Starting phenix.real_space_refine on Wed Mar 4 09:01:43 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f0j_31399/03_2026/7f0j_31399.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f0j_31399/03_2026/7f0j_31399.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7f0j_31399/03_2026/7f0j_31399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f0j_31399/03_2026/7f0j_31399.map" model { file = "/net/cci-nas-00/data/ceres_data/7f0j_31399/03_2026/7f0j_31399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f0j_31399/03_2026/7f0j_31399.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 64 5.16 5 C 8036 2.51 5 N 2112 2.21 5 O 2208 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12424 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3105 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 14, 'TRANS': 371} Chain breaks: 2 Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 788 SG CYS B 132 60.801 38.204 86.720 1.00 41.28 S ATOM 794 SG CYS B 133 61.054 41.812 88.010 1.00 40.69 S Restraints were copied for chains: C, F, H Time building chain proxies: 2.22, per 1000 atoms: 0.18 Number of scatterers: 12424 At special positions: 0 Unit cell: (105.825, 105.825, 134.045, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 64 16.00 O 2208 8.00 N 2112 7.00 C 8036 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: 0.97 Conformation dependent library (CDL) restraints added in 605.0 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" ND1 HIS B 105 " pdb="ZN ZN B 701 " - pdb=" SG CYS H 111 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 132 " pdb="ZN ZN B 701 " - pdb=" SG CYS B 133 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" ND1 HIS C 105 " pdb="ZN ZN C 701 " - pdb=" SG CYS B 111 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 132 " pdb="ZN ZN C 701 " - pdb=" SG CYS C 133 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" ND1 HIS F 105 " pdb="ZN ZN F 701 " - pdb=" SG CYS C 111 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 132 " pdb="ZN ZN F 701 " - pdb=" SG CYS F 133 " pdb=" ZN H 701 " pdb="ZN ZN H 701 " - pdb=" ND1 HIS H 105 " pdb="ZN ZN H 701 " - pdb=" SG CYS F 111 " pdb="ZN ZN H 701 " - pdb=" SG CYS H 132 " pdb="ZN ZN H 701 " - pdb=" SG CYS H 133 " Number of angles added : 12 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2928 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 4 sheets defined 75.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'B' and resid 56 through 60 Processing helix chain 'B' and resid 69 through 75 removed outlier: 4.081A pdb=" N ASP B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE B 92 " --> pdb=" O ASP B 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS B 94 " --> pdb=" O ASP B 90 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 122 Processing helix chain 'B' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE B 128 " --> pdb=" O ILE B 125 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE B 129 " --> pdb=" O PRO B 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 125 through 129' Processing helix chain 'B' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG B 147 " --> pdb=" O GLU B 143 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 158 No H-bonds generated for 'chain 'B' and resid 156 through 158' Processing helix chain 'B' and resid 166 through 166 No H-bonds generated for 'chain 'B' and resid 166 through 166' Processing helix chain 'B' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL B 171 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP B 172 " --> pdb=" O ARG B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 182 through 205 Processing helix chain 'B' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE B 230 " --> pdb=" O ALA B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 253 through 260 Processing helix chain 'B' and resid 260 through 280 Proline residue: B 272 - end of helix Processing helix chain 'B' and resid 281 through 283 No H-bonds generated for 'chain 'B' and resid 281 through 283' Processing helix chain 'B' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR B 291 " --> pdb=" O GLY B 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG B 296 " --> pdb=" O LEU B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE B 303 " --> pdb=" O ILE B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG B 311 " --> pdb=" O SER B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 320 through 347 Processing helix chain 'B' and resid 356 through 369 removed outlier: 4.024A pdb=" N TRP B 362 " --> pdb=" O PRO B 358 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR B 363 " --> pdb=" O ALA B 359 " (cutoff:3.500A) Processing helix chain 'B' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU B 392 " --> pdb=" O SER B 388 " (cutoff:3.500A) Processing helix chain 'B' and resid 401 through 435 Processing helix chain 'C' and resid 56 through 60 Processing helix chain 'C' and resid 69 through 75 removed outlier: 4.081A pdb=" N ASP C 73 " --> pdb=" O SER C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE C 92 " --> pdb=" O ASP C 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS C 94 " --> pdb=" O ASP C 90 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 122 Processing helix chain 'C' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE C 128 " --> pdb=" O ILE C 125 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 129 " --> pdb=" O PRO C 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 125 through 129' Processing helix chain 'C' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG C 147 " --> pdb=" O GLU C 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 156 through 158 No H-bonds generated for 'chain 'C' and resid 156 through 158' Processing helix chain 'C' and resid 166 through 166 No H-bonds generated for 'chain 'C' and resid 166 through 166' Processing helix chain 'C' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL C 171 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP C 172 " --> pdb=" O ARG C 168 " (cutoff:3.500A) Processing helix chain 'C' and resid 182 