Starting phenix.real_space_refine on Thu Mar 5 00:35:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6lmv_0921/03_2026/6lmv_0921.cif Found real_map, /net/cci-nas-00/data/ceres_data/6lmv_0921/03_2026/6lmv_0921.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6lmv_0921/03_2026/6lmv_0921.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6lmv_0921/03_2026/6lmv_0921.map" model { file = "/net/cci-nas-00/data/ceres_data/6lmv_0921/03_2026/6lmv_0921.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6lmv_0921/03_2026/6lmv_0921.cif" } resolution = 3.6 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= 0.001 sd= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 11538 2.51 5 N 2943 2.21 5 O 3168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 153 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 17766 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1974 Number of conformers: 1 Conformer: "" Number of residues, atoms: 247, 1974 Classifications: {'peptide': 247} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 236} Chain breaks: 1 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'ARG:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 9 Restraints were copied for chains: B, C, D, E, F, G, H, I Time building chain proxies: 1.78, per 1000 atoms: 0.10 Number of scatterers: 17766 At special positions: 0 Unit cell: (138.084, 136.631, 103.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 3168 8.00 N 2943 7.00 C 11538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=27, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 131 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 176 " distance=2.03 Simple disulfide: pdb=" SG CYS A 138 " - pdb=" SG CYS A 174 " distance=2.03 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 131 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 131 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 131 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 131 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 131 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 131 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 131 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 131 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 176 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 176 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 176 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 176 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 176 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 176 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 176 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 176 " distance=2.03 Simple disulfide: pdb=" SG CYS B 138 " - pdb=" SG CYS B 174 " distance=2.03 Simple disulfide: pdb=" SG CYS C 138 " - pdb=" SG CYS C 174 " distance=2.03 Simple disulfide: pdb=" SG CYS D 138 " - pdb=" SG CYS D 174 " distance=2.03 Simple disulfide: pdb=" SG CYS E 138 " - pdb=" SG CYS E 174 " distance=2.03 Simple disulfide: pdb=" SG CYS F 138 " - pdb=" SG CYS F 174 " distance=2.03 Simple disulfide: pdb=" SG CYS G 138 " - pdb=" SG CYS G 174 " distance=2.03 Simple disulfide: pdb=" SG CYS H 138 " - pdb=" SG CYS H 174 " distance=2.03 Simple disulfide: pdb=" SG CYS I 138 " - pdb=" SG CYS I 174 " 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: 1.86 Conformation dependent library (CDL) restraints added in 704.8 milliseconds 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4266 Finding SS restraints... Secondary structure from input PDB file: 135 helices and 0 sheets defined 80.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'A' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR A 55 " --> pdb=" O PRO A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA A 66 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN A 76 " --> pdb=" O GLY A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP A 80 " --> pdb=" O ASN A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 94 Processing helix chain 'A' and resid 96 through 112 Processing helix chain 'A' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE A 116 " --> pdb=" O SER A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 126 through 134 Processing helix chain 'A' and resid 135 through 137 No H-bonds generated for 'chain 'A' and resid 135 through 137' Processing helix chain 'A' and resid 149 through 154 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 179 through 215 Processing helix chain 'A' and resid 219 through 258 Processing helix chain 'A' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP A 267 " --> pdb=" O THR A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 306 Processing helix chain 'B' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR B 55 " --> pdb=" O PRO B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA B 66 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN B 76 " --> pdb=" O GLY B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP B 80 " --> pdb=" O ASN B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 94 Processing helix chain 'B' and resid 96 through 112 Processing helix chain 'B' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE B 116 " --> pdb=" O SER B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 126 through 134 Processing helix chain 'B' and resid 135 through 137 No H-bonds generated for 'chain 'B' and resid 135 through 137' Processing helix chain 'B' and resid 149 through 154 Processing helix chain 'B' and resid 157 through 162 Processing helix chain 'B' and resid 171 through 177 Processing helix chain 'B' and resid 179 through 215 Processing helix chain 'B' and resid 219 through 258 Processing helix chain 'B' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP B 267 " --> pdb=" O THR B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 298 through 306 Processing helix chain 'C' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR C 55 " --> pdb=" O PRO C 51 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA C 66 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN C 76 " --> pdb=" O GLY C 72 " (cutoff:3.500A) Processing helix chain 'C' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP C 80 " --> pdb=" O ASN C 76 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 94 Processing helix chain 'C' and resid 96 through 112 Processing helix chain 'C' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE C 116 " --> pdb=" O SER C 112 " (cutoff:3.500A) Processing helix chain 'C' and resid 126 through 134 Processing helix chain 'C' and resid 135 through 137 No H-bonds generated for 'chain 'C' and resid 135 through 137' Processing helix chain 'C' and resid 149 through 154 Processing helix chain 'C' and resid 157 through 162 Processing helix chain 'C' and resid 171 through 177 Processing helix chain 'C' and resid 179 through 215 Processing helix chain 'C' and resid 219 through 258 Processing helix chain 'C' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP C 267 " --> pdb=" O THR C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 298 through 306 Processing helix chain 'D' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR D 55 " --> pdb=" O PRO D 51 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP D 80 " --> pdb=" O ASN D 76 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 94 Processing helix chain 'D' and resid 96 through 112 Processing helix chain 'D' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE D 116 " --> pdb=" O SER D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 126 through 134 Processing helix chain 'D' and resid 135 through 137 No H-bonds generated for 'chain 'D' and resid 135 through 137' Processing helix chain 'D' and resid 149 through 154 Processing helix chain 'D' and resid 157 through 162 Processing helix chain 'D' and resid 171 through 177 Processing helix chain 'D' and resid 179 through 215 Processing helix chain 'D' and resid 219 through 258 Processing helix chain 'D' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP D 267 " --> pdb=" O THR D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 298 through 306 Processing helix chain 'E' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR E 55 " --> pdb=" O PRO E 51 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA E 66 " --> pdb=" O PHE E 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN E 76 " --> pdb=" O GLY E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 84 removed outlier: 3.979A pdb=" N TRP E 80 " --> pdb=" O ASN E 76 " (cutoff:3.500A) Processing helix chain 'E' and resid 90 through 94 Processing helix chain 'E' and resid 96 through 112 Processing helix chain 'E' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE E 116 " --> pdb=" O SER E 112 " (cutoff:3.500A) Processing helix chain 'E' and resid 126 through 134 Processing helix chain 'E' and resid 135 through 137 No H-bonds generated for 'chain 'E' and resid 135 through 137' Processing helix chain 'E' and resid 149 through 154 Processing helix chain 'E' and resid 157 through 162 Processing helix chain 'E' and resid 171 through 177 Processing helix chain 'E' and resid 179 through 215 Processing helix chain 'E' and resid 219 through 258 Processing helix chain 'E' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP E 267 " --> pdb=" O THR E 263 " (cutoff:3.500A) Processing helix chain 'E' and resid 298 through 306 Processing helix chain 'F' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR F 55 " --> pdb=" O PRO F 51 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA F 66 " --> pdb=" O PHE F 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN F 76 " --> pdb=" O GLY F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP F 80 " --> pdb=" O ASN F 76 " (cutoff:3.500A) Processing helix chain 'F' and resid 90 through 94 Processing helix chain 'F' and resid 96 through 112 Processing helix chain 'F' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE F 116 " --> pdb=" O SER F 112 " (cutoff:3.500A) Processing helix chain 'F' and resid 126 through 134 Processing helix chain 'F' and resid 135 through 137 No H-bonds generated for 'chain 'F' and resid 135 through 137' Processing helix chain 'F' and resid 149 through 154 Processing helix chain 'F' and resid 157 through 162 Processing helix chain 'F' and resid 171 through 177 Processing helix chain 'F' and resid 179 through 215 Processing helix chain 'F' and resid 219 through 258 Processing helix chain 'F' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP F 267 " --> pdb=" O THR F 263 " (cutoff:3.500A) Processing helix chain 'F' and resid 298 through 306 Processing helix chain 'G' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR G 55 " --> pdb=" O PRO G 51 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA G 66 " --> pdb=" O PHE G 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN G 76 " --> pdb=" O GLY G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP G 80 " --> pdb=" O ASN G 76 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 94 Processing helix chain 'G' and resid 96 through 112 Processing helix chain 'G' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE G 116 " --> pdb=" O SER G 112 " (cutoff:3.500A) Processing helix chain 'G' and resid 126 through 134 Processing helix chain 'G' and resid 135 through 137 No H-bonds generated for 'chain 'G' and resid 135 through 137' Processing helix chain 'G' and resid 149 through 154 Processing helix chain 'G' and resid 157 through 162 Processing helix chain 'G' and resid 171 through 177 Processing helix chain 'G' and resid 179 through 215 Processing helix chain 'G' and resid 219 through 258 Processing helix chain 'G' and resid 263 through 271 removed outlier: 3.747A pdb=" N TRP G 267 " --> pdb=" O THR G 263 " (cutoff:3.500A) Processing helix chain 'G' and resid 298 through 306 Processing helix chain 'H' and resid 51 through 62 removed outlier: 4.020A pdb=" N TYR H 55 " --> pdb=" O PRO H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASN H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 76 through 84 removed outlier: 3.980A pdb=" N TRP H 80 " --> pdb=" O ASN H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 94 Processing helix chain 'H' and resid 96 through 112 Processing helix chain 'H' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE H 116 " --> pdb=" O SER H 112 " (cutoff:3.500A) Processing helix chain 'H' and resid 126 through 134 Processing helix chain 'H' and resid 135 through 137 No H-bonds generated for 'chain 'H' and resid 135 through 137' Processing helix chain 'H' and resid 149 through 154 Processing helix chain 'H' and resid 157 through 162 Processing helix chain 'H' and resid 171 through 177 Processing helix chain 'H' and resid 179 through 215 Processing helix chain 'H' and resid 219 through 258 Processing helix chain 'H' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP H 267 " --> pdb=" O THR H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 298 through 306 Processing helix chain 'I' and resid 51 through 62 removed outlier: 4.021A pdb=" N TYR I 55 " --> pdb=" O PRO I 51 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 76 removed outlier: 3.951A pdb=" N ALA I 66 " --> pdb=" O PHE I 62 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ASN I 76 " --> pdb=" O GLY I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 76 through 84 removed outlier: 3.981A pdb=" N TRP I 80 " --> pdb=" O ASN I 76 " (cutoff:3.500A) Processing helix chain 'I' and resid 90 through 94 Processing helix chain 'I' and resid 96 through 112 Processing helix chain 'I' and resid 112 through 125 removed outlier: 3.908A pdb=" N ILE I 116 " --> pdb=" O SER I 112 " (cutoff:3.500A) Processing helix chain 'I' and resid 126 through 134 Processing helix chain 'I' and resid 135 through 137 No H-bonds generated for 'chain 'I' and resid 135 through 137' Processing helix chain 'I' and resid 149 through 154 Processing helix chain 'I' and resid 157 through 162 Processing helix chain 'I' and resid 171 through 177 Processing helix chain 'I' and resid 179 through 215 Processing helix chain 'I' and resid 219 through 258 Processing helix chain 'I' and resid 263 through 271 removed outlier: 3.748A pdb=" N TRP I 267 " --> pdb=" O THR I 263 " (cutoff:3.500A) Processing helix chain 'I' and resid 298 through 306 1206 hydrogen bonds defined for protein. 3564 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: 3.15 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5274 1.34 - 1.45: 3669 1.45 - 1.57: 9228 1.57 - 1.69: 0 1.69 - 1.81: 135 Bond restraints: 18306 Sorted by residual: bond pdb=" CA PRO I 51 " pdb=" C PRO I 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.61e+00 bond pdb=" CA PRO B 51 " pdb=" C PRO B 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA PRO D 51 " pdb=" C PRO D 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.59e+00 bond pdb=" CA PRO G 51 " pdb=" C PRO G 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.52e+00 bond pdb=" CA PRO C 51 " pdb=" C PRO C 51 " ideal model delta sigma weight residual 1.524 1.492 0.032 2.00e-02 2.50e+03 2.50e+00 ... (remaining 18301 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 23827 2.04 - 4.07: 948 4.07 - 6.11: 128 6.11 - 8.15: 36 8.15 - 10.18: 27 Bond angle restraints: 24966 Sorted by residual: angle pdb=" N SER F 141 " pdb=" CA SER F 141 " pdb=" C SER F 141 " ideal model delta sigma weight residual 114.62 106.09 8.53 1.14e+00 7.69e-01 5.60e+01 angle pdb=" N SER H 141 " pdb=" CA SER H 141 " pdb=" C SER H 141 " ideal model delta sigma weight residual 114.62 106.10 8.52 1.14e+00 7.69e-01 5.59e+01 angle pdb=" N SER C 141 " pdb=" CA SER C 141 " pdb=" C SER C 141 " ideal model delta sigma weight residual 114.62 106.10 8.52 1.14e+00 7.69e-01 5.58e+01 angle pdb=" N SER E 141 " pdb=" CA SER E 141 " pdb=" C SER E 141 " ideal model delta sigma weight residual 114.62 106.11 8.51 1.14e+00 7.69e-01 5.57e+01 angle pdb=" N SER A 141 " pdb=" CA SER A 141 " pdb=" C SER A 141 " ideal model delta sigma weight residual 114.62 106.11 8.51 1.14e+00 7.69e-01 5.57e+01 ... (remaining 24961 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 9581 17.92 - 35.83: 832 35.83 - 53.75: 171 53.75 - 71.67: 18 71.67 - 89.59: 18 Dihedral angle restraints: 10620 sinusoidal: 4032 harmonic: 6588 Sorted by residual: dihedral pdb=" CB CYS C 46 " pdb=" SG CYS C 46 " pdb=" SG CYS C 131 " pdb=" CB CYS C 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.41 -89.59 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS I 46 " pdb=" SG CYS I 46 " pdb=" SG CYS I 131 " pdb=" CB CYS I 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.42 -89.58 1 1.00e+01 1.00e-02 9.53e+01 dihedral pdb=" CB CYS E 46 " pdb=" SG CYS E 46 " pdb=" SG CYS E 131 " pdb=" CB CYS E 131 " ideal model delta sinusoidal sigma weight residual 93.00 -177.42 -89.58 1 1.00e+01 1.00e-02 9.53e+01 ... (remaining 10617 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1174 0.032 - 0.065: 997 0.065 - 0.097: 360 0.097 - 0.130: 102 0.130 - 0.162: 103 Chirality restraints: 2736 Sorted by residual: chirality pdb=" CA PRO A 64 " pdb=" N PRO A 64 " pdb=" C PRO A 64 " pdb=" CB PRO A 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.59e-01 chirality pdb=" CA PRO H 64 " pdb=" N PRO H 64 " pdb=" C PRO H 64 " pdb=" CB PRO H 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.55e-01 chirality pdb=" CA PRO G 64 " pdb=" N PRO G 64 " pdb=" C PRO G 64 " pdb=" CB PRO G 64 " both_signs ideal model delta sigma weight residual False 2.72 2.56 0.16 2.00e-01 2.50e+01 6.49e-01 ... (remaining 2733 not shown) Planarity restraints: 3105 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY F 63 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO F 64 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO F 64 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO F 64 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 63 " 0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO C 64 " -0.122 5.00e-02 4.00e+02 pdb=" CA PRO C 64 " 0.036 5.00e-02 4.00e+02 pdb=" CD PRO C 64 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY G 63 " -0.047 5.00e-02 4.00e+02 7.04e-02 7.93e+00 pdb=" N PRO G 64 " 0.122 5.00e-02 4.00e+02 pdb=" CA PRO G 64 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 64 " -0.039 5.00e-02 4.00e+02 ... (remaining 3102 not shown) Histogram of nonbonded interaction distances: 2.34 - 2.85: 6452 2.85 - 3.37: 17082 3.37 - 3.88: 28066 3.88 - 4.39: 32115 4.39 - 4.90: 55564 Nonbonded interactions: 139279 Sorted by model distance: nonbonded pdb=" O ALA I 143 " pdb=" NZ LYS I 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA A 143 " pdb=" NZ LYS A 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA H 143 " pdb=" NZ LYS H 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA E 143 " pdb=" NZ LYS E 147 " model vdw 2.342 3.120 nonbonded pdb=" O ALA F 143 " pdb=" NZ LYS F 147 " model vdw 2.342 3.120 ... (remaining 139274 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: 0.05 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' } 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: 0.500 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.170 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:1.430 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 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 : 0.009 0.076 18333 Z= 0.360 Angle : 1.011 10.185 25020 Z= 0.600 Chirality : 0.055 0.162 2736 Planarity : 0.008 0.070 3105 Dihedral : 14.135 88.921 6273 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.94 % Allowed : 4.72 % Favored : 94.