Starting phenix.real_space_refine on Thu Aug 6 20:49:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9tg3_55889/08_2026/9tg3_55889.cif Found real_map, /net/cci-nas-00/data/ceres_data/9tg3_55889/08_2026/9tg3_55889.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9tg3_55889/08_2026/9tg3_55889.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9tg3_55889/08_2026/9tg3_55889.map" model { file = "/net/cci-nas-00/data/ceres_data/9tg3_55889/08_2026/9tg3_55889.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9tg3_55889/08_2026/9tg3_55889.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.022 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: 6 Type Number sf(0) Gaussians K 2 8.98 5 S 68 5.16 5 C 5572 2.51 5 N 1392 2.21 5 O 1544 1.98 5 H 8112 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 16690 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4172 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "B" Number of atoms: 4172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4172 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "C" Number of atoms: 4172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4172 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "D" Number of atoms: 4172 Number of conformers: 1 Conformer: "" Number of residues, atoms: 283, 4172 Classifications: {'peptide': 283} Link IDs: {'PTRANS': 15, 'TRANS': 267} Chain breaks: 2 Unresolved non-hydrogen bonds: 119 Unresolved non-hydrogen angles: 151 Unresolved non-hydrogen dihedrals: 101 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 4, 'ASP:plan': 1, 'TRP:plan': 1, 'ASN:plan1': 3, 'GLU:plan': 4, 'PHE:plan': 1, 'GLN:plan1': 2, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 83 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' K': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.85, per 1000 atoms: 0.17 Number of scatterers: 16690 At special positions: 0 Unit cell: (89.7, 91, 118.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 2 19.00 S 68 16.00 O 1544 8.00 N 1392 7.00 C 5572 6.00 H 8112 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 99 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 99 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 99 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 99 " - pdb=" SG CYS D 131 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.50 Conformation dependent library (CDL) restraints added in 478.8 milliseconds 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2160 Finding SS restraints... Secondary structure from input PDB file: 28 helices and 18 sheets defined 36.1% alpha, 22.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 39 through 48 Processing helix chain 'A' and resid 52 through 83 removed outlier: 3.687A pdb=" N PHE A 64 " --> pdb=" O PHE A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 118 removed outlier: 3.583A pdb=" N LEU A 118 " --> pdb=" O LEU A 114 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 161 removed outlier: 3.561A pdb=" N ILE A 135 " --> pdb=" O CYS A 131 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 184 Processing helix chain 'A' and resid 253 through 258 removed outlier: 3.803A pdb=" N LEU A 257 " --> pdb=" O LEU A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 291 No H-bonds generated for 'chain 'A' and resid 289 through 291' Processing helix chain 'B' and resid 39 through 48 Processing helix chain 'B' and resid 52 through 83 removed outlier: 3.712A pdb=" N PHE B 64 " --> pdb=" O PHE B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 119 removed outlier: 3.688A pdb=" N LEU B 118 " --> pdb=" O LEU B 114 " (cutoff:3.500A) Processing helix chain 'B' and resid 131 through 161 removed outlier: 3.520A pdb=" N ILE B 135 " --> pdb=" O CYS B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 180 through 184 Processing helix chain 'B' and resid 253 through 258 removed outlier: 3.725A pdb=" N LEU B 257 " --> pdb=" O LEU B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 291 No H-bonds generated for 'chain 'B' and resid 289 through 291' Processing helix chain 'C' and resid 39 through 48 Processing helix chain 'C' and resid 52 through 83 removed outlier: 3.610A pdb=" N PHE C 64 " --> pdb=" O PHE C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 119 removed outlier: 3.550A pdb=" N LEU C 118 " --> pdb=" O LEU C 114 " (cutoff:3.500A) Processing helix chain 'C' and resid 131 through 161 removed outlier: 3.541A pdb=" N ILE C 135 " --> pdb=" O CYS C 131 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 184 Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.663A pdb=" N LEU C 257 " --> pdb=" O LEU C 253 " (cutoff:3.500A) Processing helix chain 'C' and resid 289 through 291 No H-bonds generated for 'chain 'C' and resid 289 through 291' Processing helix chain 'D' and resid 39 through 48 Processing helix chain 'D' and resid 52 through 83 removed outlier: 3.626A pdb=" N PHE D 64 " --> pdb=" O PHE D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 119 removed outlier: 3.638A pdb=" N LEU D 118 " --> pdb=" O LEU D 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 131 through 161 Processing helix chain 'D' and resid 180 through 184 Processing helix chain 'D' and resid 253 through 258 removed outlier: 3.739A pdb=" N LEU D 257 " --> pdb=" O LEU D 253 " (cutoff:3.500A) Processing helix chain 'D' and resid 289 through 293 Processing sheet with id=AA1, first strand: chain 'A' and resid 170 through 172 Processing sheet with id=AA2, first strand: chain 'A' and resid 170 through 172 removed outlier: 3.522A pdb=" N MET A 294 " --> pdb=" O ALA A 176 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.710A pdb=" N ALA A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 220 through 222 removed outlier: 3.710A pdb=" N ALA A 206 " --> pdb=" O VAL A 222 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N SER A 201 " --> pdb=" O MET A 274 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N MET A 274 " --> pdb=" O SER A 201 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 297 through 298 Processing sheet with id=AA6, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA7, first strand: chain 'B' and resid 170 through 172 Processing sheet with id=AA8, first strand: chain 'B' and resid 217 through 222 removed outlier: 3.609A pdb=" N ALA B 206 " --> pdb=" O VAL B 222 " (cutoff:3.500A) removed outlier: 5.695A pdb=" N SER B 201 " --> pdb=" O MET B 274 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N MET B 274 " --> pdb=" O SER B 201 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 297 through 298 Processing sheet with id=AB1, first strand: chain 'C' and resid 170 through 172 Processing sheet with id=AB2, first strand: chain 'C' and resid 170 through 172 removed outlier: 3.544A pdb=" N MET C 294 " --> pdb=" O ALA C 176 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.629A pdb=" N ALA C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 220 through 222 removed outlier: 3.629A pdb=" N ALA C 206 " --> pdb=" O VAL C 222 " (cutoff:3.500A) removed outlier: 4.246A pdb=" N VAL C 202 " --> pdb=" O SER C 272 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N SER C 272 " --> pdb=" O VAL C 202 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N VAL C 204 " --> pdb=" O PHE C 270 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N PHE C 270 " --> pdb=" O VAL C 204 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N ALA C 206 " --> pdb=" O VAL C 268 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N VAL C 268 " --> pdb=" O ALA C 206 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 297 through 298 Processing sheet with id=AB6, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AB7, first strand: chain 'D' and resid 170 through 172 Processing sheet with id=AB8, first strand: chain 'D' and resid 221 through 222 removed outlier: 3.619A pdb=" N ALA D 206 " --> pdb=" O VAL D 222 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N VAL D 202 " --> pdb=" O SER D 272 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N SER D 272 " --> pdb=" O VAL D 202 " (cutoff:3.500A) removed outlier: 4.521A pdb=" N VAL D 204 " --> pdb=" O PHE D 270 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N PHE D 270 " --> pdb=" O VAL D 204 " (cutoff:3.500A) removed outlier: 4.482A pdb=" N ALA D 206 " --> pdb=" O VAL D 268 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL D 268 " --> pdb=" O ALA D 206 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N LEU D 208 " --> pdb=" O GLU D 266 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLU D 266 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 297 through 298 437 hydrogen bonds defined for protein. 1209 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: 3.43 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 8100 1.03 - 1.23: 13 1.23 - 1.42: 3759 1.42 - 1.62: 4936 1.62 - 1.81: 116 Bond restraints: 16924 Sorted by residual: bond pdb=" N ARG D 18 " pdb=" CA ARG D 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.07e+00 bond pdb=" N ARG C 18 " pdb=" CA ARG C 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.99e+00 bond pdb=" N ARG B 18 " pdb=" CA ARG B 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.97e+00 bond pdb=" N ARG A 18 " pdb=" CA ARG A 18 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 2.93e+00 bond pdb=" N ARG B 18 " pdb=" H ARG B 18 " ideal model delta sigma weight residual 0.860 0.891 -0.031 2.00e-02 2.50e+03 2.41e+00 ... (remaining 16919 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.92: 27467 0.92 - 1.85: 2801 1.85 - 2.77: 122 2.77 - 3.69: 74 3.69 - 4.61: 8 Bond angle restraints: 30472 Sorted by residual: angle pdb=" N ILE A 238 " pdb=" CA ILE A 238 " pdb=" C ILE A 238 " ideal model delta sigma weight residual 111.62 108.50 3.12 7.90e-01 1.60e+00 1.56e+01 angle pdb=" N ILE D 238 " pdb=" CA ILE D 238 " pdb=" C ILE D 238 " ideal model delta sigma weight residual 111.62 109.06 2.56 7.90e-01 1.60e+00 1.05e+01 angle pdb=" N ILE B 238 " pdb=" CA ILE B 238 " pdb=" C ILE B 238 " ideal model delta sigma weight residual 111.62 109.44 2.18 7.90e-01 1.60e+00 7.63e+00 angle pdb=" N ARG B 166 " pdb=" CA ARG B 166 " pdb=" C ARG B 166 " ideal model delta sigma weight residual 114.39 111.03 3.36 1.45e+00 4.76e-01 5.38e+00 angle pdb=" N ARG A 166 " pdb=" CA ARG A 166 " pdb=" C ARG A 166 " ideal model delta sigma weight residual 114.39 111.05 3.34 1.45e+00 4.76e-01 5.32e+00 ... (remaining 30467 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 7405 17.94 - 35.89: 557 35.89 - 53.83: 149 53.83 - 71.78: 42 