Starting phenix.real_space_refine on Sat Aug 8 20:36:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zk2_60165/08_2026/8zk2_60165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zk2_60165/08_2026/8zk2_60165.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2026/8zk2_60165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2026/8zk2_60165.map" model { file = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2026/8zk2_60165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zk2_60165/08_2026/8zk2_60165.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 4470 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians Fe 5 7.16 5 P 7 5.49 5 Mg 55 5.21 5 S 133 5.16 5 C 18777 2.51 5 N 3834 2.21 5 O 4137 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 26948 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2618 Classifications: {'peptide': 342} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 314} Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2163 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2269 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 269} Chain: "H" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1906 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "J" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "O" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "P" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "R" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "U" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "V" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "W" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Z" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "a" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "e" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "h" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "i" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "j" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {' MG': 3, '8K6': 1, 'HEC': 4, 'PGV': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 338 Unusual residues: {'8K6': 5, 'BCL': 2, 'BPH': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 401 Unusual residues: {' FE': 1, '8K6': 1, 'BCL': 2, 'BPH': 1, 'CRT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 171 Unusual residues: {' MG': 1, '8K6': 4, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 227 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "a" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 212 Unusual residues: {'8K6': 2, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 5.29, per 1000 atoms: 0.20 Number of scatterers: 26948 At special positions: 0 Unit cell: (139.36, 126.88, 133.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Fe 5 26.01 S 133 16.00 P 7 15.00 Mg 55 11.99 O 4137 8.00 N 3834 7.00 C 18777 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=63, symmetry=0 Number of additional bonds: simple=63, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.37 Conformation dependent library (CDL) restraints added in 636.9 milliseconds 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5122 Finding SS restraints... Secondary structure from input PDB file: 104 helices and 9 sheets defined 62.1% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'C' and resid 26 through 45 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 76 through 80 Processing helix chain 'C' and resid 94 through 99 removed outlier: 3.538A pdb=" N VAL C 98 " --> pdb=" O LEU C 94 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 124 Processing helix chain 'C' and resid 128 through 133 removed outlier: 3.888A pdb=" N ASN C 131 " --> pdb=" O GLU C 128 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N CYS C 133 " --> pdb=" O CYS C 130 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 164 removed outlier: 3.823A pdb=" N ILE C 148 " --> pdb=" O PRO C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 169 Processing helix chain 'C' and resid 174 through 179 removed outlier: 4.301A pdb=" N CYS C 178 " --> pdb=" O THR C 174 " (cutoff:3.500A) Processing helix chain 'C' and resid 212 through 216 Processing helix chain 'C' and resid 224 through 229 Processing helix chain 'C' and resid 252 through 271 Processing helix chain 'C' and resid 273 through 277 Processing helix chain 'C' and resid 291 through 310 removed outlier: 3.581A pdb=" N THR C 295 " --> pdb=" O PRO C 291 " (cutoff:3.500A) Processing helix chain 'C' and resid 314 through 318 Processing helix chain 'C' and resid 333 through 339 removed outlier: 4.113A pdb=" N CYS C 337 " --> pdb=" O ASN C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 343 through 348 removed outlier: 3.542A pdb=" N GLU C 348 " --> pdb=" O MET C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 359 removed outlier: 3.997A pdb=" N ALA C 359 " --> pdb=" O SER C 356 " (cutoff:3.500A) Processing helix chain 'L' and resid 7 through 11 Processing helix chain 'L' and resid 33 through 56 Processing helix chain 'L' and resid 72 through 76 Processing helix chain 'L' and resid 85 through 114 Processing helix chain 'L' and resid 117 through 135 removed outlier: 3.617A pdb=" N PHE L 125 " --> pdb=" O PHE L 121 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ALA L 126 " --> pdb=" O ALA L 122 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 142 Processing helix chain 'L' and resid 143 through 147 Processing helix chain 'L' and resid 153 through 165 removed outlier: 3.506A pdb=" N ASP L 157 " --> pdb=" O MET L 153 " (cutoff:3.500A) Processing helix chain 'L' and resid 166 through 167 No H-bonds generated for 'chain 'L' and resid 166 through 167' Processing helix chain 'L' and resid 168 through 171 Processing helix chain 'L' and resid 172 through 201 Processing helix chain 'L' and resid 210 through 222 removed outlier: 3.657A pdb=" N PHE L 218 " --> pdb=" O GLU L 214 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 252 removed outlier: 3.509A pdb=" N ILE L 231 " --> pdb=" O GLY L 227 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N HIS L 232 " --> pdb=" O THR L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 261 through 264 Processing helix