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -5.49 (0.11), residues: 2187 helix: -3.69 (0.07), residues: 1629 sheet: None (None), residues: 0 loop : -2.57 (0.23), residues: 558 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG C 265 TYR 0.027 0.002 TYR E 155 PHE 0.016 0.002 PHE I 237 TRP 0.013 0.002 TRP E 262 HIS 0.007 0.002 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00869 (18306) covalent geometry : angle 1.00208 (24966) SS BOND : bond 0.00305 ( 27) SS BOND : angle 3.05965 ( 54) hydrogen bonds : bond 0.26146 ( 1206) hydrogen bonds : angle 8.74460 ( 3564) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 466 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 448 time to evaluate : 0.645 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.8692 (p) cc_final: 0.8414 (p) REVERT: A 95 HIS cc_start: 0.6952 (m90) cc_final: 0.6688 (m-70) REVERT: A 125 ASP cc_start: 0.8127 (t0) cc_final: 0.7923 (t70) REVERT: A 200 PHE cc_start: 0.7494 (t80) cc_final: 0.7200 (m-10) REVERT: A 236 LYS cc_start: 0.8644 (mmmt) cc_final: 0.8411 (mmmm) REVERT: A 238 ASP cc_start: 0.8462 (m-30) cc_final: 0.8040 (t0) REVERT: A 269 TRP cc_start: 0.7846 (t-100) cc_final: 0.7473 (t-100) REVERT: A 307 LYS cc_start: 0.5497 (mmtt) cc_final: 0.5268 (tmtt) REVERT: B 125 ASP cc_start: 0.8114 (t0) cc_final: 0.7881 (t70) REVERT: B 200 PHE cc_start: 0.7793 (t80) cc_final: 0.7437 (m-10) REVERT: B 227 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8064 (mm-30) REVERT: B 230 LYS cc_start: 0.8189 (mttt) cc_final: 0.7744 (mttm) REVERT: B 235 GLN cc_start: 0.8752 (tm-30) cc_final: 0.8396 (tm-30) REVERT: B 236 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8289 (mmmt) REVERT: B 251 HIS cc_start: 0.7765 (m90) cc_final: 0.7544 (t-90) REVERT: B 260 LYS cc_start: 0.5995 (mmtt) cc_final: 0.5650 (mmtt) REVERT: B 261 ASP cc_start: 0.8226 (t70) cc_final: 0.7999 (t70) REVERT: C 269 TRP cc_start: 0.7761 (t-100) cc_final: 0.7458 (t-100) REVERT: C 297 TYR cc_start: 0.5609 (m-80) cc_final: 0.5251 (m-80) REVERT: D 110 GLN cc_start: 0.8606 (tp-100) cc_final: 0.8135 (tp-100) REVERT: D 222 GLN cc_start: 0.8796 (tt0) cc_final: 0.8419 (tt0) REVERT: D 236 LYS cc_start: 0.8596 (mmmt) cc_final: 0.8306 (tppt) REVERT: D 250 GLU cc_start: 0.7976 (tp30) cc_final: 0.7495 (tp30) REVERT: D 251 HIS cc_start: 0.7905 (m90) cc_final: 0.7591 (t-90) REVERT: E 222 GLN cc_start: 0.8892 (tt0) cc_final: 0.8640 (tt0) REVERT: E 227 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7728 (mm-30) REVERT: E 230 LYS cc_start: 0.8197 (mttt) cc_final: 0.7746 (mtmt) REVERT: E 235 GLN cc_start: 0.8651 (tm-30) cc_final: 0.8353 (tm-30) REVERT: E 236 LYS cc_start: 0.8647 (mmmt) cc_final: 0.8218 (mmmm) REVERT: E 250 GLU cc_start: 0.8026 (tp30) cc_final: 0.7141 (tp30) REVERT: E 269 TRP cc_start: 0.7748 (t-100) cc_final: 0.7533 (t-100) REVERT: E 297 TYR cc_start: 0.5632 (m-80) cc_final: 0.5155 (m-80) REVERT: F 200 PHE cc_start: 0.7944 (t80) cc_final: 0.7391 (m-10) REVERT: F 250 GLU cc_start: 0.7900 (tp30) cc_final: 0.7530 (tm-30) REVERT: F 254 ARG cc_start: 0.8385 (mmt180) cc_final: 0.8013 (mmt-90) REVERT: F 306 ASN cc_start: 0.8354 (m110) cc_final: 0.7921 (p0) REVERT: G 61 MET cc_start: 0.8051 (mtp) cc_final: 0.7705 (mtp) REVERT: G 200 PHE cc_start: 0.7689 (t80) cc_final: 0.7304 (m-10) REVERT: G 222 GLN cc_start: 0.8755 (tt0) cc_final: 0.8444 (tt0) REVERT: G 223 ARG cc_start: 0.8064 (tpp-160) cc_final: 0.7836 (tpp-160) REVERT: G 232 VAL cc_start: 0.8693 (t) cc_final: 0.8438 (p) REVERT: G 235 GLN cc_start: 0.8369 (tm-30) cc_final: 0.8159 (tm-30) REVERT: G 250 GLU cc_start: 0.8181 (tp30) cc_final: 0.7619 (tp30) REVERT: G 251 HIS cc_start: 0.7960 (m90) cc_final: 0.7538 (t-170) REVERT: G 269 TRP cc_start: 0.7912 (t-100) cc_final: 0.7697 (t-100) REVERT: G 297 TYR cc_start: 0.5592 (m-80) cc_final: 0.5030 (m-10) REVERT: H 110 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8391 (tp-100) REVERT: H 177 VAL cc_start: 0.8579 (t) cc_final: 0.8292 (p) REVERT: H 200 PHE cc_start: 0.7844 (t80) cc_final: 0.7279 (m-10) REVERT: H 222 GLN cc_start: 0.8876 (tt0) cc_final: 0.8674 (tt0) REVERT: H 227 GLU cc_start: 0.8150 (mm-30) cc_final: 0.7733 (mm-30) REVERT: H 250 GLU cc_start: 0.8195 (tp30) cc_final: 0.7667 (tm-30) REVERT: H 254 ARG cc_start: 0.7862 (mmt180) cc_final: 0.7330 (mmt-90) REVERT: H 269 TRP cc_start: 0.7771 (t-100) cc_final: 0.7545 (t-100) REVERT: I 125 ASP cc_start: 0.8319 (t0) cc_final: 0.8084 (t70) REVERT: I 251 HIS cc_start: 0.7964 (m90) cc_final: 0.7606 (t-170) outliers start: 18 outliers final: 18 residues processed: 466 average time/residue: 0.1767 time to fit residues: 111.9406 Evaluate side-chains 368 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 350 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 48 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 48 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain H residue 48 CYS Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain I residue 48 CYS Chi-restraints excluded: chain I residue 176 CYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 107 optimal weight: 20.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.9980 chunk 200 optimal weight: 0.6980 chunk 212 optimal weight: 3.9990 chunk 77 optimal weight: 3.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 84 HIS A 110 GLN A 135 HIS A 162 ASN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 84 HIS B 135 HIS B 162 ASN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 HIS C 110 GLN C 135 HIS C 162 ASN C 251 HIS ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 HIS D 110 GLN D 135 HIS D 162 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 84 HIS E 110 GLN E 135 HIS E 162 ASN E 231 ASN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 84 HIS F 110 GLN F 135 HIS F 162 ASN F 251 HIS ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 HIS G 135 HIS G 162 ASN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 HIS H 110 GLN H 135 HIS H 162 ASN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 84 HIS I 110 GLN I 135 HIS I 162 ASN I 222 GLN Total number of N/Q/H flips: 38 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.145163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.112783 restraints weight = 25100.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.116119 restraints weight = 14249.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.118227 restraints weight = 10156.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.119312 restraints weight = 8392.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.120131 restraints weight = 7589.807| |-----------------------------------------------------------------------------| r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7833 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18333 Z= 0.134 Angle : 0.591 6.908 25020 Z= 0.318 Chirality : 0.039 0.145 2736 Planarity : 0.006 0.060 3105 Dihedral : 6.556 54.846 2421 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 4.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 2.83 % Allowed : 12.00 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.49 (0.16), residues: 2187 helix: -0.53 (0.11), residues: 1647 sheet: None (None), residues: 0 loop : -2.03 (0.25), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 254 TYR 0.009 0.001 TYR A 297 PHE 0.015 0.001 PHE E 200 TRP 0.012 0.001 TRP D 269 HIS 0.007 0.001 HIS C 251 Details of bonding type rmsd covalent geometry : bond 0.00282 (18306) covalent geometry : angle 0.58837 (24966) SS BOND : bond 0.00090 ( 27) SS BOND : angle 1.26849 ( 54) hydrogen bonds : bond 0.05455 ( 1206) hydrogen bonds : angle 4.37885 ( 3564) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 448 time to evaluate : 0.669 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 48 CYS cc_start: 0.7311 (OUTLIER) cc_final: 0.6919 (m) REVERT: A 176 CYS cc_start: 0.6170 (OUTLIER) cc_final: 0.5735 (m) REVERT: A 220 LEU cc_start: 0.8092 (tp) cc_final: 0.7778 (tp) REVERT: A 236 LYS cc_start: 0.8799 (mmmt) cc_final: 0.8358 (mmtp) REVERT: A 307 LYS cc_start: 0.5750 (mmtt) cc_final: 0.5491 (tmtt) REVERT: B 176 CYS cc_start: 0.6599 (OUTLIER) cc_final: 0.5898 (m) REVERT: B 200 PHE cc_start: 0.7993 (t80) cc_final: 0.7682 (m-10) REVERT: B 210 THR cc_start: 0.8579 (m) cc_final: 0.8303 (m) REVERT: B 230 LYS cc_start: 0.8175 (mttt) cc_final: 0.7939 (mttm) REVERT: B 235 GLN cc_start: 0.8793 (tm-30) cc_final: 0.8545 (tm-30) REVERT: B 250 GLU cc_start: 0.8170 (tp30) cc_final: 0.7622 (tm-30) REVERT: B 254 ARG cc_start: 0.8165 (mmt90) cc_final: 0.7924 (mmt-90) REVERT: B 260 LYS cc_start: 0.5811 (mmtt) cc_final: 0.5371 (mmtp) REVERT: C 130 ARG cc_start: 0.8395 (ttm170) cc_final: 0.8164 (ttm170) REVERT: C 176 CYS cc_start: 0.5656 (OUTLIER) cc_final: 0.5030 (m) REVERT: C 213 ARG cc_start: 0.8261 (mmt90) cc_final: 0.7955 (mmt90) REVERT: C 222 GLN cc_start: 0.8732 (tt0) cc_final: 0.8379 (tt0) REVERT: C 236 LYS cc_start: 0.9171 (tppt) cc_final: 0.8971 (mmtp) REVERT: C 265 ARG cc_start: 0.8190 (ptm160) cc_final: 0.7540 (ttt90) REVERT: D 48 CYS cc_start: 0.7369 (OUTLIER) cc_final: 0.7046 (m) REVERT: D 69 LEU cc_start: 0.8621 (tp) cc_final: 0.8415 (tt) REVERT: D 110 GLN cc_start: 0.8021 (tp40) cc_final: 0.7791 (tp-100) REVERT: D 176 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6299 (m) REVERT: D 222 GLN cc_start: 0.8675 (tt0) cc_final: 0.8355 (tt0) REVERT: D 236 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8605 (mmmm) REVERT: D 238 ASP cc_start: 0.8445 (OUTLIER) cc_final: 0.8192 (t0) REVERT: E 176 CYS cc_start: 0.6577 (OUTLIER) cc_final: 0.5984 (m) REVERT: E 213 ARG cc_start: 0.8149 (mmt90) cc_final: 0.7941 (mmt-90) REVERT: E 230 LYS cc_start: 0.8241 (mttt) cc_final: 0.7969 (mtmt) REVERT: E 235 GLN cc_start: 0.8552 (tm-30) cc_final: 0.7959 (tm-30) REVERT: E 236 LYS cc_start: 0.8509 (mmmt) cc_final: 0.8065 (mmmm) REVERT: E 297 TYR cc_start: 0.5715 (m-80) cc_final: 0.5220 (m-10) REVERT: F 48 CYS cc_start: 0.7429 (OUTLIER) cc_final: 0.7197 (m) REVERT: F 176 CYS cc_start: 0.5556 (OUTLIER) cc_final: 0.4854 (m) REVERT: F 235 GLN cc_start: 0.8615 (tm-30) cc_final: 0.8140 (tm-30) REVERT: F 236 LYS cc_start: 0.9216 (tppt) cc_final: 0.8125 (mmmt) REVERT: F 250 GLU cc_start: 0.8049 (tp30) cc_final: 0.7423 (tp30) REVERT: G 48 CYS cc_start: 0.7355 (OUTLIER) cc_final: 0.7093 (m) REVERT: G 176 CYS cc_start: 0.6363 (OUTLIER) cc_final: 0.5839 (m) REVERT: G 213 ARG cc_start: 0.8270 (mmt90) cc_final: 0.8007 (mmt90) REVERT: G 222 GLN cc_start: 0.8691 (tt0) cc_final: 0.8480 (tt0) REVERT: G 223 ARG cc_start: 0.8326 (tpp-160) cc_final: 0.8055 (tpp-160) REVERT: G 224 GLN cc_start: 0.8257 (mt0) cc_final: 0.8015 (mt0) REVERT: G 265 ARG cc_start: 0.8100 (ptm-80) cc_final: 0.7655 (ttt90) REVERT: G 297 TYR cc_start: 0.6053 (m-80) cc_final: 0.5495 (m-10) REVERT: H 110 GLN cc_start: 0.8396 (tp40) cc_final: 0.8193 (tp-100) REVERT: H 176 CYS cc_start: 0.5672 (OUTLIER) cc_final: 0.5267 (m) REVERT: H 177 VAL cc_start: 0.8456 (t) cc_final: 0.8215 (p) REVERT: H 250 GLU cc_start: 0.8122 (tp30) cc_final: 0.7640 (tm-30) REVERT: I 176 CYS cc_start: 0.6437 (OUTLIER) cc_final: 0.5768 (m) REVERT: I 222 GLN cc_start: 0.8625 (tt0) cc_final: 0.8356 (tt0) REVERT: I 269 TRP cc_start: 0.8068 (t-100) cc_final: 0.7823 (t-100) outliers start: 54 outliers final: 28 residues processed: 482 average time/residue: 0.1560 time to fit residues: 105.7480 Evaluate side-chains 399 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 357 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 CYS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 95 HIS Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 48 CYS Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain G residue 48 CYS Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 142 ASP Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 142 ASP Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 214 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 126 optimal weight: 4.9990 chunk 54 optimal weight: 0.9980 chunk 155 optimal weight: 30.0000 chunk 84 optimal weight: 10.0000 chunk 104 optimal weight: 0.5980 chunk 61 optimal weight: 0.0470 chunk 5 optimal weight: 4.9990 chunk 215 optimal weight: 9.9990 chunk 168 optimal weight: 0.7980 chunk 190 optimal weight: 9.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.2880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 251 HIS ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN E 191 GLN F 110 GLN G 251 HIS ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138074 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.105802 restraints weight = 26402.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.108703 restraints weight = 15230.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.110531 restraints weight = 11155.496| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.111592 restraints weight = 9412.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.112204 restraints weight = 8570.715| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18333 Z= 0.134 Angle : 0.545 6.082 25020 Z= 0.289 Chirality : 0.039 0.142 2736 Planarity : 0.005 0.045 3105 Dihedral : 5.746 59.661 2416 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 4.66 % Allowed : 12.84 % Favored : 82.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 0.68 (0.17), residues: 2187 helix: 1.21 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -2.03 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 265 TYR 0.009 0.001 TYR G 297 PHE 0.017 0.001 PHE H 200 TRP 0.010 0.001 TRP I 195 HIS 0.007 0.001 HIS D 251 Details of bonding type rmsd covalent geometry : bond 0.00301 (18306) covalent geometry : angle 0.54398 (24966) SS BOND : bond 0.00355 ( 27) SS BOND : angle 0.97114 ( 54) hydrogen bonds : bond 0.04381 ( 1206) hydrogen bonds : angle 3.91737 ( 3564) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 382 time to evaluate : 0.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.6268 (OUTLIER) cc_final: 0.5751 (m) REVERT: A 197 LEU cc_start: 0.8498 (OUTLIER) cc_final: 0.8279 (tp) REVERT: A 236 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8403 (mmtp) REVERT: A 238 ASP cc_start: 0.8417 (m-30) cc_final: 0.8145 (t0) REVERT: B 176 CYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6421 (m) REVERT: B 200 PHE cc_start: 0.7962 (t80) cc_final: 0.7642 (m-10) REVERT: B 222 GLN cc_start: 0.8943 (tt0) cc_final: 0.8649 (tt0) REVERT: B 235 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8611 (tm-30) REVERT: B 250 GLU cc_start: 0.8233 (tp30) cc_final: 0.7517 (tm-30) REVERT: B 254 ARG cc_start: 0.8150 (mmt90) cc_final: 0.7698 (mmt90) REVERT: B 260 LYS cc_start: 0.5811 (mmtt) cc_final: 0.5472 (mmtp) REVERT: C 130 ARG cc_start: 0.8472 (ttm170) cc_final: 0.8133 (ttm170) REVERT: C 176 CYS cc_start: 0.6553 (OUTLIER) cc_final: 0.5984 (m) REVERT: C 197 LEU cc_start: 0.8659 (OUTLIER) cc_final: 0.8444 (tp) REVERT: C 222 GLN cc_start: 0.8710 (tt0) cc_final: 0.8371 (tt0) REVERT: D 94 ARG cc_start: 0.8191 (mmt90) cc_final: 0.7806 (mtt90) REVERT: D 110 GLN cc_start: 0.8085 (tp40) cc_final: 0.7840 (tp-100) REVERT: D 163 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7336 (ttmt) REVERT: D 176 CYS cc_start: 0.6479 (OUTLIER) cc_final: 0.5959 (m) REVERT: D 222 GLN cc_start: 0.8613 (tt0) cc_final: 0.8273 (tt0) REVERT: D 238 ASP cc_start: 0.8331 (OUTLIER) cc_final: 0.8099 (t0) REVERT: E 176 CYS cc_start: 0.6605 (OUTLIER) cc_final: 0.6067 (m) REVERT: E 213 ARG cc_start: 0.8034 (mmt90) cc_final: 0.7810 (mmt-90) REVERT: E 235 GLN cc_start: 0.8693 (tm-30) cc_final: 0.8439 (tm-30) REVERT: E 236 LYS cc_start: 0.8607 (mmmt) cc_final: 0.8290 (mmmm) REVERT: E 297 TYR cc_start: 0.5679 (m-80) cc_final: 0.5373 (m-10) REVERT: F 176 CYS cc_start: 0.6122 (OUTLIER) cc_final: 0.5518 (m) REVERT: F 222 GLN cc_start: 0.8752 (tt0) cc_final: 0.8515 (tt0) REVERT: F 235 GLN cc_start: 0.8611 (tm-30) cc_final: 0.8111 (tm-30) REVERT: F 236 LYS cc_start: 0.9202 (tppt) cc_final: 0.7993 (mmmt) REVERT: F 250 GLU cc_start: 0.7865 (tp30) cc_final: 0.7038 (tp30) REVERT: F 254 ARG cc_start: 0.8328 (mmt-90) cc_final: 0.7813 (mmt-90) REVERT: G 176 CYS cc_start: 0.6474 (OUTLIER) cc_final: 0.5860 (m) REVERT: G 222 GLN cc_start: 0.8751 (tt0) cc_final: 0.8503 (tt0) REVERT: G 250 GLU cc_start: 0.7980 (tp30) cc_final: 0.7548 (tp30) REVERT: G 269 TRP cc_start: 0.8112 (t-100) cc_final: 0.7769 (t-100) REVERT: G 297 TYR cc_start: 0.5219 (m-80) cc_final: 0.4855 (m-10) REVERT: H 176 CYS cc_start: 0.6475 (OUTLIER) cc_final: 0.5971 (m) REVERT: H 269 TRP cc_start: 0.8062 (t-100) cc_final: 0.7859 (t-100) REVERT: I 97 TRP cc_start: 0.5646 (OUTLIER) cc_final: 0.5372 (m-10) REVERT: I 176 CYS cc_start: 0.6905 (OUTLIER) cc_final: 0.6393 (m) outliers start: 89 outliers final: 49 residues processed: 440 average time/residue: 0.1626 time to fit residues: 99.1896 Evaluate side-chains 395 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 333 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 197 LEU Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 210 THR Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 113 VAL Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 210 THR Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 176 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 160 optimal weight: 1.9990 chunk 99 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 158 optimal weight: 1.9990 chunk 142 optimal weight: 0.0060 chunk 98 optimal weight: 0.7980 chunk 104 optimal weight: 0.9990 chunk 11 optimal weight: 9.9990 chunk 60 optimal weight: 4.9990 chunk 53 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 overall best weight: 1.1602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 224 GLN E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN H 222 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.138415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.106025 restraints weight = 26291.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.108929 restraints weight = 15236.509| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.110747 restraints weight = 11197.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.111825 restraints weight = 9435.