Starting phenix.real_space_refine on Wed Aug 5 11:57:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.cif Found real_map, /net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.cif" model { file = "/net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8j3r_35965/08_2026/8j3r_35965.cif" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 sd= 0.076 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 140 5.49 5 Mg 3 5.21 5 S 32 5.16 5 C 5481 2.51 5 N 1731 2.21 5 O 2138 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 9526 Number of models: 1 Model: "" Number of chains: 7 Chain: "A" Number of atoms: 3429 Number of conformers: 1 Conformer: "" Number of residues, atoms: 422, 3429 Classifications: {'peptide': 422} Link IDs: {'PTRANS': 10, 'TRANS': 411} Chain: "D" Number of atoms: 466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 466 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "E" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 166 Classifications: {'DNA': 8} Link IDs: {'rna3p': 7} Chain: "C" Number of atoms: 2345 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 2345 Classifications: {'RNAv2': 109} Modifications used: {'rna2p_pur': 10, 'rna2p_pyr': 2, 'rna3p_pur': 56, 'rna3p_pyr': 41} Link IDs: {'rna2p': 12, 'rna3p': 96} Chain: "B" Number of atoms: 3116 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 3116 Classifications: {'peptide': 387} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PTRANS': 9, 'TRANS': 377} Chain breaks: 4 Unresolved non-hydrogen bonds: 39 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 2, 'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 19 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 1, ' ZN': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' MG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 3055 SG CYS A 372 88.301 55.825 32.384 1.00103.10 S ATOM 3076 SG CYS A 375 91.722 54.642 33.836 1.00 97.25 S ATOM 3193 SG CYS A 391 90.472 58.181 34.340 1.00116.70 S ATOM 3215 SG CYS A 394 91.398 56.126 32.490 1.00100.31 S Time building chain proxies: 1.97, per 1000 atoms: 0.21 Number of scatterers: 9526 At special positions: 0 Unit cell: (102.3, 117.7, 113.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 32 16.00 P 140 15.00 Mg 3 11.99 O 2138 8.00 N 1731 7.00 C 5481 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 278.7 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 501 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 394 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 391 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 372 " pdb="ZN ZN A 501 " - pdb=" SG CYS A 375 " Number of angles added : 6 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 8 sheets defined 49.3% alpha, 17.6% beta 46 base pairs and 86 stacking pairs defined. Time for finding SS restraints: 1.24 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: 2.14 Time building geometry restraints manager: 1.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2190 1.33 - 1.45: 2776 1.45 - 1.57: 4700 1.57 - 1.69: 277 1.69 - 1.81: 54 Bond restraints: 9997 Sorted by residual: bond pdb=" C1' DT E -7 " pdb=" N1 DT E -7 " ideal model delta sigma weight residual 1.468 1.518 -0.050 1.40e-02 5.10e+03 1.28e+01 bond pdb=" C3' DG E 0 " pdb=" C2' DG E 0 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.68e+00 bond pdb=" C3' DC D 10 " pdb=" C2' DC D 10 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.55e+00 bond pdb=" C3' DT D 15 " pdb=" C2' DT D 15 " ideal model delta sigma weight residual 1.516 1.535 -0.019 8.00e-03 1.56e+04 5.52e+00 bond pdb=" C1' DC D 10 " pdb=" N1 DC D 10 " ideal model delta sigma weight residual 1.468 1.501 -0.033 1.40e-02 5.10e+03 5.47e+00 ... (remaining 9992 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.53: 13489 1.53 - 3.06: 570 3.06 - 4.58: 65 4.58 - 6.11: 17 6.11 - 7.64: 2 Bond angle restraints: 14143 Sorted by residual: angle pdb=" N3 DT D 19 " pdb=" C4 DT D 19 " pdb=" O4 DT D 19 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT D 16 " pdb=" C4 DT D 16 " pdb=" O4 DT D 16 " ideal model delta sigma weight residual 119.90 122.41 -2.51 6.00e-01 2.78e+00 1.75e+01 angle pdb=" N3 DT D 15 " pdb=" C4 DT D 15 " pdb=" O4 DT D 15 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT E -7 " pdb=" C4 DT E -7 " pdb=" O4 DT E -7 " ideal model delta sigma weight residual 119.90 122.38 -2.48 6.00e-01 2.78e+00 1.71e+01 angle pdb=" N3 DT D 23 " pdb=" C4 DT D 23 " pdb=" O4 DT D 23 " ideal model delta sigma weight residual 119.90 122.37 -2.47 6.00e-01 2.78e+00 1.70e+01 ... (remaining 14138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 4786 17.52 - 35.05: 503 35.05 - 52.57: 273 52.57 - 70.10: 123 70.10 - 87.62: 23 Dihedral angle restraints: 5708 sinusoidal: 3341 harmonic: 2367 Sorted by residual: dihedral pdb=" C4' G C -43 " pdb=" C3' G C -43 " pdb=" C2' G C -43 " pdb=" C1' G C -43 " ideal model delta sinusoidal sigma weight residual 36.34 -36.63 72.97 1 3.10e+00 1.04e-01 7.06e+02 dihedral pdb=" C4' G C -12 " pdb=" C3' G C -12 " pdb=" C2' G C -12 " pdb=" C1' G C -12 " ideal model delta sinusoidal sigma weight residual 36.34 -36.01 72.35 1 3.10e+00 1.04e-01 6.96e+02 dihedral pdb=" C4' G C 0 " pdb=" C3' G C 0 " pdb=" C2' G C 0 " pdb=" C1' G C 0 " ideal model delta sinusoidal sigma weight residual 36.34 -35.99 72.33 1 3.10e+00 1.04e-01 6.96e+02 ... (remaining 5705 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1313 0.059 - 0.119: 170 0.119 - 0.178: 12 0.178 - 0.237: 91 0.237 - 0.297: 42 Chirality restraints: 1628 Sorted by residual: chirality pdb=" P A C -11 " pdb=" OP1 A C -11 " pdb=" OP2 A C -11 " pdb=" O5' A C -11 " both_signs ideal model delta sigma weight residual True 2.17 -2.47 -0.30 2.00e-01 2.50e+01 2.20e+00 chirality pdb=" C2' A C -36 " pdb=" C3' A C -36 " pdb=" O2' A C -36 " pdb=" C1' A C -36 " both_signs ideal model delta sigma weight residual False -2.79 -2.50 -0.28 2.00e-01 2.50e+01 2.03e+00 chirality pdb=" C2' A C -57 " pdb=" C3' A C -57 " pdb=" O2' A C -57 " pdb=" C1' A C -57 " both_signs ideal model delta sigma weight residual False -2.79 -2.51 -0.28 2.00e-01 2.50e+01 2.02e+00 ... (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: 0.210 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: 0.030 Process input model: 11.860 Find NCS groups from input model: 0.120 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:9.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5092 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 10001 Z= 0.233 Angle : 0.897 56.945 14149 Z= 0.411 Chirality : 0.077 0.297 1628 Planarity : 0.003 0.034 1293 Dihedral : 19.091 87.620 4192 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.46 % Allowed : 11.01 % Favored : 86.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.29), residues: 797 helix: 1.90 (0.26), residues: 361 sheet: 0.11 (0.39), residues: 162 loop : -0.90 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 197 TYR 0.011 0.001 TYR A 119 PHE 0.007 0.001 PHE B 102 TRP 0.008 0.001 TRP A 43 HIS 0.003 0.001 HIS A 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.23 ( 9997) covalent geometry : angle 0.68580 / 0.40 (14143) hydrogen bonds : bond 0.22544 / 14.29 ( 462) hydrogen bonds : angle 6.19927 / 4.61 ( 1238) metal coordination : bond 0.03778 / 1.89 ( 4) metal coordination : angle 28.09070 / 11.61 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1594 Ramachandran restraints generated. 797 Oldfield, 0 Emsley, 797 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 152 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 204 ASN cc_start: 0.6649 (OUTLIER) cc_final: 0.6447 (m110) REVERT: A 377 ASN cc_start: 0.6732 (t0) cc_final: 0.6497 (t0) REVERT: B 141 ASP cc_start: 0.6652 (OUTLIER) cc_final: 0.6234 (m-30) REVERT: B 142 TYR cc_start: 0.2633 (m-80) cc_final: 0.1485 (m-80) REVERT: B 288 GLU cc_start: 0.4753 (OUTLIER) cc_final: 0.4004 (tm-30) outliers start: 17 outliers final: 2 residues processed: 164 average time/residue: 0.5354 time to fit residues: 93.4916 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 : 0.200 ------------------------------------------------------------------------------- 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: 7.9990 chunk 53 optimal weight: 5.9990 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: 8.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 74 optimal weight: 3.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 131 ASN A 204 ASN B 186 GLN B 322 GLN B 403 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3874 r_free = 0.3874 target = 0.141445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115759 restraints weight = 15055.776| |-----------------------------------------------------------------------------| r_work (start): 0.3521 rms_B_bonded: 1.88 r_work: 0.3389 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6277 moved from start: 0.3530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.098 10001 Z= 0.312 Angle : 1.291 32.223 14149 Z= 0.549 Chirality : 0.096 0.945 1628 Planarity : 0.006 0.040 1293 Dihedral : 19.777 145.533 2571 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 9.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 3.33 % Allowed : 18.84 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.29), residues: 797 helix: 1.76 (0.25), residues: 373 sheet: -0.21 (0.38), residues: 157 loop : -1.06 (0.36), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 214 TYR 0.022 0.002 TYR B 119 PHE 0.028 0.003 PHE B 33 TRP 0.019 0.003 TRP B 201 HIS 0.006 0.002 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00638 / 0.31 ( 9997) covalent geometry : angle 1.25145 / 0.55 (14143) hydrogen bonds : bond 0.06681 / 4.06 ( 462) hydrogen bonds : angle 4.39576 / 3.25 ( 1238) metal coordination : bond 0.01479 / 0.74 ( 4) metal coordination : angle 15.40623 / 5.81 ( 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 168 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 145 time to evaluate : 0.