.283 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8413 (OUTLIER) cc_final: 0.8200 (t) REVERT: A 105 TYR cc_start: 0.8885 (m-80) cc_final: 0.8672 (m-80) REVERT: A 137 MET cc_start: 0.8618 (mmm) cc_final: 0.8344 (mmm) REVERT: A 141 ASP cc_start: 0.8240 (p0) cc_final: 0.7981 (p0) REVERT: A 236 PHE cc_start: 0.8600 (OUTLIER) cc_final: 0.8382 (m-80) REVERT: A 261 ARG cc_start: 0.8528 (OUTLIER) cc_final: 0.8153 (ttp80) REVERT: A 270 TYR cc_start: 0.8722 (p90) cc_final: 0.8134 (p90) REVERT: A 288 GLU cc_start: 0.8113 (tm-30) cc_final: 0.7628 (tm-30) REVERT: A 325 ASP cc_start: 0.8223 (t0) cc_final: 0.8007 (t0) REVERT: A 415 LYS cc_start: 0.7937 (mmmm) cc_final: 0.7671 (mmmm) REVERT: A 420 SER cc_start: 0.7896 (m) cc_final: 0.7532 (p) REVERT: B 22 THR cc_start: 0.8756 (m) cc_final: 0.8510 (p) REVERT: B 39 THR cc_start: 0.8883 (OUTLIER) cc_final: 0.8620 (p) REVERT: B 46 MET cc_start: 0.8962 (tpp) cc_final: 0.8584 (mmt) REVERT: B 118 SER cc_start: 0.8858 (t) cc_final: 0.8590 (p) REVERT: B 120 LYS cc_start: 0.8981 (mmmm) cc_final: 0.8723 (tppp) REVERT: B 150 SER cc_start: 0.8436 (t) cc_final: 0.8235 (t) REVERT: B 155 GLN cc_start: 0.8410 (tp-100) cc_final: 0.8074 (tp-100) REVERT: B 157 MET cc_start: 0.8647 (mpp) cc_final: 0.8224 (mpp) REVERT: B 159 VAL cc_start: 0.5974 (OUTLIER) cc_final: 0.5623 (m) REVERT: B 178 ASP cc_start: 0.7821 (m-30) cc_final: 0.7486 (m-30) REVERT: B 233 TYR cc_start: 0.8371 (OUTLIER) cc_final: 0.8014 (t80) REVERT: B 249 GLU cc_start: 0.7167 (tp30) cc_final: 0.6889 (tp30) REVERT: B 261 ARG cc_start: 0.8438 (ttm170) cc_final: 0.8189 (ttm170) REVERT: B 262 ILE cc_start: 0.8737 (tp) cc_final: 0.8531 (tt) REVERT: B 289 GLN cc_start: 0.7647 (tp40) cc_final: 0.7373 (tp40) REVERT: B 291 ARG cc_start: 0.7576 (ttm110) cc_final: 0.7348 (ttm110) REVERT: B 315 LYS cc_start: 0.8529 (OUTLIER) cc_final: 0.8196 (tttt) REVERT: B 355 GLU cc_start: 0.8460 (tt0) cc_final: 0.8243 (tm-30) REVERT: B 413 ILE cc_start: 0.7198 (tp) cc_final: 0.6798 (mm) outliers start: 47 outliers final: 12 residues processed: 227 average time/residue: 0.7240 time to fit residues: 173.4253 Evaluate side-chains 207 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 236 PHE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 29 GLN 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 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 315 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 8 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 30 optimal weight: 0.8980 chunk 67 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 18 optimal weight: 0.0670 chunk 39 optimal weight: 8.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 93 GLN A 106 GLN A 131 ASN A 186 GLN A 237 GLN A 366 GLN B 87 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.135845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.107021 restraints weight = 14683.952| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 1.92 r_work: 0.3194 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3038 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3038 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 1.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 10001 Z= 0.127 Angle : 0.568 8.606 14149 Z= 0.305 Chirality : 0.038 0.161 1628 Planarity : 0.004 0.049 1293 Dihedral : 21.553 85.871 2931 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 4.06 % Allowed : 31.45 % Favored : 64.