71.78 - 89.72: 27 Dihedral angle restraints: 8180 sinusoidal: 4120 harmonic: 4060 Sorted by residual: dihedral pdb=" CB GLU B 233 " pdb=" CG GLU B 233 " pdb=" CD GLU B 233 " pdb=" OE1 GLU B 233 " ideal model delta sinusoidal sigma weight residual 0.00 89.72 -89.72 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" CG ARG A 19 " pdb=" CD ARG A 19 " pdb=" NE ARG A 19 " pdb=" CZ ARG A 19 " ideal model delta sinusoidal sigma weight residual 180.00 137.17 42.83 2 1.50e+01 4.44e-03 9.86e+00 dihedral pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " pdb=" CE MET B 125 " ideal model delta sinusoidal sigma weight residual -180.00 -120.62 -59.38 3 1.50e+01 4.44e-03 9.48e+00 ... (remaining 8177 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 836 0.026 - 0.052: 357 0.052 - 0.077: 82 0.077 - 0.103: 75 0.103 - 0.129: 46 Chirality restraints: 1396 Sorted by residual: chirality pdb=" CA VAL B 191 " pdb=" N VAL B 191 " pdb=" C VAL B 191 " pdb=" CB VAL B 191 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.15e-01 chirality pdb=" CA ILE C 98 " pdb=" N ILE C 98 " pdb=" C ILE C 98 " pdb=" CB ILE C 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE B 98 " pdb=" N ILE B 98 " pdb=" C ILE B 98 " pdb=" CB ILE B 98 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 ... (remaining 1393 not shown) Planarity restraints: 2572 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP A 50 " 0.007 2.00e-02 2.50e+03 1.33e-02 1.78e+00 pdb=" CG ASP A 50 " -0.023 2.00e-02 2.50e+03 pdb=" OD1 ASP A 50 " 0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP A 50 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG C 19 " 0.096 9.50e-02 1.11e+02 3.22e-02 1.24e+00 pdb=" NE ARG C 19 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG C 19 " 0.004 2.00e-02 2.50e+03 pdb=" NH1 ARG C 19 " -0.004 2.00e-02 2.50e+03 pdb=" NH2 ARG C 19 " -0.000 2.00e-02 2.50e+03 pdb="HH11 ARG C 19 " -0.004 2.00e-02 2.50e+03 pdb="HH12 ARG C 19 " 0.005 2.00e-02 2.50e+03 pdb="HH21 ARG C 19 " 0.000 2.00e-02 2.50e+03 pdb="HH22 ARG C 19 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP C 223 " 0.005 2.00e-02 2.50e+03 1.01e-02 1.02e+00 pdb=" C ASP C 223 " -0.017 2.00e-02 2.50e+03 pdb=" O ASP C 223 " 0.007 2.00e-02 2.50e+03 pdb=" N PHE C 224 " 0.006 2.00e-02 2.50e+03 ... (remaining 2569 not shown) Histogram of nonbonded interaction distances: 1.51 - 2.24: 1616 2.24 - 2.96: 42017 2.96 - 3.69: 58042 3.69 - 4.41: 88105 4.41 - 5.14: 139569 Nonbonded interactions: 329349 Sorted by model distance: nonbonded pdb=" HE1 TRP C 68 " pdb=" OE1 GLN C 117 " model vdw 1.511 2.450 nonbonded pdb=" HE1 TRP D 68 " pdb=" OE1 GLN D 117 " model vdw 1.538 2.450 nonbonded pdb=" HE1 TRP A 68 " pdb=" OE1 GLN A 117 " model vdw 1.542 2.450 nonbonded pdb=" HE1 TRP B 68 " pdb=" OE1 GLN B 117 " model vdw 1.558 2.450 nonbonded pdb=" HZ1 LYS C 23 " pdb=" OE1 GLU C 292 " model vdw 1.587 2.450 ... (remaining 329344 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: 0.01 Found NCS groups: ncs_group { reference = (chain 'A' and resid 18 through 324) selection = (chain 'B' and resid 18 through 324) selection = chain 'C' selection = chain 'D' } 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 group one per residue 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: 5.650 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: 0.070 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.930 Find NCS groups from input model: 0.290 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8816 Z= 0.126 Angle : 0.537 4.508 12036 Z= 0.316 Chirality : 0.039 0.129 1396 Planarity : 0.003 0.041 1512 Dihedral : 13.989 89.722 2976 Min Nonbonded Distance : 1.979 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 0.79 % Allowed : 9.50 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.78 (0.26), residues: 1108 helix: 1.31 (0.29), residues: 344 sheet: -0.73 (0.32), residues: 240 loop : 0.82 (0.28), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 19 TYR 0.006 0.001 TYR C 122 PHE 0.013 0.001 PHE B 236 TRP 0.005 0.000 TRP B 162 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00251 / 0.13 ( 8812) covalent geometry : angle 0.53674 / 0.32 (12028) SS BOND : bond 0.00233 / 0.12 ( 4) SS BOND : angle 0.27606 / 0.19 ( 8) hydrogen bonds : bond 0.21730 / 14.71 ( 423) hydrogen bonds : angle 8.60758 / 6.08 ( 1209) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 148 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 141 time to evaluate : 0.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6006 (ttp) cc_final: 0.5636 (ttm) REVERT: A 323 PRO cc_start: 0.6786 (Cg_endo) cc_final: 0.6359 (Cg_exo) REVERT: B 297 HIS cc_start: 0.6400 (m-70) cc_final: 0.5266 (m-70) REVERT: C 50 ASP cc_start: 0.6798 (p0) cc_final: 0.6308 (p0) REVERT: C 294 MET cc_start: 0.6789 (ptt) cc_final: 0.6556 (ptt) REVERT: D 297 HIS cc_start: 0.6610 (m-70) cc_final: 0.5481 (m-70) outliers start: 7 outliers final: 6 residues processed: 146 average time/residue: 0.1523 time to fit residues: 34.0580 Evaluate side-chains 144 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 286 THR Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 287 SER Chi-restraints excluded: chain D residue 61 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 0.5980 chunk 49 optimal weight: 1.