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 79 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6907 (pt) REVERT: A 130 GLU cc_start: 0.7592 (tm-30) cc_final: 0.7253 (tm-30) REVERT: A 347 GLN cc_start: 0.7986 (tm-30) cc_final: 0.7745 (tp-100) REVERT: A 377 ASN cc_start: 0.7671 (t0) cc_final: 0.7416 (t0) REVERT: B 39 THR cc_start: 0.7328 (t) cc_final: 0.6983 (m) REVERT: B 90 ASN cc_start: 0.7716 (m-40) cc_final: 0.7406 (m-40) REVERT: B 233 TYR cc_start: 0.4103 (OUTLIER) cc_final: 0.3794 (m-10) REVERT: B 312 MET cc_start: 0.5869 (mmm) cc_final: 0.4714 (mmm) outliers start: 23 outliers final: 6 residues processed: 158 average time/residue: 0.5072 time to fit residues: 85.6557 Evaluate side-chains 126 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 118 time to evaluate : 0.254 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 ILE Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain B residue 4 VAL Chi-restraints excluded: chain B residue 27 LEU Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 249 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 23 optimal weight: 3.9990 chunk 89 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 28 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 60 optimal weight: 8.9990 chunk 44 optimal weight: 6.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 131 ASN A 139 HIS B 77 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3936 r_free = 0.3936 target = 0.147991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3582 r_free = 0.3582 target = 0.121632 restraints weight = 15235.999| |-----------------------------------------------------------------------------| r_work (start): 0.3566 rms_B_bonded: 1.95 r_work: 0.3435 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3435 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7218 moved from start: 0.6562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.131 10001 Z= 0.272 Angle : 1.106 17.297 14149 Z= 0.495 Chirality : 0.075 0.636 1628 Planarity : 0.007 0.077 1293 Dihedral : 19.859 167.966 2562 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 5.07 % Allowed : 20.14 % Favored : 74.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 797 helix: 1.55 (0.25), residues: 374 sheet: -0.50 (0.40), residues: 146 loop : -1.39 (0.35), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG A 121 TYR 0.023 0.003 TYR A 5 PHE 0.020 0.003 PHE A 336 TRP 0.032 0.004 TRP A 201 HIS 0.017 0.003 HIS B 123 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.27 ( 9997) covalent geometry : angle 1.09198 / 0.49 (14143) hydrogen bonds : bond 0.08221 / 4.77 ( 462) hydrogen bonds : angle 4.36377 / 3.22 ( 1238) metal coordination : bond 0.00784 / 0.38 ( 4) metal coordination : angle 8.53111 / 3.74 ( 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 210 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 175 time to evaluate : 0.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 46 MET cc_start: 0.7961 (OUTLIER) cc_final: 0.7636 (ttm) REVERT: A 82 LYS cc_start: 0.8074 (mttt) cc_final: 0.7792 (mttt) REVERT: A 294 ILE cc_start: 0.8438 (mt) cc_final: 0.8212 (mp) REVERT: A 332 ILE cc_start: 0.6294 (OUTLIER) cc_final: 0.6082 (pp) REVERT: B 33 PHE cc_start: 0.7203 (t80) cc_final: 0.6975 (t80) REVERT: B 107 LYS cc_start: 0.8347 (OUTLIER) cc_final: 0.8088 (mttp) REVERT: B 126 ASP cc_start: 0.7252 (m-30) cc_final: 0.6929 (m-30) REVERT: B 147 SER cc_start: 0.7830 (OUTLIER) cc_final: 0.7563 (t) REVERT: B 264 MET cc_start: 0.6037 (mmt) cc_final: 0.5802 (mmt) outliers start: 35 outliers final: 11 residues processed: 193 average time/residue: 0.5311 time to fit residues: 109.1201 Evaluate side-chains 159 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.192 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 114 MET Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 332 ILE Chi-restraints excluded: chain B residue 9 ILE Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 107 LYS Chi-restraints excluded: chain B residue 147 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 41 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 6.9990 chunk 87 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 88 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.6980 overall best weight: 3.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 106 GLN ** A 131 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 347 GLN B 87 ASN B 338 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3873 r_free = 0.3873 target = 0.143111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.115127 restraints weight = 15215.967| |-----------------------------------------------------------------------------| r_work (start): 0.3466 rms_B_bonded: 2.02 r_work: 0.3331 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3331 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7868 moved from start: 0.9214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 10001 Z= 0.309 Angle : 1.128 15.289 14149 Z= 0.513 Chirality : 0.079 0.675 1628 Planarity : 0.007 0.072 1293 Dihedral : 19.419 154.440 2562 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 10.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 7.54 % Allowed : 20.87 % Favored : 71.