chain 'L' and resid 265 through 270 Processing helix chain 'M' and resid 39 through 44 removed outlier: 3.832A pdb=" N ILE M 43 " --> pdb=" O TRP M 39 " (cutoff:3.500A) Processing helix chain 'M' and resid 53 through 78 Processing helix chain 'M' and resid 82 through 90 Processing helix chain 'M' and resid 99 through 103 Processing helix chain 'M' and resid 109 through 112 Processing helix chain 'M' and resid 113 through 141 Processing helix chain 'M' and resid 145 through 163 removed outlier: 3.640A pdb=" N TRP M 149 " --> pdb=" O THR M 145 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N SER M 153 " --> pdb=" O TRP M 149 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA M 154 " --> pdb=" O ALA M 150 " (cutoff:3.500A) Processing helix chain 'M' and resid 163 through 170 Processing helix chain 'M' and resid 171 through 175 Processing helix chain 'M' and resid 180 through 194 removed outlier: 3.806A pdb=" N LEU M 184 " --> pdb=" O ILE M 180 " (cutoff:3.500A) Processing helix chain 'M' and resid 196 through 199 Processing helix chain 'M' and resid 200 through 227 Processing helix chain 'M' and resid 228 through 231 Processing helix chain 'M' and resid 234 through 241 Processing helix chain 'M' and resid 243 through 258 removed outlier: 3.614A pdb=" N TRP M 253 " --> pdb=" O ALA M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 264 through 287 removed outlier: 3.937A pdb=" N THR M 278 " --> pdb=" O ALA M 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 294 through 302 Processing helix chain 'H' and resid 10 through 34 Processing helix chain 'H' and resid 101 through 106 Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 200 through 202 No H-bonds generated for 'chain 'H' and resid 200 through 202' Processing helix chain 'H' and resid 217 through 222 removed outlier: 3.552A pdb=" N ALA H 222 " --> pdb=" O ALA H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 252 removed outlier: 3.809A pdb=" N THR H 249 " --> pdb=" O TYR H 245 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N LEU H 250 " --> pdb=" O ALA H 246 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 47 removed outlier: 3.663A pdb=" N VAL B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 5 through 11 removed outlier: 3.959A pdb=" N TRP A 9 " --> pdb=" O HIS A 6 " (cutoff:3.500A) Processing helix chain 'A' and resid 13 through 38 Processing helix chain 'D' and resid 14 through 47 Processing helix chain 'E' and resid 5 through 11 removed outlier: 3.875A pdb=" N TRP E 9 " --> pdb=" O HIS E 6 " (cutoff:3.500A) Processing helix chain 'E' and resid 13 through 38 Processing helix chain 'F' and resid 14 through 47 removed outlier: 3.569A pdb=" N LYS F 19 " --> pdb=" O GLU F 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 11 removed outlier: 3.750A pdb=" N TRP G 9 " --> pdb=" O HIS G 6 " (cutoff:3.500A) Processing helix chain 'G' and resid 13 through 38 Processing helix chain 'I' and resid 14 through 47 Processing helix chain 'J' and resid 5 through 11 removed outlier: 3.752A pdb=" N TRP J 9 " --> pdb=" O HIS J 6 " (cutoff:3.500A) Processing helix chain 'J' and resid 13 through 38 Processing helix chain 'K' and resid 14 through 47 Processing helix chain 'N' and resid 5 through 11 removed outlier: 3.766A pdb=" N VAL N 8 " --> pdb=" O THR N 5 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N TRP N 9 " --> pdb=" O HIS N 6 " (cutoff:3.500A) Processing helix chain 'N' and resid 13 through 38 Processing helix chain 'O' and resid 16 through 47 removed outlier: 3.562A pdb=" N VAL O 24 " --> pdb=" O GLU O 20 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 11 removed outlier: 3.786A pdb=" N TRP P 9 " --> pdb=" O HIS P 6 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU P 10 " --> pdb=" O LYS P 7 " (cutoff:3.500A) Processing helix chain 'P' and resid 13 through 38 Processing helix chain 'Q' and resid 14 through 47 Processing helix chain 'R' and resid 5 through 11 removed outlier: 3.777A pdb=" N VAL R 8 " --> pdb=" O THR R 5 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N TRP R 9 " --> pdb=" O HIS R 6 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 38 Processing helix chain 'S' and resid 14 through 47 Processing helix chain 'T' and resid 5 through 11 removed outlier: 3.583A pdb=" N VAL T 8 " --> pdb=" O THR T 5 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N TRP T 9 " --> pdb=" O HIS T 6 " (cutoff:3.500A) Processing helix chain 'T' and resid 13 through 38 Processing helix chain 'U' and resid 14 through 47 Processing helix chain 'V' and resid 5 through 11 removed outlier: 3.830A pdb=" N VAL V 8 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP V 9 " --> pdb=" O HIS V 6 " (cutoff:3.500A) Processing helix chain 'V' and resid 13 through 38 Processing helix chain 'W' and resid 14 through 47 Processing helix chain 'X' and resid 5 through 11 removed outlier: 3.536A pdb=" N VAL X 8 " --> pdb=" O THR X 5 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TRP X 9 " --> pdb=" O HIS X 6 " (cutoff:3.500A) Processing helix chain 'X' and resid 13 through 38 Processing helix chain 'Y' and resid 14 through 47 Processing helix chain 'Z' and resid 6 through 11 removed outlier: 4.406A pdb=" N TRP Z 9 " --> pdb=" O HIS Z 6 " (cutoff:3.500A) Processing helix chain 'Z' and resid 13 through 38 Processing helix chain 'a' and resid 14 through 47 Processing helix chain 'b' and resid 5 through 11 removed outlier: 3.662A pdb=" N VAL b 8 " --> pdb=" O THR b 5 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP b 9 " --> pdb=" O HIS b 6 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 38 Processing helix chain 'c' and resid 14 through 47 Processing helix chain 'd' and resid 5 through 11 removed outlier: 3.564A pdb=" N VAL d 8 " --> pdb=" O THR d 5 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TRP d 9 " --> pdb=" O HIS d 6 " (cutoff:3.500A) Processing helix chain 'd' and resid 13 through 38 removed outlier: 4.882A pdb=" N VAL d 19 " --> pdb=" O ARG d 15 " (cutoff:3.500A) removed outlier: 5.080A pdb=" N ALA d 20 " --> pdb=" O SER d 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 16 through 47 Processing