Starting phenix.real_space_refine on Wed Jul 30 12:46:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f0j_31399/07_2025/7f0j_31399.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f0j_31399/07_2025/7f0j_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_31399/07_2025/7f0j_31399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f0j_31399/07_2025/7f0j_31399.map" model { file = "/net/cci-nas-00/data/ceres_data/7f0j_31399/07_2025/7f0j_31399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f0j_31399/07_2025/7f0j_31399.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12424 Number of models: 1 Model: "" Number of chains: 2 Chain: "H" 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: "H" 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 10103 SG CYS H 132 38.204 43.613 86.720 1.00 41.16 S ATOM 10109 SG CYS H 133 41.812 43.360 88.010 1.00 40.55 S Restraints were copied for chains: C, B, F Time building chain proxies: 5.76, per 1000 atoms: 0.46 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: 2.84 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 1.07 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: 3.17 Time building geometry restraints manager: 3.38 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: 0.09 Found NCS groups: ncs_group { reference = chain 'H' selection = chain 'C' selection = chain 'B' selection = chain 'F' } 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: 0.500 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 28.160 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 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:12.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.540 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.008 0.001 TRP C 362 HIS 0.002 0.000 HIS H 306 PHE 0.010 0.001 PHE C 338 TYR 0.015 0.001 TYR F 413 ARG 0.002 0.000 ARG C 296 Details of bonding type rmsd hydrogen bonds : bond 0.11370 ( 792) hydrogen bonds : angle 4.48092 ( 2316) metal coordination : bond 0.00511 ( 16) metal coordination : angle 1.78044 ( 12) covalent geometry : bond 0.00239 (12720) covalent geometry : angle 0.53769 (17232) *********************** 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 : 1.246 Fit side-chains REVERT: B 109 HIS cc_start: 0.7478 (p-80) cc_final: 0.6199 (m170) REVERT: B 233 ASP cc_start: 0.7941 (t0) cc_final: 0.7531 (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: 1.0408 time to fit residues: 320.6849 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 : 1.331 ------------------------------------------------------------------------------- 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 128 optimal weight: 1.9990 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 4.9990 chunk 39 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 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 = 0.4435 r_free = 0.4435 target = 0.223558 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.190183 restraints weight = 13975.434| |-----------------------------------------------------------------------------| r_work (start): 0.4111 rms_B_bonded: 1.79 r_work: 0.3700 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3628 rms_B_bonded: 3.38 restraints_weight: 0.2500 r_work (final): 0.3628 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 12736 Z= 0.218 Angle : 0.624 7.613 17244 Z= 0.338 Chirality : 0.044 0.151 1928 Planarity : 0.006 0.065 2180 Dihedral : 4.631 33.578 1744 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.01 % Allowed : 12.27 % Favored : 84.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.21), residues: 1520 helix: 1.35 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP H 362 HIS 0.004 0.001 HIS H 414 PHE 0.025 0.002 PHE B 386 TYR 0.019 0.002 TYR H 188 ARG 0.006 0.000 ARG B 51 Details of bonding type rmsd hydrogen bonds : bond 0.04970 ( 792) hydrogen bonds : angle 3.96728 ( 2316) metal coordination : bond 0.00681 ( 16) metal coordination : angle 2.54368 ( 12) covalent geometry : bond 0.00530 (12720) covalent geometry : angle 0.62029 (17232) *********************** 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 228 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 1.258 Fit side-chains REVERT: B 60 GLU cc_start: 0.6841 (mt-10) cc_final: 0.6430 (pp20) REVERT: B 183 MET cc_start: 0.4851 (OUTLIER) cc_final: 0.4603 (ttp) REVERT: B 233 ASP cc_start: 0.8353 (t0) cc_final: 0.7802 (t0) REVERT: C 60 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6429 (pp20) REVERT: C 109 HIS cc_start: 0.7720 (p-80) cc_final: 0.6141 (m170) REVERT: C 183 MET cc_start: 0.4857 (OUTLIER) cc_final: 0.4609 (ttp) REVERT: C 233 ASP cc_start: 0.8341 (t0) cc_final: 0.7787 (t0) REVERT: F 60 GLU cc_start: 0.6831 (mt-10) cc_final: 0.6428 (pp20) REVERT: F 183 MET cc_start: 0.4874 (OUTLIER) cc_final: 0.4630 (ttp) REVERT: F 233 ASP cc_start: 0.8358 (t0) cc_final: 0.7801 (t0) REVERT: H 60 GLU cc_start: 0.6829 (mt-10) cc_final: 0.6434 (pp20) REVERT: H 183 MET cc_start: 0.4869 (OUTLIER) cc_final: 0.4623 (ttp) REVERT: H 233 ASP cc_start: 0.8355 (t0) cc_final: 0.7800 (t0) outliers start: 40 outliers final: 8 residues processed: 208 average time/residue: 1.0987 time to fit residues: 250.8476 Evaluate side-chains 184 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 183 MET 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 279 MET Chi-restraints excluded: chain F residue 413 TYR 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 20 optimal weight: 8.9990 chunk 40 optimal weight: 10.0000 chunk 50 optimal weight: 4.9990 chunk 49 optimal weight: 5.9990 chunk 11 optimal weight: 0.0570 chunk 47 optimal weight: 4.9990 chunk 46 optimal weight: 4.9990 chunk 101 optimal weight: 3.9990 chunk 79 optimal weight: 7.9990 chunk 73 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 overall best weight: 2.6104 ------------------------------------------------------------------------------- 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 C 46 ASN C 56 GLN F 46 ASN F 56 GLN H 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4416 r_free = 0.4416 target = 0.221478 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4019 r_free = 0.4019 target = 0.179673 restraints weight = 13938.939| |-----------------------------------------------------------------------------| r_work (start): 0.3998 rms_B_bonded: 2.84 r_work: 0.3349 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3349 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 12736 Z= 0.262 Angle : 0.651 7.897 17244 Z= 0.353 Chirality : 0.046 0.145 1928 Planarity : 0.006 0.060 2180 Dihedral : 4.641 19.849 1736 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.84 % Favored : 93.16 % Rotamer: Outliers : 4.82 % Allowed : 14.46 % Favored : 80.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.21), residues: 1520 helix: 1.08 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.34 (0.28), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP H 362 HIS 0.005 0.001 HIS H 306 PHE 0.033 0.002 PHE F 386 TYR 0.024 0.002 TYR C 188 ARG 0.003 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.05462 ( 792) hydrogen bonds : angle 4.13327 ( 2316) metal coordination : bond 0.00511 ( 16) metal coordination : angle 3.53667 ( 12) covalent geometry : bond 0.00648 (12720) covalent geometry : angle 0.64411 (17232) *********************** 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 244 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 180 time to evaluate : 1.703 Fit side-chains REVERT: B 60 GLU cc_start: 0.7537 (mt-10) cc_final: 0.6575 (pp20) REVERT: B 131 ASP cc_start: 0.6458 (OUTLIER) cc_final: 0.6122 (t70) REVERT: B 183 MET cc_start: 0.4435 (OUTLIER) cc_final: 0.4211 (ttp) REVERT: B 225 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.6393 (m-10) REVERT: B 233 ASP cc_start: 0.8522 (t0) cc_final: 0.7841 (t0) REVERT: C 60 GLU cc_start: 0.7538 (mt-10) cc_final: 0.6580 (pp20) REVERT: C 131 ASP cc_start: 0.6456 (OUTLIER) cc_final: 0.6123 (t70) REVERT: C 183 MET cc_start: 0.4399 (OUTLIER) cc_final: 0.4184 (ttp) REVERT: C 225 TYR cc_start: 0.6650 (OUTLIER) cc_final: 0.6392 (m-10) REVERT: C 233 ASP cc_start: 0.8511 (t0) cc_final: 0.7828 (t0) REVERT: F 60 GLU cc_start: 0.7554 (mt-10) cc_final: 0.6591 (pp20) REVERT: F 131 ASP cc_start: 0.6454 (OUTLIER) cc_final: 0.6121 (t70) REVERT: F 183 MET cc_start: 0.4431 (OUTLIER) cc_final: 0.4207 (ttp) REVERT: F 225 TYR cc_start: 0.6690 (OUTLIER) cc_final: 0.6439 (m-10) REVERT: F 233 ASP cc_start: 0.8531 (t0) cc_final: 0.7860 (t0) REVERT: H 60 GLU cc_start: 0.7521 (mt-10) cc_final: 0.6592 (pp20) REVERT: H 131 ASP cc_start: 0.6452 (OUTLIER) cc_final: 0.6117 (t70) REVERT: H 183 MET cc_start: 0.4452 (OUTLIER) cc_final: 0.4228 (ttp) REVERT: H 225 TYR cc_start: 0.6662 (OUTLIER) cc_final: 0.6409 (m-10) REVERT: H 233 ASP cc_start: 0.8519 (t0) cc_final: 0.7843 (t0) outliers start: 64 outliers final: 16 residues processed: 212 average time/residue: 1.1236 time to fit residues: 262.8465 Evaluate side-chains 181 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 153 time to evaluate : 1.