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.07 (0.28), residues: 797 helix: 1.28 (0.25), residues: 373 sheet: -0.45 (0.39), residues: 153 loop : -1.66 (0.33), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 254 TYR 0.032 0.003 TYR B 202 PHE 0.024 0.003 PHE B 253 TRP 0.024 0.003 TRP B 45 HIS 0.008 0.002 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00663 / 0.31 ( 9997) covalent geometry : angle 1.11818 / 0.51 (14143) hydrogen bonds : bond 0.06035 / 3.66 ( 462) hydrogen bonds : angle 4.13662 / 3.05 ( 1238) metal coordination : bond 0.01020 / 0.50 ( 4) metal coordination : angle 7.43510 / 3.07 ( 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 241 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 189 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7679 (t70) cc_final: 0.7410 (t70) REVERT: A 120 LYS cc_start: 0.8454 (pttt) cc_final: 0.8226 (pttt) REVERT: A 175 THR cc_start: 0.8642 (m) cc_final: 0.8409 (p) REVERT: A 234 MET cc_start: 0.8130 (OUTLIER) cc_final: 0.7769 (mtt) REVERT: A 261 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.7445 (ttp80) REVERT: A 294 ILE cc_start: 0.8710 (mt) cc_final: 0.8485 (mp) REVERT: A 322 GLN cc_start: 0.8359 (mt0) cc_final: 0.8057 (mt0) REVERT: A 355 GLU cc_start: 0.7809 (tp30) cc_final: 0.7480 (tt0) REVERT: A 406 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7315 (mtp85) REVERT: B 18 LYS cc_start: 0.7673 (tppt) cc_final: 0.7423 (tppt) REVERT: B 25 ARG cc_start: 0.8063 (tpp80) cc_final: 0.7822 (tpp80) REVERT: B 51 ASP cc_start: 0.7233 (p0) cc_final: 0.6985 (p0) REVERT: B 118 SER cc_start: 0.8291 (m) cc_final: 0.8008 (p) REVERT: B 132 ILE cc_start: 0.6913 (mp) cc_final: 0.6711 (mt) REVERT: B 312 MET cc_start: 0.7024 (mmm) cc_final: 0.6473 (mmt) REVERT: B 401 ASP cc_start: 0.5764 (m-30) cc_final: 0.5543 (m-30) outliers start: 52 outliers final: 15 residues processed: 214 average time/residue: 0.6031 time to fit residues: 136.6254 Evaluate side-chains 185 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 0.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 261 ARG Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 358 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 17 optimal weight: 0.1980 chunk 48 optimal weight: 7.9990 chunk 75 optimal weight: 5.9990 chunk 35 optimal weight: 4.9990 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 56 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 93 GLN A 155 GLN A 347 GLN ** 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 = 0.3863 r_free = 0.3863 target = 0.140556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3467 r_free = 0.3467 target = 0.112089 restraints weight = 15208.070| |-----------------------------------------------------------------------------| r_work (start): 0.3468 rms_B_bonded: 2.02 r_work: 0.3332 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.9725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10001 Z= 0.159 Angle : 0.860 13.694 14149 Z= 0.387 Chirality : 0.066 0.527 1628 Planarity : 0.005 0.057 1293 Dihedral : 19.411 168.788 2562 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 5.07 % Allowed : 25.36 % Favored : 69.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.29), residues: 797 helix: 1.92 (0.26), residues: 371 sheet: -0.39 (0.38), residues: 157 loop : -1.46 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 298 TYR 0.021 0.002 TYR B 185 PHE 0.014 0.002 PHE B 253 TRP 0.012 0.002 TRP B 43 HIS 0.005 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00337 / 0.16 ( 9997) covalent geometry : angle 0.84930 / 0.39 (14143) hydrogen bonds : bond 0.05315 / 3.21 ( 462) hydrogen bonds : angle 3.90386 / 2.91 ( 1238) metal coordination : bond 0.00749 / 0.36 ( 4) metal coordination : angle 6.52575 / 2.59 ( 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 220 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7697 (t70) cc_final: 0.7443 (t70) REVERT: A 28 GLN cc_start: 0.8297 (mt0) cc_final: 0.7988 (mt0) REVERT: A 51 ASP cc_start: 0.7423 (m-30) cc_final: 0.7216 (m-30) REVERT: A 79 ILE cc_start: 0.7943 (pt) cc_final: 0.7724 (pt) REVERT: A 129 LYS cc_start: 0.9241 (OUTLIER) cc_final: 0.9029 (ttmt) REVERT: A 134 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8596 (t) REVERT: A 179 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7969 (mtt90) REVERT: A 234 MET cc_start: 0.8246 (OUTLIER) cc_final: 0.7812 (mtt) REVERT: A 406 ARG cc_start: 0.7497 (OUTLIER) cc_final: 0.6993 (mtp85) REVERT: B 25 ARG cc_start: 0.8129 (tpp80) cc_final: 0.7862 (tpp80) REVERT: B 51 ASP cc_start: 0.7436 (p0) cc_final: 0.7234 (p0) REVERT: B 103 LYS cc_start: 0.8242 (tppp) cc_final: 0.7957 (ttmm) REVERT: B 233 TYR cc_start: 0.6794 (OUTLIER) cc_final: 0.6376 (m-80) REVERT: B 264 MET cc_start: 0.6563 (mmt) cc_final: 0.6137 (mmt) REVERT: B 401 ASP cc_start: 0.5883 (m-30) cc_final: 0.5629 (m-30) outliers start: 35 outliers final: 7 residues processed: 205 average time/residue: 0.5893 time to fit residues: 127.6217 Evaluate side-chains 192 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 179 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 LYS Chi-restraints excluded: chain A residue 129 LYS Chi-restraints excluded: chain A residue 132 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 320 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 34 optimal weight: 0.7980 chunk 8 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 67 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 93 GLN A 155 GLN A 289 GLN B 87 ASN B 135 ASN ** B 322 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.139730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111255 restraints weight = 14908.590| |-----------------------------------------------------------------------------| r_work (start): 0.3459 rms_B_bonded: 2.01 r_work: 0.3324 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 1.0148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10001 Z= 0.163 Angle : 0.843 13.761 14149 Z= 0.379 Chirality : 0.065 0.511 1628 Planarity : 0.005 0.062 1293 Dihedral : 19.324 169.333 2562 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.78 % Allowed : 27.83 % Favored : 67.