helix chain 'f' and resid 5 through 11 removed outlier: 3.997A pdb=" N VAL f 8 " --> pdb=" O THR f 5 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N TRP f 9 " --> pdb=" O HIS f 6 " (cutoff:3.500A) Processing helix chain 'f' and resid 13 through 38 removed outlier: 3.565A pdb=" N LEU f 18 " --> pdb=" O PRO f 14 " (cutoff:3.500A) Processing helix chain 'g' and resid 14 through 47 removed outlier: 3.654A pdb=" N VAL g 24 " --> pdb=" O GLU g 20 " (cutoff:3.500A) Processing helix chain 'h' and resid 5 through 11 removed outlier: 3.655A pdb=" N VAL h 8 " --> pdb=" O THR h 5 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N TRP h 9 " --> pdb=" O HIS h 6 " (cutoff:3.500A) Processing helix chain 'h' and resid 13 through 39 Processing helix chain 'i' and resid 14 through 47 Processing helix chain 'j' and resid 5 through 11 removed outlier: 3.550A pdb=" N VAL j 8 " --> pdb=" O THR j 5 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N TRP j 9 " --> pdb=" O HIS j 6 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 38 Processing sheet with id=AA1, first strand: chain 'C' and resid 50 through 53 Processing sheet with id=AA2, first strand: chain 'C' and resid 188 through 189 Processing sheet with id=AA3, first strand: chain 'L' and resid 25 through 27 removed outlier: 3.643A pdb=" N PHE L 25 " --> pdb=" O VAL L 32 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'M' and resid 35 through 36 removed outlier: 3.687A pdb=" N THR M 35 " --> pdb=" O ILE M 48 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'M' and resid 94 through 95 Processing sheet with id=AA6, first strand: chain 'H' and resid 61 through 64 Processing sheet with id=AA7, first strand: chain 'H' and resid 85 through 86 Processing sheet with id=AA8, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.386A pdb=" N GLY H 161 " --> pdb=" O LEU H 182 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N LEU H 182 " --> pdb=" O GLY H 161 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL H 163 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL H 180 " --> pdb=" O VAL H 163 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N ASP H 165 " --> pdb=" O LEU H 178 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N LEU H 178 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 6.764A pdb=" N TRP H 167 " --> pdb=" O ARG H 176 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE H 174 " --> pdb=" O ASP H 169 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 129 through 131 removed outlier: 6.638A pdb=" N THR H 159 " --> pdb=" O ALA H 154 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ALA H 154 " --> pdb=" O THR H 159 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLY H 161 " --> pdb=" O VAL H 152 " (cutoff:3.500A) 1319 hydrogen bonds defined for protein. 3735 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: 4.26 Time building geometry restraints manager: 2.86 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 8759 1.38 - 1.58: 18873 1.58 - 1.79: 88 1.79 - 2.00: 176 2.00 - 2.20: 191 Bond restraints: 28087 Sorted by residual: bond pdb=" NA BCL M 403 " pdb="MG BCL M 403 " ideal model delta sigma weight residual 2.170 1.977 0.193 2.40e-02 1.74e+03 6.45e+01 bond pdb=" NA BCL G 101 " pdb="MG BCL G 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.09e+01 bond pdb=" NA BCL P 101 " pdb="MG BCL P 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.05e+01 bond pdb=" NA BCL M 402 " pdb="MG BCL M 402 " ideal model delta sigma weight residual 2.170 1.984 0.186 2.40e-02 1.74e+03 6.02e+01 bond pdb=" NA BCL f 101 " pdb="MG BCL f 101 " ideal model delta sigma weight residual 2.170 1.985 0.185 2.40e-02 1.74e+03 5.96e+01 ... (remaining 28082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 38046 6.73 - 13.46: 722 13.46 - 20.19: 52 20.19 - 26.92: 2 26.92 - 33.65: 2 Bond angle restraints: 38824 Sorted by residual: angle pdb=" ND BCL M 403 " pdb="MG BCL M 403 " pdb=" NA BCL M 403 " ideal model delta sigma weight residual 88.02 97.69 -9.66 1.29e+00 6.02e-01 5.62e+01 angle pdb=" C1D BCL d 102 " pdb=" C2D BCL d 102 " pdb=" CMD BCL d 102 " ideal model delta sigma weight residual 125.57 139.08 -13.50 1.83e+00 2.99e-01 5.46e+01 angle pdb=" ND BCL J 101 " pdb="MG BCL J 101 " pdb=" NA BCL J 101 " ideal model delta sigma weight residual 88.02 97.51 -9.48 1.29e+00 6.02e-01 5.41e+01 angle pdb=" ND BCL f 101 " pdb="MG BCL f 101 " pdb=" NA BCL f 101 " ideal model delta sigma weight residual 88.02 97.37 -9.35 1.29e+00 6.02e-01 5.26e+01 angle pdb=" ND BCL h 101 " pdb="MG BCL h 101 " pdb=" NA BCL h 101 " ideal model delta sigma weight residual 88.02 97.30 -9.27 1.29e+00 6.02e-01 5.18e+01 ... (remaining 38819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 14210 35.82 - 71.63: 639 71.63 - 107.45: 62 107.45 - 143.26: 15 143.26 - 179.08: 10 Dihedral angle restraints: 14936 sinusoidal: 7021 harmonic: 7915 Sorted by residual: dihedral pdb=" C1 BCL h 102 " pdb=" CGA BCL h 102 " pdb=" O2A BCL h 102 " pdb=" CBA BCL h 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.92 -179.08 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual -180.00 -1.96 -178.04 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL V 102 " pdb=" CGA BCL V 102 " pdb=" O2A BCL V 102 " pdb=" CBA BCL V 102 " ideal model delta sinusoidal sigma weight residual 180.00 2.41 177.59 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 14933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3215 0.066 - 0.132: 431 0.132 - 0.198: 104 0.198 - 0.263: 19 0.263 - 0.329: 11 Chirality restraints: 3780 Sorted by residual: chirality pdb=" CBD BCL I 101 " pdb=" CAD BCL I 101 " pdb=" CGD BCL I 101 " pdb=" CHA BCL I 101 " both_signs ideal model delta sigma weight residual False 2.62 2.29 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CBD BCL B 101 " pdb=" CAD BCL B 101 " pdb=" CGD BCL B 101 " pdb=" CHA BCL B 101 " both_signs ideal model delta sigma weight residual False 2.62 2.30 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA VAL W 57 " pdb=" N VAL W 57 " pdb=" C VAL W 57 " pdb=" CB VAL W 57 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3777 not shown) Planarity restraints: 