through 205 Processing helix chain 'C' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE C 230 " --> pdb=" O ALA C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 260 Processing helix chain 'C' and resid 260 through 280 Proline residue: C 272 - end of helix Processing helix chain 'C' and resid 281 through 283 No H-bonds generated for 'chain 'C' and resid 281 through 283' Processing helix chain 'C' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR C 291 " --> pdb=" O GLY C 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG C 296 " --> pdb=" O LEU C 292 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE C 303 " --> pdb=" O ILE C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG C 311 " --> pdb=" O SER C 307 " (cutoff:3.500A) Processing helix chain 'C' and resid 320 through 347 Processing helix chain 'C' and resid 356 through 369 removed outlier: 4.024A pdb=" N TRP C 362 " --> pdb=" O PRO C 358 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR C 363 " --> pdb=" O ALA C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU C 392 " --> pdb=" O SER C 388 " (cutoff:3.500A) Processing helix chain 'C' and resid 401 through 435 Processing helix chain 'F' and resid 56 through 60 Processing helix chain 'F' and resid 69 through 75 removed outlier: 4.080A pdb=" N ASP F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE F 92 " --> pdb=" O ASP F 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS F 94 " --> pdb=" O ASP F 90 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 122 Processing helix chain 'F' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE F 128 " --> pdb=" O ILE F 125 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE F 129 " --> pdb=" O PRO F 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 125 through 129' Processing helix chain 'F' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG F 147 " --> pdb=" O GLU F 143 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 158 No H-bonds generated for 'chain 'F' and resid 156 through 158' Processing helix chain 'F' and resid 166 through 166 No H-bonds generated for 'chain 'F' and resid 166 through 166' Processing helix chain 'F' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL F 171 " --> pdb=" O ALA F 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP F 172 " --> pdb=" O ARG F 168 " (cutoff:3.500A) Processing helix chain 'F' and resid 182 through 205 Processing helix chain 'F' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE F 230 " --> pdb=" O ALA F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 253 through 260 Processing helix chain 'F' and resid 260 through 280 Proline residue: F 272 - end of helix Processing helix chain 'F' and resid 281 through 283 No H-bonds generated for 'chain 'F' and resid 281 through 283' Processing helix chain 'F' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR F 291 " --> pdb=" O GLY F 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 296 " --> pdb=" O LEU F 292 " (cutoff:3.500A) Processing helix chain 'F' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE F 303 " --> pdb=" O ILE F 300 " (cutoff:3.500A) Processing helix chain 'F' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG F 311 " --> pdb=" O SER F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 320 through 347 Processing helix chain 'F' and resid 356 through 369 removed outlier: 4.025A pdb=" N TRP F 362 " --> pdb=" O PRO F 358 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TYR F 363 " --> pdb=" O ALA F 359 " (cutoff:3.500A) Processing helix chain 'F' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU F 392 " --> pdb=" O SER F 388 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 435 Processing helix chain 'H' and resid 56 through 60 Processing helix chain 'H' and resid 69 through 75 removed outlier: 4.081A pdb=" N ASP H 73 " --> pdb=" O SER H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 101 removed outlier: 3.612A pdb=" N PHE H 92 " --> pdb=" O ASP H 88 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N HIS H 94 " --> pdb=" O ASP H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 122 Processing helix chain 'H' and resid 125 through 129 removed outlier: 3.617A pdb=" N ILE H 128 " --> pdb=" O ILE H 125 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N ILE H 129 " --> pdb=" O PRO H 126 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 125 through 129' Processing helix chain 'H' and resid 133 through 155 removed outlier: 3.623A pdb=" N ARG H 147 " --> pdb=" O GLU H 143 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 158 No H-bonds generated for 'chain 'H' and resid 156 through 158' Processing helix chain 'H' and resid 166 through 166 No H-bonds generated for 'chain 'H' and resid 166 through 166' Processing helix chain 'H' and resid 167 through 175 removed outlier: 3.980A pdb=" N VAL H 171 " --> pdb=" O ALA H 167 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N TRP H 172 " --> pdb=" O ARG H 168 " (cutoff:3.500A) Processing helix chain 'H' and resid 182 through 205 Processing helix chain 'H' and resid 226 through 251 removed outlier: 4.177A pdb=" N PHE H 230 " --> pdb=" O ALA H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 253 through 260 Processing helix chain 'H' and resid 260 through 280 Proline residue: H 272 - end of helix Processing helix chain 'H' and resid 281 through 283 No H-bonds generated for 'chain 'H' and resid 281 through 283' Processing helix chain 'H' and resid 287 through 296 removed outlier: 4.012A pdb=" N THR H 291 " --> pdb=" O GLY H 287 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG H 296 " --> pdb=" O LEU H 292 " (cutoff:3.500A) Processing helix chain 'H' and resid 297 through 305 removed outlier: 3.501A pdb=" N PHE H 303 " --> pdb=" O ILE H 300 " (cutoff:3.500A) Processing helix chain 'H' and resid 307 through 320 removed outlier: 3.702A pdb=" N ARG H 311 " --> pdb=" O SER H 307 " (cutoff:3.500A) Processing helix chain 'H' and resid 320 through 347 Processing helix chain 'H' and resid 356 through 369 removed outlier: 4.025A pdb=" N TRP H 362 " --> pdb=" O PRO H 358 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TYR H 363 " --> pdb=" O ALA H 359 " (cutoff:3.500A) Processing helix chain 'H' and resid 380 through 400 removed outlier: 3.697A pdb=" N LEU H 392 " --> pdb=" O SER H 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 401 through 435 Processing sheet with id=AA1, first strand: chain 'B' and resid 42 through 44 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 44 Processing sheet with id=AA3, first strand: chain 'F' and resid 42 through 44 Processing sheet with id=AA4, first strand: chain 'H' and resid 42 through 44 792 hydrogen bonds defined for protein. 