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 797 helix: 2.18 (0.26), residues: 371 sheet: -0.29 (0.38), residues: 159 loop : -1.24 (0.35), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG A 161 TYR 0.018 0.002 TYR B 351 PHE 0.014 0.001 PHE B 253 TRP 0.011 0.001 TRP B 43 HIS 0.005 0.001 HIS A 238 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.16 ( 9997) covalent geometry : angle 0.83445 / 0.38 (14143) hydrogen bonds : bond 0.04692 / 2.86 ( 462) hydrogen bonds : angle 3.80202 / 2.84 ( 1238) metal coordination : bond 0.00681 / 0.33 ( 4) metal coordination : angle 5.80664 / 2.33 ( 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 217 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.7602 (t70) cc_final: 0.7315 (t70) REVERT: A 79 ILE cc_start: 0.8085 (pt) cc_final: 0.7878 (pt) REVERT: A 134 VAL cc_start: 0.8821 (OUTLIER) cc_final: 0.8534 (t) REVERT: A 179 ARG cc_start: 0.8213 (OUTLIER) cc_final: 0.7961 (mtt90) REVERT: A 197 ARG cc_start: 0.8718 (tmt90) cc_final: 0.8361 (ttp-170) REVERT: A 234 MET cc_start: 0.8266 (OUTLIER) cc_final: 0.7733 (mtt) REVERT: A 406 ARG cc_start: 0.7610 (OUTLIER) cc_final: 0.7215 (mtp85) REVERT: B 25 ARG cc_start: 0.8123 (tpp80) cc_final: 0.7869 (tpp80) REVERT: B 46 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8471 (mmm) REVERT: B 103 LYS cc_start: 0.8279 (tppp) cc_final: 0.8006 (ttmm) REVERT: B 233 TYR cc_start: 0.7091 (OUTLIER) cc_final: 0.6682 (m-80) REVERT: B 264 MET cc_start: 0.6701 (mmt) cc_final: 0.6184 (mmt) REVERT: B 299 ASP cc_start: 0.7402 (t70) cc_final: 0.6954 (t0) REVERT: B 362 LYS cc_start: 0.7451 (OUTLIER) cc_final: 0.6955 (mmmm) REVERT: B 401 ASP cc_start: 0.5986 (m-30) cc_final: 0.5726 (m-30) outliers start: 33 outliers final: 11 residues processed: 197 average time/residue: 0.5986 time to fit residues: 124.4571 Evaluate side-chains 191 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 173 time to evaluate : 0.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 168 ILE Chi-restraints excluded: chain A residue 179 ARG Chi-restraints excluded: chain A residue 234 MET Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 46 MET Chi-restraints excluded: chain B residue 134 VAL Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 180 ILE Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 320 THR Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 362 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 64 optimal weight: 0.7980 chunk 49 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 55 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 90 optimal weight: 8.9990 chunk 15 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 4.9990 overall best weight: 2.8986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 29 GLN A 87 ASN A 93 GLN A 131 ASN A 155 GLN A 186 GLN A 289 GLN B 77 HIS B 87 ASN B 252 ASN B 322 GLN B 339 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.138083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3399 r_free = 0.3399 target = 0.109642 restraints weight = 14802.382| |-----------------------------------------------------------------------------| r_work (start): 0.3380 rms_B_bonded: 1.93 r_work: 0.3237 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3080 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 1.1595 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 10001 Z= 0.254 Angle : 0.968 12.761 14149 Z= 0.449 Chirality : 0.069 0.456 1628 Planarity : 0.007 0.099 1293 Dihedral : 19.272 170.186 2562 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 6.81 % Allowed : 27.97 % Favored : 65.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.28), residues: 797 helix: 1.77 (0.26), residues: 367 sheet: -0.47 (0.37), residues: 157 loop : -1.42 (0.34), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.050 0.001 ARG B 242 TYR 0.023 0.003 TYR B 185 PHE 0.013 0.002 PHE A 236 TRP 0.017 0.003 TRP B 43 HIS 0.006 0.002 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00557 / 0.25 ( 9997) covalent geometry : angle 0.95847 / 0.45 (14143) hydrogen bonds : bond 0.05690 / 3.44 ( 462) hydrogen bonds : angle 3.96821 / 2.93 ( 1238) metal coordination : bond 0.00857 / 0.41 ( 4) metal coordination : angle 6.63640 / 2.87 ( 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 250 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 203 time to evaluate : 0.