4704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL G 102 " -0.350 3.00e-02 1.11e+03 2.87e-01 4.58e+02 pdb=" CBA BCL G 102 " -0.176 3.00e-02 1.11e+03 pdb=" CGA BCL G 102 " 0.081 3.00e-02 1.11e+03 pdb=" O1A BCL G 102 " -0.054 3.00e-02 1.11e+03 pdb=" O2A BCL G 102 " 0.499 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL J 102 " -0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL J 102 " -0.190 3.00e-02 1.11e+03 pdb=" CGA BCL J 102 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL J 102 " -0.034 3.00e-02 1.11e+03 pdb=" O2A BCL J 102 " 0.491 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 402 " -0.327 3.00e-02 1.11e+03 2.71e-01 4.07e+02 pdb=" CBA BCL M 402 " -0.152 3.00e-02 1.11e+03 pdb=" CGA BCL M 402 " 0.064 3.00e-02 1.11e+03 pdb=" O1A BCL M 402 " -0.063 3.00e-02 1.11e+03 pdb=" O2A BCL M 402 " 0.478 3.00e-02 1.11e+03 ... (remaining 4701 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 259 2.62 - 3.19: 20984 3.19 - 3.76: 45735 3.76 - 4.33: 69564 4.33 - 4.90: 110746 Nonbonded interactions: 247288 Sorted by model distance: nonbonded pdb=" NE2 HIS C 338 " pdb="FE HEC C 504 " model vdw 2.047 3.080 nonbonded pdb=" OD2 ASP C 214 " pdb="MG MG C 506 " model vdw 2.070 2.170 nonbonded pdb=" OD1 ASP C 194 " pdb="MG MG C 506 " model vdw 2.073 2.170 nonbonded pdb=" NE2 HIS L 192 " pdb="FE FE M 401 " model vdw 2.144 2.340 nonbonded pdb=" NE2 HIS M 220 " pdb="FE FE M 401 " model vdw 2.147 2.340 ... (remaining 247283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 51) selection = (chain 'E' and resid 6 through 51) selection = (chain 'G' and resid 6 through 51) selection = (chain 'J' and resid 6 through 51) selection = (chain 'N' and resid 6 through 51) selection = (chain 'P' and resid 6 through 51) selection = (chain 'R' and resid 6 through 51) selection = (chain 'T' and resid 6 through 51) selection = (chain 'V' and resid 6 through 51) selection = (chain 'X' and resid 6 through 51) selection = (chain 'Z' and resid 6 through 51) selection = (chain 'b' and resid 6 through 51) selection = (chain 'd' and resid 6 through 51) selection = (chain 'f' and resid 6 through 51) selection = (chain 'h' and resid 6 through 51) selection = (chain 'j' and resid 6 through 51) } ncs_group { reference = (chain 'B' and resid 9 through 101) selection = chain 'D' selection = chain 'F' selection = (chain 'I' and resid 9 through 101) selection = (chain 'K' and resid 9 through 101) selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = (chain 'U' and resid 9 through 101) selection = (chain 'W' and resid 9 through 101) selection = (chain 'Y' and resid 9 through 101) selection = (chain 'a' and resid 9 through 101) selection = chain 'c' selection = (chain 'e' and resid 9 through 101) selection = chain 'g' selection = (chain 'i' and resid 9 through 101) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.050 Process input model: 20.090 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.800 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 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 : 0.022 0.348 28150 Z= 1.025 Angle : 2.009 33.654 38824 Z= 0.905 Chirality : 0.055 0.329 3780 Planarity : 0.021 0.287 4704 Dihedral : 19.507 179.077 9814 Min Nonbonded Distance : 2.047 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.05 % Allowed : 0.41 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.75 (0.16), residues: 2698 helix: 2.14 (0.13), residues: 1492 sheet: 0.58 (0.98), residues: 26 loop : -0.05 (0.18), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 57 TYR 0.021 0.002 TYR M 194 PHE 0.058 0.002 PHE L 218 TRP 0.014 0.001 TRP U 50 HIS 0.016 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.02085 / 0.91 (28087) covalent geometry : angle 2.00870 / 0.91 (38824) hydrogen bonds : bond 0.12040 / 8.28 ( 1317) hydrogen bonds : angle 4.73226 / 3.47 ( 3735) Misc. bond : bond 0.11981 / 8.28 ( 63) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 311 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 310 time to evaluate : 0.818 Fit side-chains REVERT: H 1 MET cc_start: 0.7285 (mmt) cc_final: 0.6864 (mpt) REVERT: E 1 MET cc_start: 0.7695 (ttm) cc_final: 0.7183 (mtp) REVERT: F 27 GLN cc_start: 0.8063 (mt0) cc_final: 0.7854 (mt0) REVERT: U 27 GLN cc_start: 0.7945 (mt0) cc_final: 0.7634 (mt0) REVERT: V 46 GLU cc_start: 0.8138 (tp30) cc_final: 0.7934 (mm-30) outliers start: 1 outliers final: 0 residues processed: 311 average time/residue: 0.6525 time to fit residues: 232.8292 Evaluate side-chains 273 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 0.7980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.1980 chunk 132 optimal weight: 0.9990 chunk 248 optimal weight: 0.7980 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.9980 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 0.9990 chunk 111 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 146 HIS L 168 HIS H 90 ASN ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 253 ASN T 39 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3298 r_free = 0.3298 target = 0.114938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.097172 restraints weight = 31378.554| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 1.17 r_work: 0.2959 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8464 moved from start: 0.0889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.398 28150 Z= 0.155 Angle : 0.813 13.480 38824 Z= 0.301 Chirality : 0.037 0.173 3780 Planarity : 0.005 0.069 4704 Dihedral : 19.232 179.476 5265 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 0.73 % Allowed : 6.47 % Favored : 92.