Starting phenix.real_space_refine on Mon Dec 30 05:58:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7f0j_31399/12_2024/7f0j_31399.cif Found real_map, /net/cci-nas-00/data/ceres_data/7f0j_31399/12_2024/7f0j_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_31399/12_2024/7f0j_31399.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7f0j_31399/12_2024/7f0j_31399.map" model { file = "/net/cci-nas-00/data/ceres_data/7f0j_31399/12_2024/7f0j_31399.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7f0j_31399/12_2024/7f0j_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-5532/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: 5.88, per 1000 atoms: 0.47 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: 3.45 Conformation dependent library (CDL) restraints added in 1.7 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: 1.19 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: 3.68 Time building geometry restraints manager: 3.91 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: 0.00 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'F' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.500 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: 0.500 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 30.280 Find NCS groups from input model: 0.450 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:14.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.100 ------------------------------------------------------------------------------- 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 12720 Z= 0.155 Angle : 0.538 6.566 17232 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 *********************** 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 : 1.432 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: 1.0662 time to fit residues: 328.2397 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 : 1.447 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7191 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 12720 Z= 0.342 Angle : 0.620 7.613 17232 Z= 0.337 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 *********************** 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 : 1.441 Fit side-chains REVERT: B 233 ASP cc_start: 0.8017 (t0) cc_final: 0.7563 (t0) REVERT: C 109 HIS cc_start: 0.7705 (p-80) cc_final: 0.6230 (m170) REVERT: C 233 ASP cc_start: 0.8010 (t0) cc_final: 0.7556 (t0) REVERT: F 233 ASP cc_start: 0.8012 (t0) cc_final: 0.7555 (t0) REVERT: H 233 ASP cc_start: 0.8020 (t0) cc_final: 0.7563 (t0) outliers start: 40 outliers final: 8 residues processed: 208 average time/residue: 1.1355 time to fit residues: 259.0639 Evaluate side-chains 180 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 172 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR 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 76 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 0.9990 chunk 138 optimal weight: 0.4980 chunk 149 optimal weight: 0.0050 chunk 123 optimal weight: 5.9990 chunk 137 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 110 optimal weight: 0.6980 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 46 ASN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.2053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12720 Z= 0.204 Angle : 0.540 8.172 17232 Z= 0.292 Chirality : 0.041 0.122 1928 Planarity : 0.005 0.059 2180 Dihedral : 4.097 16.338 1736 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.33 % Allowed : 16.64 % Favored : 81.02 % 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: 0.69 (0.22), residues: 1520 helix: 1.53 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.22 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 362 HIS 0.002 0.001 HIS H 306 PHE 0.019 0.002 PHE F 289 TYR 0.016 0.001 TYR B 188 ARG 0.003 0.000 ARG F 51 *********************** 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 227 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 196 time to evaluate : 1.