Starting phenix.real_space_refine on Sun Jul 5 20:47:29 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zk2_60165/07_2026/8zk2_60165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zk2_60165/07_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_60165/07_2026/8zk2_60165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zk2_60165/07_2026/8zk2_60165.map" model { file = "/net/cci-nas-00/data/ceres_data/8zk2_60165/07_2026/8zk2_60165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zk2_60165/07_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-dev-6108/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, 400 Ad-hoc single atom residues: {' FE': 1} Unusual residues: {'8K6': 1, 'BCL': 2, 'BPH': 1, 'CRT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain breaks: 1 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: 5.04, per 1000 atoms: 0.19 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: 2.13 Conformation dependent library (CDL) restraints added in 798.5 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: 0.51 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: 2.84 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 3.080 nonbonded pdb=" NE2 HIS M 220 " pdb="FE FE M 401 " model vdw 2.147 3.080 ... (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: 3.590 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: 0.380 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 21.450 Find NCS groups from input model: 0.590 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.450 ------------------------------------------------------------------------------- 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 : 0.896 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: 0.6944 time to fit residues: 247.8352 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 : 0.890 ------------------------------------------------------------------------------- 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 ** L 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 90 ASN ** H 232 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 39 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.115264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.097394 restraints weight = 31341.652| |-----------------------------------------------------------------------------| r_work (start): 0.3084 rms_B_bonded: 1.19 r_work: 0.2962 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2861 rms_B_bonded: 2.92 restraints_weight: 0.2500 r_work (final): 0.2861 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.383 28150 Z= 0.152 Angle : 0.824 13.550 38824 Z= 0.301 Chirality : 0.037 0.167 3780 Planarity : 0.005 0.067 4704 Dihedral : 19.248 179.511 5265 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 10.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.68 % Allowed : 6.70 % Favored : 92.62 % 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: 2.29 (0.12), residues: 1495 sheet: 0.61 (1.03), residues: 26 loop : -0.00 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG j 15 TYR 0.024 0.002 TYR M 194 PHE 0.030 0.002 PHE L 218 TRP 0.013 0.001 TRP M 172 HIS 0.014 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.15 (28087) covalent geometry : angle 0.82423 / 0.30 (38824) hydrogen bonds : bond 0.04300 / 2.92 ( 1317) hydrogen bonds : angle 3.98567 / 2.92 ( 3735) Misc. bond : bond 0.13138 / 9.40 ( 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 308 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 293 time to evaluate : 0.729 Fit side-chains REVERT: C 214 ASP cc_start: 0.8589 (m-30) cc_final: 0.8183 (m-30) REVERT: E 1 MET cc_start: 0.7243 (ttm) cc_final: 0.6979 (mtp) REVERT: F 27 GLN cc_start: 0.8495 (mt0) cc_final: 0.8269 (mt0) REVERT: F 54 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7546 (pp20) REVERT: U 27 GLN cc_start: 0.8231 (mt0) cc_final: 0.7933 (mt0) REVERT: f 11 MET cc_start: 0.8480 (OUTLIER) cc_final: 0.8183 (ttm) REVERT: i 19 LYS cc_start: 0.7995 (tttt) cc_final: 0.7721 (tttm) outliers start: 15 outliers final: 3 residues processed: 300 average time/residue: 0.6639 time to fit residues: 229.8251 Evaluate side-chains 267 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 262 time to evaluate : 0.812 ------------------------------------------------------------------------------- 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 