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 131 ASP Chi-restraints excluded: chain B residue 183 MET Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 225 TYR Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 405 ILE Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 131 ASP Chi-restraints excluded: chain C residue 183 MET Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 225 TYR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 405 ILE Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 131 ASP Chi-restraints excluded: chain F residue 183 MET Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 225 TYR Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 405 ILE Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 131 ASP Chi-restraints excluded: chain H residue 183 MET Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 225 TYR Chi-restraints excluded: chain H residue 279 MET Chi-restraints excluded: chain H residue 405 ILE 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 24 optimal weight: 0.8980 chunk 146 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 46 optimal weight: 5.9990 chunk 102 optimal weight: 2.9990 chunk 100 optimal weight: 0.9990 chunk 43 optimal weight: 6.9990 chunk 105 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 138 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 46 ASN B 56 GLN B 416 ASN C 46 ASN C 56 GLN 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.224925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.186788 restraints weight = 13982.377| |-----------------------------------------------------------------------------| r_work (start): 0.4080 rms_B_bonded: 1.92 r_work: 0.3575 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.133 Angle : 0.544 8.871 17244 Z= 0.294 Chirality : 0.041 0.125 1928 Planarity : 0.005 0.054 2180 Dihedral : 4.200 17.268 1736 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 4.44 % Allowed : 15.66 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.21), residues: 1520 helix: 1.50 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.23 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 362 HIS 0.002 0.001 HIS H 306 PHE 0.016 0.001 PHE H 175 TYR 0.016 0.001 TYR B 188 ARG 0.002 0.000 ARG C 51 Details of bonding type rmsd hydrogen bonds : bond 0.04065 ( 792) hydrogen bonds : angle 3.78409 ( 2316) metal coordination : bond 0.00445 ( 16) metal coordination : angle 2.80785 ( 12) covalent geometry : bond 0.00303 (12720) covalent geometry : angle 0.53884 (17232) *********************** 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 243 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 184 time to evaluate : 1.281 Fit side-chains REVERT: B 60 GLU cc_start: 0.7676 (mt-10) cc_final: 0.6722 (pp20) REVERT: B 109 HIS cc_start: 0.7617 (p-80) cc_final: 0.5635 (m170) REVERT: B 147 ARG cc_start: 0.5616 (tmm-80) cc_final: 0.4917 (ttp-110) REVERT: B 225 TYR cc_start: 0.6180 (OUTLIER) cc_final: 0.5936 (m-10) REVERT: B 233 ASP cc_start: 0.8395 (t0) cc_final: 0.7826 (t0) REVERT: B 238 MET cc_start: 0.7375 (ttm) cc_final: 0.7095 (ttp) REVERT: B 346 GLU cc_start: 0.9022 (mm-30) cc_final: 0.7878 (tp30) REVERT: B 413 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.5195 (m-80) REVERT: C 60 GLU cc_start: 0.7692 (mt-10) cc_final: 0.6726 (pp20) REVERT: C 147 ARG cc_start: 0.5582 (tmm-80) cc_final: 0.4897 (ttp-110) REVERT: C 225 TYR cc_start: 0.6179 (OUTLIER) cc_final: 0.5934 (m-10) REVERT: C 233 ASP cc_start: 0.8380 (t0) cc_final: 0.7805 (t0) REVERT: C 238 MET cc_start: 0.7362 (ttm) cc_final: 0.7084 (ttp) REVERT: C 346 GLU cc_start: 0.9014 (mm-30) cc_final: 0.7862 (tp30) REVERT: C 413 TYR cc_start: 0.6596 (OUTLIER) cc_final: 0.5196 (m-80) REVERT: F 60 GLU cc_start: 0.7722 (mt-10) cc_final: 0.6735 (pp20) REVERT: F 147 ARG cc_start: 0.5587 (tmm-80) cc_final: 0.4902 (ttp-110) REVERT: F 225 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5926 (m-10) REVERT: F 233 ASP cc_start: 0.8395 (t0) cc_final: 0.7822 (t0) REVERT: F 238 MET cc_start: 0.7375 (ttm) cc_final: 0.7094 (ttp) REVERT: F 346 GLU cc_start: 0.9006 (mm-30) cc_final: 0.7858 (tp30) REVERT: F 413 TYR cc_start: 0.6615 (OUTLIER) cc_final: 0.5214 (m-80) REVERT: H 60 GLU cc_start: 0.7716 (mt-10) cc_final: 0.6745 (pp20) REVERT: H 147 ARG cc_start: 0.5591 (tmm-80) cc_final: 0.5017 (ttp-110) REVERT: H 225 TYR cc_start: 0.6171 (OUTLIER) cc_final: 0.5927 (m-10) REVERT: H 233 ASP cc_start: 0.8393 (t0) cc_final: 0.7816 (t0) REVERT: H 238 MET cc_start: 0.7404 (ttm) cc_final: 0.7123 (ttp) REVERT: H 346 GLU cc_start: 0.9018 (mm-30) cc_final: 0.7880 (tp30) REVERT: H 413 TYR cc_start: 0.6592 (OUTLIER) cc_final: 0.5193 (m-80) outliers start: 59 outliers final: 8 residues processed: 214 average time/residue: 1.3339 time to fit residues: 310.0341 Evaluate side-chains 179 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 1.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 225 TYR 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 225 TYR 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 225 TYR 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 225 TYR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 37 optimal weight: 5.9990 chunk 72 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 42 optimal weight: 8.9990 chunk 100 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 141 optimal weight: 0.8980 chunk 145 optimal weight: 0.4980 chunk 69 optimal weight: 0.7980 chunk 13 optimal weight: 10.0000 chunk 73 optimal weight: 1.