2316 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.86 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3952 1.34 - 1.46: 2801 1.46 - 1.58: 5871 1.58 - 1.69: 0 1.69 - 1.81: 96 Bond restraints: 12720 Sorted by residual: bond pdb=" C TYR C 106 " pdb=" O TYR C 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" C TYR B 106 " pdb=" O TYR B 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" C TYR H 106 " pdb=" O TYR H 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" C TYR F 106 " pdb=" O TYR F 106 " ideal model delta sigma weight residual 1.248 1.237 0.011 1.26e-02 6.30e+03 7.69e-01 bond pdb=" CB PRO B 401 " pdb=" CG PRO B 401 " ideal model delta sigma weight residual 1.492 1.533 -0.041 5.00e-02 4.00e+02 6.80e-01 ... (remaining 12715 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 16671 1.31 - 2.63: 445 2.63 - 3.94: 88 3.94 - 5.25: 20 5.25 - 6.57: 8 Bond angle restraints: 17232 Sorted by residual: angle pdb=" C ILE B 270 " pdb=" N LEU B 271 " pdb=" CA LEU B 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" C ILE C 270 " pdb=" N LEU C 271 " pdb=" CA LEU C 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" C ILE H 270 " pdb=" N LEU H 271 " pdb=" CA LEU H 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" C ILE F 270 " pdb=" N LEU F 271 " pdb=" CA LEU F 271 " ideal model delta sigma weight residual 120.09 123.61 -3.52 1.25e+00 6.40e-01 7.95e+00 angle pdb=" N ASN C 46 " pdb=" CA ASN C 46 " pdb=" C ASN C 46 " ideal model delta sigma weight residual 110.23 113.34 -3.11 1.45e+00 4.76e-01 4.61e+00 ... (remaining 17227 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 6476 14.14 - 28.27: 716 28.27 - 42.41: 272 42.41 - 56.55: 36 56.55 - 70.68: 4 Dihedral angle restraints: 7504 sinusoidal: 2964 harmonic: 4540 Sorted by residual: dihedral pdb=" CA ASN B 46 " pdb=" C ASN B 46 " pdb=" N VAL B 47 " pdb=" CA VAL B 47 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN C 46 " pdb=" C ASN C 46 " pdb=" N VAL C 47 " pdb=" CA VAL C 47 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CA ASN H 46 " pdb=" C ASN H 46 " pdb=" N VAL H 47 " pdb=" CA VAL H 47 " ideal model delta harmonic sigma weight residual 180.00 163.50 16.50 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 7501 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 1109 0.026 - 0.052: 452 0.052 - 0.077: 237 0.077 - 0.103: 94 0.103 - 0.128: 36 Chirality restraints: 1928 Sorted by residual: chirality pdb=" CA GLN F 417 " pdb=" N GLN F 417 " pdb=" C GLN F 417 " pdb=" CB GLN F 417 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA GLN C 417 " pdb=" N GLN C 417 " pdb=" C GLN C 417 " pdb=" CB GLN C 417 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA GLN H 417 " pdb=" N GLN H 417 " pdb=" C GLN H 417 " pdb=" CB GLN H 417 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.12e-01 ... (remaining 1925 not shown) Planarity restraints: 2180 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL F 402 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO F 403 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO F 403 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO F 403 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL H 402 " 0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO H 403 " -0.132 5.00e-02 4.00e+02 pdb=" CA PRO H 403 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 403 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL C 402 " -0.050 5.00e-02 4.00e+02 7.63e-02 9.32e+00 pdb=" N PRO C 403 " 0.132 5.00e-02 4.00e+02 pdb=" CA PRO C 403 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 403 " -0.042 5.00e-02 4.00e+02 ... (remaining 2177 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3376 2.81 - 3.33: 12628 3.33 - 3.85: 20757 3.85 - 4.38: 23097 4.38 - 4.90: 39616 Nonbonded interactions: 99474 Sorted by model distance: nonbonded pdb=" O CYS C 231 " pdb=" OG1 THR C 234 " model vdw 2.281 3.040 nonbonded pdb=" O CYS F 231 " pdb=" OG1 THR F 234 " model vdw 2.281 3.040 nonbonded pdb=" O CYS B 231 " pdb=" OG1 THR B 234 " model vdw 2.281 3.040 nonbonded pdb=" O CYS H 231 " pdb=" OG1 THR H 234 " model vdw 2.281 3.040 nonbonded pdb=" OD1 ASP F 86 " pdb=" NH1 ARG H 100 " model vdw 2.318 3.120 ... (remaining 99469 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: 0.04 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'H' } 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: 0.550 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: 0.160 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 12.750 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7076 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12736 Z= 0.115 Angle : 0.540 6.566 17244 Z= 0.292 Chirality : 0.039 0.128 1928 Planarity : 0.006 0.076 2180 Dihedral : 13.592 70.682 4576 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.21), residues: 1520 helix: 1.50 (0.16), residues: 1056 sheet: None (None), residues: 0 loop : -2.12 (0.26), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 296 TYR 0.015 0.001 TYR F 413 PHE 0.010 0.001 PHE C 338 TRP 0.008 0.001 TRP C 362 HIS 0.002 0.000 HIS H 306 Details of bonding type rmsd covalent geometry : bond 0.00239 (12720) covalent geometry : angle 0.53769 (17232) hydrogen bonds : bond 0.11370 ( 792) hydrogen bonds : angle 4.48092 ( 2316) metal coordination : bond 0.00511 ( 16) metal coordination : angle 1.78044 ( 12) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.456 Fit side-chains