Starting phenix.real_space_refine on Thu Jun 26 05:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zk2_60165/06_2025/8zk2_60165.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zk2_60165/06_2025/8zk2_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_60165/06_2025/8zk2_60165.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zk2_60165/06_2025/8zk2_60165.map" model { file = "/net/cci-nas-00/data/ceres_data/8zk2_60165/06_2025/8zk2_60165.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zk2_60165/06_2025/8zk2_60165.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.065 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): 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 26948 Number of models: 1 Model: "" Number of chains: 72 Chain: "C" Number of atoms: 2618 Number of conformers: 1 Conformer: "" Number of residues, atoms: 342, 2618 Classifications: {'peptide': 342} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 314} Chain: "L" Number of atoms: 2163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 273, 2163 Classifications: {'peptide': 273} Link IDs: {'PTRANS': 15, 'TRANS': 257} Chain: "M" Number of atoms: 2269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2269 Classifications: {'peptide': 287} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 269} Chain: "H" Number of atoms: 1906 Number of conformers: 1 Conformer: "" Number of residues, atoms: 245, 1906 Classifications: {'peptide': 245} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 18, 'TRANS': 224} Chain breaks: 1 Chain: "B" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "A" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "D" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "E" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "F" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "G" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "I" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "J" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "K" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "N" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "O" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "P" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Q" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "R" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "S" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "T" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "U" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "V" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "W" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "X" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "Y" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "Z" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 369 Classifications: {'peptide': 46} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "a" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "b" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "c" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "d" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "e" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "f" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "g" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "h" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "i" Number of atoms: 377 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 377 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 2, 'TRANS': 46} Chain: "j" Number of atoms: 424 Number of conformers: 1 Conformer: "" Number of residues, atoms: 53, 424 Classifications: {'peptide': 53} Link IDs: {'PTRANS': 2, 'TRANS': 50} Chain: "C" Number of atoms: 229 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 229 Unusual residues: {' MG': 3, '8K6': 1, 'HEC': 4, 'PGV': 1} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 15 Chain: "L" Number of atoms: 338 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 338 Unusual residues: {'8K6': 5, 'BCL': 2, 'BPH': 1, 'LMT': 1, 'PGV': 1} Classifications: {'undetermined': 10} Link IDs: {None: 9} Unresolved non-hydrogen bonds: 35 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 34 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PGV:plan-3': 1} Unresolved non-hydrogen planarities: 4 Chain: "M" Number of atoms: 401 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 401 Unusual residues: {' FE': 1, '8K6': 1, 'BCL': 2, 'BPH': 1, 'CRT': 1, 'MQ8': 1, 'PGV': 2} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 16 Unresolved non-hydrogen chiralities: 2 Chain: "H" Number of atoms: 171 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 171 Unusual residues: {' MG': 1, '8K6': 4, 'PGV': 2} Classifications: {'undetermined': 7} Link IDs: {None: 6} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 176 Unusual residues: {'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 163 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "O" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 194 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 194 Unusual residues: {'8K6': 1, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "Q" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 227 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 227 Unusual residues: {'BCL': 2, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "S" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "U" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "V" Number of atoms: 168 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 168 Unusual residues: {'8K6': 2, 'BCL': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "W" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "X" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Y" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Z" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'CRT': 1, 'PGV': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 9 Chain: "a" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "c" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "d" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "f" Number of atoms: 150 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 150 Unusual residues: {'8K6': 1, 'BCL': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "h" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "i" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 110 Unusual residues: {'BCL': 1, 'CRT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "j" Number of atoms: 212 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 212 Unusual residues: {'8K6': 2, 'BCL': 2, 'CRT': 1} Classifications: {'undetermined': 5} Link IDs: {None: 4} Time building chain proxies: 17.13, per 1000 atoms: 0.64 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: 15.70 Conformation dependent library (CDL) restraints added in 2.9 seconds 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: 2.19 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: 8.27 Time building geometry restraints manager: 10.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.38: 8759 1.38 - 1.58: 18873 1.58 - 1.79: 88 1.79 - 2.00: 176 2.00 - 2.20: 191 Bond restraints: 28087 Sorted by residual: bond pdb=" NA BCL M 403 " pdb="MG BCL M 403 " ideal model delta sigma weight residual 2.170 1.977 0.193 2.40e-02 1.74e+03 6.45e+01 bond pdb=" NA BCL G 101 " pdb="MG BCL G 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.09e+01 bond pdb=" NA BCL P 101 " pdb="MG BCL P 101 " ideal model delta sigma weight residual 2.170 1.983 0.187 2.40e-02 1.74e+03 6.05e+01 bond pdb=" NA BCL M 402 " pdb="MG BCL M 402 " ideal model delta sigma weight residual 2.170 1.984 0.186 2.40e-02 1.74e+03 6.02e+01 bond pdb=" NA BCL f 101 " pdb="MG BCL f 101 " ideal model delta sigma weight residual 2.170 1.985 0.185 2.40e-02 1.74e+03 5.96e+01 ... (remaining 28082 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.73: 38046 6.73 - 13.46: 722 13.46 - 20.19: 52 20.19 - 26.92: 2 26.92 - 33.65: 2 Bond angle restraints: 38824 Sorted by residual: angle pdb=" ND BCL M 403 " pdb="MG BCL M 403 " pdb=" NA BCL M 403 " ideal model delta sigma weight residual 88.02 97.69 -9.66 1.29e+00 6.02e-01 5.62e+01 angle pdb=" C1D BCL d 102 " pdb=" C2D BCL d 102 " pdb=" CMD BCL d 102 " ideal model delta sigma weight residual 125.57 139.08 -13.50 1.83e+00 2.99e-01 5.46e+01 angle pdb=" ND BCL J 101 " pdb="MG BCL J 101 " pdb=" NA BCL J 101 " ideal model delta sigma weight residual 88.02 97.51 -9.48 1.29e+00 6.02e-01 5.41e+01 angle pdb=" ND BCL f 101 " pdb="MG BCL f 101 " pdb=" NA BCL f 101 " ideal model delta sigma weight residual 88.02 97.37 -9.35 1.29e+00 6.02e-01 5.26e+01 angle pdb=" ND BCL h 101 " pdb="MG BCL h 101 " pdb=" NA BCL h 101 " ideal model delta sigma weight residual 88.02 97.30 -9.27 1.29e+00 6.02e-01 5.18e+01 ... (remaining 38819 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 14210 35.82 - 71.63: 639 71.63 - 107.45: 62 107.45 - 143.26: 15 143.26 - 179.08: 10 Dihedral angle restraints: 14936 sinusoidal: 7021 harmonic: 7915 Sorted by residual: dihedral pdb=" C1 BCL h 102 " pdb=" CGA BCL h 102 " pdb=" O2A BCL h 102 " pdb=" CBA BCL h 102 " ideal model delta sinusoidal sigma weight residual -180.00 -0.92 -179.08 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL X 102 " pdb=" CGA BCL X 102 " pdb=" O2A BCL X 102 " pdb=" CBA BCL X 102 " ideal model delta sinusoidal sigma weight residual -180.00 -1.96 -178.04 1 6.00e+00 2.78e-02 5.33e+02 dihedral pdb=" C1 BCL V 102 " pdb=" CGA BCL V 102 " pdb=" O2A BCL V 102 " pdb=" CBA BCL V 102 " ideal model delta sinusoidal sigma weight residual 180.00 2.41 177.59 1 6.00e+00 2.78e-02 5.33e+02 ... (remaining 14933 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3215 0.066 - 0.132: 431 0.132 - 0.198: 104 0.198 - 0.263: 19 0.263 - 0.329: 11 Chirality restraints: 3780 Sorted by residual: chirality pdb=" CBD BCL I 101 " pdb=" CAD BCL I 101 " pdb=" CGD BCL I 101 " pdb=" CHA BCL I 101 " both_signs ideal model delta sigma weight residual False 2.62 2.29 0.33 2.00e-01 2.50e+01 2.71e+00 chirality pdb=" CBD BCL B 101 " pdb=" CAD BCL B 101 " pdb=" CGD BCL B 101 " pdb=" CHA BCL B 101 " both_signs ideal model delta sigma weight residual False 2.62 2.30 0.32 2.00e-01 2.50e+01 2.53e+00 chirality pdb=" CA VAL W 57 " pdb=" N VAL W 57 " pdb=" C VAL W 57 " pdb=" CB VAL W 57 " both_signs ideal model delta sigma weight residual False 2.44 2.74 -0.30 2.00e-01 2.50e+01 2.26e+00 ... (remaining 3777 not shown) Planarity restraints: 4704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL G 102 " -0.350 3.00e-02 1.11e+03 2.87e-01 4.58e+02 pdb=" CBA BCL G 102 " -0.176 3.00e-02 1.11e+03 pdb=" CGA BCL G 102 " 0.081 3.00e-02 