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.29), residues: 797 helix: 2.26 (0.26), residues: 379 sheet: -0.13 (0.39), residues: 160 loop : -1.09 (0.35), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 111 TYR 0.013 0.001 TYR B 351 PHE 0.008 0.001 PHE A 253 TRP 0.013 0.001 TRP B 45 HIS 0.006 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00277 ( 9997) covalent geometry : angle 0.56070 (14143) hydrogen bonds : bond 0.04278 ( 462) hydrogen bonds : angle 3.64817 ( 1238) metal coordination : bond 0.00547 ( 4) metal coordination : angle 4.58043 ( 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 235 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 207 time to evaluate : 0.241 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.8274 (m) cc_final: 0.8064 (t) REVERT: A 130 GLU cc_start: 0.8017 (tm-30) cc_final: 0.7698 (tm-30) REVERT: A 155 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8332 (mm-40) REVERT: A 178 ASP cc_start: 0.8525 (m-30) cc_final: 0.8230 (m-30) REVERT: A 261 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8163 (ttp80) REVERT: A 266 ARG cc_start: 0.8164 (mtt180) cc_final: 0.7899 (mtt90) REVERT: A 270 TYR cc_start: 0.8602 (p90) cc_final: 0.8159 (p90) REVERT: A 288 GLU cc_start: 0.7982 (tm-30) cc_final: 0.7486 (tm-30) REVERT: A 346 GLN cc_start: 0.8755 (mt0) cc_final: 0.8514 (mt0) REVERT: A 351 TYR cc_start: 0.7542 (OUTLIER) cc_final: 0.7264 (t80) REVERT: A 415 LYS cc_start: 0.7849 (mmmm) cc_final: 0.7539 (mmmm) REVERT: A 420 SER cc_start: 0.7818 (m) cc_final: 0.7488 (p) REVERT: B 22 THR cc_start: 0.8677 (m) cc_final: 0.8472 (p) REVERT: B 46 MET cc_start: 0.8925 (tpp) cc_final: 0.8567 (mmt) REVERT: B 118 SER cc_start: 0.8603 (t) cc_final: 0.8307 (p) REVERT: B 120 LYS cc_start: 0.8928 (mmmm) cc_final: 0.8723 (tppp) REVERT: B 155 GLN cc_start: 0.8297 (tp-100) cc_final: 0.8025 (tp-100) REVERT: B 157 MET cc_start: 0.8555 (mpp) cc_final: 0.8160 (mpp) REVERT: B 178 ASP cc_start: 0.7758 (m-30) cc_final: 0.7386 (m-30) REVERT: B 190 SER cc_start: 0.8548 (p) cc_final: 0.8306 (m) REVERT: B 199 ASN cc_start: 0.8637 (t0) cc_final: 0.8434 (t0) REVERT: B 233 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7959 (t80) REVERT: B 243 TYR cc_start: 0.8069 (m-80) cc_final: 0.7633 (m-80) REVERT: B 249 GLU cc_start: 0.6895 (tp30) cc_final: 0.6642 (tp30) REVERT: B 261 ARG cc_start: 0.8260 (ttm170) cc_final: 0.8038 (ttm170) REVERT: B 262 ILE cc_start: 0.8752 (tp) cc_final: 0.8505 (tt) REVERT: B 289 GLN cc_start: 0.7504 (tp40) cc_final: 0.7157 (tp40) REVERT: B 293 LYS cc_start: 0.8566 (mmtt) cc_final: 0.8328 (mmpt) REVERT: B 346 GLN cc_start: 0.8041 (tt0) cc_final: 0.7743 (tp40) REVERT: B 413 ILE cc_start: 0.7197 (tp) cc_final: 0.6985 (mm) outliers start: 28 outliers final: 9 residues processed: 220 average time/residue: 0.7206 time to fit residues: 167.6199 Evaluate side-chains 210 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 198 time to evaluate : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 126 ASP Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain B residue 133 SER 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 310 VAL Chi-restraints excluded: chain B residue 324 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 0.6980 chunk 49 optimal weight: 9.9990 chunk 8 optimal weight: 0.6980 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 90 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 4.9990 chunk 30 optimal weight: 6.9990 overall best weight: 2.