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 7.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 106 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 283 GLN B 190 GLN B 283 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.302914 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.254284 restraints weight = 24129.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.254297 restraints weight = 23518.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.254297 restraints weight = 22781.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.254297 restraints weight = 22779.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.254297 restraints weight = 22779.366| |-----------------------------------------------------------------------------| r_work (final): 0.4722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8816 Z= 0.157 Angle : 0.538 4.404 12036 Z= 0.290 Chirality : 0.041 0.134 1396 Planarity : 0.004 0.023 1512 Dihedral : 4.384 36.249 1190 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.58 % Allowed : 8.48 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.25), residues: 1108 helix: 1.88 (0.27), residues: 348 sheet: -0.61 (0.31), residues: 240 loop : 0.77 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 19 TYR 0.009 0.001 TYR C 122 PHE 0.017 0.002 PHE A 106 TRP 0.006 0.001 TRP D 75 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.16 ( 8812) covalent geometry : angle 0.53748 / 0.29 (12028) SS BOND : bond 0.00253 / 0.13 ( 4) SS BOND : angle 0.67503 / 0.61 ( 8) hydrogen bonds : bond 0.05084 / 3.48 ( 423) hydrogen bonds : angle 5.08946 / 3.57 ( 1209) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 145 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6167 (ttp) cc_final: 0.5761 (ttm) REVERT: B 297 HIS cc_start: 0.6202 (m-70) cc_final: 0.5331 (m-70) REVERT: C 50 ASP cc_start: 0.5419 (p0) cc_final: 0.5054 (p0) REVERT: D 297 HIS cc_start: 0.6457 (m-70) cc_final: 0.5519 (m-70) outliers start: 14 outliers final: 10 residues processed: 153 average time/residue: 0.1396 time to fit residues: 33.1830 Evaluate side-chains 150 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 64 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 86 optimal weight: 9.9990 chunk 68 optimal weight: 1.9990 chunk 65 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5054 r_free = 0.5054 target = 0.301961 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4716 r_free = 0.4716 target = 0.255497 restraints weight = 24347.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 100)---------------| | r_work = 0.4525 r_free = 0.4525 target = 0.236121 restraints weight = 21298.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.239302 restraints weight = 16304.446| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.242312 restraints weight = 14492.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4591 r_free = 0.4591 target = 0.243966 restraints weight = 12989.817| |-----------------------------------------------------------------------------| r_work (final): 0.4645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 8816 Z= 0.135 Angle : 0.492 4.940 12036 Z= 0.258 Chirality : 0.040 0.133 1396 Planarity : 0.003 0.027 1512 Dihedral : 3.977 17.548 1186 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.58 % Allowed : 8.37 % Favored : 90.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.48 (0.25), residues: 1108 helix: 2.55 (0.27), residues: 348 sheet: -0.28 (0.33), residues: 220 loop : 0.63 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.009 0.001 TYR D 244 PHE 0.013 0.001 PHE B 106 TRP 0.004 0.001 TRP D 53 HIS 0.005 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 ( 8812) covalent geometry : angle 0.49173 / 0.26 (12028) SS BOND : bond 0.00380 / 0.19 ( 4) SS BOND : angle 0.69672 / 0.50 ( 8) hydrogen bonds : bond 0.04140 / 2.80 ( 423) hydrogen bonds : angle 4.56277 / 3.21 ( 1209) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 163 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 149 time to evaluate : 0.596 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6236 (ttp) cc_final: 0.5831 (ttm) REVERT: B 297 HIS cc_start: 0.6635 (m-70) cc_final: 0.5535 (m-70) REVERT: C 50 ASP cc_start: 0.6887 (p0) cc_final: 0.6344 (p0) REVERT: D 54 ARG cc_start: 0.6006 (tpt170) cc_final: 0.5577 (mpp80) REVERT: D 297 HIS cc_start: 0.6653 (m-70) cc_final: 0.5525 (m-70) outliers start: 14 outliers final: 11 residues processed: 157 average time/residue: 0.1593 time to fit residues: 38.1965 Evaluate side-chains 153 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 88 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 57 optimal weight: 10.0000 chunk 64 optimal weight: 0.9990 chunk 77 optimal weight: 1.9990 chunk 41 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 85 optimal weight: 9.9990 chunk 105 optimal weight: 0.2980 chunk 29 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5044 r_free = 0.5044 target = 0.300770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 139)---------------| | r_work = 0.4577 r_free = 0.4577 target = 0.238617 restraints weight = 23610.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4567 r_free = 0.4567 target = 0.238988 restraints weight = 18665.