REVERT: B 109 HIS cc_start: 0.7478 (p-80) cc_final: 0.6198 (m170) REVERT: B 233 ASP cc_start: 0.7941 (t0) cc_final: 0.7532 (t0) REVERT: B 262 MET cc_start: 0.6732 (mmm) cc_final: 0.6250 (mmm) REVERT: C 233 ASP cc_start: 0.7936 (t0) cc_final: 0.7527 (t0) REVERT: C 262 MET cc_start: 0.6796 (mmm) cc_final: 0.6269 (mmm) REVERT: F 233 ASP cc_start: 0.7939 (t0) cc_final: 0.7529 (t0) REVERT: F 262 MET cc_start: 0.6796 (mmm) cc_final: 0.6271 (mmm) REVERT: H 233 ASP cc_start: 0.7943 (t0) cc_final: 0.7531 (t0) REVERT: H 262 MET cc_start: 0.6800 (mmm) cc_final: 0.6268 (mmm) outliers start: 0 outliers final: 4 residues processed: 280 average time/residue: 0.5084 time to fit residues: 155.9421 Evaluate side-chains 190 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 186 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain C residue 112 ILE Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain H residue 112 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 98 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 0.0770 chunk 124 optimal weight: 8.9990 chunk 103 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 7.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 3.9990 overall best weight: 1.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 416 ASN C 46 ASN C 416 ASN F 46 ASN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 46 ASN H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.225288 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.192350 restraints weight = 14094.378| |-----------------------------------------------------------------------------| r_work (start): 0.4131 rms_B_bonded: 1.76 r_work: 0.3698 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7688 moved from start: 0.1742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12736 Z= 0.168 Angle : 0.579 7.781 17244 Z= 0.313 Chirality : 0.042 0.140 1928 Planarity : 0.006 0.064 2180 Dihedral : 4.411 32.787 1744 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.71 % Allowed : 12.35 % Favored : 84.94 % 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: 0.69 (0.22), residues: 1520 helix: 1.56 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.30 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 51 TYR 0.017 0.002 TYR F 188 PHE 0.022 0.002 PHE B 175 TRP 0.013 0.002 TRP H 362 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00396 (12720) covalent geometry : angle 0.57646 (17232) hydrogen bonds : bond 0.04470 ( 792) hydrogen bonds : angle 3.83372 ( 2316) metal coordination : bond 0.00400 ( 16) metal coordination : angle 2.19964 ( 12) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 188 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 HIS cc_start: 0.7534 (p-80) cc_final: 0.6083 (m170) REVERT: B 183 MET cc_start: 0.4833 (OUTLIER) cc_final: 0.4560 (ttp) REVERT: B 233 ASP cc_start: 0.8367 (t0) cc_final: 0.7818 (t0) REVERT: C 183 MET cc_start: 0.4837 (OUTLIER) cc_final: 0.4569 (ttp) REVERT: C 233 ASP cc_start: 0.8366 (t0) cc_final: 0.7814 (t0) REVERT: F 183 MET cc_start: 0.4860 (OUTLIER) cc_final: 0.4596 (ttp) REVERT: F 233 ASP cc_start: 0.8374 (t0) cc_final: 0.7820 (t0) REVERT: H 183 MET cc_start: 0.4850 (OUTLIER) cc_final: 0.4583 (ttp) REVERT: H 233 ASP cc_start: 0.8369 (t0) cc_final: 0.7816 (t0) outliers start: 36 outliers final: 12 residues processed: 204 average time/residue: 0.4977 time to fit residues: 111.2488 Evaluate side-chains 181 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 165 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 121 PHE Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 chunk 133 optimal weight: 6.9990 chunk 29 optimal weight: 0.9980 chunk 77 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 56 GLN B 416 ASN C 46 ASN C 56 GLN C 416 ASN F 46 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 46 ASN H 56 GLN H 416 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.226232 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.191921 restraints weight = 14161.126| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.78 r_work: 0.3701 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3626 rms_B_bonded: 3.53 restraints_weight: 0.2500 r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 12736 Z= 0.129 Angle : 0.534 7.825 17244 Z= 0.287 Chirality : 0.040 0.120 1928 Planarity : 0.005 0.060 2180 Dihedral : 3.921 16.029 1736 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 3.61 % Allowed : 14.38 % Favored : 82.00 % 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 (0.22), residues: 1520 helix: 1.61 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.27 (0.27), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 51 TYR 0.016 0.001 TYR H 188 PHE 0.020 0.002 PHE F 289 TRP 0.011 0.001 TRP C 362 HIS 0.003 0.001 HIS B 306 Details of bonding type rmsd covalent geometry : bond 0.00286 (12720) covalent geometry : angle 0.52951 (17232) hydrogen bonds : bond 0.03858 ( 792) hydrogen bonds : angle 3.70879 ( 2316) metal coordination : bond 0.00426 ( 16) metal coordination : angle 2.66918 ( 12) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 192 time to evaluate : 0.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 HIS cc_start: 0.7497 (p-80) cc_final: 0.6082 (m170) REVERT: B 122 PHE cc_start: 0.8526 (m-80) cc_final: 0.8204 (m-80) REVERT: B 233 ASP cc_start: 0.8304 (t0) cc_final: 0.7751 (t0) REVERT: B 238 MET cc_start: 0.7272 (ttm) cc_final: 0.7006 (ttp) REVERT: C 122 PHE cc_start: 0.8518 (m-80) cc_final: 0.8199 (m-80) REVERT: C 233 ASP cc_start: 0.8305 (t0) cc_final: 0.7745 (t0) REVERT: C 238 MET cc_start: 0.7282 (ttm) cc_final: 0.7022 (ttp) REVERT: F 122 PHE cc_start: 0.8525 (m-80) cc_final: 0.8211 (m-80) REVERT: F 233 ASP cc_start: 0.8324 (t0) cc_final: 0.7766 (t0) REVERT: F 238 MET cc_start: 0.7270 (ttm) cc_final: 0.7008 (ttp) REVERT: H 122 PHE cc_start: 0.8529 (m-80) cc_final: 0.8216 (m-80) REVERT: H 233 ASP cc_start: 0.8325 (t0) cc_final: 0.7761 (t0) REVERT: H 238 MET cc_start: 0.7240 (ttm) cc_final: 0.6978 (ttp) outliers start: 48 outliers final: 4 residues processed: 220 average time/residue: 