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 26 GLN A 87 ASN A 93 GLN A 106 GLN A 131 ASN A 237 GLN A 377 ASN ** B 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.129964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.101163 restraints weight = 14777.273| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.92 r_work: 0.3152 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 1.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10001 Z= 0.186 Angle : 0.619 10.115 14149 Z= 0.325 Chirality : 0.040 0.259 1628 Planarity : 0.005 0.068 1293 Dihedral : 21.582 83.464 2931 Min Nonbonded Distance : 1.962 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 3.48 % Allowed : 33.19 % Favored : 63.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.16 (0.29), residues: 797 helix: 2.39 (0.26), residues: 374 sheet: -0.16 (0.38), residues: 159 loop : -1.02 (0.35), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 111 TYR 0.010 0.001 TYR B 185 PHE 0.008 0.001 PHE A 253 TRP 0.013 0.002 TRP B 45 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 9997) covalent geometry : angle 0.60929 (14143) hydrogen bonds : bond 0.04527 ( 462) hydrogen bonds : angle 3.65381 ( 1238) metal coordination : bond 0.01208 ( 4) metal coordination : angle 5.35156 ( 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 225 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 201 time to evaluate : 0.289 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.8312 (OUTLIER) cc_final: 0.8066 (t) REVERT: A 129 LYS cc_start: 0.9346 (OUTLIER) cc_final: 0.9038 (ttmm) REVERT: A 130 GLU cc_start: 0.8073 (tm-30) cc_final: 0.7782 (tm-30) REVERT: A 155 GLN cc_start: 0.8682 (mm-40) cc_final: 0.8383 (mm-40) REVERT: A 261 ARG cc_start: 0.8497 (OUTLIER) cc_final: 0.8176 (ttp80) REVERT: A 270 TYR cc_start: 0.8606 (p90) cc_final: 0.8121 (p90) REVERT: A 288 GLU cc_start: 0.8055 (tm-30) cc_final: 0.7518 (tm-30) REVERT: A 351 TYR cc_start: 0.7532 (OUTLIER) cc_final: 0.7154 (t80) REVERT: A 415 LYS cc_start: 0.7879 (mmmm) cc_final: 0.7616 (mmmm) REVERT: A 420 SER cc_start: 0.7914 (m) cc_final: 0.7611 (p) REVERT: B 39 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8605 (m) REVERT: B 46 MET cc_start: 0.8995 (tpp) cc_final: 0.8654 (mmt) REVERT: B 118 SER cc_start: 0.8683 (t) cc_final: 0.8376 (p) REVERT: B 155 GLN cc_start: 0.8439 (tp-100) cc_final: 0.8190 (tp-100) REVERT: B 157 MET cc_start: 0.8636 (mpp) cc_final: 0.8293 (mpp) REVERT: B 177 MET cc_start: 0.8051 (mmt) cc_final: 0.7733 (tpp) REVERT: B 178 ASP cc_start: 0.7771 (m-30) cc_final: 0.7366 (m-30) REVERT: B 233 TYR cc_start: 0.8215 (OUTLIER) cc_final: 0.7774 (t80) REVERT: B 249 GLU cc_start: 0.6996 (tp30) cc_final: 0.6692 (tp30) REVERT: B 261 ARG cc_start: 0.8301 (ttm170) cc_final: 0.8074 (ttm170) REVERT: B 262 ILE cc_start: 0.8711 (tp) cc_final: 0.8470 (tt) REVERT: B 289 GLN cc_start: 0.7590 (tp40) cc_final: 0.7272 (tp40) REVERT: B 293 LYS cc_start: 0.8583 (mmtt) cc_final: 0.8349 (mmpt) REVERT: B 335 ARG cc_start: 0.7608 (mtt-85) cc_final: 0.7138 (mtt-85) REVERT: B 416 ILE cc_start: 0.7792 (pp) cc_final: 0.7473 (mt) outliers start: 24 outliers final: 12 residues processed: 214 average time/residue: 0.7323 time to fit residues: 165.4123 Evaluate side-chains 223 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 205 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 133 SER 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 310 VAL 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: 0.9990 chunk 29 optimal weight: 1.9990 chunk 84 optimal weight: 9.9990 chunk 38 optimal weight: 0.7980 chunk 42 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 49 optimal weight: 10.0000 chunk 70 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 44 optimal weight: 7.9990 chunk 63 optimal weight: 5.