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4583 r_free = 0.4583 target = 0.241288 restraints weight = 16075.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.243272 restraints weight = 14201.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.244177 restraints weight = 12878.589| |-----------------------------------------------------------------------------| r_work (final): 0.4651 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.1631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8816 Z= 0.137 Angle : 0.491 5.040 12036 Z= 0.256 Chirality : 0.040 0.137 1396 Planarity : 0.003 0.026 1512 Dihedral : 3.871 18.017 1186 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.58 % Allowed : 8.48 % Favored : 89.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.56 (0.26), residues: 1108 helix: 2.84 (0.27), residues: 348 sheet: -0.46 (0.33), residues: 240 loop : 0.65 (0.28), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.011 0.001 TYR C 122 PHE 0.014 0.002 PHE C 71 TRP 0.004 0.001 TRP D 53 HIS 0.004 0.001 HIS B 89 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.14 ( 8812) covalent geometry : angle 0.49105 / 0.26 (12028) SS BOND : bond 0.00346 / 0.17 ( 4) SS BOND : angle 0.83790 / 0.56 ( 8) hydrogen bonds : bond 0.03536 / 2.38 ( 423) hydrogen bonds : angle 4.40671 / 3.09 ( 1209) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6418 (ttp) cc_final: 0.6059 (ttm) REVERT: B 57 MET cc_start: 0.6528 (ttp) cc_final: 0.6195 (ttt) REVERT: B 297 HIS cc_start: 0.6520 (m-70) cc_final: 0.5550 (m-70) REVERT: C 50 ASP cc_start: 0.6370 (p0) cc_final: 0.5885 (p0) REVERT: D 50 ASP cc_start: 0.6399 (p0) cc_final: 0.6129 (p0) REVERT: D 57 MET cc_start: 0.6485 (ttp) cc_final: 0.6036 (ttm) outliers start: 14 outliers final: 13 residues processed: 155 average time/residue: 0.1460 time to fit residues: 34.5101 Evaluate side-chains 152 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 139 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 104 optimal weight: 1.9990 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 0.9990 chunk 63 optimal weight: 0.5980 chunk 25 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 96 optimal weight: 0.9990 chunk 47 optimal weight: 0.0870 chunk 7 optimal weight: 2.9990 overall best weight: 0.6762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5047 r_free = 0.5047 target = 0.304279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.4594 r_free = 0.4594 target = 0.240466 restraints weight = 23929.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.243351 restraints weight = 22118.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.246553 restraints weight = 17520.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4622 r_free = 0.4622 target = 0.246730 restraints weight = 14417.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4624 r_free = 0.4624 target = 0.246878 restraints weight = 14422.041| |-----------------------------------------------------------------------------| r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 8816 Z= 0.124 Angle : 0.472 4.298 12036 Z= 0.246 Chirality : 0.040 0.132 1396 Planarity : 0.003 0.025 1512 Dihedral : 3.800 18.410 1185 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.70 % Allowed : 8.14 % Favored : 90.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.26), residues: 1108 helix: 3.08 (0.27), residues: 348 sheet: -0.49 (0.32), residues: 248 loop : 0.76 (0.29), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.008 0.001 TYR D 244 PHE 0.019 0.001 PHE B 270 TRP 0.004 0.000 TRP D 53 HIS 0.004 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.12 ( 8812) covalent geometry : angle 0.47134 / 0.25 (12028) SS BOND : bond 0.00364 / 0.18 ( 4) SS BOND : angle 0.89172 / 0.59 ( 8) hydrogen bonds : bond 0.03410 / 2.28 ( 423) hydrogen bonds : angle 4.31275 / 3.02 ( 1209) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 MET cc_start: 0.6438 (ttp) cc_final: 0.6088 (ttm) REVERT: B 57 MET cc_start: 0.6554 (ttp) cc_final: 0.6211 (ttm) REVERT: B 297 HIS cc_start: 0.6472 (m-70) cc_final: 0.5577 (m-70) REVERT: C 50 ASP cc_start: 0.6103 (p0) cc_final: 0.5582 (p0) REVERT: D 50 ASP cc_start: 0.6152 (p0) cc_final: 0.5917 (p0) REVERT: D 57 MET cc_start: 0.6486 (ttp) cc_final: 0.6072 (ttm) outliers start: 15 outliers final: 14 residues processed: 154 average time/residue: 0.1365 time to fit residues: 31.8126 Evaluate side-chains 153 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 35 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 102 optimal weight: 0.6980 chunk 51 optimal weight: 5.9990 chunk 23 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 82 optimal weight: 0.5980 chunk 43 optimal weight: 1.9990 chunk 80 optimal weight: 0.5980 chunk 87 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5016 r_free = 0.5016 target = 0.295340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 115)---------------| | r_work = 0.4554 r_free = 0.4554 target = 0.235785 restraints weight = 23345.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 78)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.229977 restraints weight = 22014.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4525 r_free = 0.4525 target = 0.234406 restraints weight = 19243.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.236241 restraints weight = 15582.