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.112412 restraints weight = 8576.675| |-----------------------------------------------------------------------------| r_work (final): 0.3330 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18333 Z= 0.122 Angle : 0.518 6.001 25020 Z= 0.273 Chirality : 0.039 0.141 2736 Planarity : 0.004 0.046 3105 Dihedral : 5.592 59.635 2412 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 5.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 4.82 % Allowed : 14.10 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.71 (0.18), residues: 2187 helix: 2.01 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.90 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 254 TYR 0.010 0.001 TYR I 218 PHE 0.011 0.001 PHE H 200 TRP 0.014 0.001 TRP B 267 HIS 0.003 0.001 HIS C 56 Details of bonding type rmsd covalent geometry : bond 0.00280 (18306) covalent geometry : angle 0.51701 (24966) SS BOND : bond 0.00230 ( 27) SS BOND : angle 0.85408 ( 54) hydrogen bonds : bond 0.03867 ( 1206) hydrogen bonds : angle 3.70599 ( 3564) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 440 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 348 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7212 (OUTLIER) cc_final: 0.6942 (m-70) REVERT: A 176 CYS cc_start: 0.6419 (OUTLIER) cc_final: 0.6080 (m) REVERT: A 235 GLN cc_start: 0.8910 (tm-30) cc_final: 0.8155 (tm-30) REVERT: A 236 LYS cc_start: 0.8797 (mmmt) cc_final: 0.8125 (mmtp) REVERT: B 176 CYS cc_start: 0.6754 (OUTLIER) cc_final: 0.6072 (m) REVERT: B 200 PHE cc_start: 0.7958 (t80) cc_final: 0.7641 (m-10) REVERT: B 222 GLN cc_start: 0.8843 (tt0) cc_final: 0.8587 (tt0) REVERT: B 235 GLN cc_start: 0.8818 (tm-30) cc_final: 0.8563 (tm-30) REVERT: B 250 GLU cc_start: 0.8227 (tp30) cc_final: 0.7427 (tm-30) REVERT: B 254 ARG cc_start: 0.8079 (mmt90) cc_final: 0.7734 (mmt90) REVERT: B 260 LYS cc_start: 0.5680 (mmtt) cc_final: 0.5328 (mmtp) REVERT: C 130 ARG cc_start: 0.8452 (ttm170) cc_final: 0.8133 (ttm170) REVERT: C 176 CYS cc_start: 0.6561 (OUTLIER) cc_final: 0.5955 (m) REVERT: C 222 GLN cc_start: 0.8675 (tt0) cc_final: 0.8339 (tt0) REVERT: C 265 ARG cc_start: 0.8224 (ttt180) cc_final: 0.7986 (ttt-90) REVERT: D 94 ARG cc_start: 0.8280 (mmt90) cc_final: 0.7926 (mtt90) REVERT: D 110 GLN cc_start: 0.8127 (tp40) cc_final: 0.7864 (tp-100) REVERT: D 163 LYS cc_start: 0.7734 (ttmt) cc_final: 0.7354 (ttmt) REVERT: D 176 CYS cc_start: 0.6609 (OUTLIER) cc_final: 0.6028 (m) REVERT: D 222 GLN cc_start: 0.8585 (tt0) cc_final: 0.8265 (tt0) REVERT: E 163 LYS cc_start: 0.7629 (OUTLIER) cc_final: 0.7384 (tttp) REVERT: E 176 CYS cc_start: 0.6592 (OUTLIER) cc_final: 0.6053 (m) REVERT: E 235 GLN cc_start: 0.8660 (tm-30) cc_final: 0.8363 (tm-30) REVERT: E 236 LYS cc_start: 0.8696 (mmmt) cc_final: 0.8220 (mmmm) REVERT: F 176 CYS cc_start: 0.6468 (OUTLIER) cc_final: 0.5969 (m) REVERT: F 250 GLU cc_start: 0.7886 (tp30) cc_final: 0.7058 (mm-30) REVERT: G 176 CYS cc_start: 0.6592 (OUTLIER) cc_final: 0.5930 (m) REVERT: G 222 GLN cc_start: 0.8718 (tt0) cc_final: 0.8474 (tt0) REVERT: G 250 GLU cc_start: 0.8046 (tp30) cc_final: 0.7811 (tp30) REVERT: G 297 TYR cc_start: 0.5287 (m-80) cc_final: 0.4957 (m-10) REVERT: H 176 CYS cc_start: 0.6427 (OUTLIER) cc_final: 0.5956 (m) REVERT: H 297 TYR cc_start: 0.5520 (m-80) cc_final: 0.5299 (m-10) REVERT: I 176 CYS cc_start: 0.6594 (OUTLIER) cc_final: 0.6079 (m) outliers start: 92 outliers final: 56 residues processed: 413 average time/residue: 0.1566 time to fit residues: 90.7595 Evaluate side-chains 391 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 324 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 197 LEU Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 176 CYS Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 217 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 115 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 101 optimal weight: 10.0000 chunk 46 optimal weight: 10.0000 chunk 69 optimal weight: 5.9990 chunk 31 optimal weight: 0.0980 chunk 63 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 2.9990 chunk 24 optimal weight: 20.0000 chunk 139 optimal weight: 0.7980 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 251 HIS ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.140276 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.107919 restraints weight = 25933.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.110938 restraints weight = 14879.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.112834 restraints weight = 10891.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.113957 restraints weight = 9165.204| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.114477 restraints weight = 8333.690| |-----------------------------------------------------------------------------| r_work (final): 0.3359 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7974 moved from start: 0.3425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 18333 Z= 0.213 Angle : 0.609 8.875 25020 Z= 0.318 Chirality : 0.043 0.140 2736 Planarity : 0.005 0.055 3105 Dihedral : 5.720 59.272 2412 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Rotamer: Outliers : 5.19 % Allowed : 17.98 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.80 (0.18), residues: 2187 helix: 2.09 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.91 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG G 254 TYR 0.014 0.001 TYR E 218 PHE 0.012 0.001 PHE G 237 TRP 0.013 0.001 TRP B 267 HIS 0.005 0.001 HIS E 251 Details of bonding type rmsd covalent geometry : bond 0.00496 (18306) covalent geometry : angle 0.60790 (24966) SS BOND : bond 0.00229 ( 27) SS BOND : angle 0.95190 ( 54) hydrogen bonds : bond 0.04763 ( 1206) hydrogen bonds : angle 3.86248 ( 3564) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 342 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 176 CYS cc_start: 0.6593 (OUTLIER) cc_final: 0.6317 (m) REVERT: A 210 THR cc_start: 0.9110 (OUTLIER) cc_final: 0.8886 (t) REVERT: A 222 GLN cc_start: 0.8580 (tt0) cc_final: 0.8295 (tt0) REVERT: A 236 LYS cc_start: 0.8856 (mmmt) cc_final: 0.8407 (mmtp) REVERT: A 238 ASP cc_start: 0.8239 (m-30) cc_final: 0.8004 (t0) REVERT: B 176 CYS cc_start: 0.7018 (OUTLIER) cc_final: 0.6289 (m) REVERT: B 200 PHE cc_start: 0.7935 (t80) cc_final: 0.7704 (m-10) REVERT: B 235 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8534 (tm-30) REVERT: B 250 GLU cc_start: 0.8257 (tp30) cc_final: 0.7757 (tm-30) REVERT: B 268 ASP cc_start: 0.8233 (m-30) cc_final: 0.7670 (m-30) REVERT: C 176 CYS cc_start: 0.6800 (OUTLIER) cc_final: 0.6158 (m) REVERT: C 197 LEU cc_start: 0.8628 (OUTLIER) cc_final: 0.8377 (tp) REVERT: C 222 GLN cc_start: 0.8689 (tt0) cc_final: 0.8394 (tt0) REVERT: C 265 ARG cc_start: 0.8334 (ttt180) cc_final: 0.8022 (ttt-90) REVERT: D 94 ARG cc_start: 0.8298 (mmt90) cc_final: 0.8009 (mtt90) REVERT: D 110 GLN cc_start: 0.8082 (tp40) cc_final: 0.7867 (tp-100) REVERT: D 222 GLN cc_start: 0.8680 (tt0) cc_final: 0.8362 (tt0) REVERT: D 269 TRP cc_start: 0.7790 (t-100) cc_final: 0.7557 (t-100) REVERT: E 163 LYS cc_start: 0.7806 (OUTLIER) cc_final: 0.7503 (tttt) REVERT: E 176 CYS cc_start: 0.6718 (OUTLIER) cc_final: 0.6232 (m) REVERT: E 235 GLN cc_start: 0.8640 (tm-30) cc_final: 0.8309 (tm-30) REVERT: E 236 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8291 (mmtm) REVERT: E 247 GLN cc_start: 0.8264 (mt0) cc_final: 0.7940 (mt0) REVERT: F 176 CYS cc_start: 0.6863 (OUTLIER) cc_final: 0.6565 (m) REVERT: G 163 LYS cc_start: 0.8069 (ttmt) cc_final: 0.7740 (ttpt) REVERT: G 176 CYS cc_start: 0.6878 (OUTLIER) cc_final: 0.6373 (m) REVERT: G 268 ASP cc_start: 0.8332 (m-30) cc_final: 0.8043 (m-30) REVERT: G 269 TRP cc_start: 0.8168 (t-100) cc_final: 0.7905 (t60) REVERT: G 297 TYR cc_start: 0.5559 (m-80) cc_final: 0.5235 (m-10) REVERT: H 176 CYS cc_start: 0.7060 (OUTLIER) cc_final: 0.6414 (m) REVERT: H 297 TYR cc_start: 0.5595 (m-80) cc_final: 0.5316 (m-10) REVERT: I 176 CYS cc_start: 0.6947 (OUTLIER) cc_final: 0.6381 (m) outliers start: 99 outliers final: 72 residues processed: 404 average time/residue: 0.1578 time to fit residues: 90.0405 Evaluate side-chains 416 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 333 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 210 THR Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain B residue 232 VAL Chi-restraints excluded: chain B residue 306 ASN Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain C residue 210 THR Chi-restraints excluded: chain C residue 232 VAL Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 217 LYS Chi-restraints excluded: chain D residue 232 VAL Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain D residue 306 ASN Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 232 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 113 VAL Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 233 GLU Chi-restraints excluded: chain I residue 306 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 38 optimal weight: 0.8980 chunk 118 optimal weight: 7.9990 chunk 146 optimal weight: 1.9990 chunk 170 optimal weight: 0.0020 chunk 27 optimal weight: 0.9990 chunk 201 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 167 optimal weight: 0.9990 chunk 75 optimal weight: 0.7980 chunk 185 optimal weight: 3.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 153 ASN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.146676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.113977 restraints weight = 25586.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.117289 restraints weight = 14268.