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: 0.9990 chunk 124 optimal weight: 0.9990 chunk 251 optimal weight: 0.0040 chunk 52 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 243 optimal weight: 0.5980 chunk 4 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 244 optimal weight: 1.9990 chunk 146 optimal weight: 1.9990 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 90 ASN H 232 GLN 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 = 0.3314 r_free = 0.3314 target = 0.116139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.098271 restraints weight = 31458.968| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.19 r_work: 0.2973 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 2.90 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.301 28150 Z= 0.130 Angle : 0.707 14.610 38824 Z= 0.273 Chirality : 0.036 0.139 3780 Planarity : 0.005 0.061 4704 Dihedral : 18.499 178.830 5265 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.19 % Allowed : 8.20 % Favored : 90.61 % 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: 2.20 (0.15), residues: 2698 helix: 2.55 (0.12), residues: 1495 sheet: 0.59 (1.06), residues: 26 loop : 0.07 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG M 248 TYR 0.021 0.001 TYR M 194 PHE 0.019 0.002 PHE L 218 TRP 0.011 0.001 TRP M 253 HIS 0.010 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.13 (28087) covalent geometry : angle 0.70731 / 0.27 (38824) hydrogen bonds : bond 0.04037 / 2.73 ( 1317) hydrogen bonds : angle 3.77486 / 2.76 ( 3735) Misc. bond : bond 0.10990 / 8.06 ( 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 315 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 289 time to evaluate : 0.923 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8772 (OUTLIER) cc_final: 0.7418 (ptm-80) REVERT: C 214 ASP cc_start: 0.8631 (m-30) cc_final: 0.8231 (m-30) REVERT: L 225 SER cc_start: 0.7524 (p) cc_final: 0.7150 (m) REVERT: M 80 ASP cc_start: 0.8139 (m-30) cc_final: 0.7820 (m-30) REVERT: M 137 ARG cc_start: 0.8091 (mmm160) cc_final: 0.7837 (mmp-170) REVERT: E 1 MET cc_start: 0.7382 (ttm) cc_final: 0.7174 (mtp) REVERT: F 27 GLN cc_start: 0.8471 (mt0) cc_final: 0.8232 (mt0) REVERT: U 27 GLN cc_start: 0.8240 (mt0) cc_final: 0.7956 (mt0) REVERT: c 15 GLU cc_start: 0.7431 (OUTLIER) cc_final: 0.6375 (tm-30) REVERT: f 11 MET cc_start: 0.8477 (OUTLIER) cc_final: 0.8106 (ttm) REVERT: i 19 LYS cc_start: 0.8043 (tttt) cc_final: 0.7772 (tttp) outliers start: 26 outliers final: 9 residues processed: 301 average time/residue: 0.6666 time to fit residues: 230.7804 Evaluate side-chains 283 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 271 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain L residue 168 HIS 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 J residue 52 THR Chi-restraints excluded: chain P residue 35 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: 3.9990 chunk 60 optimal weight: 0.5980 chunk 116 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 20 optimal weight: 0.8980 chunk 114 optimal weight: 1.9990 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: 1.8986 ------------------------------------------------------------------------------- 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 = 0.3299 r_free = 0.3299 target = 0.114589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098355 restraints weight = 31586.681| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 1.00 r_work: 0.2961 rms_B_bonded: 1.57 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.65 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.1392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.411 28150 Z= 0.235 Angle : 0.846 12.631 38824 Z= 0.327 Chirality : 0.041 0.150 3780 Planarity : 0.005 0.060 4704 Dihedral : 19.119 179.909 5265 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.60 % Allowed : 8.80 % Favored : 89.61 % 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: 1.82 (0.15), residues: 2698 helix: 2.17 (0.12), residues: 1495 sheet: 0.58 (1.09), residues: 26 loop : 0.00 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.028 0.002 TYR M 194 PHE 0.023 0.002 PHE H 19 TRP 0.016 0.002 TRP L 265 HIS 0.010 0.002 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00582 / 0.23 (28087) covalent geometry : angle 0.84646 / 0.33 (38824) hydrogen bonds : bond 0.04731 / 3.21 ( 1317) hydrogen bonds : angle 4.03554 / 2.95 ( 3735) Misc. bond : bond 0.12930 / 9.43 ( 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: 35 poor density : 284 time to evaluate : 1.