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4555 r_free = 0.4555 target = 0.237878 restraints weight = 13481.009| |-----------------------------------------------------------------------------| r_work (final): 0.4530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8816 Z= 0.181 Angle : 0.507 4.580 12036 Z= 0.268 Chirality : 0.041 0.134 1396 Planarity : 0.003 0.026 1512 Dihedral : 3.893 19.142 1185 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.81 % Allowed : 8.37 % Favored : 89.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.52 (0.26), residues: 1108 helix: 2.99 (0.28), residues: 348 sheet: -0.77 (0.35), residues: 212 loop : 0.56 (0.28), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.014 0.001 TYR C 122 PHE 0.017 0.002 PHE B 106 TRP 0.005 0.001 TRP B 68 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.18 ( 8812) covalent geometry : angle 0.50660 / 0.27 (12028) SS BOND : bond 0.00477 / 0.24 ( 4) SS BOND : angle 1.03462 / 0.61 ( 8) hydrogen bonds : bond 0.03453 / 2.32 ( 423) hydrogen bonds : angle 4.39581 / 3.07 ( 1209) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 144 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6821 (p0) cc_final: 0.6501 (p0) REVERT: A 57 MET cc_start: 0.6412 (ttp) cc_final: 0.6035 (ttm) REVERT: B 57 MET cc_start: 0.6562 (ttp) cc_final: 0.6205 (ttm) REVERT: C 50 ASP cc_start: 0.6378 (p0) cc_final: 0.5817 (p0) REVERT: D 57 MET cc_start: 0.6492 (ttp) cc_final: 0.6090 (ttm) outliers start: 16 outliers final: 15 residues processed: 153 average time/residue: 0.1614 time to fit residues: 36.4956 Evaluate side-chains 157 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 142 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 13 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 chunk 77 optimal weight: 2.9990 chunk 86 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5028 r_free = 0.5028 target = 0.298201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.4544 r_free = 0.4544 target = 0.233191 restraints weight = 23680.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 60)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.233021 restraints weight = 22460.538| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.235644 restraints weight = 17616.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.237074 restraints weight = 14944.672| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4560 r_free = 0.4560 target = 0.239101 restraints weight = 13450.213| |-----------------------------------------------------------------------------| r_work (final): 0.4603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7259 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8816 Z= 0.168 Angle : 0.500 4.259 12036 Z= 0.265 Chirality : 0.041 0.164 1396 Planarity : 0.003 0.028 1512 Dihedral : 3.917 19.423 1185 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.04 % Allowed : 8.48 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.51 (0.26), residues: 1108 helix: 3.00 (0.28), residues: 348 sheet: -0.71 (0.36), residues: 208 loop : 0.49 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 203 TYR 0.010 0.001 TYR C 122 PHE 0.014 0.002 PHE B 106 TRP 0.006 0.001 TRP D 53 HIS 0.007 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.17 ( 8812) covalent geometry : angle 0.49986 / 0.26 (12028) SS BOND : bond 0.00430 / 0.22 ( 4) SS BOND : angle 1.03193 / 0.64 ( 8) hydrogen bonds : bond 0.03359 / 2.24 ( 423) hydrogen bonds : angle 4.35689 / 3.05 ( 1209) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 164 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 146 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6797 (p0) cc_final: 0.6438 (p0) REVERT: A 57 MET cc_start: 0.6402 (ttp) cc_final: 0.6031 (ttm) REVERT: A 188 ILE cc_start: 0.8411 (OUTLIER) cc_final: 0.8126 (pt) REVERT: B 18 ARG cc_start: 0.6608 (ptm160) cc_final: 0.6336 (ptm160) REVERT: B 57 MET cc_start: 0.6502 (ttp) cc_final: 0.6176 (ttm) REVERT: C 50 ASP cc_start: 0.6339 (p0) cc_final: 0.5746 (p0) REVERT: D 57 MET cc_start: 0.6466 (ttp) cc_final: 0.6093 (ttm) outliers start: 18 outliers final: 16 residues processed: 157 average time/residue: 0.1752 time to fit residues: 40.2121 Evaluate side-chains 156 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 57 MET Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 77 optimal weight: 2.9990 chunk 89 optimal weight: 0.7980 chunk 78 optimal weight: 0.4980 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 66 optimal weight: 0.6980 chunk 65 optimal weight: 0.0980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5048 r_free = 0.5048 target = 0.297820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 112)---------------| | r_work = 0.4514 r_free = 0.4514 target = 0.234495 restraints weight = 23441.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.234158 restraints weight = 17885.222| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4544 r_free = 0.4544 target = 0.238386 restraints weight = 14803.