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119378 restraints weight = 10237.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.120600 restraints weight = 8513.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3455 r_free = 0.3455 target = 0.121315 restraints weight = 7695.107| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7877 moved from start: 0.3787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18333 Z= 0.108 Angle : 0.513 8.097 25020 Z= 0.270 Chirality : 0.038 0.140 2736 Planarity : 0.005 0.048 3105 Dihedral : 5.426 59.704 2411 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 4.56 % Allowed : 19.86 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.43 (0.18), residues: 2187 helix: 2.58 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.82 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 254 TYR 0.012 0.001 TYR F 229 PHE 0.009 0.001 PHE B 256 TRP 0.010 0.001 TRP H 267 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00240 (18306) covalent geometry : angle 0.51157 (24966) SS BOND : bond 0.00079 ( 27) SS BOND : angle 0.93769 ( 54) hydrogen bonds : bond 0.03609 ( 1206) hydrogen bonds : angle 3.54004 ( 3564) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 427 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 340 time to evaluate : 0.463 Fit side-chains revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7015 (OUTLIER) cc_final: 0.6794 (m-70) REVERT: A 176 CYS cc_start: 0.6684 (OUTLIER) cc_final: 0.6310 (m) REVERT: A 235 GLN cc_start: 0.8832 (tm-30) cc_final: 0.7937 (tm-30) REVERT: A 236 LYS cc_start: 0.8800 (mmmt) cc_final: 0.8053 (mmtp) REVERT: B 89 ARG cc_start: 0.7841 (OUTLIER) cc_final: 0.6994 (ttt-90) REVERT: B 176 CYS cc_start: 0.6735 (OUTLIER) cc_final: 0.6028 (m) REVERT: B 200 PHE cc_start: 0.7958 (t80) cc_final: 0.7700 (m-10) REVERT: B 235 GLN cc_start: 0.8776 (tm-30) cc_final: 0.8566 (tm-30) REVERT: B 250 GLU cc_start: 0.8193 (tp30) cc_final: 0.7774 (tm-30) REVERT: B 260 LYS cc_start: 0.5878 (mmtt) cc_final: 0.5523 (mmtp) REVERT: C 130 ARG cc_start: 0.8334 (ttm170) cc_final: 0.8052 (ttm170) REVERT: C 176 CYS cc_start: 0.6713 (OUTLIER) cc_final: 0.6079 (m) REVERT: C 213 ARG cc_start: 0.8577 (mmt-90) cc_final: 0.8235 (mmt-90) REVERT: C 222 GLN cc_start: 0.8627 (tt0) cc_final: 0.8294 (tt0) REVERT: C 265 ARG cc_start: 0.8305 (ttt180) cc_final: 0.7984 (ttt-90) REVERT: D 82 LEU cc_start: 0.9234 (mm) cc_final: 0.8909 (mt) REVERT: D 94 ARG cc_start: 0.8286 (mmt90) cc_final: 0.8020 (mtt90) REVERT: D 110 GLN cc_start: 0.8107 (tp40) cc_final: 0.7851 (tp-100) REVERT: D 163 LYS cc_start: 0.8226 (tppt) cc_final: 0.7792 (tppt) REVERT: D 222 GLN cc_start: 0.8531 (tt0) cc_final: 0.8222 (tt0) REVERT: D 269 TRP cc_start: 0.7744 (t-100) cc_final: 0.7451 (t-100) REVERT: E 163 LYS cc_start: 0.7700 (tttp) cc_final: 0.7464 (tttp) REVERT: E 176 CYS cc_start: 0.6639 (OUTLIER) cc_final: 0.6143 (m) REVERT: E 235 GLN cc_start: 0.8608 (tm-30) cc_final: 0.8298 (tm-30) REVERT: E 236 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8292 (mmmm) REVERT: E 247 GLN cc_start: 0.8291 (mt0) cc_final: 0.7939 (mt0) REVERT: F 176 CYS cc_start: 0.6801 (OUTLIER) cc_final: 0.6493 (m) REVERT: F 250 GLU cc_start: 0.7510 (tp30) cc_final: 0.7254 (tp30) REVERT: G 176 CYS cc_start: 0.6785 (OUTLIER) cc_final: 0.6191 (m) REVERT: G 222 GLN cc_start: 0.8664 (tt0) cc_final: 0.8451 (tt0) REVERT: G 251 HIS cc_start: 0.7690 (t-90) cc_final: 0.7472 (t-90) REVERT: G 269 TRP cc_start: 0.8030 (t-100) cc_final: 0.7647 (t-100) REVERT: H 176 CYS cc_start: 0.6971 (OUTLIER) cc_final: 0.6297 (m) REVERT: I 176 CYS cc_start: 0.6853 (OUTLIER) cc_final: 0.6284 (m) outliers start: 87 outliers final: 58 residues processed: 398 average time/residue: 0.1567 time to fit residues: 87.8973 Evaluate side-chains 385 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 317 time to evaluate : 0.617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 197 LEU Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 233 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 68 optimal weight: 5.9990 chunk 196 optimal weight: 5.9990 chunk 105 optimal weight: 0.8980 chunk 168 optimal weight: 0.5980 chunk 150 optimal weight: 1.9990 chunk 137 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 212 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 134 optimal weight: 4.9990 chunk 215 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 301 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.145342 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.112482 restraints weight = 25671.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.115750 restraints weight = 14294.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.117832 restraints weight = 10276.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.119060 restraints weight = 8558.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.119753 restraints weight = 7732.901| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7900 moved from start: 0.3886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18333 Z= 0.126 Angle : 0.527 7.518 25020 Z= 0.276 Chirality : 0.039 0.139 2736 Planarity : 0.005 0.055 3105 Dihedral : 5.377 59.798 2411 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.25 % Allowed : 20.39 % Favored : 75.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.55 (0.18), residues: 2187 helix: 2.66 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.76 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 254 TYR 0.013 0.001 TYR E 218 PHE 0.014 0.001 PHE A 200 TRP 0.009 0.001 TRP H 267 HIS 0.004 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00290 (18306) covalent geometry : angle 0.52465 (24966) SS BOND : bond 0.00125 ( 27) SS BOND : angle 1.12034 ( 54) hydrogen bonds : bond 0.03720 ( 1206) hydrogen bonds : angle 3.54009 ( 3564) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 408 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 327 time to evaluate : 0.620 Fit side-chains revert: symmetry clash REVERT: A 95 HIS cc_start: 0.6999 (OUTLIER) cc_final: 0.6767 (m-70) REVERT: A 98 LYS cc_start: 0.5649 (tptt) cc_final: 0.5381 (pttt) REVERT: A 176 CYS cc_start: 0.6579 (OUTLIER) cc_final: 0.6310 (m) REVERT: A 235 GLN cc_start: 0.8842 (tm-30) cc_final: 0.8117 (tm-30) REVERT: A 236 LYS cc_start: 0.8734 (mmmt) cc_final: 0.8124 (mmtp) REVERT: B 176 CYS cc_start: 0.6967 (OUTLIER) cc_final: 0.6219 (m) REVERT: B 200 PHE cc_start: 0.7947 (t80) cc_final: 0.7712 (m-10) REVERT: B 235 GLN cc_start: 0.8801 (tm-30) cc_final: 0.8546 (tm-30) REVERT: B 250 GLU cc_start: 0.7904 (tp30) cc_final: 0.7671 (tm-30) REVERT: B 254 ARG cc_start: 0.8336 (tpp80) cc_final: 0.7854 (mmt-90) REVERT: C 98 LYS cc_start: 0.6281 (tptt) cc_final: 0.6024 (pptt) REVERT: C 176 CYS cc_start: 0.6749 (OUTLIER) cc_final: 0.6102 (m) REVERT: C 213 ARG cc_start: 0.8564 (mmt-90) cc_final: 0.8247 (mmt-90) REVERT: C 214 MET cc_start: 0.8825 (mtm) cc_final: 0.8608 (mtm) REVERT: C 222 GLN cc_start: 0.8639 (tt0) cc_final: 0.8318 (tt0) REVERT: C 265 ARG cc_start: 0.8308 (ttt180) cc_final: 0.8024 (ttt-90) REVERT: D 82 LEU cc_start: 0.9217 (mm) cc_final: 0.8882 (mt) REVERT: D 94 ARG cc_start: 0.8380 (mmt90) cc_final: 0.8123 (mtt90) REVERT: D 110 GLN cc_start: 0.8071 (tp40) cc_final: 0.7776 (tp-100) REVERT: D 222 GLN cc_start: 0.8531 (tt0) cc_final: 0.8216 (tt0) REVERT: D 269 TRP cc_start: 0.7781 (t-100) cc_final: 0.7478 (t-100) REVERT: E 163 LYS cc_start: 0.7708 (tttp) cc_final: 0.7473 (tttt) REVERT: E 176 CYS cc_start: 0.6662 (OUTLIER) cc_final: 0.6137 (m) REVERT: E 235 GLN cc_start: 0.8599 (tm-30) cc_final: 0.8198 (tm-30) REVERT: E 236 LYS cc_start: 0.8648 (mmmt) cc_final: 0.8065 (mmtm) REVERT: E 247 GLN cc_start: 0.8256 (mt0) cc_final: 0.7867 (mt0) REVERT: F 176 CYS cc_start: 0.7016 (OUTLIER) cc_final: 0.6551 (m) REVERT: G 176 CYS cc_start: 0.6831 (OUTLIER) cc_final: 0.6232 (m) REVERT: G 269 TRP cc_start: 0.8079 (t-100) cc_final: 0.7869 (t60) REVERT: H 176 CYS cc_start: 0.7044 (OUTLIER) cc_final: 0.6413 (m) REVERT: I 176 CYS cc_start: 0.6880 (OUTLIER) cc_final: 0.6313 (m) REVERT: I 269 TRP cc_start: 0.8121 (t-100) cc_final: 0.7623 (t-100) outliers start: 81 outliers final: 64 residues processed: 381 average time/residue: 0.1518 time to fit residues: 82.1318 Evaluate side-chains 389 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 316 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 233 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 108 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 chunk 30 optimal weight: 1.9990 chunk 139 optimal weight: 0.9980 chunk 194 optimal weight: 2.9990 chunk 148 optimal weight: 0.9980 chunk 213 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 107 optimal weight: 8.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 222 GLN ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 110 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.145955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.113178 restraints weight = 25728.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.116460 restraints weight = 14341.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.118540 restraints weight = 10303.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.119776 restraints weight = 8574.