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8849 (OUTLIER) cc_final: 0.7532 (ptm-80) REVERT: L 79 PHE cc_start: 0.8481 (m-80) cc_final: 0.8104 (m-80) REVERT: M 139 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8571 (mmtt) REVERT: B 14 THR cc_start: 0.8197 (OUTLIER) cc_final: 0.7986 (p) REVERT: D 19 LYS cc_start: 0.8268 (ttmt) cc_final: 0.8011 (tttt) REVERT: E 1 MET cc_start: 0.7654 (ttm) cc_final: 0.7195 (mtp) REVERT: V 15 ARG cc_start: 0.8353 (OUTLIER) cc_final: 0.7267 (ttp-110) REVERT: Z 11 MET cc_start: 0.7734 (ttm) cc_final: 0.7511 (ttp) REVERT: b 7 LYS cc_start: 0.8978 (OUTLIER) cc_final: 0.8470 (mtpm) REVERT: c 15 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.6687 (tm-30) REVERT: f 11 MET cc_start: 0.8528 (OUTLIER) cc_final: 0.8105 (ttm) REVERT: i 19 LYS cc_start: 0.8252 (tttt) cc_final: 0.8006 (tttp) outliers start: 35 outliers final: 15 residues processed: 301 average time/residue: 0.6901 time to fit residues: 240.0591 Evaluate side-chains 298 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.899 ------------------------------------------------------------------------------- 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 139 LYS 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 B residue 14 THR 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 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 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 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: 3.9990 chunk 80 optimal weight: 1.9990 chunk 184 optimal weight: 2.9990 chunk 65 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 0.0670 chunk 10 optimal weight: 0.0010 chunk 136 optimal weight: 3.9990 chunk 49 optimal weight: 1.9990 chunk 22 optimal weight: 6.9990 chunk 212 optimal weight: 0.9990 overall best weight: 0.7528 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 27 GLN i 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.117500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.101309 restraints weight = 31245.485| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 1.04 r_work: 0.3006 rms_B_bonded: 1.60 restraints_weight: 0.5000 r_work: 0.2907 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1474 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= 0.134 Angle : 0.713 12.224 38824 Z= 0.276 Chirality : 0.036 0.136 3780 Planarity : 0.005 0.057 4704 Dihedral : 18.597 179.920 5265 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.55 % Allowed : 9.75 % 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: 2.15 (0.15), residues: 2698 helix: 2.47 (0.12), residues: 1495 sheet: 0.70 (1.11), residues: 26 loop : 0.11 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.022 0.001 TYR M 194 PHE 0.021 0.002 PHE L 41 TRP 0.013 0.001 TRP A 9 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (28087) covalent geometry : angle 0.71257 / 0.28 (38824) hydrogen bonds : bond 0.04118 / 2.79 ( 1317) hydrogen bonds : angle 3.79868 / 2.78 ( 3735) Misc. bond : bond 0.11590 / 8.64 ( 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 315 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 281 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.7524 (ptm-80) REVERT: L 79 PHE cc_start: 0.8423 (m-80) cc_final: 0.8009 (m-80) REVERT: M 80 ASP cc_start: 0.8163 (m-30) cc_final: 0.7879 (m-30) REVERT: H 126 ARG cc_start: 0.8089 (ptm-80) cc_final: 0.7719 (ptt180) REVERT: A 7 LYS cc_start: 0.8374 (mtmt) cc_final: 0.8153 (mtmm) REVERT: E 1 MET cc_start: 0.7526 (ttm) cc_final: 0.7236 (mtp) REVERT: F 27 GLN cc_start: 0.8374 (OUTLIER) cc_final: 0.8166 (mt0) REVERT: P 1 MET cc_start: 0.7790 (ttm) cc_final: 0.7579 (mtm) REVERT: U 14 THR cc_start: 0.8183 (OUTLIER) cc_final: 0.7980 (m) REVERT: V 15 ARG cc_start: 0.8290 (OUTLIER) cc_final: 0.7294 (ttp-110) REVERT: c 15 GLU cc_start: 0.7622 (OUTLIER) cc_final: 0.6634 (tm-30) REVERT: f 11 MET cc_start: 0.8486 (OUTLIER) cc_final: 0.8133 (ttm) REVERT: i 19 LYS cc_start: 0.8218 (tttt) cc_final: 0.7973 (tttm) outliers start: 34 outliers final: 14 residues processed: 298 average time/residue: 0.6865 time to fit residues: 235.7896 Evaluate