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 237 GLN A 256 GLN B 36 ASN B 87 ASN B 131 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.129318 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.100931 restraints weight = 14658.959| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 1.87 r_work: 0.3139 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8160 moved from start: 1.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 10001 Z= 0.202 Angle : 0.622 9.769 14149 Z= 0.329 Chirality : 0.041 0.212 1628 Planarity : 0.005 0.069 1293 Dihedral : 21.533 82.411 2931 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.93 % Allowed : 33.19 % Favored : 61.88 % 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 aren not related in a simple way. whole: 0.93 (0.29), residues: 797 helix: 2.00 (0.26), residues: 385 sheet: -0.02 (0.39), residues: 159 loop : -1.13 (0.35), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.001 ARG B 6 TYR 0.011 0.002 TYR B 142 PHE 0.008 0.001 PHE A 336 TRP 0.012 0.002 TRP B 45 HIS 0.005 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00451 ( 9997) covalent geometry : angle 0.61347 (14143) hydrogen bonds : bond 0.04586 ( 462) hydrogen bonds : angle 3.68840 ( 1238) metal coordination : bond 0.00919 ( 4) metal coordination : angle 5.11966 ( 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 242 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 208 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 50 SER cc_start: 0.8278 (OUTLIER) cc_final: 0.8049 (t) REVERT: A 129 LYS cc_start: 0.9360 (OUTLIER) cc_final: 0.9046 (ttmm) REVERT: A 130 GLU cc_start: 0.8038 (tm-30) cc_final: 0.7707 (tm-30) REVERT: A 155 GLN cc_start: 0.8691 (mm-40) cc_final: 0.8399 (mm-40) REVERT: A 178 ASP cc_start: 0.8579 (m-30) cc_final: 0.8249 (m-30) REVERT: A 228 VAL cc_start: 0.8476 (m) cc_final: 0.8209 (p) REVERT: A 261 ARG cc_start: 0.8505 (OUTLIER) cc_final: 0.8203 (ttp80) REVERT: A 270 TYR cc_start: 0.8629 (p90) cc_final: 0.8179 (p90) REVERT: A 288 GLU cc_start: 0.7949 (tm-30) cc_final: 0.7395 (tm-30) REVERT: A 351 TYR cc_start: 0.7503 (OUTLIER) cc_final: 0.7185 (t80) REVERT: A 415 LYS cc_start: 0.7847 (mmmm) cc_final: 0.7588 (mmmm) REVERT: A 420 SER cc_start: 0.7917 (m) cc_final: 0.7631 (p) REVERT: B 46 MET cc_start: 0.9022 (tpp) cc_final: 0.8682 (mmt) REVERT: B 118 SER cc_start: 0.8681 (t) cc_final: 0.8357 (p) REVERT: B 157 MET cc_start: 0.8669 (mpp) cc_final: 0.8385 (mpp) REVERT: B 177 MET cc_start: 0.8163 (mmt) cc_final: 0.7890 (tpp) REVERT: B 178 ASP cc_start: 0.7863 (m-30) cc_final: 0.7500 (m-30) REVERT: B 233 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.7822 (t80) REVERT: B 249 GLU cc_start: 0.6998 (tp30) cc_final: 0.6697 (tp30) REVERT: B 261 ARG cc_start: 0.8314 (ttm170) cc_final: 0.8095 (ttm170) REVERT: B 262 ILE cc_start: 0.8793 (tp) cc_final: 0.8565 (tt) REVERT: B 289 GLN cc_start: 0.7620 (tp40) cc_final: 