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.93 (0.16), residues: 2698 helix: 2.30 (0.12), residues: 1495 sheet: 0.60 (1.03), residues: 26 loop : -0.01 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 15 TYR 0.023 0.002 TYR M 194 PHE 0.035 0.002 PHE L 218 TRP 0.012 0.001 TRP A 9 HIS 0.009 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00376 / 0.15 (28087) covalent geometry : angle 0.81268 / 0.30 (38824) hydrogen bonds : bond 0.04374 / 2.97 ( 1317) hydrogen bonds : angle 3.99363 / 2.93 ( 3735) Misc. bond : bond 0.13252 / 9.49 ( 63) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 290 time to evaluate : 0.948 Fit side-chains REVERT: C 214 ASP cc_start: 0.8644 (m-30) cc_final: 0.8242 (m-30) REVERT: M 80 ASP cc_start: 0.8027 (m-30) cc_final: 0.7693 (m-30) REVERT: E 1 MET cc_start: 0.7182 (ttm) cc_final: 0.6888 (mtp) REVERT: F 27 GLN cc_start: 0.8448 (mt0) cc_final: 0.8222 (mt0) REVERT: F 54 GLU cc_start: 0.7883 (OUTLIER) cc_final: 0.7501 (pp20) REVERT: U 27 GLN cc_start: 0.8203 (mt0) cc_final: 0.7900 (mt0) REVERT: f 11 MET cc_start: 0.8484 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: i 19 LYS cc_start: 0.7959 (tttt) cc_final: 0.7685 (tttm) outliers start: 16 outliers final: 4 residues processed: 298 average time/residue: 0.6569 time to fit residues: 225.7787 Evaluate side-chains 269 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 263 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 21 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 251 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 243 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 244 optimal weight: 0.6980 chunk 146 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.112598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.095445 restraints weight = 31624.597| |-----------------------------------------------------------------------------| r_work (start): 0.3047 rms_B_bonded: 1.09 r_work: 0.2925 rms_B_bonded: 1.61 restraints_weight: 0.5000 r_work: 0.2824 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.2824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.379 28150 Z= 0.185 Angle : 0.784 14.663 38824 Z= 0.304 Chirality : 0.039 0.149 3780 Planarity : 0.005 0.062 4704 Dihedral : 19.040 179.876 5265 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.46 % Allowed : 7.61 % Favored : 90.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.90 (0.15), residues: 2698 helix: 2.27 (0.12), residues: 1495 sheet: 0.52 (1.05), residues: 26 loop : -0.01 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG d 15 TYR 0.025 0.002 TYR M 194 PHE 0.028 0.002 PHE L 218 TRP 0.012 0.001 TRP f 9 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00451 / 0.18 (28087) covalent geometry : angle 0.78434 / 0.30 (38824) hydrogen bonds : bond 0.04447 / 3.01 ( 1317) hydrogen bonds : angle 3.94244 / 2.89 ( 3735) Misc. bond : bond 0.11993 / 8.68 ( 63) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 285 time to evaluate : 0.871 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8765 (OUTLIER) cc_final: 0.7454 (ptm-80) REVERT: L 79 PHE cc_start: 0.8464 (m-80) cc_final: 0.8104 (m-80) REVERT: L 226 ILE cc_start: 0.7863 (tp) cc_final: 0.7662 (tt) REVERT: M 80 ASP cc_start: 0.8113 (m-30) cc_final: 0.7800 (m-30) REVERT: H 121 LYS cc_start: 0.8541 (mmtm) cc_final: 0.8185 (mmtp) REVERT: E 1 MET cc_start: 0.7514 (ttm) cc_final: 0.7010 (mtp) REVERT: U 27 GLN cc_start: 0.8317 (mt0) cc_final: 0.8061 (mt0) REVERT: V 15 ARG cc_start: 0.8249 (OUTLIER) cc_final: 0.7207 (ttp-110) REVERT: c 15 GLU cc_start: 0.7602 (OUTLIER) cc_final: 0.6570 (tm-30) REVERT: f 11 MET cc_start: 0.8505 (OUTLIER) cc_final: 0.8074 (ttm) REVERT: i 19 LYS cc_start: 0.8142 (tttt) cc_final: 0.7888 (tttm) outliers start: 32 outliers final: 13 residues processed: 299 average time/residue: 0.7359 time to fit residues: 253.3101 Evaluate side-chains 291 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 274 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 165 optimal weight: 3.9990 chunk 247 optimal weight: 0.0570 chunk 60 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 20 optimal weight: 0.0010 chunk 114 optimal weight: 0.9990 chunk 7 optimal weight: 9.9990 chunk 62 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 215 optimal weight: 1.9990 overall best weight: 1.0110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.113458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.096024 restraints weight = 31403.118| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.17 r_work: 0.2937 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2838 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2838 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.344 28150 Z= 0.153 Angle : 0.736 11.658 38824 Z= 0.284 Chirality : 0.037 0.140 3780 Planarity : 0.005 0.058 4704 Dihedral : 18.740 179.938 5265 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 9.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.55 % Allowed : 8.93 % Favored : 89.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.08 (0.15), residues: 2698 helix: 2.42 (0.12), residues: 1495 sheet: 0.63 (1.08), residues: 26 loop : 0.07 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.023 0.002 TYR M 194 PHE 0.028 0.002 PHE L 218 TRP 0.013 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (28087) covalent geometry : angle 0.73554 / 0.28 (38824) hydrogen bonds : bond 0.04214 / 2.85 ( 1317) hydrogen bonds : angle 3.84166 / 2.81 ( 3735) Misc. bond : bond 0.11843 / 8.72 ( 63) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 285 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8766 (OUTLIER) cc_final: 0.7460 (ptm-80) REVERT: L 79 PHE cc_start: 0.8432 (m-80) cc_final: 0.8004 (m-80) REVERT: L 215 ASN cc_start: 0.8483 (m-40) cc_final: 0.8163 (m-40) REVERT: L 225 SER cc_start: 0.7703 (p) cc_final: 0.7313 (m) REVERT: M 80 ASP cc_start: 0.8172 (m-30) cc_final: 0.7872 (m-30) REVERT: H 126 ARG cc_start: 0.8033 (ptm-80) cc_final: 0.7540 (ptt180) REVERT: E 1 MET cc_start: 0.7447 (ttm) cc_final: 0.7169 (mtp) REVERT: F 27 GLN cc_start: 0.8332 (OUTLIER) cc_final: 0.8069 (mt0) REVERT: U 27 GLN cc_start: 0.8270 (mt0) cc_final: 0.8002 (mt0) REVERT: V 15 ARG cc_start: 0.8155 (OUTLIER) cc_final: 0.7093 (ttp-110) REVERT: c 15 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.6589 (tm-30) REVERT: f 11 MET cc_start: 0.8436 (OUTLIER) cc_final: 0.8067 (ttm) REVERT: i 19 LYS cc_start: 0.8133 (tttt) cc_final: 0.7887 (tttm) outliers start: 34 outliers final: 14 residues processed: 301 average time/residue: 0.6858 time to fit residues: 237.6073 Evaluate side-chains 292 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 273 