side-chains 292 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 M residue 51 ILE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain U residue 14 THR 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 d residue 4 SER Chi-restraints excluded: chain f residue 11 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 101 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 176 optimal weight: 7.9990 chunk 142 optimal weight: 6.9990 chunk 244 optimal weight: 2.9990 chunk 186 optimal weight: 0.9990 chunk 72 optimal weight: 0.0770 chunk 135 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 197 optimal weight: 4.9990 chunk 88 optimal weight: 0.0570 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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 = 0.3300 r_free = 0.3300 target = 0.115201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.097975 restraints weight = 31379.053| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.13 r_work: 0.2968 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.331 28150 Z= 0.128 Angle : 0.690 11.967 38824 Z= 0.268 Chirality : 0.036 0.136 3780 Planarity : 0.004 0.056 4704 Dihedral : 18.246 179.799 5265 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 1.37 % Allowed : 10.30 % 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: 2.31 (0.15), residues: 2698 helix: 2.61 (0.12), residues: 1495 sheet: 0.59 (1.09), residues: 26 loop : 0.17 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.021 0.001 TYR M 194 PHE 0.017 0.001 PHE L 218 TRP 0.012 0.001 TRP B 56 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.13 (28087) covalent geometry : angle 0.69020 / 0.27 (38824) hydrogen bonds : bond 0.03973 / 2.69 ( 1317) hydrogen bonds : angle 3.71870 / 2.72 ( 3735) Misc. bond : bond 0.10991 / 8.20 ( 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 306 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 276 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8758 (OUTLIER) cc_final: 0.7442 (ptm-80) REVERT: C 214 ASP cc_start: 0.8639 (m-30) cc_final: 0.8248 (m-30) REVERT: L 79 PHE cc_start: 0.8317 (m-80) cc_final: 0.7906 (m-80) REVERT: M 80 ASP cc_start: 0.8077 (m-30) cc_final: 0.7816 (m-30) REVERT: M 139 LYS cc_start: 0.8624 (OUTLIER) cc_final: 0.8265 (mmpt) REVERT: H 1 MET cc_start: 0.7511 (mpt) cc_final: 0.7130 (mpt) REVERT: A 7 LYS cc_start: 0.8297 (mtmt) cc_final: 0.8068 (mtmm) REVERT: E 1 MET cc_start: 0.7326 (ttm) cc_final: 0.7086 (mtp) REVERT: U 14 THR cc_start: 0.8029 (OUTLIER) cc_final: 0.7828 (m) REVERT: V 15 ARG cc_start: 0.8111 (OUTLIER) cc_final: 0.7091 (ttp-110) REVERT: c 15 GLU cc_start: 0.7379 (OUTLIER) cc_final: 0.6342 (tm-30) REVERT: f 11 MET cc_start: 0.8353 (OUTLIER) cc_final: 0.8012 (ttm) REVERT: i 19 LYS cc_start: 0.8084 (tttt) cc_final: 0.7818 (tttm) outliers start: 30 outliers final: 15 residues processed: 290 average time/residue: 0.7153 time to fit residues: 238.2425 Evaluate side-chains 290 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 269 time to evaluate : 0.879 ------------------------------------------------------------------------------- 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 104 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 168 HIS Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 139 LYS Chi-restraints excluded: chain H residue 7 SER 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 Q residue 57 VAL Chi-restraints excluded: chain U residue 14 THR 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 d residue 4 SER Chi-restraints excluded: chain f residue 11 MET 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: 3.9990 chunk 139 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 145 optimal weight: 0.8980 chunk 159 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- 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 = 0.3277 r_free = 0.3277 target = 0.113284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.096239 restraints weight = 31162.756| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.09 r_work: 0.2938 rms_B_bonded: 1.62 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 2.75 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.348 28150 Z= 0.165 Angle : 0.738 12.752 38824 Z= 0.287 Chirality : 0.037 0.141 3780 Planarity : 0.005 0.055 4704 Dihedral : 18.436 179.950 5265 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.46 % Allowed : 10.57 % Favored : 87.97 % 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: 2.17 (0.15), residues: 2698 helix: 2.48 (0.12), residues: 1495 sheet: 0.53 (1.08), residues: 26 loop : 0.13 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 13 TYR 0.025 0.002 TYR M 194 PHE 0.020 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 0.00400 / 0.16 (28087) covalent geometry : angle 0.73778 / 0.29 (38824) hydrogen bonds : bond 0.04227 / 2.86 ( 1317) hydrogen bonds : angle 3.81753 / 2.79 ( 3735) Misc. bond : bond 0.11265 / 8.40 ( 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 304 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 272 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.7526 (ptm-80) REVERT: M 80 ASP cc_start: 0.8111 (m-30) cc_final: 0.7859 (m-30) REVERT: M 139 LYS cc_start: 0.8644 (OUTLIER) cc_final: 0.8285 (mmpt) REVERT: H 221 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8678 (m-80) REVERT: E 1 MET cc_start: 0.7383 (ttm) cc_final: 0.7115 (mtp) REVERT: V 15 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7097 (ttp-110) REVERT: c 15 GLU cc_start: 0.7450 (OUTLIER) cc_final: 0.6391 (tm-30) REVERT: i 19 LYS cc_start: 0.8136 (tttt) cc_final: 0.7888 (tttm) outliers start: 32 outliers final: 21 residues processed: 290 average time/residue: 0.6838 time to fit residues: 228.8052 Evaluate side-chains 295 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 269 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain M residue 139 LYS 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 221 PHE 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 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 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 d residue 4 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 236 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 119 optimal weight: 4.9990 chunk 9 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 106 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 123 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 212 optimal weight: 0.9980 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.113868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.096576 restraints weight = 31335.822| |-----------------------------------------------------------------------------| r_work (start): 0.3070 rms_B_bonded: 1.13 r_work: 0.2949 rms_B_bonded: 1.65 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 2.79 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.348 28150 Z= 0.148 Angle : 0.718 12.497 38824 Z= 0.280 Chirality : 0.036 0.137 3780 Planarity : 0.005 0.054 4704 Dihedral : 18.357 179.800 5265 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.55 % Allowed : 10.76 % Favored : 87.69 % 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: 2.22 (0.15), residues: 2698 helix: 2.52 (0.12), residues: 1495 sheet: 0.55 (1.09), residues: 26 loop : 0.15 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 13 TYR 0.023 0.001 TYR M 194 PHE 0.020 0.002 PHE L 218 TRP 0.012 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (28087) covalent geometry : angle 0.71791 / 0.28 (38824) hydrogen bonds : bond 0.04132 / 2.80 ( 1317) hydrogen bonds : angle 3.78051 / 2.77 ( 3735) Misc. bond : bond 0.11168 / 8.30 ( 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 308 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 274 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8724 (OUTLIER) cc_final: 0.7480 (ptm-80) REVERT: M 80 ASP cc_start: 0.8086 (m-30) cc_final: 0.7831 (m-30) REVERT: H 1 MET cc_start: 0.7510 (mpt) cc_final: 0.7128 (mpt) REVERT: H 126 ARG cc_start: 0.7946 (OUTLIER) cc_final: 0.7668 (ptt180) REVERT: H 221 PHE cc_start: 0.8903 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: B 20 GLU cc_start: 0.7173 (tt0) cc_final: 0.6852 (pt0) REVERT: E 1 MET cc_start: 0.7289 (ttm) cc_final: 0.6944 (mtp) REVERT: F 27 GLN cc_start: 0.8285 (OUTLIER) cc_final: 0.8080 (mt0) REVERT: V 15 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7062 (ttp-110) REVERT: c 15 GLU cc_start: 0.7403 (OUTLIER) cc_final: 0.6332 (tm-30) REVERT: f 11 MET cc_start: 0.8181 (ttm) cc_final: 0.7954 (ttm) REVERT: i 19 LYS cc_start: 0.8040 (tttt) cc_final: 0.7799 (tttp) outliers start: 34 outliers final: 19 residues processed: 293 average time/residue: 0.7279 time