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 ** H 109 HIS ** 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 = 0.4451 r_free = 0.4451 target = 0.225000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4098 r_free = 0.4098 target = 0.188015 restraints weight = 13958.730| |-----------------------------------------------------------------------------| r_work (start): 0.4078 rms_B_bonded: 1.84 r_work: 0.3578 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12736 Z= 0.142 Angle : 0.543 8.486 17244 Z= 0.291 Chirality : 0.041 0.145 1928 Planarity : 0.005 0.054 2180 Dihedral : 4.150 17.009 1736 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 4.14 % Allowed : 16.64 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1520 helix: 1.59 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.30 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 362 HIS 0.003 0.001 HIS B 306 PHE 0.021 0.002 PHE C 289 TYR 0.017 0.001 TYR H 188 ARG 0.002 0.000 ARG C 147 Details of bonding type rmsd hydrogen bonds : bond 0.04172 ( 792) hydrogen bonds : angle 3.73143 ( 2316) metal coordination : bond 0.00429 ( 16) metal coordination : angle 2.95839 ( 12) covalent geometry : bond 0.00338 (12720) covalent geometry : angle 0.53743 (17232) *********************** 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 240 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 185 time to evaluate : 1.338 Fit side-chains REVERT: B 60 GLU cc_start: 0.7413 (mt-10) cc_final: 0.6657 (pp20) REVERT: B 109 HIS cc_start: 0.7633 (p-80) cc_final: 0.5722 (m170) REVERT: B 233 ASP cc_start: 0.8456 (t0) cc_final: 0.7878 (t0) REVERT: B 238 MET cc_start: 0.7321 (ttm) cc_final: 0.7019 (ttp) REVERT: B 310 LEU cc_start: 0.8813 (mp) cc_final: 0.8448 (mt) REVERT: B 413 TYR cc_start: 0.6533 (OUTLIER) cc_final: 0.4888 (m-80) REVERT: C 60 GLU cc_start: 0.7442 (mt-10) cc_final: 0.6664 (pp20) REVERT: C 233 ASP cc_start: 0.8433 (t0) cc_final: 0.7848 (t0) REVERT: C 238 MET cc_start: 0.7298 (ttm) cc_final: 0.7003 (ttp) REVERT: C 310 LEU cc_start: 0.8811 (mp) cc_final: 0.8452 (mt) REVERT: C 413 TYR cc_start: 0.6563 (OUTLIER) cc_final: 0.4917 (m-80) REVERT: F 60 GLU cc_start: 0.7437 (mt-10) cc_final: 0.6665 (pp20) REVERT: F 233 ASP cc_start: 0.8454 (t0) cc_final: 0.7870 (t0) REVERT: F 238 MET cc_start: 0.7306 (ttm) cc_final: 0.7011 (ttp) REVERT: F 310 LEU cc_start: 0.8819 (mp) cc_final: 0.8449 (mt) REVERT: F 413 TYR cc_start: 0.6564 (OUTLIER) cc_final: 0.4908 (m-80) REVERT: H 60 GLU cc_start: 0.7453 (mt-10) cc_final: 0.6679 (pp20) REVERT: H 147 ARG cc_start: 0.5644 (tmm-80) cc_final: 0.4811 (ttp-110) REVERT: H 233 ASP cc_start: 0.8468 (t0) cc_final: 0.7884 (t0) REVERT: H 238 MET cc_start: 0.7330 (ttm) cc_final: 0.7023 (ttp) REVERT: H 310 LEU cc_start: 0.8825 (mp) cc_final: 0.8468 (mt) REVERT: H 413 TYR cc_start: 0.6548 (OUTLIER) cc_final: 0.4906 (m-80) outliers start: 55 outliers final: 16 residues processed: 212 average time/residue: 1.2112 time to fit residues: 279.9928 Evaluate side-chains 178 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 158 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 44 VAL 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 44 VAL 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 44 VAL 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 44 VAL 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 45 optimal weight: 0.8980 chunk 59 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 136 optimal weight: 1.9990 chunk 81 optimal weight: 3.9990 chunk 10 optimal weight: 8.9990 chunk 102 optimal weight: 2.9990 chunk 131 optimal weight: 6.9990 chunk 71 optimal weight: 0.7980 chunk 37 optimal weight: 10.0000 chunk 138 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- 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 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.224676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.190415 restraints weight = 14084.670| |-----------------------------------------------------------------------------| r_work (start): 0.4114 rms_B_bonded: 1.82 r_work: 0.3653 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12736 Z= 0.148 Angle : 0.558 8.817 17244 Z= 0.293 Chirality : 0.041 0.171 1928 Planarity : 0.005 0.054 2180 Dihedral : 4.133 16.697 1736 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 4.37 % Allowed : 17.24 % Favored : 78.