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120497 restraints weight = 7730.407| |-----------------------------------------------------------------------------| r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18333 Z= 0.122 Angle : 0.529 8.675 25020 Z= 0.277 Chirality : 0.039 0.140 2736 Planarity : 0.005 0.047 3105 Dihedral : 5.336 59.917 2411 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 4.66 % Allowed : 20.13 % Favored : 75.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.63 (0.18), residues: 2187 helix: 2.73 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.76 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 254 TYR 0.010 0.001 TYR B 218 PHE 0.010 0.001 PHE F 237 TRP 0.011 0.001 TRP I 267 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00280 (18306) covalent geometry : angle 0.52732 (24966) SS BOND : bond 0.00111 ( 27) SS BOND : angle 0.97538 ( 54) hydrogen bonds : bond 0.03625 ( 1206) hydrogen bonds : angle 3.51009 ( 3564) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 406 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 317 time to evaluate : 0.714 Fit side-chains REVERT: A 95 HIS cc_start: 0.7027 (OUTLIER) cc_final: 0.6827 (m-70) REVERT: A 98 LYS cc_start: 0.5632 (tptt) cc_final: 0.5367 (pttt) REVERT: A 176 CYS cc_start: 0.6581 (OUTLIER) cc_final: 0.6292 (m) REVERT: A 222 GLN cc_start: 0.8486 (tt0) cc_final: 0.8180 (tt0) REVERT: A 235 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8052 (tm-30) REVERT: A 236 LYS cc_start: 0.8737 (mmmt) cc_final: 0.8128 (mmtp) REVERT: B 89 ARG cc_start: 0.7830 (OUTLIER) cc_final: 0.7007 (ttt-90) REVERT: B 176 CYS cc_start: 0.6903 (OUTLIER) cc_final: 0.6147 (m) REVERT: B 200 PHE cc_start: 0.7951 (t80) cc_final: 0.7699 (m-10) REVERT: B 235 GLN cc_start: 0.8828 (tm-30) cc_final: 0.8560 (tm-30) REVERT: B 250 GLU cc_start: 0.7911 (tp30) cc_final: 0.7683 (tm-30) REVERT: B 254 ARG cc_start: 0.8365 (tpp80) cc_final: 0.7856 (mmt-90) REVERT: B 260 LYS cc_start: 0.5923 (mmtt) cc_final: 0.5515 (mttm) REVERT: C 98 LYS cc_start: 0.6249 (tptt) cc_final: 0.5993 (pptt) REVERT: C 176 CYS cc_start: 0.6725 (OUTLIER) cc_final: 0.6087 (m) REVERT: C 213 ARG cc_start: 0.8563 (mmt-90) cc_final: 0.8242 (mmt-90) REVERT: C 214 MET cc_start: 0.8840 (mtm) cc_final: 0.8613 (mtm) REVERT: C 222 GLN cc_start: 0.8634 (tt0) cc_final: 0.8310 (tt0) REVERT: C 265 ARG cc_start: 0.8288 (ttt180) cc_final: 0.7958 (ttt-90) REVERT: D 82 LEU cc_start: 0.9215 (mm) cc_final: 0.8887 (mt) REVERT: D 110 GLN cc_start: 0.8120 (tp40) cc_final: 0.7751 (tp-100) REVERT: D 222 GLN cc_start: 0.8521 (tt0) cc_final: 0.8219 (tt0) REVERT: D 250 GLU cc_start: 0.8091 (tp30) cc_final: 0.7758 (mm-30) REVERT: D 269 TRP cc_start: 0.7775 (t-100) cc_final: 0.7425 (t-100) REVERT: E 163 LYS cc_start: 0.7689 (OUTLIER) cc_final: 0.7482 (tttp) REVERT: E 176 CYS cc_start: 0.6628 (OUTLIER) cc_final: 0.6124 (m) REVERT: E 235 GLN cc_start: 0.8597 (tm-30) cc_final: 0.8260 (tm-30) REVERT: E 247 GLN cc_start: 0.8162 (mt0) cc_final: 0.7841 (mt0) REVERT: F 176 CYS cc_start: 0.6989 (OUTLIER) cc_final: 0.6527 (m) REVERT: G 176 CYS cc_start: 0.6824 (OUTLIER) cc_final: 0.6200 (m) REVERT: G 269 TRP cc_start: 0.7994 (t-100) cc_final: 0.7636 (t-100) REVERT: H 176 CYS cc_start: 0.7089 (OUTLIER) cc_final: 0.6415 (m) REVERT: I 136 GLU cc_start: 0.8177 (pt0) cc_final: 0.7927 (pt0) REVERT: I 176 CYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6337 (m) outliers start: 89 outliers final: 72 residues processed: 376 average time/residue: 0.1484 time to fit residues: 79.6740 Evaluate side-chains 382 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 299 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 113 VAL Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 61 MET Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 163 LYS Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 210 THR Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain F residue 222 GLN Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 155 TYR Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 82 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 113 VAL Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 233 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 0.5980 chunk 166 optimal weight: 7.9990 chunk 96 optimal weight: 0.0050 chunk 98 optimal weight: 0.4980 chunk 83 optimal weight: 8.9990 chunk 192 optimal weight: 5.9990 chunk 106 optimal weight: 10.0000 chunk 89 optimal weight: 6.9990 chunk 93 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 overall best weight: 1.0196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 GLN ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 110 GLN C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.146690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.113923 restraints weight = 25501.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117223 restraints weight = 14248.286| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.119282 restraints weight = 10251.865| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120533 restraints weight = 8546.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.120965 restraints weight = 7718.353| |-----------------------------------------------------------------------------| r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.4109 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18333 Z= 0.114 Angle : 0.522 8.178 25020 Z= 0.274 Chirality : 0.038 0.138 2736 Planarity : 0.005 0.047 3105 Dihedral : 5.267 59.709 2411 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.84 % Favored : 96.16 % Rotamer: Outliers : 4.25 % Allowed : 21.07 % Favored : 74.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.73 (0.18), residues: 2187 helix: 2.80 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.74 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 254 TYR 0.012 0.001 TYR G 218 PHE 0.010 0.001 PHE A 44 TRP 0.016 0.001 TRP I 267 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00261 (18306) covalent geometry : angle 0.52060 (24966) SS BOND : bond 0.00102 ( 27) SS BOND : angle 1.03643 ( 54) hydrogen bonds : bond 0.03478 ( 1206) hydrogen bonds : angle 3.46808 ( 3564) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 311 time to evaluate : 0.584 Fit side-chains revert: symmetry clash REVERT: A 95 HIS cc_start: 0.7030 (OUTLIER) cc_final: 0.6817 (m-70) REVERT: A 98 LYS cc_start: 0.5608 (tptt) cc_final: 0.5351 (pttt) REVERT: A 176 CYS cc_start: 0.6611 (OUTLIER) cc_final: 0.6333 (m) REVERT: A 235 GLN cc_start: 0.8809 (tm-30) cc_final: 0.8044 (tm-30) REVERT: A 236 LYS cc_start: 0.8716 (mmmt) cc_final: 0.8153 (mmtp) REVERT: A 247 GLN cc_start: 0.8429 (mt0) cc_final: 0.8124 (mt0) REVERT: B 89 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.7000 (ttt-90) REVERT: B 176 CYS cc_start: 0.6894 (OUTLIER) cc_final: 0.6140 (m) REVERT: B 200 PHE cc_start: 0.7947 (t80) cc_final: 0.7710 (m-10) REVERT: B 235 GLN cc_start: 0.8830 (tm-30) cc_final: 0.8572 (tm-30) REVERT: C 130 ARG cc_start: 0.8325 (ttm170) cc_final: 0.8099 (ttm170) REVERT: C 176 CYS cc_start: 0.6720 (OUTLIER) cc_final: 0.6076 (m) REVERT: C 214 MET cc_start: 0.8834 (mtm) cc_final: 0.8606 (mtm) REVERT: C 222 GLN cc_start: 0.8616 (tt0) cc_final: 0.8302 (tt0) REVERT: C 265 ARG cc_start: 0.8260 (ttt180) cc_final: 0.7984 (ttt-90) REVERT: D 82 LEU cc_start: 0.9216 (mm) cc_final: 0.8892 (mt) REVERT: D 110 GLN cc_start: 0.8092 (tp40) cc_final: 0.7712 (tp-100) REVERT: D 222 GLN cc_start: 0.8462 (tt0) cc_final: 0.8177 (tt0) REVERT: D 250 GLU cc_start: 0.8088 (tp30) cc_final: 0.7886 (mm-30) REVERT: D 269 TRP cc_start: 0.7670 (t-100) cc_final: 0.7450 (t-100) REVERT: E 176 CYS cc_start: 0.6602 (OUTLIER) cc_final: 0.6092 (m) REVERT: E 235 GLN cc_start: 0.8622 (tm-30) cc_final: 0.8270 (tm-30) REVERT: E 247 GLN cc_start: 0.8162 (mt0) cc_final: 0.7831 (mt0) REVERT: F 176 CYS cc_start: 0.6985 (OUTLIER) cc_final: 0.6509 (m) REVERT: G 163 LYS cc_start: 0.7598 (ttmt) cc_final: 0.7340 (tttt) REVERT: G 176 CYS cc_start: 0.6925 (OUTLIER) cc_final: 0.6370 (m) REVERT: G 250 GLU cc_start: 0.7822 (tp30) cc_final: 0.7310 (tt0) REVERT: G 269 TRP cc_start: 0.8012 (t-100) cc_final: 0.7654 (t-100) REVERT: H 163 LYS cc_start: 0.7503 (ttmt) cc_final: 0.7151 (ttmt) REVERT: H 176 CYS cc_start: 0.7112 (OUTLIER) cc_final: 0.6440 (m) REVERT: I 176 CYS cc_start: 0.6891 (OUTLIER) cc_final: 0.6337 (m) REVERT: I 247 GLN cc_start: 0.8725 (tt0) cc_final: 0.8326 (mt0) REVERT: I 269 TRP cc_start: 0.7940 (t-100) cc_final: 0.7514 (t-100) outliers start: 81 outliers final: 65 residues processed: 367 average time/residue: 0.1429 time to fit residues: 75.5315 Evaluate side-chains 370 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 295 time to evaluate : 0.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 95 HIS Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain D residue 238 ASP Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 233 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 143 optimal weight: 0.8980 chunk 188 optimal weight: 6.9990 chunk 196 optimal weight: 5.9990 chunk 162 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 62 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 165 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 60 optimal weight: 6.9990 chunk 90 optimal weight: 5.9990 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 110 GLN ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 110 GLN ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.146777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.113925 restraints weight = 25611.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.117218 restraints weight = 14337.