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 HIS cc_start: 0.7600 (p-80) cc_final: 0.6171 (m170) REVERT: B 233 ASP cc_start: 0.7974 (t0) cc_final: 0.7507 (t0) REVERT: C 233 ASP cc_start: 0.7966 (t0) cc_final: 0.7502 (t0) REVERT: F 233 ASP cc_start: 0.7971 (t0) cc_final: 0.7503 (t0) REVERT: H 233 ASP cc_start: 0.7974 (t0) cc_final: 0.7506 (t0) outliers start: 31 outliers final: 12 residues processed: 215 average time/residue: 1.1324 time to fit residues: 267.6310 Evaluate side-chains 164 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 152 time to evaluate : 1.563 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 279 MET Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 279 MET Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 279 MET Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 279 MET 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 136 optimal weight: 0.9990 chunk 103 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 138 optimal weight: 0.8980 chunk 146 optimal weight: 0.9980 chunk 72 optimal weight: 0.8980 chunk 131 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 12720 Z= 0.208 Angle : 0.528 7.998 17232 Z= 0.287 Chirality : 0.040 0.122 1928 Planarity : 0.005 0.059 2180 Dihedral : 4.043 16.090 1736 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 3.61 % Allowed : 15.36 % Favored : 81.02 % 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: 1.58 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.29 (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 H 306 PHE 0.018 0.001 PHE F 175 TYR 0.015 0.001 TYR B 188 ARG 0.001 0.000 ARG H 51 *********************** 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 232 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 184 time to evaluate : 1.501 Fit side-chains REVERT: B 109 HIS cc_start: 0.7651 (p-80) cc_final: 0.5880 (m170) REVERT: B 233 ASP cc_start: 0.7956 (t0) cc_final: 0.7508 (t0) REVERT: C 233 ASP cc_start: 0.7949 (t0) cc_final: 0.7500 (t0) REVERT: F 233 ASP cc_start: 0.7952 (t0) cc_final: 0.7500 (t0) REVERT: H 233 ASP cc_start: 0.7960 (t0) cc_final: 0.7506 (t0) outliers start: 48 outliers final: 12 residues processed: 212 average time/residue: 1.2171 time to fit residues: 281.5954 Evaluate side-chains 168 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 156 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR 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 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.9980 chunk 83 optimal weight: 3.9990 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 0.8980 chunk 60 optimal weight: 2.9990 chunk 125 optimal weight: 8.9990 chunk 101 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 131 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 overall best weight: 1.9784 ------------------------------------------------------------------------------- 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 56 GLN H 46 ASN H 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7211 moved from start: 0.2615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 12720 Z= 0.338 Angle : 0.591 7.977 17232 Z= 0.319 Chirality : 0.044 0.137 1928 Planarity : 0.006 0.061 2180 Dihedral : 4.364 18.731 1736 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.58 % Favored : 93.42 % Rotamer: Outliers : 4.44 % Allowed : 16.94 % Favored : 78.61 % 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: 0.52 (0.21), residues: 1520 helix: 1.41 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -2.31 (0.26), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 362 HIS 0.003 0.001 HIS B 306 PHE 0.028 0.002 PHE H 386 TYR 0.020 0.002 TYR F 188 ARG 0.002 0.000 ARG C 299 *********************** 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 223 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 1.442 Fit side-chains REVERT: B 147 ARG cc_start: 0.5201 (tmm-80) cc_final: 0.4692 (ttp-110) REVERT: B 225 TYR cc_start: 0.5167 (m-10) cc_final: 0.4932 (m-10) REVERT: B 233 ASP cc_start: 0.7998 (t0) cc_final: 0.7568 (t0) REVERT: C 147 ARG cc_start: 0.5199 (tmm-80) cc_final: 0.4688 (ttp-110) REVERT: C 225 TYR cc_start: 0.5159 (m-10) cc_final: 0.4926 (m-10) REVERT: C 233 ASP cc_start: 0.7994 (t0) cc_final: 0.7564 (t0) REVERT: F 147 ARG cc_start: 0.5200 (tmm-80) cc_final: 0.4688 (ttp-110) REVERT: F 225 TYR cc_start: 0.5161 (m-10) cc_final: 0.4926 (m-10) REVERT: F 233 ASP cc_start: 0.7996 (t0) cc_final: 0.7565 (t0) REVERT: H 147 ARG cc_start: 0.5198 (tmm-80) cc_final: 0.4684 (ttp-110) REVERT: H 225 TYR cc_start: 0.5162 (m-10) cc_final: 0.4926 (m-10) REVERT: H 233 ASP cc_start: 0.7998 (t0) cc_final: 0.7566 (t0) outliers start: 59 outliers final: 12 residues processed: 207 average time/residue: 1.1905 time to fit residues: 269.4836 Evaluate side-chains 171 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 1.