0.7302 (tp40) REVERT: B 293 LYS cc_start: 0.8590 (mmtt) cc_final: 0.8355 (mmpt) REVERT: B 335 ARG cc_start: 0.7622 (mtt-85) cc_final: 0.7197 (mtt-85) REVERT: B 349 ILE cc_start: 0.7501 (mm) cc_final: 0.7012 (tt) REVERT: B 355 GLU cc_start: 0.8486 (tt0) cc_final: 0.8258 (tm-30) outliers start: 34 outliers final: 15 residues processed: 225 average time/residue: 0.7532 time to fit residues: 178.9910 Evaluate side-chains 218 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain B residue 190 SER 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 310 VAL Chi-restraints excluded: chain B residue 324 GLU Chi-restraints excluded: chain B residue 343 TYR 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: 3.9990 chunk 66 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 7.9990 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 8.9990 chunk 82 optimal weight: 0.9980 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 366 GLN A 377 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.126779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.098510 restraints weight = 14659.163| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 1.90 r_work: 0.3091 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 1.3997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 10001 Z= 0.275 Angle : 0.700 10.707 14149 Z= 0.365 Chirality : 0.044 0.343 1628 Planarity : 0.006 0.077 1293 Dihedral : 21.578 85.361 2931 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 4.35 % Allowed : 34.78 % Favored : 60.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.29), residues: 797 helix: 1.87 (0.26), residues: 376 sheet: -0.15 (0.39), residues: 159 loop : -1.22 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 111 TYR 0.049 0.002 TYR B 243 PHE 0.009 0.002 PHE A 102 TRP 0.012 0.002 TRP A 43 HIS 0.005 0.001 HIS B 72 Details of bonding type rmsd covalent geometry : bond 0.00617 ( 9997) covalent geometry : angle 0.69048 (14143) hydrogen bonds : bond 0.05048 ( 462) hydrogen bonds : angle 3.84928 ( 1238) metal coordination : bond 0.01207 ( 4) metal coordination : angle 5.75422 ( 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 233 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 203 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8234 (OUTLIER) cc_final: 0.8014 (t) REVERT: A 129 LYS cc_start: 0.9353 (OUTLIER) cc_final: 0.9047 (ttmm) REVERT: A 130 GLU cc_start: 0.8003 (tm-30) cc_final: 0.7664 (tm-30) REVERT: A 155 GLN cc_start: 0.8702 (mm-40) cc_final: 0.8416 (mm-40) REVERT: A 258 GLU cc_start: 0.8765 (tt0) cc_final: 0.8517 (tp30) REVERT: A 261 ARG cc_start: 0.8469 (OUTLIER) cc_final: 0.8071 (ttp80) REVERT: A 289 GLN cc_start: 0.8275 (OUTLIER) cc_final: 0.7746 (mp10) REVERT: A 351 TYR cc_start: 0.7539 (OUTLIER) cc_final: 0.7141 (t80) REVERT: A 390 LYS cc_start: 0.8350 (mmmt) cc_final: 0.8122 (mmmt) REVERT: A 415 LYS cc_start: 0.7875 (mmmm) cc_final: 0.7611 (mmmm) REVERT: A 420 SER cc_start: 0.7908 (m) cc_final: 0.7616 (p) REVERT: B 118 SER cc_start: 0.8750 (t) cc_final: 0.8449 (p) REVERT: B 155 GLN cc_start: 0.8470 (tp-100) cc_final: 0.7974 (tm-30) REVERT: B 157 MET cc_start: 0.8697 (mpp) cc_final: 0.8418 (mpp) REVERT: B 159 VAL cc_start: 0.6481 (OUTLIER) cc_final: 0.6095 (m) REVERT: B 178 ASP cc_start: 0.7943 (m-30) cc_final: 0.7665 (m-30) REVERT: B 184 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7975 (mp0) REVERT: B 