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.119287 restraints weight = 10321.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.120488 restraints weight = 8599.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3454 r_free = 0.3454 target = 0.121061 restraints weight = 7768.545| |-----------------------------------------------------------------------------| r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 18333 Z= 0.118 Angle : 0.531 9.516 25020 Z= 0.278 Chirality : 0.039 0.140 2736 Planarity : 0.005 0.048 3105 Dihedral : 5.254 59.695 2411 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 4.14 % Allowed : 21.28 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.72 (0.18), residues: 2187 helix: 2.79 (0.12), residues: 1665 sheet: None (None), residues: 0 loop : -1.72 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 254 TYR 0.009 0.001 TYR E 218 PHE 0.011 0.001 PHE A 44 TRP 0.016 0.001 TRP I 267 HIS 0.003 0.001 HIS A 56 Details of bonding type rmsd covalent geometry : bond 0.00271 (18306) covalent geometry : angle 0.52968 (24966) SS BOND : bond 0.00105 ( 27) SS BOND : angle 0.98714 ( 54) hydrogen bonds : bond 0.03514 ( 1206) hydrogen bonds : angle 3.45499 ( 3564) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4374 Ramachandran restraints generated. 2187 Oldfield, 0 Emsley, 2187 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 384 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 305 time to evaluate : 0.637 Fit side-chains REVERT: A 98 LYS cc_start: 0.5607 (tptt) cc_final: 0.5346 (pttt) REVERT: A 176 CYS cc_start: 0.6624 (OUTLIER) cc_final: 0.6353 (m) REVERT: A 222 GLN cc_start: 0.8518 (tt0) cc_final: 0.8259 (tt0) REVERT: A 235 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8000 (tm-30) REVERT: A 247 GLN cc_start: 0.8335 (mt0) cc_final: 0.7993 (mt0) REVERT: B 89 ARG cc_start: 0.7821 (OUTLIER) cc_final: 0.6984 (ttt-90) REVERT: B 176 CYS cc_start: 0.6916 (OUTLIER) cc_final: 0.6161 (m) REVERT: B 200 PHE cc_start: 0.7948 (t80) cc_final: 0.7717 (m-10) REVERT: B 233 GLU cc_start: 0.8700 (tm-30) cc_final: 0.8441 (tp30) REVERT: B 235 GLN cc_start: 0.8844 (tm-30) cc_final: 0.8580 (tm-30) REVERT: B 260 LYS cc_start: 0.6005 (mmtt) cc_final: 0.5635 (mttm) REVERT: C 176 CYS cc_start: 0.6734 (OUTLIER) cc_final: 0.6089 (m) REVERT: C 213 ARG cc_start: 0.8468 (mmt-90) cc_final: 0.7726 (mpt180) REVERT: C 214 MET cc_start: 0.8840 (mtm) cc_final: 0.8600 (mtm) REVERT: C 222 GLN cc_start: 0.8609 (tt0) cc_final: 0.8300 (tt0) REVERT: C 265 ARG cc_start: 0.8281 (ttt180) cc_final: 0.7999 (ttt-90) REVERT: D 82 LEU cc_start: 0.9222 (mm) cc_final: 0.8891 (mt) REVERT: D 110 GLN cc_start: 0.8082 (tp40) cc_final: 0.7696 (tp-100) REVERT: D 222 GLN cc_start: 0.8462 (tt0) cc_final: 0.8172 (tt0) REVERT: D 269 TRP cc_start: 0.7669 (t-100) cc_final: 0.7425 (t-100) REVERT: E 176 CYS cc_start: 0.6531 (OUTLIER) cc_final: 0.6012 (m) REVERT: E 235 GLN cc_start: 0.8732 (tm-30) cc_final: 0.8329 (tm-30) REVERT: E 247 GLN cc_start: 0.8159 (mt0) cc_final: 0.7827 (mt0) REVERT: F 176 CYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6512 (m) REVERT: G 176 CYS cc_start: 0.6931 (OUTLIER) cc_final: 0.6348 (m) REVERT: G 250 GLU cc_start: 0.7891 (tp30) cc_final: 0.7105 (tt0) REVERT: G 269 TRP cc_start: 0.8001 (t-100) cc_final: 0.7647 (t-100) REVERT: H 163 LYS cc_start: 0.7519 (ttmt) cc_final: 0.7174 (ttmt) REVERT: H 176 CYS cc_start: 0.7139 (OUTLIER) cc_final: 0.6465 (m) REVERT: I 163 LYS cc_start: 0.7547 (tttt) cc_final: 0.7259 (tttt) REVERT: I 176 CYS cc_start: 0.6914 (OUTLIER) cc_final: 0.6367 (m) REVERT: I 247 GLN cc_start: 0.8718 (tt0) cc_final: 0.8314 (mt0) outliers start: 79 outliers final: 66 residues processed: 359 average time/residue: 0.1443 time to fit residues: 74.6491 Evaluate side-chains 366 residues out of total 1962 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 75 poor density : 291 time to evaluate : 0.453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 122 VAL Chi-restraints excluded: chain A residue 176 CYS Chi-restraints excluded: chain A residue 201 SER Chi-restraints excluded: chain B residue 59 VAL Chi-restraints excluded: chain B residue 73 ILE Chi-restraints excluded: chain B residue 79 THR Chi-restraints excluded: chain B residue 89 ARG Chi-restraints excluded: chain B residue 122 VAL Chi-restraints excluded: chain B residue 131 CYS Chi-restraints excluded: chain B residue 176 CYS Chi-restraints excluded: chain C residue 59 VAL Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 95 HIS Chi-restraints excluded: chain C residue 122 VAL Chi-restraints excluded: chain C residue 123 PHE Chi-restraints excluded: chain C residue 131 CYS Chi-restraints excluded: chain C residue 176 CYS Chi-restraints excluded: chain C residue 238 ASP Chi-restraints excluded: chain D residue 59 VAL Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 122 VAL Chi-restraints excluded: chain D residue 130 ARG Chi-restraints excluded: chain D residue 197 LEU Chi-restraints excluded: chain E residue 59 VAL Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 95 HIS Chi-restraints excluded: chain E residue 97 TRP Chi-restraints excluded: chain E residue 122 VAL Chi-restraints excluded: chain E residue 176 CYS Chi-restraints excluded: chain E residue 197 LEU Chi-restraints excluded: chain E residue 238 ASP Chi-restraints excluded: chain F residue 59 VAL Chi-restraints excluded: chain F residue 79 THR Chi-restraints excluded: chain F residue 95 HIS Chi-restraints excluded: chain F residue 122 VAL Chi-restraints excluded: chain F residue 131 CYS Chi-restraints excluded: chain F residue 176 CYS Chi-restraints excluded: chain F residue 197 LEU Chi-restraints excluded: chain F residue 201 SER Chi-restraints excluded: chain F residue 208 VAL Chi-restraints excluded: chain G residue 59 VAL Chi-restraints excluded: chain G residue 79 THR Chi-restraints excluded: chain G residue 97 TRP Chi-restraints excluded: chain G residue 122 VAL Chi-restraints excluded: chain G residue 176 CYS Chi-restraints excluded: chain G residue 201 SER Chi-restraints excluded: chain G residue 238 ASP Chi-restraints excluded: chain H residue 59 VAL Chi-restraints excluded: chain H residue 79 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 97 TRP Chi-restraints excluded: chain H residue 122 VAL Chi-restraints excluded: chain H residue 176 CYS Chi-restraints excluded: chain H residue 197 LEU Chi-restraints excluded: chain H residue 199 LEU Chi-restraints excluded: chain H residue 201 SER Chi-restraints excluded: chain H residue 222 GLN Chi-restraints excluded: chain H residue 238 ASP Chi-restraints excluded: chain I residue 59 VAL Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 82 LEU Chi-restraints excluded: chain I residue 97 TRP Chi-restraints excluded: chain I residue 113 VAL Chi-restraints excluded: chain I residue 122 VAL Chi-restraints excluded: chain I residue 123 PHE Chi-restraints excluded: chain I residue 131 CYS Chi-restraints excluded: chain I residue 176 CYS Chi-restraints excluded: chain I residue 181 THR Chi-restraints excluded: chain I residue 197 LEU Chi-restraints excluded: chain I residue 201 SER Chi-restraints excluded: chain I residue 233 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 43 optimal weight: 0.9980 chunk 159 optimal weight: 0.6980 chunk 165 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 135 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 210 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 95 HIS ** B 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 224 GLN ** D 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 110 GLN ** G 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 110 GLN ** I 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 222 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.147642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3382 r_free = 0.3382 target = 0.114866 restraints weight = 25713.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.118173 restraints weight = 14288.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.120258 restraints weight = 10256.472| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.121497 restraints weight = 8510.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.122134 restraints weight = 7693.761| |-----------------------------------------------------------------------------| r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 18333 Z= 0.110 Angle : 0.520 9.054 25020 Z= 0.272 Chirality : 0.038 0.139 2736 Planarity : 0.005 0.047 3105 Dihedral : 5.207 59.310 2411 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 5.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 4.14 % Allowed : 21.33 % Favored : 74.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 2.82 (0.18), residues: 2187 helix: 2.86 (0.12), residues: 1674 sheet: None (None), residues: 0 loop : -1.77 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG I 254 TYR 0.010 0.001 TYR G 218 PHE 0.008 0.001 PHE G 256 TRP 0.015 0.001 TRP B 267 HIS 0.003 0.001 HIS B 56 Details of bonding type rmsd covalent geometry : bond 0.00249 (18306) covalent geometry : angle 0.51823 (24966) SS BOND : bond 0.00088 ( 27) SS BOND : angle 0.98503 ( 54) hydrogen bonds : bond 0.03366 ( 1206) hydrogen bonds : angle 3.41261 ( 3564) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2921.43 seconds wall clock time: 51 minutes 13.71 seconds (3073.71 seconds total)