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.21), residues: 1520 helix: 1.62 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.30 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 362 HIS 0.003 0.001 HIS H 306 PHE 0.017 0.001 PHE B 386 TYR 0.017 0.001 TYR C 188 ARG 0.008 0.000 ARG F 147 Details of bonding type rmsd hydrogen bonds : bond 0.04209 ( 792) hydrogen bonds : angle 3.73611 ( 2316) metal coordination : bond 0.00308 ( 16) metal coordination : angle 2.40622 ( 12) covalent geometry : bond 0.00353 (12720) covalent geometry : angle 0.55457 (17232) *********************** 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 225 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 167 time to evaluate : 1.353 Fit side-chains REVERT: B 60 GLU cc_start: 0.7224 (mt-10) cc_final: 0.6575 (pp20) REVERT: B 109 HIS cc_start: 0.7729 (p-80) cc_final: 0.5801 (m170) REVERT: B 183 MET cc_start: 0.4505 (OUTLIER) cc_final: 0.4267 (ttp) REVERT: B 233 ASP cc_start: 0.8410 (t0) cc_final: 0.7850 (t0) REVERT: B 238 MET cc_start: 0.7337 (ttm) cc_final: 0.7033 (ttp) REVERT: B 310 LEU cc_start: 0.8807 (mp) cc_final: 0.8363 (mt) REVERT: C 60 GLU cc_start: 0.7228 (mt-10) cc_final: 0.6575 (pp20) REVERT: C 183 MET cc_start: 0.4511 (OUTLIER) cc_final: 0.4268 (ttp) REVERT: C 233 ASP cc_start: 0.8404 (t0) cc_final: 0.7831 (t0) REVERT: C 238 MET cc_start: 0.7342 (ttm) cc_final: 0.7037 (ttp) REVERT: C 310 LEU cc_start: 0.8799 (mp) cc_final: 0.8356 (mt) REVERT: F 60 GLU cc_start: 0.7240 (mt-10) cc_final: 0.6580 (pp20) REVERT: F 183 MET cc_start: 0.4510 (OUTLIER) cc_final: 0.4273 (ttp) REVERT: F 233 ASP cc_start: 0.8423 (t0) cc_final: 0.7850 (t0) REVERT: F 238 MET cc_start: 0.7316 (ttm) cc_final: 0.7010 (ttp) REVERT: F 310 LEU cc_start: 0.8811 (mp) cc_final: 0.8384 (mt) REVERT: H 60 GLU cc_start: 0.7275 (mt-10) cc_final: 0.6558 (pp20) REVERT: H 183 MET cc_start: 0.4492 (OUTLIER) cc_final: 0.4256 (ttp) REVERT: H 233 ASP cc_start: 0.8441 (t0) cc_final: 0.7867 (t0) REVERT: H 238 MET cc_start: 0.7328 (ttm) cc_final: 0.7021 (ttp) REVERT: H 310 LEU cc_start: 0.8814 (mp) cc_final: 0.8376 (mt) outliers start: 58 outliers final: 20 residues processed: 198 average time/residue: 1.2077 time to fit residues: 260.7098 Evaluate side-chains 181 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 157 time to evaluate : 1.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU 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 66 LEU 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 66 LEU 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 66 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 17 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 11 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 6.9990 chunk 109 optimal weight: 0.6980 chunk 6 optimal weight: 5.9990 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 0.5980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 ** H 109 HIS ** 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 = 0.4441 r_free = 0.4441 target = 0.224108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.189552 restraints weight = 13964.395| |-----------------------------------------------------------------------------| r_work (start): 0.4107 rms_B_bonded: 1.78 r_work: 0.3655 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12736 Z= 0.157 Angle : 0.562 9.091 17244 Z= 0.297 Chirality : 0.042 0.195 1928 Planarity : 0.005 0.053 2180 Dihedral : 4.155 17.083 1736 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.61 % Allowed : 18.67 % Favored : 77.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1520 helix: 1.62 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.33 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 362 HIS 0.003 0.001 HIS B 306 PHE 0.023 0.002 PHE F 289 TYR 0.018 0.002 TYR F 188 ARG 0.010 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.04348 ( 792) hydrogen bonds : angle 3.73626 ( 2316) metal coordination : bond 0.00304 ( 16) metal coordination : angle 2.35926 ( 12) covalent geometry : bond 0.00378 (12720) covalent geometry : angle 0.55856 (17232) *********************** 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 218 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 170 time to evaluate : 1.375 Fit side-chains REVERT: B 60 GLU cc_start: 0.7142 (mt-10) cc_final: 0.6586 (pp20) REVERT: B 109 HIS cc_start: 0.7680 (p-80) cc_final: 0.5948 (m170) REVERT: B 183 MET cc_start: 0.4402 (OUTLIER) cc_final: 0.4186 (ttp) REVERT: B 225 TYR cc_start: 0.5523 (m-10) cc_final: 0.5097 (m-10) REVERT: B 233 ASP cc_start: 0.8338 (t0) cc_final: 0.7770 (t0) REVERT: B 413 TYR cc_start: 0.6339 (OUTLIER) cc_final: 0.4689 (m-80) REVERT: C 60 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6530 (pp20) REVERT: C 183 MET cc_start: 0.4406 (OUTLIER) cc_final: 0.4185 (ttp) REVERT: C 233 ASP cc_start: 0.8329 (t0) cc_final: 0.7760 (t0) REVERT: C 413 TYR cc_start: 0.6335 (OUTLIER) cc_final: 0.4687 (m-80) REVERT: F 60 GLU cc_start: 0.7132 (mt-10) cc_final: 0.6541 (pp20) REVERT: F 183 MET cc_start: 0.4407 (OUTLIER) cc_final: 0.4190 (ttp) REVERT: F 233 ASP cc_start: 0.8333 (t0) cc_final: 0.7762 (t0) REVERT: F 413 TYR cc_start: 0.6332 (OUTLIER) cc_final: 0.4678 (m-80) REVERT: H 60 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6539 (pp20) REVERT: H 183 MET cc_start: 0.4400 (OUTLIER) cc_final: 0.4184 (ttp) REVERT: H 225 TYR cc_start: 0.5539 (m-10) cc_final: 0.5112 (m-10) REVERT: H 233 ASP cc_start: 0.8348 (t0) cc_final: 0.7772 (t0) REVERT: H 413 TYR cc_start: 0.6334 (OUTLIER) cc_final: 0.4681 (m-80) outliers start: 48 outliers final: 21 residues processed: 198 average time/residue: 1.1636 time to fit residues: 252.0404 Evaluate side-chains 190 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 161 time to evaluate : 1.