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.240136 restraints weight = 12394.632| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4576 r_free = 0.4576 target = 0.242124 restraints weight = 11442.833| |-----------------------------------------------------------------------------| r_work (final): 0.4638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 8816 Z= 0.114 Angle : 0.470 4.066 12036 Z= 0.244 Chirality : 0.040 0.139 1396 Planarity : 0.003 0.028 1512 Dihedral : 3.749 19.400 1185 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 1.47 % Allowed : 9.16 % Favored : 89.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.73 (0.27), residues: 1108 helix: 3.21 (0.28), residues: 348 sheet: -0.57 (0.36), residues: 208 loop : 0.61 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 203 TYR 0.007 0.001 TYR A 122 PHE 0.013 0.001 PHE A 71 TRP 0.013 0.001 TRP D 53 HIS 0.006 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00261 / 0.11 ( 8812) covalent geometry : angle 0.46986 / 0.24 (12028) SS BOND : bond 0.00332 / 0.17 ( 4) SS BOND : angle 1.02752 / 0.70 ( 8) hydrogen bonds : bond 0.03163 / 2.10 ( 423) hydrogen bonds : angle 4.21480 / 2.94 ( 1209) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 152 time to evaluate : 0.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6995 (p0) cc_final: 0.6669 (p0) REVERT: A 57 MET cc_start: 0.6344 (ttp) cc_final: 0.5983 (ttm) REVERT: B 18 ARG cc_start: 0.6676 (ptm160) cc_final: 0.6410 (ptm160) REVERT: B 57 MET cc_start: 0.6395 (ttp) cc_final: 0.6071 (ttm) REVERT: B 294 MET cc_start: 0.6541 (ptt) cc_final: 0.6237 (ptt) REVERT: B 297 HIS cc_start: 0.6588 (m-70) cc_final: 0.5579 (m-70) REVERT: C 50 ASP cc_start: 0.6515 (p0) cc_final: 0.5901 (p0) REVERT: C 175 THR cc_start: 0.7269 (m) cc_final: 0.6873 (t) REVERT: D 57 MET cc_start: 0.6465 (ttp) cc_final: 0.6094 (ttm) outliers start: 13 outliers final: 12 residues processed: 160 average time/residue: 0.1511 time to fit residues: 35.2431 Evaluate side-chains 159 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 147 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 31 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 63 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 96 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 297 HIS D 180 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5006 r_free = 0.5006 target = 0.290290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 117)---------------| | r_work = 0.4536 r_free = 0.4536 target = 0.232527 restraints weight = 23093.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 71)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.229154 restraints weight = 21055.082| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.232416 restraints weight = 18570.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.234134 restraints weight = 15329.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.235282 restraints weight = 13279.854| |-----------------------------------------------------------------------------| r_work (final): 0.4604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.2871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 8816 Z= 0.171 Angle : 0.507 4.223 12036 Z= 0.267 Chirality : 0.041 0.159 1396 Planarity : 0.003 0.029 1512 Dihedral : 3.843 19.937 1185 Min Nonbonded Distance : 2.278 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 1.70 % Allowed : 9.28 % Favored : 89.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.59 (0.27), residues: 1108 helix: 3.14 (0.28), residues: 348 sheet: -0.66 (0.36), residues: 208 loop : 0.48 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.016 0.001 TYR C 122 PHE 0.016 0.002 PHE B 106 TRP 0.006 0.001 TRP D 53 HIS 0.007 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00398 / 0.17 ( 8812) covalent geometry : angle 0.50616 / 0.27 (12028) SS BOND : bond 0.00492 / 0.25 ( 4) SS BOND : angle 1.13684 / 0.68 ( 8) hydrogen bonds : bond 0.03284 / 2.20 ( 423) hydrogen bonds : angle 4.30177 / 3.00 ( 1209) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 165 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 150 time to evaluate : 0.447 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6814 (p0) cc_final: 0.6462 (p0) REVERT: A 57 MET cc_start: 0.6436 (ttp) cc_final: 0.6060 (ttm) REVERT: A 188 ILE cc_start: 0.8475 (OUTLIER) cc_final: 0.8165 (pt) REVERT: B 57 MET cc_start: 0.6479 (ttp) cc_final: 0.6163 (ttm) REVERT: B 294 MET cc_start: 0.6601 (ptt) cc_final: 0.6351 (ptt) REVERT: C 50 ASP cc_start: 0.6254 (p0) cc_final: 0.5680 (p0) REVERT: C 175 THR cc_start: 0.7285 (OUTLIER) cc_final: 0.6903 (t) REVERT: D 57 MET cc_start: 0.6539 (ttp) cc_final: 0.6176 (ttm) outliers start: 15 outliers final: 13 residues processed: 161 average time/residue: 0.1721 time to fit residues: 39.9299 Evaluate side-chains 162 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 147 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 188 ILE Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 91 optimal weight: 0.5980 chunk 86 optimal weight: 10.0000 chunk 81 optimal weight: 6.9990 chunk 63 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 108 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 110 optimal weight: 0.9980 chunk 23 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5020 r_free = 0.5020 target = 0.293171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 114)---------------| | r_work = 0.4559 r_free = 0.4559 target = 0.236563 restraints weight = 23167.