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 14 ASP cc_start: 0.8143 (t70) cc_final: 0.7798 (t70) REVERT: A 29 GLN cc_start: 0.8130 (tp40) cc_final: 0.7927 (mm-40) REVERT: A 50 SER cc_start: 0.8415 (m) cc_final: 0.8153 (t) REVERT: A 51 ASP cc_start: 0.8015 (m-30) cc_final: 0.7746 (m-30) REVERT: A 85 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8582 (mtt90) REVERT: A 134 VAL cc_start: 0.8956 (OUTLIER) cc_final: 0.8622 (t) REVERT: A 160 LYS cc_start: 0.8530 (tmmm) cc_final: 0.8209 (tmmm) REVERT: A 197 ARG cc_start: 0.8875 (tmt90) cc_final: 0.8570 (ttp-170) REVERT: A 262 ILE cc_start: 0.8650 (mt) cc_final: 0.8449 (mm) REVERT: A 289 GLN cc_start: 0.8488 (tp40) cc_final: 0.8222 (tp40) REVERT: A 293 LYS cc_start: 0.8676 (tptp) cc_final: 0.8470 (tttm) REVERT: A 342 TYR cc_start: 0.8754 (m-80) cc_final: 0.8511 (m-80) REVERT: A 403 ASN cc_start: 0.8433 (t0) cc_final: 0.8191 (t0) REVERT: A 406 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7878 (ttp80) REVERT: B 103 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8294 (ttmm) REVERT: B 118 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8213 (p) REVERT: B 120 LYS cc_start: 0.8966 (mmmm) cc_final: 0.8399 (tppp) REVERT: B 150 SER cc_start: 0.7947 (t) cc_final: 0.7671 (p) REVERT: B 162 LYS cc_start: 0.7430 (OUTLIER) cc_final: 0.7187 (mttm) REVERT: B 249 GLU cc_start: 0.7722 (tp30) cc_final: 0.7417 (tp30) REVERT: B 264 MET cc_start: 0.7578 (mmt) cc_final: 0.7257 (mmt) REVERT: B 346 GLN cc_start: 0.7892 (tt0) cc_final: 0.7399 (mp10) outliers start: 47 outliers final: 18 residues processed: 226 average time/residue: 0.5369 time to fit residues: 128.4474 Evaluate side-chains 217 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 193 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 85 ARG Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 318 CYS Chi-restraints excluded: chain A residue 348 LYS Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 31 THR Chi-restraints excluded: chain B residue 39 THR Chi-restraints excluded: chain B residue 103 LYS Chi-restraints excluded: chain B residue 118 SER Chi-restraints excluded: chain B residue 145 SER Chi-restraints excluded: chain B residue 159 VAL Chi-restraints excluded: chain B residue 162 LYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 239 THR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 349 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 30 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 84 optimal weight: 9.9990 chunk 38 optimal weight: 0.0000 chunk 42 optimal weight: 50.0000 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 7.9990 chunk 70 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 186 GLN B 36 ASN B 303 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.136927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.108543 restraints weight = 14804.465| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 1.89 r_work: 0.3296 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3143 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.3143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8285 moved from start: 1.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 10001 Z= 0.153 Angle : 0.853 12.751 14149 Z= 0.390 Chirality : 0.064 0.427 1628 Planarity : 0.006 0.067 1293 Dihedral : 19.203 173.407 2561 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.75 % Allowed : 33.04 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.29), residues: 797 helix: 2.10 (0.26), residues: 372 sheet: -0.40 (0.38), residues: 150 loop : -1.23 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 25 TYR 0.019 0.001 TYR B 7 PHE 0.013 0.001 PHE B 253 TRP 0.013 0.002 TRP B 45 HIS 0.003 0.001 HIS A 139 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.15 ( 9997) covalent geometry : angle 0.84600 / 0.39 (14143) hydrogen bonds : bond 0.04674 / 2.87 ( 462) hydrogen bonds : angle 3.82324 / 2.83 ( 1238) metal coordination : bond 0.00695 / 0.33 ( 4) metal coordination : angle 5.52500 / 2.30 ( 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 201 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.192 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8103 (tp40) cc_final: 0.7819 (mm-40) REVERT: A 51 ASP cc_start: 0.8071 (m-30) cc_final: 0.7753 (m-30) REVERT: A 160 LYS cc_start: 0.8446 (tmmm) cc_final: 0.8123 (tmmm) REVERT: A 161 ARG cc_start: 0.8062 (mmm-85) cc_final: 0.7768 (mmm-85) REVERT: A 197 ARG cc_start: 0.8873 (tmt90) cc_final: 0.8561 (ttp-170) REVERT: A 293 LYS cc_start: 0.8684 (tptp) cc_final: 0.8466 (tttp) REVERT: A 342 TYR cc_start: 0.8695 (m-80) cc_final: 0.8418 (m-80) REVERT: A 347 GLN cc_start: 0.8585 (tp40) cc_final: 0.8348 (tp40) REVERT: A 403 ASN cc_start: 0.8387 (t0) cc_final: 0.8117 (t0) REVERT: A 406 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7875 (ttp80) REVERT: B 46 MET cc_start: 0.8960 (tpp) cc_final: 0.8522 (mmm) REVERT: B 103 LYS cc_start: 0.8498 (tppp) cc_final: 0.8284 (ttmm) REVERT: B 118 SER cc_start: 0.8442 (m) cc_final: 0.8106 (p) REVERT: B 150 SER cc_start: 0.7871 (t) cc_final: 0.7586 (p) REVERT: B 162 LYS cc_start: 0.7276 (tppp) cc_final: 0.7034 (mttm) REVERT: B 233 TYR cc_start: 0.7816 (OUTLIER) cc_final: 0.7353 (m-80) REVERT: B 249 GLU cc_start: 0.7569 (tp30) cc_final: 0.7233 (tp30) REVERT: B 264 MET cc_start: 0.7499 (mmt) cc_final: 0.7216 (mmt) REVERT: B 315 LYS cc_start: 0.8493 (ttpt) cc_final: 0.8201 (tttt) REVERT: B 346 GLN cc_start: 0.7825 (tt0) cc_final: 0.7254 (mp10) outliers start: 19 outliers final: 8 residues processed: 193 average time/residue: 0.5574 time to fit residues: 113.8018 Evaluate side-chains 190 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 180 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 52 optimal weight: 9.9990 chunk 87 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 43 optimal weight: 10.0000 chunk 44 optimal weight: 6.