to fit residues: 244.7971 Evaluate side-chains 294 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 269 time to evaluate : 0.919 ------------------------------------------------------------------------------- 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 70 LEU 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 51 ILE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 219 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 J residue 52 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 191 optimal weight: 0.7980 chunk 254 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 73 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 229 optimal weight: 0.1980 chunk 187 optimal weight: 0.5980 chunk 94 optimal weight: 0.7980 chunk 162 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 43 optimal weight: 6.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... W 27 GLN i 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.115589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.098295 restraints weight = 31302.322| |-----------------------------------------------------------------------------| r_work (start): 0.3093 rms_B_bonded: 1.16 r_work: 0.2972 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.339 28150 Z= 0.124 Angle : 0.680 12.180 38824 Z= 0.266 Chirality : 0.035 0.136 3780 Planarity : 0.004 0.054 4704 Dihedral : 18.027 179.350 5265 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.05 % Allowed : 11.67 % Favored : 87.28 % 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: 2.37 (0.15), residues: 2698 helix: 2.65 (0.12), residues: 1495 sheet: 0.54 (1.09), residues: 26 loop : 0.21 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 13 TYR 0.021 0.001 TYR M 194 PHE 0.019 0.001 PHE L 41 TRP 0.014 0.001 TRP A 9 HIS 0.007 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.12 (28087) covalent geometry : angle 0.68016 / 0.27 (38824) hydrogen bonds : bond 0.03933 / 2.66 ( 1317) hydrogen bonds : angle 3.69400 / 2.70 ( 3735) Misc. bond : bond 0.10380 / 7.78 ( 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 295 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 272 time to evaluate : 0.933 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7443 (ptm-80) REVERT: C 214 ASP cc_start: 0.8681 (m-30) cc_final: 0.8294 (m-30) REVERT: L 191 MET cc_start: 0.8771 (mtm) cc_final: 0.8491 (mtp) REVERT: M 80 ASP cc_start: 0.8075 (m-30) cc_final: 0.7830 (m-30) REVERT: H 24 PHE cc_start: 0.7914 (m-10) cc_final: 0.7645 (m-80) REVERT: H 126 ARG cc_start: 0.7890 (OUTLIER) cc_final: 0.7631 (ptt180) REVERT: H 221 PHE cc_start: 0.8932 (OUTLIER) cc_final: 0.8692 (m-80) REVERT: B 20 GLU cc_start: 0.7260 (tt0) cc_final: 0.6897 (pt0) REVERT: E 1 MET cc_start: 0.7222 (ttm) cc_final: 0.7008 (mtp) REVERT: F 27 GLN cc_start: 0.8339 (OUTLIER) cc_final: 0.8134 (mt0) REVERT: V 15 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7107 (ttp-110) REVERT: c 15 GLU cc_start: 0.7315 (OUTLIER) cc_final: 0.6234 (tm-30) REVERT: i 19 LYS cc_start: 0.8080 (tttt) cc_final: 0.7818 (tttm) outliers start: 23 outliers final: 17 residues processed: 282 average time/residue: 0.7206 time to fit residues: 233.2863 Evaluate side-chains 291 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 268 time to evaluate : 0.575 ------------------------------------------------------------------------------- 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 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 126 ARG Chi-restraints excluded: chain H residue 219 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 J residue 52 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 c residue 15 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 226 optimal weight: 5.9990 chunk 42 optimal weight: 0.0970 chunk 253 optimal weight: 0.8980 chunk 190 optimal weight: 0.6980 chunk 137 optimal weight: 5.9990 chunk 16 optimal weight: 0.1980 chunk 183 optimal weight: 2.9990 chunk 198 optimal weight: 0.0970 chunk 204 optimal weight: 5.9990 chunk 152 optimal weight: 2.9990 chunk 248 optimal weight: 4.9990 overall best weight: 0.3976 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 6 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 = 0.3328 r_free = 0.3328 target = 0.117397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.100089 restraints weight = 