214 ARG cc_start: 0.7407 (OUTLIER) cc_final: 0.7001 (ptp-110) REVERT: B 233 TYR cc_start: 0.8302 (OUTLIER) cc_final: 0.7809 (t80) REVERT: B 249 GLU cc_start: 0.7082 (tp30) cc_final: 0.6768 (tp30) REVERT: B 261 ARG cc_start: 0.8370 (ttm170) cc_final: 0.8150 (ttm170) REVERT: B 262 ILE cc_start: 0.8782 (tp) cc_final: 0.8554 (tt) REVERT: B 289 GLN cc_start: 0.7675 (tp40) cc_final: 0.7319 (tp40) REVERT: B 293 LYS cc_start: 0.8598 (mmtt) cc_final: 0.8361 (mmpt) REVERT: B 335 ARG cc_start: 0.7697 (mtt-85) cc_final: 0.7266 (mtt-85) REVERT: B 349 ILE cc_start: 0.7626 (mm) cc_final: 0.7108 (tt) outliers start: 30 outliers final: 15 residues processed: 219 average time/residue: 0.7403 time to fit residues: 171.3372 Evaluate side-chains 216 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 192 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 221 ILE Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 283 ARG Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 324 GLU Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 133 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 184 GLU Chi-restraints excluded: chain B residue 187 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 Chi-restraints excluded: chain B residue 410 ILE 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: 0.7980 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 5.9990 chunk 54 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 78 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 186 GLN A 237 GLN A 366 GLN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.132212 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.104069 restraints weight = 14604.552| |-----------------------------------------------------------------------------| r_work (start): 0.3338 rms_B_bonded: 1.87 r_work: 0.3200 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3047 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3047 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 1.4104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 10001 Z= 0.133 Angle : 0.629 12.452 14149 Z= 0.328 Chirality : 0.039 0.205 1628 Planarity : 0.005 0.077 1293 Dihedral : 21.556 83.042 2931 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.61 % Allowed : 37.10 % Favored : 60.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.04 (0.29), residues: 797 helix: 2.22 (0.26), residues: 376 sheet: 0.00 (0.39), residues: 159 loop : -1.16 (0.34), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 111 TYR 0.022 0.001 TYR B 351 PHE 0.008 0.001 PHE A 253 TRP 0.011 0.001 TRP B 45 HIS 0.004 0.001 HIS B 194 Details of bonding type rmsd covalent geometry : bond 0.00294 ( 9997) covalent geometry : angle 0.62320 (14143) hydrogen bonds : bond 0.04094 ( 462) hydrogen bonds : angle 3.63526 ( 1238) metal coordination : bond 0.00469 ( 4) metal coordination : angle 4.26562 ( 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 210 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 192 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 50 SER cc_start: 0.8177 (OUTLIER) cc_final: 0.7968 (t) REVERT: A 130 GLU cc_start: 0.8022 (tm-30) cc_final: 0.7672 (tm-30) REVERT: A 155 GLN cc_start: 0.8713 (mm-40) cc_final: 0.8439 (mm-40) REVERT: A 161 ARG cc_start: 0.8258 (mtt-85) cc_final: 0.8041 (mtp85) REVERT: A 261 ARG cc_start: 0.8477 (OUTLIER) cc_final: 0.8244 (ttp80) REVERT: A 270 TYR cc_start: 0.8358 (p90) cc_final: 0.7615 (p90) REVERT: A 289 GLN cc_start: 0.8152 (OUTLIER) cc_final: 0.7639 (mp10) REVERT: A 351 TYR cc_start: 0.7426 (OUTLIER) cc_final: 0.7159 (t80) REVERT: A 420 SER cc_start: 0.7811 (m) cc_final: 0.7556 (p) REVERT: B 6 ARG cc_start: 0.8167 (ttm110) cc_final: 0.7632 (ttm110) REVERT: B 46 MET cc_start: 0.8893 (tpp) cc_final: 0.8615 (mmt) REVERT: B 118 SER cc_start: 0.8631 (t) cc_final: 0.8300 (p) REVERT: B 157 MET cc_start: 0.8586 (mpp) cc_final: 0.8274 (mpp) REVERT: B 184 GLU cc_start: 0.8218 (mt-10) cc_final: 0.7890 (mp0) REVERT: B 214 ARG cc_start: 0.7257 (OUTLIER) cc_final: 0.6870 (ptp-110) REVERT: B 233 TYR cc_start: 0.8481 (OUTLIER) cc_final: 0.8141 (t80) REVERT: B 249 GLU cc_start: 0.6930 (tp30) cc_final: 0.6617 (tp30) REVERT: B 261 ARG cc_start: 0.8297 (ttm170) cc_final: 0.8094 (ttm170) REVERT: B 289 GLN cc_start: 0.7586 (tp40) cc_final: 0.7239 (tp40) REVERT: B 291 ARG cc_start: 0.7480 (ttm170) cc_final: 0.7203 (tmm160) REVERT: B 293 LYS cc_start: 0.8586 (mmtt) cc_final: 0.8347 (mmpt) REVERT: B 335 ARG cc_start: 0.7540 (mtt-85) cc_final: 0.7162 (mtt-85) outliers start: 18 outliers final: 6 residues processed: 202 average time/residue: 0.7671 time to fit residues: 163.5948 Evaluate side-chains 206 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 194 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 4 VAL Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 289 GLN Chi-restraints excluded: chain A residue 351 TYR Chi-restraints excluded: chain A residue 394 CYS 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 410 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 58 optimal weight: 4.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 10.0000 chunk 71 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 21 optimal weight: 0.0970 overall best weight: 1.3580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 186 GLN A 366 GLN B 70 ASN ** B 87 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 407 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.131624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.103573 restraints weight = 14557.418| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 1.86 r_work: 0.3187 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3031 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 1.4153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 10001 Z= 0.145 Angle : 0.616 9.405 14149 Z= 0.321 Chirality : 0.039 0.209 1628 Planarity : 0.005 0.078 1293 Dihedral : 21.534 83.727 2931 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.19 % Allowed : 36.23 % Favored : 60.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.09 (0.29), residues: 797 helix: 2.22 (0.26), residues: 380 sheet: 0.09 (0.39), residues: 159 loop : -1.17 (0.34), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.016 0.001 ARG B 6 TYR 0.020 0.001 TYR B 351 PHE 0.007 0.001 PHE A 253 TRP 0.013 0.001 TRP B 45 HIS 0.004 0.001 HIS A 278 Details of bonding type rmsd covalent geometry : bond 0.00324 ( 9997) covalent geometry : angle 0.61011 (14143) hydrogen bonds : bond 0.03991 ( 462) hydrogen bonds : angle 3.60997 ( 1238) metal coordination : bond 0.00618 ( 4) metal coordination : angle 4.31067 ( 6) =============================================================================== Job complete usr+sys time: 4163.40 seconds wall clock time: 71 minutes 32.66 seconds (4292.66 seconds total)