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 64 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 184 optimal weight: 3.9990 chunk 65 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 48 optimal weight: 0.3980 chunk 10 optimal weight: 2.9990 chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.099089 restraints weight = 31633.822| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.00 r_work: 0.2976 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2878 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.378 28150 Z= 0.191 Angle : 0.782 13.057 38824 Z= 0.303 Chirality : 0.039 0.144 3780 Planarity : 0.005 0.058 4704 Dihedral : 18.859 179.881 5265 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 1.82 % Allowed : 9.48 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 1.98 (0.15), residues: 2698 helix: 2.30 (0.12), residues: 1495 sheet: 0.63 (1.10), residues: 26 loop : 0.08 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.026 0.002 TYR M 194 PHE 0.029 0.002 PHE L 218 TRP 0.014 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00466 / 0.19 (28087) covalent geometry : angle 0.78219 / 0.30 (38824) hydrogen bonds : bond 0.04447 / 3.01 ( 1317) hydrogen bonds : angle 3.93015 / 2.87 ( 3735) Misc. bond : bond 0.12290 / 9.00 ( 63) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 279 time to evaluate : 0.747 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8838 (OUTLIER) cc_final: 0.7554 (ptm-80) REVERT: L 79 PHE cc_start: 0.8458 (m-80) cc_final: 0.8008 (m-80) REVERT: M 80 ASP cc_start: 0.8152 (m-30) cc_final: 0.7852 (m-30) REVERT: H 126 ARG cc_start: 0.8092 (ptm-80) cc_final: 0.7575 (ptt180) REVERT: E 1 MET cc_start: 0.7582 (ttm) cc_final: 0.7149 (mtp) REVERT: K 14 THR cc_start: 0.8041 (OUTLIER) cc_final: 0.7821 (p) REVERT: P 11 MET cc_start: 0.8264 (ttm) cc_final: 0.7981 (ttm) REVERT: S 45 MET cc_start: 0.8804 (mtm) cc_final: 0.8590 (mtm) REVERT: V 15 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.7219 (ttp-110) REVERT: b 7 LYS cc_start: 0.8958 (OUTLIER) cc_final: 0.8465 (mtpm) REVERT: c 15 GLU cc_start: 0.7674 (OUTLIER) cc_final: 0.6676 (tm-30) REVERT: f 11 MET cc_start: 0.8518 (ttp) cc_final: 0.8142 (ttm) REVERT: i 19 LYS cc_start: 0.8219 (tttt) cc_final: 0.7980 (tttp) outliers start: 40 outliers final: 22 residues processed: 301 average time/residue: 0.7420 time to fit residues: 256.9877 Evaluate side-chains 302 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 275 time to evaluate : 0.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 101 optimal weight: 1.9990 chunk 179 optimal weight: 2.9990 chunk 176 optimal weight: 7.9990 chunk 142 optimal weight: 5.9990 chunk 244 skipped: trial refinement blew up (Bond distance > max_reasonable_bond_distance: 53.2217 > 50:) chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 chunk 70 optimal weight: 0.6980 chunk 197 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.116108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.099551 restraints weight = 31381.858| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.05 r_work: 0.2983 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 2.71 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8610 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.347 28150 Z= 0.158 Angle : 0.738 12.378 38824 Z= 0.286 Chirality : 0.037 0.141 3780 Planarity : 0.005 0.056 4704 Dihedral : 18.652 179.546 5265 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.91 % Allowed : 9.75 % Favored : 88.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.10 (0.15), residues: 2698 helix: 2.41 (0.12), residues: 1495 sheet: 0.69 (1.10), residues: 26 loop : 0.11 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 13 TYR 0.024 0.002 TYR M 194 PHE 0.028 0.002 PHE L 218 TRP 0.013 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00380 / 0.16 (28087) covalent geometry : angle 0.73831 / 0.29 (38824) hydrogen bonds : bond 0.04240 / 2.87 ( 1317) hydrogen bonds : angle 3.84784 / 2.81 ( 3735) Misc. bond : bond 0.11597 / 8.54 ( 63) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 277 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.7493 (ptm-80) REVERT: L 191 MET cc_start: 0.8893 (OUTLIER) cc_final: 0.8621 (mtp) REVERT: M 80 ASP cc_start: 0.8190 (m-30) cc_final: 0.7920 (m-30) REVERT: H 126 ARG cc_start: 0.8047 (ptm-80) cc_final: 0.7586 (ptt180) REVERT: H 221 PHE cc_start: 0.9036 (OUTLIER) cc_final: 0.8776 (m-80) REVERT: B 20 GLU cc_start: 0.7267 (tt0) cc_final: 0.6951 (pt0) REVERT: E 1 MET cc_start: 0.7528 (ttm) cc_final: 0.7126 (mtp) REVERT: F 27 GLN cc_start: 0.8413 (mt0) cc_final: 0.8161 (mt0) REVERT: K 14 THR cc_start: 0.8076 (OUTLIER) cc_final: 0.7851 (p) REVERT: P 1 MET cc_start: 0.7911 (ttm) cc_final: 0.7686 (mtm) REVERT: P 11 MET cc_start: 0.8259 (ttm) cc_final: 0.7985 (ttm) REVERT: V 15 ARG cc_start: 0.8267 (OUTLIER) cc_final: 0.7231 (ttp-110) REVERT: W 54 GLU cc_start: 0.8028 (pm20) cc_final: 0.7822 (pm20) REVERT: b 7 LYS cc_start: 0.8964 (OUTLIER) cc_final: 0.8485 (mtpm) REVERT: c 15 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.6620 (tm-30) REVERT: f 11 MET cc_start: 0.8510 (ttp) cc_final: 0.8122 (ttm) REVERT: i 19 LYS cc_start: 0.8247 (tttt) cc_final: 0.7996 (tttm) outliers start: 42 outliers final: 23 residues processed: 301 average time/residue: 0.7264 time to fit residues: 251.5401 Evaluate side-chains 301 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 271 time to evaluate : 0.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain L residue 191 MET Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 11 MET Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 205 optimal weight: 0.7980 chunk 161 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 139 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 145 optimal weight: 0.7980 chunk 159 optimal weight: 1.9990 chunk 247 optimal weight: 0.0670 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.0030 chunk 87 optimal weight: 0.8980 overall best weight: 0.4728 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.116053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.098862 restraints weight = 31203.377| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.15 r_work: 0.2980 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.335 28150 Z= 0.117 Angle : 0.672 11.994 38824 Z= 0.261 Chirality : 0.035 0.140 3780 Planarity : 0.004 0.055 4704 Dihedral : 18.207 179.394 5265 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 1.32 % Allowed : 10.39 % Favored : 88.