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 22 optimal weight: 10.0000 chunk 61 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 186 GLN B 194 HIS B 252 ASN B 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.137268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.108344 restraints weight = 14925.843| |-----------------------------------------------------------------------------| r_work (start): 0.3369 rms_B_bonded: 2.01 r_work: 0.3230 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3076 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 1.2135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 10001 Z= 0.192 Angle : 0.872 12.448 14149 Z= 0.398 Chirality : 0.064 0.400 1628 Planarity : 0.006 0.075 1293 Dihedral : 19.151 175.099 2561 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.46 % Allowed : 33.91 % Favored : 63.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.83 (0.29), residues: 797 helix: 2.09 (0.26), residues: 377 sheet: -0.22 (0.38), residues: 157 loop : -1.25 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG B 6 TYR 0.055 0.002 TYR B 402 PHE 0.012 0.002 PHE B 253 TRP 0.012 0.002 TRP B 43 HIS 0.003 0.001 HIS B 72 Details of bonding type rmsd/Z covalent geometry : bond 0.00430 / 0.19 ( 9997) covalent geometry : angle 0.86397 / 0.40 (14143) hydrogen bonds : bond 0.04819 / 2.91 ( 462) hydrogen bonds : angle 3.81985 / 2.85 ( 1238) metal coordination : bond 0.00779 / 0.38 ( 4) metal coordination : angle 5.62263 / 2.39 ( 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 210 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 193 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8133 (tp40) cc_final: 0.7899 (mm-40) REVERT: A 50 SER cc_start: 0.8314 (m) cc_final: 0.8033 (t) REVERT: A 51 ASP cc_start: 0.8090 (m-30) cc_final: 0.7890 (m-30) REVERT: A 160 LYS cc_start: 0.8573 (tmmm) cc_final: 0.8316 (tmmm) REVERT: A 161 ARG cc_start: 0.8125 (mmm-85) cc_final: 0.7863 (mmm160) REVERT: A 197 ARG cc_start: 0.8912 (tmt90) cc_final: 0.8637 (ttp-170) REVERT: A 262 ILE cc_start: 0.8738 (mm) cc_final: 0.8476 (tp) REVERT: A 291 ARG cc_start: 0.8061 (ttp-170) cc_final: 0.7650 (ttm170) REVERT: A 347 GLN cc_start: 0.8559 (tp40) cc_final: 0.8330 (tp40) REVERT: A 403 ASN cc_start: 0.8392 (t0) cc_final: 0.8121 (t0) REVERT: A 406 ARG cc_start: 0.8161 (OUTLIER) cc_final: 0.7866 (ttp80) REVERT: A 420 SER cc_start: 0.7726 (m) cc_final: 0.7462 (p) REVERT: B 46 MET cc_start: 0.8964 (tpp) cc_final: 0.8710 (mmt) REVERT: B 103 LYS cc_start: 0.8492 (tppp) cc_final: 0.8271 (ttmm) REVERT: B 118 SER cc_start: 0.8552 (m) cc_final: 0.8222 (p) REVERT: B 150 SER cc_start: 0.7973 (t) cc_final: 0.7564 (p) REVERT: B 157 MET cc_start: 0.8226 (mmp) cc_final: 0.7672 (mpp) REVERT: B 233 TYR cc_start: 0.8081 (OUTLIER) cc_final: 0.7657 (m-80) REVERT: B 249 GLU cc_start: 0.7631 (tp30) cc_final: 0.7278 (tp30) REVERT: B 264 MET cc_start: 0.7641 (mmt) cc_final: 0.7313 (mmt) REVERT: B 315 LYS cc_start: 0.8467 (ttpt) cc_final: 0.8267 (tttt) REVERT: B 346 GLN cc_start: 0.7911 (tt0) cc_final: 0.7256 (mp10) REVERT: B 362 LYS cc_start: 0.8357 (OUTLIER) cc_final: 0.8143 (mmmm) REVERT: B 402 TYR cc_start: 0.7334 (t80) cc_final: 0.6966 (m-80) outliers start: 17 outliers final: 13 residues processed: 202 average time/residue: 0.6044 time to fit residues: 128.7438 Evaluate side-chains 212 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 196 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 ILE Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 361 ILE Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 339 ASN Chi-restraints excluded: chain B residue 349 ILE Chi-restraints excluded: chain B residue 362 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 92 random chunks: chunk 57 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 1.9990 chunk 43 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 85 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 14 optimal weight: 2.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 87 ASN A 93 GLN A 131 ASN A 186 GLN B 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.138506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3401 r_free = 0.3401 target = 0.109840 restraints weight = 14821.210| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.99 r_work: 0.3248 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.3092 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3092 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8288 moved from start: 1.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10001 Z= 0.158 Angle : 0.848 12.343 14149 Z= 0.389 Chirality : 0.063 0.387 1628 Planarity : 0.005 0.067 1293 Dihedral : 19.155 176.803 2561 Min Nonbonded Distance : 2.005 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.17 % Allowed : 34.93 % Favored : 62.