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU 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 318 LYS Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 66 LEU 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 402 VAL Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 66 LEU 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 402 VAL Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 66 LEU 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 402 VAL 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 148 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 110 optimal weight: 0.9990 chunk 96 optimal weight: 8.9990 chunk 68 optimal weight: 0.0770 chunk 128 optimal weight: 3.9990 chunk 105 optimal weight: 0.9990 chunk 65 optimal weight: 0.6980 chunk 73 optimal weight: 0.0020 chunk 9 optimal weight: 5.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- 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 415 GLN B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 415 GLN C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 415 GLN F 416 ASN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 415 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 = 0.4459 r_free = 0.4459 target = 0.226260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.195770 restraints weight = 14154.596| |-----------------------------------------------------------------------------| r_work (start): 0.4166 rms_B_bonded: 1.75 r_work: 0.3678 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3556 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7712 moved from start: 0.2744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12736 Z= 0.118 Angle : 0.543 9.594 17244 Z= 0.284 Chirality : 0.040 0.197 1928 Planarity : 0.005 0.051 2180 Dihedral : 3.936 15.460 1736 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.86 % Allowed : 19.50 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.21), residues: 1520 helix: 1.77 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.24 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 362 HIS 0.004 0.001 HIS H 109 PHE 0.017 0.001 PHE B 175 TYR 0.015 0.001 TYR B 188 ARG 0.008 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.03773 ( 792) hydrogen bonds : angle 3.59758 ( 2316) metal coordination : bond 0.00445 ( 16) metal coordination : angle 2.04107 ( 12) covalent geometry : bond 0.00266 (12720) covalent geometry : angle 0.54002 (17232) *********************** 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 222 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 184 time to evaluate : 1.360 Fit side-chains REVERT: B 60 GLU cc_start: 0.7125 (mt-10) cc_final: 0.6738 (pp20) REVERT: B 109 HIS cc_start: 0.7645 (p-80) cc_final: 0.5798 (m170) REVERT: B 233 ASP cc_start: 0.8393 (t0) cc_final: 0.7834 (t0) REVERT: B 238 MET cc_start: 0.7310 (ttm) cc_final: 0.7013 (ttp) REVERT: B 310 LEU cc_start: 0.8821 (mp) cc_final: 0.8370 (mt) REVERT: B 346 GLU cc_start: 0.9043 (mm-30) cc_final: 0.7876 (tp30) REVERT: B 413 TYR cc_start: 0.6362 (OUTLIER) cc_final: 0.5007 (m-80) REVERT: C 60 GLU cc_start: 0.7121 (mt-10) cc_final: 0.6737 (pp20) REVERT: C 233 ASP cc_start: 0.8394 (t0) cc_final: 0.7810 (t0) REVERT: C 238 MET cc_start: 0.7253 (ttm) cc_final: 0.6946 (ttp) REVERT: C 310 LEU cc_start: 0.8818 (mp) cc_final: 0.8352 (mt) REVERT: C 346 GLU cc_start: 0.9027 (mm-30) cc_final: 0.7865 (tp30) REVERT: C 413 TYR cc_start: 0.6366 (OUTLIER) cc_final: 0.5015 (m-80) REVERT: F 60 GLU cc_start: 0.7130 (mt-10) cc_final: 0.6749 (pp20) REVERT: F 205 GLU cc_start: 0.8737 (OUTLIER) cc_final: 0.8444 (pt0) REVERT: F 233 ASP cc_start: 0.8415 (t0) cc_final: 0.7830 (t0) REVERT: F 238 MET cc_start: 0.7225 (ttm) cc_final: 0.6916 (ttp) REVERT: F 310 LEU cc_start: 0.8835 (mp) cc_final: 0.8387 (mt) REVERT: F 346 GLU cc_start: 0.9021 (mm-30) cc_final: 0.7873 (tp30) REVERT: F 413 TYR cc_start: 0.6376 (OUTLIER) cc_final: 0.5024 (m-80) REVERT: H 60 GLU cc_start: 0.7151 (mt-10) cc_final: 0.6770 (pp20) REVERT: H 205 GLU cc_start: 0.8747 (OUTLIER) cc_final: 0.8453 (pt0) REVERT: H 233 ASP cc_start: 0.8418 (t0) cc_final: 0.7828 (t0) REVERT: H 238 MET cc_start: 0.7319 (ttm) cc_final: 0.7017 (ttp) REVERT: H 310 LEU cc_start: 0.8837 (mp) cc_final: 0.8394 (mt) REVERT: H 346 GLU cc_start: 0.9033 (mm-30) cc_final: 0.7866 (tp30) REVERT: H 413 TYR cc_start: 0.6379 (OUTLIER) cc_final: 0.5019 (m-80) outliers start: 38 outliers final: 14 residues processed: 209 average time/residue: 1.3223 time to fit residues: 303.4277 Evaluate side-chains 175 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 155 time to evaluate : 2.