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR 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 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 0.5980 chunk 86 optimal weight: 9.9990 chunk 36 optimal weight: 7.9990 chunk 147 optimal weight: 0.9980 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 0.3980 chunk 12 optimal weight: 0.3980 chunk 48 optimal weight: 7.9990 chunk 77 optimal weight: 9.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- 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 H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.2754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12720 Z= 0.247 Angle : 0.553 9.181 17232 Z= 0.299 Chirality : 0.042 0.179 1928 Planarity : 0.005 0.056 2180 Dihedral : 4.222 17.312 1736 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.56 % Allowed : 18.83 % Favored : 78.61 % 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: 0.69 (0.21), residues: 1520 helix: 1.55 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : -2.26 (0.27), residues: 456 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 362 HIS 0.003 0.001 HIS F 306 PHE 0.018 0.001 PHE F 386 TYR 0.018 0.002 TYR B 188 ARG 0.001 0.000 ARG F 247 *********************** 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 204 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 170 time to evaluate : 1.425 Fit side-chains REVERT: B 109 HIS cc_start: 0.7711 (p-80) cc_final: 0.5846 (m170) REVERT: B 147 ARG cc_start: 0.5003 (tmm-80) cc_final: 0.4702 (ttp-110) REVERT: B 225 TYR cc_start: 0.5119 (m-80) cc_final: 0.4881 (m-10) REVERT: B 233 ASP cc_start: 0.8028 (t0) cc_final: 0.7583 (t0) REVERT: B 415 GLN cc_start: 0.6987 (OUTLIER) cc_final: 0.6763 (mt0) REVERT: C 147 ARG cc_start: 0.4995 (tmm-80) cc_final: 0.4697 (ttp-110) REVERT: C 225 TYR cc_start: 0.5115 (m-80) cc_final: 0.4879 (m-10) REVERT: C 233 ASP cc_start: 0.8022 (t0) cc_final: 0.7577 (t0) REVERT: C 415 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: F 147 ARG cc_start: 0.4999 (tmm-80) cc_final: 0.4696 (ttp-110) REVERT: F 225 TYR cc_start: 0.5116 (m-80) cc_final: 0.4879 (m-10) REVERT: F 233 ASP cc_start: 0.8025 (t0) cc_final: 0.7577 (t0) REVERT: F 415 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6778 (mt0) REVERT: H 147 ARG cc_start: 0.4998 (tmm-80) cc_final: 0.4694 (ttp-110) REVERT: H 225 TYR cc_start: 0.5117 (m-80) cc_final: 0.4877 (m-10) REVERT: H 233 ASP cc_start: 0.8029 (t0) cc_final: 0.7580 (t0) REVERT: H 415 GLN cc_start: 0.6984 (OUTLIER) cc_final: 0.6770 (mt0) outliers start: 34 outliers final: 12 residues processed: 192 average time/residue: 1.2754 time to fit residues: 266.4507 Evaluate side-chains 170 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 154 time to evaluate : 1.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain B residue 415 GLN 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 C residue 415 GLN 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 F residue 415 GLN Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 413 TYR Chi-restraints excluded: chain H residue 415 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 83 optimal weight: 4.9990 chunk 107 optimal weight: 0.7980 chunk 123 optimal weight: 0.9990 chunk 82 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 91 optimal weight: 0.6980 chunk 89 optimal weight: 10.0000 chunk 67 optimal weight: 0.9980 chunk 90 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 416 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 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 12720 Z= 0.206 Angle : 0.533 9.362 17232 Z= 0.287 Chirality : 0.041 0.190 1928 Planarity : 0.005 0.055 