0.4777 time to fit residues: 115.0410 Evaluate side-chains 160 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 156 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 148 optimal weight: 2.9990 chunk 112 optimal weight: 5.9990 chunk 18 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 75 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 109 optimal weight: 0.5980 chunk 14 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 127 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 416 ASN C 46 ASN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 46 ASN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 46 ASN H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.226191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.191898 restraints weight = 14088.273| |-----------------------------------------------------------------------------| r_work (start): 0.4133 rms_B_bonded: 1.84 r_work: 0.3625 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2162 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12736 Z= 0.125 Angle : 0.517 7.876 17244 Z= 0.278 Chirality : 0.040 0.119 1928 Planarity : 0.005 0.061 2180 Dihedral : 3.873 15.842 1736 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.71 % Allowed : 15.89 % Favored : 81.40 % 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: 0.77 (0.21), residues: 1520 helix: 1.64 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 51 TYR 0.016 0.001 TYR C 188 PHE 0.024 0.001 PHE C 121 TRP 0.010 0.001 TRP F 362 HIS 0.003 0.001 HIS F 306 Details of bonding type rmsd covalent geometry : bond 0.00289 (12720) covalent geometry : angle 0.51351 (17232) hydrogen bonds : bond 0.03859 ( 792) hydrogen bonds : angle 3.62460 ( 2316) metal coordination : bond 0.00802 ( 16) metal coordination : angle 2.38508 ( 12) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 185 time to evaluate : 0.428 Fit side-chains REVERT: B 109 HIS cc_start: 0.7511 (p-80) cc_final: 0.6024 (m170) REVERT: B 183 MET cc_start: 0.4447 (OUTLIER) cc_final: 0.4207 (ttp) REVERT: B 233 ASP cc_start: 0.8365 (t0) cc_final: 0.7821 (t0) REVERT: B 238 MET cc_start: 0.7439 (ttm) cc_final: 0.7161 (ttp) REVERT: C 183 MET cc_start: 0.4461 (OUTLIER) cc_final: 0.4217 (ttp) REVERT: C 233 ASP cc_start: 0.8357 (t0) cc_final: 0.7806 (t0) REVERT: C 238 MET cc_start: 0.7431 (ttm) cc_final: 0.7156 (ttp) REVERT: F 183 MET cc_start: 0.4468 (OUTLIER) cc_final: 0.4227 (ttp) REVERT: F 233 ASP cc_start: 0.8367 (t0) cc_final: 0.7822 (t0) REVERT: F 238 MET cc_start: 0.7409 (ttm) cc_final: 0.7136 (ttp) REVERT: H 183 MET cc_start: 0.4462 (OUTLIER) cc_final: 0.4224 (ttp) REVERT: H 233 ASP cc_start: 0.8372 (t0) cc_final: 0.7816 (t0) REVERT: H 238 MET cc_start: 0.7403 (ttm) cc_final: 0.7124 (ttp) outliers start: 36 outliers final: 16 residues processed: 209 average time/residue: 0.5566 time to fit residues: 126.2341 Evaluate side-chains 176 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 156 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 121 PHE Chi-restraints excluded: chain B residue 143 GLU Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 121 PHE Chi-restraints excluded: chain C residue 143 GLU Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 121 PHE Chi-restraints excluded: chain F residue 143 GLU Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 121 PHE Chi-restraints excluded: chain H residue 143 GLU Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 29 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 48 optimal weight: 9.9990 chunk 58 optimal weight: 0.4980 chunk 30 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 144 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 77 optimal weight: 10.0000 chunk 148 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.225652 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.191120 restraints weight = 14221.702| |-----------------------------------------------------------------------------| r_work (start): 0.4127 rms_B_bonded: 1.82 r_work: 0.3643 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3519 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7754 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12736 Z= 0.130 Angle : 0.523 8.276 17244 Z= 0.280 Chirality : 0.040 0.119 1928 Planarity : 0.005 0.060 2180 Dihedral : 3.898 17.194 1736 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.53 % Favored : 94.47 % Rotamer: Outliers : 2.41 % Allowed : 17.09 % Favored : 80.50 % 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: 0.81 (0.21), residues: 1520 helix: 1.66 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 87 TYR 0.016 0.001 TYR H 188 PHE 0.020 0.002 PHE B 289 TRP 0.011 0.001 TRP F 362 HIS 0.003 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00300 (12720) covalent geometry : angle 0.52021 (17232) hydrogen bonds : bond 0.03881 ( 792) hydrogen bonds : angle 3.63373 ( 2316) metal coordination : bond 0.00457 ( 16) metal coordination : angle 2.21876 ( 12) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 206 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.453 Fit side-chains REVERT: B 109 HIS cc_start: 0.7537 (p-80) cc_final: 0.6040 (m170) REVERT: B 147 ARG cc_start: 0.5497 (tmm-80) cc_final: 0.4722 (ttp-110) REVERT: B 183 MET cc_start: 0.4457 (OUTLIER) cc_final: 0.4189 (ttp) REVERT: B 233 ASP cc_start: 0.8372 (t0) cc_final: 0.7789 (t0) REVERT: B 238 MET cc_start: 0.7474 (ttm) cc_final: 0.7189 (ttp) REVERT: B 416 ASN cc_start: 0.7488 (t160) cc_final: 0.7225 (t0) REVERT: C 147 ARG cc_start: 0.5482 (tmm-80) cc_final: 0.4708 (ttp-110) REVERT: C 183 MET cc_start: 0.4477 (OUTLIER) cc_final: 0.4207 (ttp) REVERT: C 233 ASP cc_start: 0.8379 (t0) cc_final: 0.7793 (t0) REVERT: C 238 MET cc_start: 0.7473 (ttm) cc_final: 0.7191 (ttp) REVERT: C 416 ASN cc_start: 0.7475 (t160) cc_final: 0.7218 (t0) REVERT: F 147 ARG cc_start: 0.5493 (tmm-80) cc_final: 0.4716 (ttp-110) REVERT: F 183 MET cc_start: 0.4488 (OUTLIER) cc_final: 0.4223 (ttp) REVERT: F 233 ASP cc_start: 0.8382 (t0) cc_final: 0.7798 (t0) REVERT: F 238 MET cc_start: 0.7451 (ttm) cc_final: 0.7166 (ttp) REVERT: F 289 PHE cc_start: 0.7293 (t80) cc_final: 0.7076 (t80) REVERT: F 416 ASN cc_start: 0.7493 (t160) cc_final: 0.7244 (t0) REVERT: H 147 ARG cc_start: 0.5489 (tmm-80) cc_final: 0.4844 (ttp-110) REVERT: H 183 MET cc_start: 0.4475 (OUTLIER) cc_final: 0.4209 (ttp) REVERT: H 233 ASP cc_start: 0.8395 (t0) cc_final: 0.7808 (t0) REVERT: H 238 MET cc_start: 0.7449 (ttm) cc_final: 0.7161 (ttp) REVERT: H 416 ASN cc_start: 0.7499 (t160) cc_final: 0.7242 (t0) outliers start: 32 outliers final: 12 residues processed: 194 average time/residue: 0.5399 time to fit residues: 113.6235 Evaluate side-chains 174 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 158 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 5.9990 chunk 133 optimal weight: 0.9980 chunk 26 optimal weight: 3.9990 chunk 65 optimal weight: 0.7980 chunk 118 optimal weight: 2.9990 chunk 78 optimal weight: 0.0370 chunk 131 optimal weight: 0.0970 chunk 51 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 137 optimal weight: 10.0000 chunk 8 optimal weight: 0.2980 overall best weight: 0.4456 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 ASN H 56 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.226620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.191258 restraints weight = 14167.168| |-----------------------------------------------------------------------------| r_work (start): 0.4130 rms_B_bonded: 1.88 r_work: 0.3625 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12736 Z= 0.113 Angle : 0.517 8.544 17244 Z= 0.274 Chirality : 0.040 0.155 1928 Planarity : 0.005 0.059 2180 Dihedral : 3.746 16.355 1736 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.09 % Allowed : 17.47 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.93 (0.21), residues: 1520 helix: 1.77 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 51 TYR 0.016 0.001 TYR F 188 PHE 0.018 0.001 PHE C 175 TRP 0.010 0.001 TRP C 362 HIS 0.003 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00247 (12720) covalent geometry : angle 0.51370 (17232) hydrogen bonds : bond 0.03607 ( 792) hydrogen bonds : angle 3.53648 ( 2316) metal coordination : bond 0.00618 ( 16) metal coordination : angle 2.13073 ( 12) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 168 time to evaluate : 0.336 Fit side-chains REVERT: B 109 HIS cc_start: 0.7431 (p-80) cc_final: 0.5881 (m170) REVERT: B 233 ASP cc_start: 0.8295 (t0) cc_final: 0.7736 (t0) REVERT: B 238 MET cc_start: 0.7204 (ttm) cc_final: 0.6905 (ttp) REVERT: B 279 MET cc_start: 0.6404 (OUTLIER) cc_final: 0.6096 (tpp) REVERT: B 310 LEU cc_start: 0.8706 (mp) cc_final: 0.8365 (mt) REVERT: C 233 ASP cc_start: 0.8297 (t0) cc_final: 0.7731 (t0) REVERT: C 238 MET cc_start: 0.7167 (ttm) cc_final: 0.6870 (ttp) REVERT: C 279 MET cc_start: 0.6432 (OUTLIER) cc_final: 0.6133 (tpp) REVERT: C 310 LEU cc_start: 0.8698 (mp) cc_final: 0.8350 (mt) REVERT: F 233 ASP cc_start: 0.8292 (t0) cc_final: 0.7741 (t0) REVERT: F 238 MET cc_start: 0.7169 (ttm) cc_final: 0.6869 (ttp) REVERT: F 279 MET cc_start: 0.6429 (OUTLIER) cc_final: 0.6130 (tpp) REVERT: F 289 PHE cc_start: 0.7182 (t80) cc_final: 0.6968 (t80) REVERT: F 310 LEU cc_start: 0.8715 (mp) cc_final: 0.8360 (mt) REVERT: H 147 ARG cc_start: 0.5408 (tmm-80) cc_final: 0.4662 (ttp-110) REVERT: H 233 ASP cc_start: 0.8317 (t0) cc_final: 0.7751 (t0) REVERT: H 238 MET cc_start: 0.7176 (ttm) cc_final: 0.6872 (ttp) REVERT: H 279 MET cc_start: 0.6419 (OUTLIER) cc_final: 0.6121 (tpp) REVERT: H 310 LEU cc_start: 0.8711 (mp) cc_final: 0.8364 (mt) outliers start: 41 outliers final: 12 residues processed: 189 average time/residue: 0.5818 time to fit residues: 119.1331 Evaluate side-chains 169 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 13 optimal weight: 7.9990 chunk 140 optimal weight: 0.6980 chunk 148 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 107 optimal weight: 0.5980 chunk 53 optimal weight: 0.0170 chunk 22 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 144 optimal weight: 0.0570 chunk 47 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.4536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 56 GLN H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.227445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.193363 restraints weight = 14130.716| |-----------------------------------------------------------------------------| r_work (start): 0.4143 rms_B_bonded: 1.97 r_work: 0.3634 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.2458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 12736 Z= 0.112 Angle : 0.513 8.819 17244 Z= 0.272 Chirality : 0.040 0.187 1928 Planarity : 0.005 0.059 2180 Dihedral : 3.720 16.071 1736 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.25 % Favored : 93.75 % Rotamer: Outliers : 2.79 % Allowed : 18.52 % Favored : 78.69 % 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: 0.97 (0.21), residues: 1520 helix: 1.79 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 147 TYR 0.015 0.001 TYR B 188 PHE 0.022 0.001 PHE H 289 TRP 0.010 0.001 TRP C 362 HIS 0.003 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00247 (12720) covalent geometry : angle 0.51003 (17232) hydrogen bonds : bond 0.03595 ( 792) hydrogen bonds : angle 3.48798 ( 2316) metal coordination : bond 0.00657 ( 16) metal coordination : angle 2.01636 ( 12) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 165 time to evaluate : 0.502 Fit side-chains REVERT: B 109 HIS cc_start: 0.7469 (p-80) cc_final: 0.5908 (m170) REVERT: B 233 ASP cc_start: 0.8288 (t0) cc_final: 0.7723 (t0) REVERT: B 238 MET cc_start: 0.7179 (ttm) cc_final: 0.6891 (ttp) REVERT: B 279 MET cc_start: 0.6290 (OUTLIER) cc_final: 0.6000 (tpp) REVERT: B 310 LEU cc_start: 0.8715 (mp) cc_final: 0.8367 (mt) REVERT: C 233 ASP cc_start: 0.8288 (t0) cc_final: 0.7709 (t0) REVERT: C 238 MET cc_start: 0.7194 (ttm) cc_final: 0.6905 (ttp) REVERT: C 279 MET cc_start: 0.6310 (OUTLIER) cc_final: 0.6020 (tpp) REVERT: C 310 LEU cc_start: 0.8709 (mp) cc_final: 0.8356 (mt) REVERT: F 233 ASP cc_start: 0.8289 (t0) cc_final: 0.7720 (t0) REVERT: F 238 MET cc_start: 0.7182 (ttm) cc_final: 0.6895 (ttp) REVERT: F 279 MET cc_start: 0.6298 (OUTLIER) cc_final: 0.6003 (tpp) REVERT: F 310 LEU cc_start: 0.8726 (mp) cc_final: 0.8373 (mt) REVERT: H 233 ASP cc_start: 0.8314 (t0) cc_final: 0.7738 (t0) REVERT: H 238 MET cc_start: 0.7176 (ttm) cc_final: 0.6885 (ttp) REVERT: H 279 MET cc_start: 0.6306 (OUTLIER) cc_final: 0.6016 (tpp) REVERT: H 310 LEU cc_start: 0.8718 (mp) cc_final: 0.8363 (mt) outliers start: 37 outliers final: 16 residues processed: 186 average time/residue: 0.5405 time to fit residues: 109.2398 Evaluate side-chains 173 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 153 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 113 optimal weight: 7.9990 chunk 58 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 103 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 85 optimal weight: 7.9990 chunk 92 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.226341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4160 r_free = 0.4160 target = 0.194483 restraints weight = 14055.754| |-----------------------------------------------------------------------------| r_work (start): 0.4160 rms_B_bonded: 1.90 r_work: 0.3705 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3602 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12736 Z= 0.128 Angle : 0.535 8.847 17244 Z= 0.285 Chirality : 0.041 0.178 1928 Planarity : 0.006 0.070 2180 Dihedral : 3.821 16.890 1736 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.56 % Allowed : 19.35 % Favored : 78.09 % 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: 0.90 (0.21), residues: 1520 helix: 1.73 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.23 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG B 147 TYR 0.016 0.001 TYR F 188 PHE 0.018 0.001 PHE F 175 TRP 0.011 0.001 TRP C 362 HIS 0.003 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00295 (12720) covalent geometry : angle 0.53387 (17232) hydrogen bonds : bond 0.03816 ( 792) hydrogen bonds : angle 3.52429 ( 2316) metal coordination : bond 0.00706 ( 16) metal coordination : angle 1.60865 ( 12) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 0.439 Fit side-chains REVERT: B 109 HIS cc_start: 0.7499 (p-80) cc_final: 0.5935 (m170) REVERT: B 183 MET cc_start: 0.4390 (OUTLIER) cc_final: 0.4142 (ttt) REVERT: B 233 ASP cc_start: 0.8349 (t0) cc_final: 0.7825 (t0) REVERT: B 238 MET cc_start: 0.7284 (ttm) cc_final: 0.7003 (ttp) REVERT: B 279 MET cc_start: 0.6540 (OUTLIER) cc_final: 0.6263 (tpp) REVERT: B 310 LEU cc_start: 0.8837 (mp) cc_final: 0.8451 (mt) REVERT: C 183 MET cc_start: 0.4392 (OUTLIER) cc_final: 0.4144 (ttt) REVERT: C 233 ASP cc_start: 0.8341 (t0) cc_final: 0.7809 (t0) REVERT: C 238 MET cc_start: 0.7260 (ttm) cc_final: 0.6983 (ttp) REVERT: C 279 MET cc_start: 0.6574 (OUTLIER) cc_final: 0.6299 (tpp) REVERT: C 310 LEU cc_start: 0.8830 (mp) cc_final: 0.8419 (mt) REVERT: F 183 MET cc_start: 0.4400 (OUTLIER) cc_final: 0.4152 (ttt) REVERT: F 233 ASP cc_start: 0.8339 (t0) cc_final: 0.7813 (t0) REVERT: F 238 MET cc_start: 0.7267 (ttm) cc_final: 0.6984 (ttp) REVERT: F 279 MET cc_start: 0.6568 (OUTLIER) cc_final: 0.6292 (tpp) REVERT: F 310 LEU cc_start: 0.8847 (mp) cc_final: 0.8429 (mt) REVERT: H 183 MET cc_start: 0.4390 (OUTLIER) cc_final: 0.4143 (ttt) REVERT: H 233 ASP cc_start: 0.8363 (t0) cc_final: 0.7833 (t0) REVERT: H 238 MET cc_start: 0.7293 (ttm) cc_final: 0.7007 (ttp) REVERT: H 279 MET cc_start: 0.6552 (OUTLIER) cc_final: 0.6278 (tpp) REVERT: H 310 LEU cc_start: 0.8845 (mp) cc_final: 0.8467 (mt) outliers start: 34 outliers final: 12 residues processed: 180 average time/residue: 0.5215 time to fit residues: 102.4317 Evaluate side-chains 172 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 152 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 27 optimal weight: 2.9990 chunk 118 optimal weight: 9.9990 chunk 114 optimal weight: 2.9990 chunk 108 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 8 optimal weight: 0.0770 chunk 82 optimal weight: 0.9990 chunk 73 optimal weight: 3.9990 chunk 119 optimal weight: 0.6980 chunk 89 optimal weight: 0.0470 chunk 88 optimal weight: 3.9990 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 56 GLN H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.227835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.189691 restraints weight = 14175.411| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 2.10 r_work: 0.3701 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3595 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.3595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 12736 Z= 0.112 Angle : 0.527 9.472 17244 Z= 0.281 Chirality : 0.039 0.127 1928 Planarity : 0.005 0.059 2180 Dihedral : 3.719 16.737 1736 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.33 % Allowed : 20.26 % Favored : 77.41 % 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: 0.97 (0.21), residues: 1520 helix: 1.78 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.23 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG B 147 TYR 0.015 0.001 TYR C 188 PHE 0.022 0.001 PHE F 289 TRP 0.010 0.001 TRP H 362 HIS 0.004 0.000 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00244 (12720) covalent geometry : angle 0.52552 (17232) hydrogen bonds : bond 0.03536 ( 792) hydrogen bonds : angle 3.47524 ( 2316) metal coordination : bond 0.00924 ( 16) metal coordination : angle 1.60464 ( 12) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 165 time to evaluate : 0.441 Fit side-chains REVERT: B 109 HIS cc_start: 0.7418 (p-80) cc_final: 0.5918 (m170) REVERT: B 233 ASP cc_start: 0.8327 (t0) cc_final: 0.7825 (t0) REVERT: B 238 MET cc_start: 0.7290 (ttm) cc_final: 0.6996 (ttp) REVERT: B 279 MET cc_start: 0.6366 (OUTLIER) cc_final: 0.6085 (tpp) REVERT: B 310 LEU cc_start: 0.8799 (mp) cc_final: 0.8409 (mt) REVERT: C 233 ASP cc_start: 0.8313 (t0) cc_final: 0.7809 (t0) REVERT: C 238 MET cc_start: 0.7275 (ttm) cc_final: 0.6983 (ttp) REVERT: C 279 MET cc_start: 0.6401 (OUTLIER) cc_final: 0.6121 (tpp) REVERT: C 310 LEU cc_start: 0.8791 (mp) cc_final: 0.8395 (mt) REVERT: F 233 ASP cc_start: 0.8301 (t0) cc_final: 0.7800 (t0) REVERT: F 238 MET cc_start: 0.7237 (ttm) cc_final: 0.6946 (ttp) REVERT: F 279 MET cc_start: 0.6394 (OUTLIER) cc_final: 0.6117 (tpp) REVERT: F 310 LEU cc_start: 0.8813 (mp) cc_final: 0.8411 (mt) REVERT: H 233 ASP cc_start: 0.8346 (t0) cc_final: 0.7841 (t0) REVERT: H 238 MET cc_start: 0.7275 (ttm) cc_final: 0.6980 (ttp) REVERT: H 279 MET cc_start: 0.6385 (OUTLIER) cc_final: 0.6115 (tpp) REVERT: H 310 LEU cc_start: 0.8810 (mp) cc_final: 0.8420 (mt) outliers start: 31 outliers final: 12 residues processed: 176 average time/residue: 0.5036 time to fit residues: 96.9178 Evaluate side-chains 169 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 153 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 73 optimal weight: 1.9990 chunk 136 optimal weight: 0.0980 chunk 88 optimal weight: 0.0270 chunk 24 optimal weight: 0.9980 chunk 141 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 9 optimal weight: 0.5980 chunk 79 optimal weight: 0.0000 chunk 115 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 overall best weight: 0.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.229039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4183 r_free = 0.4183 target = 0.196607 restraints weight = 14137.866| |-----------------------------------------------------------------------------| r_work (start): 0.4185 rms_B_bonded: 1.88 r_work: 0.3761 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3761 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7474 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 12736 Z= 0.111 Angle : 0.524 9.526 17244 Z= 0.281 Chirality : 0.039 0.137 1928 Planarity : 0.005 0.059 2180 Dihedral : 3.628 16.577 1736 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.92 % Favored : 94.08 % Rotamer: Outliers : 1.51 % Allowed : 20.86 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.04 (0.21), residues: 1520 helix: 1.81 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.13 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 147 TYR 0.015 0.001 TYR B 188 PHE 0.019 0.001 PHE B 175 TRP 0.010 0.001 TRP C 362 HIS 0.004 0.000 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00238 (12720) covalent geometry : angle 0.52251 (17232) hydrogen bonds : bond 0.03413 ( 792) hydrogen bonds : angle 3.43108 ( 2316) metal coordination : bond 0.00688 ( 16) metal coordination : angle 1.47390 ( 12) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3040 Ramachandran restraints generated. 1520 Oldfield, 0 Emsley, 1520 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 179 time to evaluate : 0.495 Fit side-chains REVERT: B 109 HIS cc_start: 0.7388 (p-80) cc_final: 0.6051 (m170) REVERT: B 233 ASP cc_start: 0.8161 (t0) cc_final: 0.7667 (t0) REVERT: B 238 MET cc_start: 0.6954 (ttm) cc_final: 0.6677 (ttp) REVERT: B 279 MET cc_start: 0.6346 (OUTLIER) cc_final: 0.6058 (tpp) REVERT: B 310 LEU cc_start: 0.8663 (mp) cc_final: 0.8340 (mt) REVERT: B 432 ARG cc_start: 0.5118 (ttt180) cc_final: 0.4874 (tmt-80) REVERT: C 233 ASP cc_start: 0.8145 (t0) cc_final: 0.7654 (t0) REVERT: C 238 MET cc_start: 0.6913 (ttm) cc_final: 0.6638 (ttp) REVERT: C 279 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6072 (tpp) REVERT: C 310 LEU cc_start: 0.8674 (mp) cc_final: 0.8345 (mt) REVERT: C 432 ARG cc_start: 0.5113 (ttt180) cc_final: 0.4907 (tmt-80) REVERT: F 233 ASP cc_start: 0.8142 (t0) cc_final: 0.7643 (t0) REVERT: F 238 MET cc_start: 0.6921 (ttm) cc_final: 0.6646 (ttp) REVERT: F 279 MET cc_start: 0.6364 (OUTLIER) cc_final: 0.6072 (tpp) REVERT: F 310 LEU cc_start: 0.8671 (mp) cc_final: 0.8341 (mt) REVERT: F 432 ARG cc_start: 0.5108 (ttt180) cc_final: 0.4902 (tmt-80) REVERT: H 233 ASP cc_start: 0.8185 (t0) cc_final: 0.7684 (t0) REVERT: H 238 MET cc_start: 0.6945 (ttm) cc_final: 0.6666 (ttp) REVERT: H 279 MET cc_start: 0.6355 (OUTLIER) cc_final: 0.6068 (tpp) REVERT: H 310 LEU cc_start: 0.8672 (mp) cc_final: 0.8334 (mt) outliers start: 20 outliers final: 12 residues processed: 187 average time/residue: 0.4962 time to fit residues: 101.7066 Evaluate side-chains 176 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 160 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 130 optimal weight: 0.0670 chunk 29 optimal weight: 0.7980 chunk 76 optimal weight: 3.9990 chunk 93 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 31 optimal weight: 0.5980 chunk 109 optimal weight: 0.7980 chunk 65 optimal weight: 0.9980 chunk 102 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 chunk 70 optimal weight: 0.9980 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 416 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.227582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.190654 restraints weight = 14103.425| |-----------------------------------------------------------------------------| r_work (start): 0.4108 rms_B_bonded: 1.96 r_work: 0.3742 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3619 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3619 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 moved from start: 0.2699 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12736 Z= 0.125 Angle : 0.553 9.419 17244 Z= 0.295 Chirality : 0.040 0.135 1928 Planarity : 0.006 0.068 2180 Dihedral : 3.753 16.011 1736 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 1.88 % Allowed : 20.93 % Favored : 77.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.21), residues: 1520 helix: 1.79 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.10 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG H 147 TYR 0.016 0.001 TYR H 273 PHE 0.021 0.001 PHE C 289 TRP 0.010 0.001 TRP B 362 HIS 0.003 0.001 HIS F 109 Details of bonding type rmsd covalent geometry : bond 0.00287 (12720) covalent geometry : angle 0.55138 (17232) hydrogen bonds : bond 0.03690 ( 792) hydrogen bonds : angle 3.51435 ( 2316) metal coordination : bond 0.01046 ( 16) metal coordination : angle 1.53376 ( 12) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3947.30 seconds wall clock time: 67 minutes 58.64 seconds (4078.64 seconds total)