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 402 VAL Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 402 VAL Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 402 VAL 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 130 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 70 optimal weight: 0.3980 chunk 50 optimal weight: 6.9990 chunk 120 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 148 optimal weight: 2.9990 chunk 33 optimal weight: 0.5980 chunk 144 optimal weight: 0.5980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** H 109 HIS ** 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 = 0.4443 r_free = 0.4443 target = 0.224437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.190281 restraints weight = 14040.600| |-----------------------------------------------------------------------------| r_work (start): 0.4113 rms_B_bonded: 1.77 r_work: 0.3662 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work (final): 0.3662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12736 Z= 0.151 Angle : 0.564 9.310 17244 Z= 0.301 Chirality : 0.042 0.195 1928 Planarity : 0.005 0.052 2180 Dihedral : 4.045 16.817 1736 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 3.16 % Allowed : 20.11 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.21), residues: 1520 helix: 1.70 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.29 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 362 HIS 0.003 0.001 HIS C 306 PHE 0.023 0.002 PHE C 289 TYR 0.018 0.002 TYR F 188 ARG 0.008 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.04205 ( 792) hydrogen bonds : angle 3.67493 ( 2316) metal coordination : bond 0.00371 ( 16) metal coordination : angle 2.02790 ( 12) covalent geometry : bond 0.00360 (12720) covalent geometry : angle 0.56137 (17232) *********************** 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 204 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 162 time to evaluate : 1.416 Fit side-chains REVERT: B 60 GLU cc_start: 0.7041 (mt-10) cc_final: 0.6760 (pp20) REVERT: B 109 HIS cc_start: 0.7657 (p-80) cc_final: 0.5943 (m170) REVERT: B 169 GLN cc_start: 0.7212 (tm-30) cc_final: 0.7001 (tm130) REVERT: B 205 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: B 233 ASP cc_start: 0.8242 (t0) cc_final: 0.7689 (t0) REVERT: C 60 GLU cc_start: 0.7032 (mt-10) cc_final: 0.6762 (pp20) REVERT: C 169 GLN cc_start: 0.7200 (tm-30) cc_final: 0.6995 (tm130) REVERT: C 205 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: C 233 ASP cc_start: 0.8222 (t0) cc_final: 0.7667 (t0) REVERT: F 60 GLU cc_start: 0.7059 (mt-10) cc_final: 0.6757 (pp20) REVERT: F 169 GLN cc_start: 0.7238 (tm-30) cc_final: 0.7018 (tm130) REVERT: F 205 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8181 (pt0) REVERT: F 233 ASP cc_start: 0.8244 (t0) cc_final: 0.7688 (t0) REVERT: H 60 GLU cc_start: 0.7096 (mt-10) cc_final: 0.6775 (pp20) REVERT: H 169 GLN cc_start: 0.7249 (tm-30) cc_final: 0.7030 (tm130) REVERT: H 205 GLU cc_start: 0.8528 (OUTLIER) cc_final: 0.8178 (pt0) REVERT: H 233 ASP cc_start: 0.8255 (t0) cc_final: 0.7694 (t0) outliers start: 42 outliers final: 22 residues processed: 191 average time/residue: 1.1081 time to fit residues: 233.0119 Evaluate side-chains 186 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 160 time to evaluate : 1.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 112 ILE 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 402 VAL Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 66 LEU Chi-restraints excluded: chain C residue 112 ILE 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 402 VAL Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 66 LEU 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 402 VAL Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 66 LEU 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 402 VAL 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 37 optimal weight: 8.9990 chunk 117 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 71 optimal weight: 0.9980 chunk 14 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 140 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 60 optimal weight: 0.6980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.224883 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.190161 restraints weight = 13961.041| |-----------------------------------------------------------------------------| r_work (start): 0.4110 rms_B_bonded: 1.71 r_work: 0.3629 rms_B_bonded: 3.02 restraints_weight: 0.5000 r_work: 0.3486 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2802 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= 0.140 Angle : 0.564 9.741 17244 Z= 0.298 Chirality : 0.041 0.182 1928 Planarity : 0.005 0.053 2180 Dihedral : 4.043 17.247 1736 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 2.18 % Allowed : 21.31 % Favored : 76.