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.29), residues: 797 helix: 2.09 (0.26), residues: 377 sheet: -0.16 (0.38), residues: 157 loop : -1.24 (0.36), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG B 6 TYR 0.036 0.002 TYR B 402 PHE 0.013 0.001 PHE B 253 TRP 0.011 0.002 TRP B 45 HIS 0.003 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 ( 9997) covalent geometry : angle 0.84121 / 0.39 (14143) hydrogen bonds : bond 0.04584 / 2.81 ( 462) hydrogen bonds : angle 3.83592 / 2.85 ( 1238) metal coordination : bond 0.00660 / 0.32 ( 4) metal coordination : angle 5.29187 / 2.21 ( 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 219 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 204 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 29 GLN cc_start: 0.8120 (tp40) cc_final: 0.7880 (mm-40) REVERT: A 50 SER cc_start: 0.8378 (m) cc_final: 0.8111 (t) REVERT: A 51 ASP cc_start: 0.8104 (m-30) cc_final: 0.7809 (m-30) REVERT: A 129 LYS cc_start: 0.9330 (ttmt) cc_final: 0.9127 (ttmm) REVERT: A 134 VAL cc_start: 0.8601 (OUTLIER) cc_final: 0.8261 (t) REVERT: A 160 LYS cc_start: 0.8590 (tmmm) cc_final: 0.8318 (tmmm) REVERT: A 161 ARG cc_start: 0.8165 (mmm-85) cc_final: 0.7862 (mmm160) REVERT: A 178 ASP cc_start: 0.8700 (m-30) cc_final: 0.8368 (m-30) REVERT: A 197 ARG cc_start: 0.8890 (tmt90) cc_final: 0.8616 (ttp-170) REVERT: A 291 ARG cc_start: 0.8050 (ttp-170) cc_final: 0.7663 (ttm170) REVERT: A 403 ASN cc_start: 0.8325 (t0) cc_final: 0.8083 (t0) REVERT: A 406 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7733 (ttp80) REVERT: A 420 SER cc_start: 0.7820 (m) cc_final: 0.7529 (p) REVERT: B 46 MET cc_start: 0.8952 (tpp) cc_final: 0.8713 (mmt) REVERT: B 103 LYS cc_start: 0.8484 (tppp) cc_final: 0.8278 (ttmm) REVERT: B 118 SER cc_start: 0.8512 (m) cc_final: 0.8175 (p) REVERT: B 120 LYS cc_start: 0.8994 (mmmm) cc_final: 0.8363 (tppp) REVERT: B 150 SER cc_start: 0.7984 (t) cc_final: 0.7543 (p) REVERT: B 157 MET cc_start: 0.8283 (mmp) cc_final: 0.7789 (mpp) REVERT: B 177 MET cc_start: 0.8125 (mmp) cc_final: 0.7690 (mmm) REVERT: B 200 LYS cc_start: 0.8011 (mttt) cc_final: 0.7124 (mttt) REVERT: B 233 TYR cc_start: 0.8034 (OUTLIER) cc_final: 0.7582 (m-80) REVERT: B 249 GLU cc_start: 0.7544 (tp30) cc_final: 0.7209 (tp30) REVERT: B 264 MET cc_start: 0.7677 (mmt) cc_final: 0.7366 (mmt) REVERT: B 289 GLN cc_start: 0.7152 (tp40) cc_final: 0.6916 (tp40) REVERT: B 346 GLN cc_start: 0.7928 (tt0) cc_final: 0.7285 (mp10) outliers start: 15 outliers final: 10 residues processed: 213 average time/residue: 0.5797 time to fit residues: 130.5102 Evaluate side-chains 205 residues out of total 700 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 192 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 ASN Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 257 VAL Chi-restraints excluded: chain A residue 294 ILE Chi-restraints excluded: chain A residue 406 ARG Chi-restraints excluded: chain B residue 26 GLN Chi-restraints excluded: chain B residue 50 SER Chi-restraints excluded: chain B residue 129 LYS Chi-restraints excluded: chain B residue 196 ASP Chi-restraints excluded: chain B residue 214 ARG Chi-restraints excluded: chain B residue 233 TYR Chi-restraints excluded: chain B residue 246 GLU Chi-restraints excluded: chain B residue 310 VAL 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: 8.9990 chunk 50 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 57 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 12 optimal weight: 0.8980 chunk 21 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 186 GLN B 87 ASN B 252 ASN B 303 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3776 r_free = 0.3776 target = 0.136223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.107620 restraints weight = 14785.252| |-----------------------------------------------------------------------------| r_work (start): 0.3353 rms_B_bonded: 1.96 r_work: 0.3215 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3059 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3059 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 1.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10001 Z= 0.223 Angle : 0.890 12.269 14149 Z= 0.409 Chirality : 0.065 0.396 1628 Planarity : 0.006 0.089 1293 Dihedral : 19.124 176.442 2561 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.75 % Allowed : 34.20 % Favored : 63.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.82 (0.29), residues: 797 helix: 2.03 (0.26), residues: 377 sheet: -0.10 (0.39), residues: 157 loop : -1.26 (0.35), residues: 263 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.020 0.001 ARG B 6 TYR 0.018 0.002 TYR B 185 PHE 0.014 0.002 PHE B 253 TRP 0.013 0.002 TRP B 43 HIS 0.005 0.001 HIS B 194 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.22 ( 9997) covalent geometry : angle 0.88284 / 0.41 (14143) hydrogen bonds : bond 0.04894 / 2.96 ( 462) hydrogen bonds : angle 3.82782 / 2.85 ( 1238) metal coordination : bond 0.00773 / 0.37 ( 4) metal coordination : angle 5.49357 / 2.35 ( 6) =============================================================================== Job complete usr+sys time: 3163.01 seconds wall clock time: 54 minutes 29.03 seconds (3269.03 seconds total)