31418.476| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 1.18 r_work: 0.2996 rms_B_bonded: 1.72 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 2.93 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.329 28150 Z= 0.112 Angle : 0.657 11.787 38824 Z= 0.258 Chirality : 0.035 0.133 3780 Planarity : 0.004 0.054 4704 Dihedral : 17.742 179.165 5265 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.05 % Allowed : 11.76 % Favored : 87.19 % 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: 2.52 (0.15), residues: 2698 helix: 2.78 (0.12), residues: 1495 sheet: -0.18 (1.50), residues: 15 loop : 0.28 (0.18), residues: 1188 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 13 TYR 0.019 0.001 TYR M 194 PHE 0.018 0.001 PHE L 41 TRP 0.012 0.001 TRP Z 9 HIS 0.008 0.001 HIS L 192 Details of bonding type rmsd/Z covalent geometry : bond 0.00260 / 0.11 (28087) covalent geometry : angle 0.65742 / 0.26 (38824) hydrogen bonds : bond 0.03780 / 2.56 ( 1317) hydrogen bonds : angle 3.62245 / 2.65 ( 3735) Misc. bond : bond 0.09738 / 7.33 ( 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 293 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 270 time to evaluate : 0.754 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7457 (ptm-80) REVERT: C 214 ASP cc_start: 0.8690 (m-30) cc_final: 0.8282 (m-30) REVERT: L 191 MET cc_start: 0.8772 (mtm) cc_final: 0.8488 (mtp) REVERT: M 80 ASP cc_start: 0.7986 (m-30) cc_final: 0.7764 (m-30) REVERT: H 121 LYS cc_start: 0.8463 (mmtm) cc_final: 0.8234 (mmtm) REVERT: H 126 ARG cc_start: 0.7855 (OUTLIER) cc_final: 0.7627 (ptt180) REVERT: H 221 PHE cc_start: 0.8909 (OUTLIER) cc_final: 0.8672 (m-80) REVERT: E 1 MET cc_start: 0.7123 (ttm) cc_final: 0.6903 (mtp) REVERT: F 27 GLN cc_start: 0.8347 (OUTLIER) cc_final: 0.8078 (mt0) REVERT: S 54 GLU cc_start: 0.8016 (pm20) cc_final: 0.7652 (mp0) REVERT: V 15 ARG cc_start: 0.8062 (OUTLIER) cc_final: 0.7038 (ttp-110) REVERT: c 15 GLU cc_start: 0.7128 (OUTLIER) cc_final: 0.6029 (tm-30) REVERT: f 11 MET cc_start: 0.8140 (ttm) cc_final: 0.7935 (ttm) REVERT: i 19 LYS cc_start: 0.8053 (tttt) cc_final: 0.7791 (tttm) outliers start: 23 outliers final: 14 residues processed: 283 average time/residue: 0.6926 time to fit residues: 225.9105 Evaluate side-chains 279 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 259 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 51 ILE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 126 ARG Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain J residue 52 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 c residue 15 GLU 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: 1.9990 chunk 154 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 139 optimal weight: 0.9990 chunk 141 optimal weight: 0.6980 chunk 82 optimal weight: 0.6980 chunk 125 optimal weight: 4.9990 chunk 228 optimal weight: 0.8980 chunk 166 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3301 r_free = 0.3301 target = 0.115149 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.097878 restraints weight = 31130.141| |-----------------------------------------------------------------------------| r_work (start): 0.3088 rms_B_bonded: 1.15 r_work: 0.2967 rms_B_bonded: 1.67 restraints_weight: 0.5000 r_work: 0.2866 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.2866 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.1743 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= 0.139 Angle : 0.693 12.261 38824 Z= 0.273 Chirality : 0.036 0.147 3780 Planarity : 0.004 0.053 4704 Dihedral : 17.851 179.248 5265 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.09 % Allowed : 12.12 % Favored : 86.78 % 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: 2.40 (0.15), residues: 2698 helix: 2.66 (0.12), residues: 1495 sheet: 0.59 (1.11), residues: 26 loop : 0.26 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 13 TYR 0.022 0.001 TYR M 194 PHE 0.020 0.002 PHE L 41 TRP 0.014 0.001 TRP M 253 HIS 0.008 0.001 HIS M 183 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (28087) covalent geometry : angle 0.69275 / 0.27 (38824) hydrogen bonds : bond 0.03976 / 2.69 ( 1317) hydrogen bonds : angle 3.69938 / 2.71 ( 3735) Misc. bond : bond 0.10347 / 7.74 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7888.99 seconds wall clock time: 135 minutes 19.37 seconds (8119.37 seconds total)