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.21), residues: 1520 helix: 1.68 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.27 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 362 HIS 0.003 0.001 HIS B 306 PHE 0.017 0.001 PHE H 175 TYR 0.017 0.001 TYR C 188 ARG 0.007 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.04069 ( 792) hydrogen bonds : angle 3.70254 ( 2316) metal coordination : bond 0.00307 ( 16) metal coordination : angle 1.99920 ( 12) covalent geometry : bond 0.00331 (12720) covalent geometry : angle 0.56200 (17232) ********************** 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 188 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 159 time to evaluate : 1.281 Fit side-chains REVERT: B 60 GLU cc_start: 0.7184 (mt-10) cc_final: 0.6714 (pp20) REVERT: B 109 HIS cc_start: 0.7575 (p-80) cc_final: 0.5870 (m170) REVERT: B 169 GLN cc_start: 0.7193 (tm-30) cc_final: 0.6948 (tm130) REVERT: B 205 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8565 (pt0) REVERT: B 233 ASP cc_start: 0.8482 (t0) cc_final: 0.7895 (t0) REVERT: B 413 TYR cc_start: 0.6520 (OUTLIER) cc_final: 0.4880 (m-80) REVERT: C 60 GLU cc_start: 0.7185 (mt-10) cc_final: 0.6708 (pp20) REVERT: C 169 GLN cc_start: 0.7179 (tm-30) cc_final: 0.6938 (tm130) REVERT: C 205 GLU cc_start: 0.8806 (OUTLIER) cc_final: 0.8529 (pt0) REVERT: C 233 ASP cc_start: 0.8409 (t0) cc_final: 0.7847 (t0) REVERT: C 413 TYR cc_start: 0.6480 (OUTLIER) cc_final: 0.4984 (m-80) REVERT: F 60 GLU cc_start: 0.7199 (mt-10) cc_final: 0.6705 (pp20) REVERT: F 169 GLN cc_start: 0.7192 (tm-30) cc_final: 0.6951 (tm130) REVERT: F 205 GLU cc_start: 0.8883 (OUTLIER) cc_final: 0.8589 (pt0) REVERT: F 233 ASP cc_start: 0.8439 (t0) cc_final: 0.7871 (t0) REVERT: F 413 TYR cc_start: 0.6495 (OUTLIER) cc_final: 0.5005 (m-80) REVERT: H 60 GLU cc_start: 0.7295 (mt-10) cc_final: 0.6760 (pp20) REVERT: H 169 GLN cc_start: 0.7219 (tm-30) cc_final: 0.6976 (tm130) REVERT: H 205 GLU cc_start: 0.8892 (OUTLIER) cc_final: 0.8597 (pt0) REVERT: H 233 ASP cc_start: 0.8500 (t0) cc_final: 0.7904 (t0) REVERT: H 413 TYR cc_start: 0.6556 (OUTLIER) cc_final: 0.4912 (m-80) outliers start: 29 outliers final: 9 residues processed: 180 average time/residue: 1.1491 time to fit residues: 226.3955 Evaluate side-chains 168 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 151 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 LEU Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 402 VAL Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 66 LEU 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 66 LEU 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 66 LEU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 81 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 chunk 148 optimal weight: 0.9980 chunk 124 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 3 optimal weight: 9.9990 chunk 103 optimal weight: 0.8980 chunk 125 optimal weight: 6.9990 chunk 90 optimal weight: 3.9990 chunk 89 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 53 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** H 109 HIS ** 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 = 0.4447 r_free = 0.4447 target = 0.225025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4132 r_free = 0.4132 target = 0.191875 restraints weight = 13888.270| |-----------------------------------------------------------------------------| r_work (start): 0.4128 rms_B_bonded: 1.73 r_work: 0.3683 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work (final): 0.3683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.2814 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= 0.139 Angle : 0.567 9.709 17244 Z= 0.298 Chirality : 0.041 0.182 1928 Planarity : 0.005 0.054 2180 Dihedral : 4.046 16.318 1736 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 3.01 % Allowed : 21.16 % Favored : 75.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.80 (0.21), residues: 1520 helix: 1.65 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.28 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 362 HIS 0.003 0.001 HIS F 306 PHE 0.022 0.002 PHE C 289 TYR 0.016 0.001 TYR F 188 ARG 0.007 0.000 ARG H 147 Details of bonding type rmsd hydrogen bonds : bond 0.04089 ( 792) hydrogen bonds : angle 3.70320 ( 2316) metal coordination : bond 0.00303 ( 16) metal coordination : angle 1.99926 ( 12) covalent geometry : bond 0.00328 (12720) covalent geometry : angle 0.56443 (17232) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8742.59 seconds wall clock time: 152 minutes 10.47 seconds (9130.47 seconds total)