2180 Dihedral : 4.052 16.373 1736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 2.64 % Allowed : 19.20 % Favored : 78.16 % 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: 0.78 (0.21), residues: 1520 helix: 1.62 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.21 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 362 HIS 0.003 0.001 HIS B 306 PHE 0.023 0.001 PHE H 289 TYR 0.016 0.001 TYR B 188 ARG 0.001 0.000 ARG B 247 *********************** 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 200 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 165 time to evaluate : 1.557 Fit side-chains REVERT: B 109 HIS cc_start: 0.7640 (p-80) cc_final: 0.5833 (m170) REVERT: B 147 ARG cc_start: 0.5140 (tmm-80) cc_final: 0.4652 (ttp-110) REVERT: B 225 TYR cc_start: 0.4978 (m-80) cc_final: 0.4711 (m-10) REVERT: B 233 ASP cc_start: 0.7991 (t0) cc_final: 0.7569 (t0) REVERT: B 413 TYR cc_start: 0.5892 (OUTLIER) cc_final: 0.4405 (m-80) REVERT: C 147 ARG cc_start: 0.5138 (tmm-80) cc_final: 0.4648 (ttp-110) REVERT: C 225 TYR cc_start: 0.4972 (m-80) cc_final: 0.4706 (m-10) REVERT: C 233 ASP cc_start: 0.7987 (t0) cc_final: 0.7563 (t0) REVERT: C 413 TYR cc_start: 0.5895 (OUTLIER) cc_final: 0.4414 (m-80) REVERT: F 147 ARG cc_start: 0.5135 (tmm-80) cc_final: 0.4644 (ttp-110) REVERT: F 225 TYR cc_start: 0.4973 (m-80) cc_final: 0.4706 (m-10) REVERT: F 233 ASP cc_start: 0.7989 (t0) cc_final: 0.7564 (t0) REVERT: F 413 TYR cc_start: 0.5897 (OUTLIER) cc_final: 0.4409 (m-80) REVERT: H 147 ARG cc_start: 0.5138 (tmm-80) cc_final: 0.4644 (ttp-110) REVERT: H 225 TYR cc_start: 0.4972 (m-80) cc_final: 0.4705 (m-10) REVERT: H 233 ASP cc_start: 0.7993 (t0) cc_final: 0.7567 (t0) REVERT: H 413 TYR cc_start: 0.5896 (OUTLIER) cc_final: 0.4408 (m-80) outliers start: 35 outliers final: 4 residues processed: 188 average time/residue: 1.2438 time to fit residues: 255.4892 Evaluate side-chains 160 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 152 time to evaluate : 1.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 232 LEU 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 58 optimal weight: 0.2980 chunk 87 optimal weight: 8.9990 chunk 44 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 10.0000 chunk 72 optimal weight: 2.9990 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 8.9990 chunk 133 optimal weight: 1.9990 chunk 140 optimal weight: 0.8980 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN C 56 GLN F 56 GLN H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7193 moved from start: 0.2911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 12720 Z= 0.297 Angle : 0.602 9.240 17232 Z= 0.321 Chirality : 0.044 0.176 1928 Planarity : 0.005 0.056 2180 Dihedral : 4.256 18.232 1736 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 3.09 % Allowed : 19.28 % 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: 0.68 (0.21), residues: 1520 helix: 1.52 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 362 HIS 0.003 0.001 HIS B 306 PHE 0.025 0.002 PHE B 386 TYR 0.019 0.002 TYR B 188 ARG 0.002 0.000 ARG H 299 *********************** 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 205 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 164 time to evaluate : 1.505 Fit side-chains REVERT: B 225 TYR cc_start: 0.5171 (m-80) cc_final: 0.4895 (m-10) REVERT: B 233 ASP cc_start: 0.8057 (t0) cc_final: 0.7589 (t0) REVERT: C 109 HIS cc_start: 0.7705 (p-80) cc_final: 0.5887 (m170) REVERT: C 225 TYR cc_start: 0.5165 (m-80) cc_final: 0.4890 (m-10) REVERT: C 233 ASP cc_start: 0.8048 (t0) cc_final: 0.7583 (t0) REVERT: F 225 TYR cc_start: 0.5167 (m-80) cc_final: 0.4893 (m-10) REVERT: F 233 ASP cc_start: 0.8060 (t0) cc_final: 0.7585 (t0) REVERT: H 225 TYR cc_start: 0.5166 (m-80) cc_final: 0.4889 (m-10) REVERT: H 233 ASP cc_start: 0.8061 (t0) cc_final: 0.7592 (t0) outliers start: 41 outliers final: 21 residues processed: 193 average time/residue: 1.3133 time to fit residues: 275.4077 Evaluate side-chains 165 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 144 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 205 GLU Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 