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.36 (0.15), residues: 2698 helix: 2.68 (0.12), residues: 1495 sheet: 0.41 (0.98), residues: 36 loop : 0.15 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 13 TYR 0.020 0.001 TYR M 194 PHE 0.023 0.001 PHE L 218 TRP 0.012 0.001 TRP Z 9 HIS 0.004 0.001 HIS e 22 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.11 (28087) covalent geometry : angle 0.67197 / 0.26 (38824) hydrogen bonds : bond 0.03872 / 2.62 ( 1317) hydrogen bonds : angle 3.68091 / 2.69 ( 3735) Misc. bond : bond 0.10411 / 7.78 ( 63) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 284 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8737 (OUTLIER) cc_final: 0.7441 (ptm-80) REVERT: C 214 ASP cc_start: 0.8699 (m-30) cc_final: 0.8294 (m-30) REVERT: L 191 MET cc_start: 0.8869 (OUTLIER) cc_final: 0.8480 (mmm) REVERT: M 80 ASP cc_start: 0.8057 (m-30) cc_final: 0.7801 (m-30) REVERT: H 221 PHE cc_start: 0.8935 (OUTLIER) cc_final: 0.8709 (m-80) REVERT: E 1 MET cc_start: 0.7200 (ttm) cc_final: 0.6961 (mtp) REVERT: F 27 GLN cc_start: 0.8343 (OUTLIER) cc_final: 0.8072 (mt0) REVERT: K 14 THR cc_start: 0.7907 (OUTLIER) cc_final: 0.7669 (p) REVERT: V 15 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7123 (ttp-110) REVERT: i 19 LYS cc_start: 0.8057 (tttt) cc_final: 0.7795 (tttm) outliers start: 29 outliers final: 12 residues processed: 297 average time/residue: 0.7192 time to fit residues: 246.0307 Evaluate side-chains 289 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 271 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 168 HIS Chi-restraints excluded: chain L residue 191 MET Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 16 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 236 optimal weight: 0.9980 chunk 87 optimal weight: 2.9990 chunk 178 optimal weight: 3.9990 chunk 119 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 3.9990 chunk 169 optimal weight: 0.9990 chunk 123 optimal weight: 0.7980 chunk 200 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS H 90 ASN W 27 GLN i 27 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.113208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.095659 restraints weight = 31458.036| |-----------------------------------------------------------------------------| r_work (start): 0.3059 rms_B_bonded: 1.16 r_work: 0.2936 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.339 28150 Z= 0.166 Angle : 0.739 13.008 38824 Z= 0.288 Chirality : 0.037 0.140 3780 Planarity : 0.005 0.054 4704 Dihedral : 18.415 179.803 5265 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 1.41 % Allowed : 10.80 % Favored : 87.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.18 (0.15), residues: 2698 helix: 2.50 (0.12), residues: 1496 sheet: 0.39 (0.98), residues: 36 loop : 0.11 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 13 TYR 0.024 0.002 TYR M 194 PHE 0.027 0.002 PHE L 218 TRP 0.013 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00404 / 0.16 (28087) covalent geometry : angle 0.73901 / 0.29 (38824) hydrogen bonds : bond 0.04217 / 2.85 ( 1317) hydrogen bonds : angle 3.81237 / 2.79 ( 3735) Misc. bond : bond 0.10953 / 8.13 ( 63) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 275 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8746 (OUTLIER) cc_final: 0.7460 (ptm-80) REVERT: C 326 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7954 (mm-30) REVERT: M 80 ASP cc_start: 0.8097 (m-30) cc_final: 0.7844 (m-30) REVERT: H 126 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7617 (ptt180) REVERT: H 221 PHE cc_start: 0.8873 (OUTLIER) cc_final: 0.8609 (m-80) REVERT: B 20 GLU cc_start: 0.7229 (tt0) cc_final: 0.6850 (pt0) REVERT: E 1 MET cc_start: 0.7279 (ttm) cc_final: 0.6882 (mtp) REVERT: F 27 GLN cc_start: 0.8311 (mt0) cc_final: 0.8040 (mt0) REVERT: K 14 THR cc_start: 0.7901 (OUTLIER) cc_final: 0.7666 (p) REVERT: V 15 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7023 (ttp-110) REVERT: f 11 MET cc_start: 0.8154 (ttm) cc_final: 0.7928 (ttm) REVERT: i 19 LYS cc_start: 0.8041 (tttt) cc_final: 0.7799 (tttp) outliers start: 31 outliers final: 18 residues processed: 294 average time/residue: 0.6811 time to fit residues: 230.4005 Evaluate side-chains 294 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 271 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 70 LEU Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 191 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 73 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 229 optimal weight: 3.9990 chunk 187 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 162 optimal weight: 20.0000 chunk 87 optimal weight: 3.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.096295 restraints weight = 31410.333| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.16 r_work: 0.2944 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.343 28150 Z= 0.147 Angle : 0.717 12.506 38824 Z= 0.279 Chirality : 0.036 0.137 3780 Planarity : 0.005 0.054 4704 Dihedral : 18.289 179.668 5265 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.32 % Allowed : 11.26 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.24 (0.15), residues: 2698 helix: 2.54 (0.12), residues: 1495 sheet: 0.61 (1.10), residues: 26 loop : 0.15 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 13 TYR 0.023 0.001 TYR M 194 PHE 0.028 0.002 PHE L 218 TRP 0.012 0.001 TRP L 265 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00354 / 0.15 (28087) covalent geometry : angle 0.71658 / 0.28 (38824) hydrogen bonds : bond 0.04121 / 2.79 ( 1317) hydrogen bonds : angle 3.77945 / 2.76 ( 3735) Misc. bond : bond 0.10750 / 7.96 ( 63) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 275 time to evaluate : 0.872 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8781 (OUTLIER) cc_final: 0.7548 (ptm-80) REVERT: C 326 GLU cc_start: 0.8599 (OUTLIER) cc_final: 0.7958 (mm-30) REVERT: M 80 ASP cc_start: 0.8082 (m-30) cc_final: 0.7827 (m-30) REVERT: M 139 LYS cc_start: 0.8631 (mmmt) cc_final: 0.8284 (mmpt) REVERT: H 126 ARG cc_start: 0.8002 (ptm-80) cc_final: 0.7711 (ptt180) REVERT: H 221 PHE cc_start: 0.8902 (OUTLIER) cc_final: 0.8640 (m-80) REVERT: H 231 GLU cc_start: 0.8012 (OUTLIER) cc_final: 0.7031 (pp20) REVERT: B 20 GLU cc_start: 0.7260 (tt0) cc_final: 0.6897 (pt0) REVERT: E 1 MET cc_start: 0.7302 (ttm) cc_final: 0.6930 (mtp) REVERT: F 27 GLN cc_start: 0.8353 (mt0) cc_final: 0.8083 (mt0) REVERT: K 14 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7699 (p) REVERT: V 15 ARG cc_start: 0.8137 (OUTLIER) cc_final: 0.7073 (ttp-110) REVERT: f 11 MET cc_start: 0.8192 (ttm) cc_final: 0.7969 (ttm) REVERT: i 19 LYS cc_start: 0.8089 (tttt) cc_final: 0.7842 (tttm) outliers start: 29 outliers final: 20 residues processed: 289 average time/residue: 0.6649 time to fit residues: 221.2624 Evaluate side-chains 298 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 272 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 137 ASP Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 226 optimal weight: 4.9990 chunk 42 optimal weight: 0.0970 chunk 253 optimal weight: 5.9990 chunk 190 optimal weight: 0.8980 chunk 137 optimal weight: 0.9980 chunk 16 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 0.9980 chunk 204 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 overall best weight: 0.7978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.114237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.096818 restraints weight = 31475.305| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.17 r_work: 0.2950 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2849 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8508 moved from start: 0.1670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.340 28150 Z= 0.138 Angle : 0.707 12.341 38824 Z= 0.277 Chirality : 0.036 0.151 3780 Planarity : 0.004 0.054 4704 Dihedral : 18.150 179.479 5265 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.37 % Allowed : 11.26 % Favored : 87.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.30 (0.15), residues: 2698 helix: 2.58 (0.12), residues: 1495 sheet: 0.63 (1.11), residues: 26 loop : 0.18 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 13 TYR 0.022 0.001 TYR M 194 PHE 0.032 0.002 PHE L 218 TRP 0.013 0.001 TRP M 253 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.14 (28087) covalent geometry : angle 0.70718 / 0.28 (38824) hydrogen bonds : bond 0.04061 / 2.75 ( 1317) hydrogen bonds : angle 3.75064 / 2.74 ( 3735) Misc. bond : bond 0.10667 / 7.86 ( 63) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5396 Ramachandran restraints generated. 2698 Oldfield, 0 Emsley, 2698 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 303 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 273 time to evaluate : 0.927 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8762 (OUTLIER) cc_final: 0.7458 (ptm-80) REVERT: C 214 ASP cc_start: 0.8726 (m-30) cc_final: 0.8344 (m-30) REVERT: C 232 ASP cc_start: 0.7290 (p0) cc_final: 0.7041 (t0) REVERT: M 80 ASP cc_start: 0.8089 (m-30) cc_final: 0.7834 (m-30) REVERT: M 139 LYS cc_start: 0.8512 (mmmt) cc_final: 0.8154 (mmpt) REVERT: H 126 ARG cc_start: 0.7911 (OUTLIER) cc_final: 0.7594 (ptt180) REVERT: H 221 PHE cc_start: 0.8893 (OUTLIER) cc_final: 0.8632 (m-80) REVERT: H 231 GLU cc_start: 0.8023 (OUTLIER) cc_final: 0.7044 (pp20) REVERT: B 20 GLU cc_start: 0.7262 (tt0) cc_final: 0.6900 (pt0) REVERT: E 1 MET cc_start: 0.7263 (ttm) cc_final: 0.6899 (mtp) REVERT: F 27 GLN cc_start: 0.8351 (mt0) cc_final: 0.8081 (mt0) REVERT: K 14 THR cc_start: 0.7927 (OUTLIER) cc_final: 0.7700 (p) REVERT: V 15 ARG cc_start: 0.8115 (OUTLIER) cc_final: 0.7073 (ttp-110) REVERT: c 15 GLU cc_start: 0.7369 (OUTLIER) cc_final: 0.6491 (tm-30) REVERT: d 7 LYS cc_start: 0.8153 (mtmm) cc_final: 0.7947 (mmmm) REVERT: f 11 MET cc_start: 0.8191 (ttm) cc_final: 0.7965 (ttm) REVERT: i 19 LYS cc_start: 0.8087 (tttt) cc_final: 0.7842 (tttm) outliers start: 30 outliers final: 18 residues processed: 288 average time/residue: 0.7443 time to fit residues: 246.1109 Evaluate side-chains 295 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 270 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 214 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 138 optimal weight: 0.8980 chunk 227 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 139 optimal weight: 0.7980 chunk 141 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 1.9990 chunk 166 optimal weight: 0.4980 chunk 196 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... L 168 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.114807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097520 restraints weight = 31176.482| |-----------------------------------------------------------------------------| r_work (start): 0.3082 rms_B_bonded: 1.15 r_work: 0.2961 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8503 moved from start: 0.1715 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.336 28150 Z= 0.131 Angle : 0.693 12.075 38824 Z= 0.271 Chirality : 0.036 0.153 3780 Planarity : 0.004 0.054 4704 Dihedral : 18.001 179.375 5265 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.28 % Allowed : 11.39 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % 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: 2.35 (0.15), residues: 2698 helix: 2.63 (0.12), residues: 1495 sheet: 0.63 (1.11), residues: 26 loop : 0.20 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 13 TYR 0.022 0.001 TYR M 194 PHE 0.030 0.001 PHE L 218 TRP 0.014 0.001 TRP M 253 HIS 0.007 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (28087) covalent geometry : angle 0.69286 / 0.27 (38824) hydrogen bonds : bond 0.03991 / 2.70 ( 1317) hydrogen bonds : angle 3.71662 / 2.72 ( 3735) Misc. bond : bond 0.10505 / 7.76 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8250.67 seconds wall clock time: 141 minutes 35.77 seconds (8495.77 seconds total)