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4540 r_free = 0.4540 target = 0.235476 restraints weight = 18703.387| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.238321 restraints weight = 16890.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4572 r_free = 0.4572 target = 0.240021 restraints weight = 14155.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4578 r_free = 0.4578 target = 0.240627 restraints weight = 12843.876| |-----------------------------------------------------------------------------| r_work (final): 0.4630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 8816 Z= 0.129 Angle : 0.485 4.840 12036 Z= 0.253 Chirality : 0.040 0.148 1396 Planarity : 0.003 0.028 1512 Dihedral : 3.779 19.778 1185 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.58 % Allowed : 9.95 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.27), residues: 1108 helix: 3.22 (0.27), residues: 348 sheet: -0.56 (0.36), residues: 208 loop : 0.58 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 203 TYR 0.008 0.001 TYR A 122 PHE 0.013 0.001 PHE A 71 TRP 0.006 0.001 TRP D 53 HIS 0.002 0.001 HIS A 297 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 8812) covalent geometry : angle 0.48453 / 0.25 (12028) SS BOND : bond 0.00338 / 0.17 ( 4) SS BOND : angle 1.09021 / 0.72 ( 8) hydrogen bonds : bond 0.03158 / 2.10 ( 423) hydrogen bonds : angle 4.19363 / 2.93 ( 1209) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2216 Ramachandran restraints generated. 1108 Oldfield, 0 Emsley, 1108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Residue LEU 29 is missing expected H atoms. Skipping. Residue MET 31 is missing expected H atoms. Skipping. Residue LEU 38 is missing expected H atoms. Skipping. Residue TYR 40 is missing expected H atoms. Skipping. Residue ILE 47 is missing expected H atoms. Skipping. Residue THR 200 is missing expected H atoms. Skipping. Residue LYS 216 is missing expected H atoms. Skipping. Residue LEU 257 is missing expected H atoms. Skipping. Residue THR 278 is missing expected H atoms. Skipping. Residue LYS 320 is missing expected H atoms. Skipping. Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 ASP cc_start: 0.6868 (p0) cc_final: 0.6515 (p0) REVERT: A 57 MET cc_start: 0.6398 (ttp) cc_final: 0.6047 (ttm) REVERT: B 57 MET cc_start: 0.6467 (ttp) cc_final: 0.6174 (ttm) REVERT: B 294 MET cc_start: 0.6582 (ptt) cc_final: 0.6335 (ptt) REVERT: B 297 HIS cc_start: 0.6497 (m-70) cc_final: 0.5581 (m-70) REVERT: C 50 ASP cc_start: 0.6291 (p0) cc_final: 0.5689 (p0) REVERT: C 175 THR cc_start: 0.7212 (OUTLIER) cc_final: 0.6836 (t) REVERT: D 57 MET cc_start: 0.6519 (ttp) cc_final: 0.6175 (ttm) outliers start: 14 outliers final: 13 residues processed: 156 average time/residue: 0.1797 time to fit residues: 40.2580 Evaluate side-chains 160 residues out of total 992 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 146 time to evaluate : 0.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 270 PHE Chi-restraints excluded: chain A residue 287 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 175 THR Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 61 SER Chi-restraints excluded: chain C residue 175 THR Chi-restraints excluded: chain C residue 238 ILE Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 287 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 109 optimal weight: 7.9990 chunk 23 optimal weight: 0.2980 chunk 68 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 24 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 29 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5042 r_free = 0.5042 target = 0.292154 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 120)---------------| | r_work = 0.4467 r_free = 0.4467 target = 0.226802 restraints weight = 22808.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 50)----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.227746 restraints weight = 18561.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.231022 restraints weight = 15267.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.233335 restraints weight = 13095.738| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.235524 restraints weight = 11495.141| |-----------------------------------------------------------------------------| r_work (final): 0.4597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 8816 Z= 0.140 Angle : 0.491 5.140 12036 Z= 0.257 Chirality : 0.040 0.138 1396 Planarity : 0.003 0.030 1512 Dihedral : 3.746 19.497 1185 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.70 % Allowed : 10.29 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.70 (0.27), residues: 1108 helix: 3.26 (0.27), residues: 348 sheet: -0.57 (0.37), residues: 208 loop : 0.53 (0.28), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 203 TYR 0.013 0.001 TYR B 122 PHE 0.013 0.001 PHE B 106 TRP 0.005 0.001 TRP D 53 HIS 0.002 0.001 HIS C 245 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.14 ( 8812) covalent geometry : angle 0.49062 / 0.26 (12028) SS BOND : bond 0.00428 / 0.22 ( 4) SS BOND : angle 1.11413 / 0.70 ( 8) hydrogen bonds : bond 0.03154 / 2.09 ( 423) hydrogen bonds : angle 4.16855 / 2.91 ( 1209) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3153.21 seconds wall clock time: 54 minutes 15.23 seconds (3255.23 seconds total)