318 LYS Chi-restraints excluded: chain B residue 413 TYR Chi-restraints excluded: chain C residue 205 GLU Chi-restraints excluded: chain C residue 232 LEU Chi-restraints excluded: chain C residue 318 LYS Chi-restraints excluded: chain C residue 413 TYR Chi-restraints excluded: chain F residue 66 LEU Chi-restraints excluded: chain F residue 112 ILE Chi-restraints excluded: chain F residue 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 318 LYS Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 66 LEU Chi-restraints excluded: chain H residue 112 ILE Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 318 LYS 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 128 optimal weight: 0.9990 chunk 136 optimal weight: 0.9980 chunk 140 optimal weight: 3.9990 chunk 82 optimal weight: 4.9990 chunk 59 optimal weight: 0.6980 chunk 107 optimal weight: 0.5980 chunk 41 optimal weight: 2.9990 chunk 123 optimal weight: 0.9980 chunk 129 optimal weight: 2.9990 chunk 89 optimal weight: 9.9990 chunk 144 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7147 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 12720 Z= 0.204 Angle : 0.565 10.482 17232 Z= 0.297 Chirality : 0.041 0.146 1928 Planarity : 0.005 0.053 2180 Dihedral : 4.073 16.632 1736 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.99 % Favored : 94.01 % Rotamer: Outliers : 2.18 % Allowed : 19.65 % Favored : 78.16 % 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: 0.83 (0.21), residues: 1520 helix: 1.65 (0.15), residues: 1060 sheet: None (None), residues: 0 loop : -2.18 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 362 HIS 0.003 0.001 HIS B 109 PHE 0.021 0.001 PHE H 289 TYR 0.016 0.001 TYR H 188 ARG 0.011 0.000 ARG H 147 *********************** 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 197 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 168 time to evaluate : 1.470 Fit side-chains REVERT: B 109 HIS cc_start: 0.7640 (p-80) cc_final: 0.5864 (m170) REVERT: B 169 GLN cc_start: 0.6980 (tm-30) cc_final: 0.6589 (tm-30) REVERT: B 205 GLU cc_start: 0.7986 (OUTLIER) cc_final: 0.7627 (pt0) REVERT: B 225 TYR cc_start: 0.5195 (m-80) cc_final: 0.4978 (m-10) REVERT: B 233 ASP cc_start: 0.7993 (t0) cc_final: 0.7563 (t0) REVERT: B 413 TYR cc_start: 0.5849 (OUTLIER) cc_final: 0.4568 (m-80) REVERT: C 169 GLN cc_start: 0.6988 (tm-30) cc_final: 0.6593 (tm-30) REVERT: C 205 GLU cc_start: 0.7988 (OUTLIER) cc_final: 0.7634 (pt0) REVERT: C 225 TYR cc_start: 0.5190 (m-80) cc_final: 0.4973 (m-10) REVERT: C 233 ASP cc_start: 0.7990 (t0) cc_final: 0.7556 (t0) REVERT: C 413 TYR cc_start: 0.5835 (OUTLIER) cc_final: 0.4568 (m-80) REVERT: F 169 GLN cc_start: 0.6991 (tm-30) cc_final: 0.6596 (tm-30) REVERT: F 205 GLU cc_start: 0.7987 (OUTLIER) cc_final: 0.7628 (pt0) REVERT: F 225 TYR cc_start: 0.5189 (m-80) cc_final: 0.4974 (m-10) REVERT: F 233 ASP cc_start: 0.7996 (t0) cc_final: 0.7560 (t0) REVERT: F 413 TYR cc_start: 0.5836 (OUTLIER) cc_final: 0.4562 (m-80) REVERT: H 169 GLN cc_start: 0.6990 (tm-30) cc_final: 0.6598 (tm-30) REVERT: H 205 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7626 (pt0) REVERT: H 225 TYR cc_start: 0.5191 (m-80) cc_final: 0.4974 (m-10) REVERT: H 233 ASP cc_start: 0.7997 (t0) cc_final: 0.7564 (t0) REVERT: H 413 TYR cc_start: 0.5837 (OUTLIER) cc_final: 0.4568 (m-80) outliers start: 29 outliers final: 7 residues processed: 186 average time/residue: 1.1526 time to fit residues: 235.1238 Evaluate side-chains 172 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 157 time to evaluate : 1.416 ------------------------------------------------------------------------------- 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 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 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 88 optimal weight: 5.9990 chunk 68 optimal weight: 0.4980 chunk 100 optimal weight: 2.9990 chunk 151 optimal weight: 7.9990 chunk 139 optimal weight: 4.9990 chunk 120 optimal weight: 3.9990 chunk 12 optimal weight: 0.0010 chunk 93 optimal weight: 6.9990 chunk 73 optimal weight: 0.5980 chunk 95 optimal weight: 2.9990 chunk 128 optimal weight: 0.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 56 GLN ** H 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 12720 Z= 0.228 Angle : 0.580 9.734 17232 Z= 0.307 Chirality : 0.041 0.139 1928 Planarity : 0.005 0.054 2180 Dihedral : 4.121 16.955 1736 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 1.81 % Allowed : 20.93 % Favored : 77.26 % 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: 0.81 (0.21), residues: 1520 helix: 1.63 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.17 (0.26), residues: 460 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 0.016 0.001 TYR C 188 ARG 0.010 0.000 ARG B 147 ********************** 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 187 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 163 time to evaluate : 1.471 Fit side-chains REVERT: B 109 HIS cc_start: 0.7626 (p-80) cc_final: 0.6120 (m-70) REVERT: B 205 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: B 233 ASP cc_start: 0.7942 (t0) cc_final: 0.7508 (t0) REVERT: B 413 TYR cc_start: 0.5882 (OUTLIER) cc_final: 0.4209 (m-80) REVERT: C 205 GLU cc_start: 0.8005 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: C 233 ASP cc_start: 0.8022 (t0) cc_final: 0.7579 (t0) REVERT: C 413 TYR cc_start: 0.5887 (OUTLIER) cc_final: 0.4219 (m-80) REVERT: F 205 GLU cc_start: 0.8006 (OUTLIER) cc_final: 0.7654 (pt0) REVERT: F 233 ASP cc_start: 0.7938 (t0) cc_final: 0.7503 (t0) REVERT: F 413 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.4219 (m-80) REVERT: H 205 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7651 (pt0) REVERT: H 233 ASP cc_start: 0.7943 (t0) cc_final: 0.7505 (t0) REVERT: H 413 TYR cc_start: 0.5891 (OUTLIER) cc_final: 0.4219 (m-80) outliers start: 24 outliers final: 8 residues processed: 179 average time/residue: 1.1916 time to fit residues: 236.4005 Evaluate side-chains 177 residues out of total 1328 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 161 time to evaluate : 1.459 ------------------------------------------------------------------------------- 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 318 LYS 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 205 GLU Chi-restraints excluded: chain F residue 232 LEU Chi-restraints excluded: chain F residue 413 TYR Chi-restraints excluded: chain H residue 205 GLU Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 318 LYS 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 36 optimal weight: 0.6980 chunk 111 optimal weight: 0.2980 chunk 17 optimal weight: 6.9990 chunk 33 optimal weight: 0.8980 chunk 120 optimal weight: 0.8980 chunk 50 optimal weight: 0.0670 chunk 124 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 106 optimal weight: 0.2980 chunk 6 optimal weight: 0.5980 overall best weight: 0.3918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 56 GLN ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 416 ASN C 56 GLN ** C 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 416 ASN F 56 GLN ** F 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 416 ASN H 56 GLN ** H 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 = 0.4463 r_free = 0.4463 target = 0.227140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4084 r_free = 0.4084 target = 0.186015 restraints weight = 13890.900| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 2.08 r_work: 0.3705 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3627 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 12720 Z= 0.175 Angle : 0.564 10.111 17232 Z= 0.294 Chirality : 0.040 0.138 1928 Planarity : 0.005 0.053 2180 Dihedral : 3.878 16.667 1736 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.13 % Favored : 94.87 % Rotamer: Outliers : 2.26 % Allowed : 21.08 % Favored : 76.66 % 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: 0.92 (0.21), residues: 1520 helix: 1.72 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -2.15 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 362 HIS 0.004 0.001 HIS F 109 PHE 0.021 0.001 PHE C 289 TYR 0.014 0.001 TYR H 188 ARG 0.011 0.000 ARG H 147 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4285.67 seconds wall clock time: 77 minutes 37.87 seconds (4657.87 seconds total)