1.11e+03 pdb=" O1A BCL G 102 " -0.054 3.00e-02 1.11e+03 pdb=" O2A BCL G 102 " 0.499 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL J 102 " -0.352 3.00e-02 1.11e+03 2.86e-01 4.55e+02 pdb=" CBA BCL J 102 " -0.190 3.00e-02 1.11e+03 pdb=" CGA BCL J 102 " 0.086 3.00e-02 1.11e+03 pdb=" O1A BCL J 102 " -0.034 3.00e-02 1.11e+03 pdb=" O2A BCL J 102 " 0.491 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL M 402 " -0.327 3.00e-02 1.11e+03 2.71e-01 4.07e+02 pdb=" CBA BCL M 402 " -0.152 3.00e-02 1.11e+03 pdb=" CGA BCL M 402 " 0.064 3.00e-02 1.11e+03 pdb=" O1A BCL M 402 " -0.063 3.00e-02 1.11e+03 pdb=" O2A BCL M 402 " 0.478 3.00e-02 1.11e+03 ... (remaining 4701 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 259 2.62 - 3.19: 20984 3.19 - 3.76: 45735 3.76 - 4.33: 69564 4.33 - 4.90: 110746 Nonbonded interactions: 247288 Sorted by model distance: nonbonded pdb=" NE2 HIS C 338 " pdb="FE HEC C 504 " model vdw 2.047 3.080 nonbonded pdb=" OD2 ASP C 214 " pdb="MG MG C 506 " model vdw 2.070 2.170 nonbonded pdb=" OD1 ASP C 194 " pdb="MG MG C 506 " model vdw 2.073 2.170 nonbonded pdb=" NE2 HIS L 192 " pdb="FE FE M 401 " model vdw 2.144 2.340 nonbonded pdb=" NE2 HIS M 220 " pdb="FE FE M 401 " model vdw 2.147 2.340 ... (remaining 247283 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 6 through 51) selection = (chain 'E' and resid 6 through 51) selection = (chain 'G' and resid 6 through 51) selection = (chain 'J' and resid 6 through 51) selection = (chain 'N' and resid 6 through 51) selection = (chain 'P' and resid 6 through 51) selection = (chain 'R' and resid 6 through 51) selection = (chain 'T' and resid 6 through 51) selection = (chain 'V' and resid 6 through 51) selection = (chain 'X' and resid 6 through 51) selection = (chain 'Z' and resid 6 through 51) selection = (chain 'b' and resid 6 through 51) selection = (chain 'd' and resid 6 through 51) selection = (chain 'f' and resid 6 through 51) selection = (chain 'h' and resid 6 through 51) selection = (chain 'j' and resid 6 through 51) } ncs_group { reference = (chain 'B' and (resid 9 through 57 or resid 101)) selection = chain 'D' selection = chain 'F' selection = (chain 'I' and (resid 9 through 57 or resid 101)) selection = (chain 'K' and (resid 9 through 57 or resid 101)) selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = (chain 'U' and (resid 9 through 57 or resid 101)) selection = (chain 'W' and (resid 9 through 57 or resid 101)) selection = (chain 'Y' and (resid 9 through 57 or resid 101)) selection = (chain 'a' and (resid 9 through 57 or resid 101)) selection = chain 'c' selection = (chain 'e' and (resid 9 through 57 or resid 101)) selection = chain 'g' selection = (chain 'i' and (resid 9 through 57 or resid 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: 3.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.200 Construct map_model_manager: 0.020 Extract box with map and model: 1.080 Check model and map are aligned: 0.190 Set scattering table: 0.270 Process input model: 60.710 Find NCS groups from input model: 1.640 Set up NCS constraints: 0.160 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:16.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 84.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 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 : 13.02 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.014 0.001 TRP U 50 HIS 0.016 0.001 HIS M 183 PHE 0.058 0.002 PHE L 218 TYR 0.021 0.002 TYR M 194 ARG 0.007 0.000 ARG C 57 Details of bonding type rmsd hydrogen bonds : bond 0.12040 ( 1317) hydrogen bonds : angle 4.73226 ( 3735) covalent geometry : bond 0.02085 (28087) covalent geometry : angle 2.00870 (38824) Misc. bond : bond 0.11981 ( 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 : 2.741 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: 2.5917 time to fit residues: 929.7475 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 : 4.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 216 optimal weight: 1.9990 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 0.9980 chunk 103 optimal weight: 2.9990 chunk 200 optimal weight: 0.9980 chunk 77 optimal weight: 0.7980 chunk 122 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 232 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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** H 253 ASN P 6 HIS T 39 HIS W 27 GLN i 27 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.113734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096418 restraints weight = 31368.325| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 1.12 r_work: 0.2946 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 2.80 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.0968 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.390 28150 Z= 0.177 Angle : 0.849 13.372 38824 Z= 0.312 Chirality : 0.039 0.189 3780 Planarity : 0.005 0.067 4704 Dihedral : 19.385 179.851 5265 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 0.87 % Allowed : 6.47 % Favored : 92.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.16), residues: 2698 helix: 2.20 (0.12), residues: 1495 sheet: 0.60 (1.03), residues: 26 loop : -0.03 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 265 HIS 0.009 0.001 HIS M 183 PHE 0.031 0.002 PHE L 218 TYR 0.025 0.002 TYR M 194 ARG 0.006 0.000 ARG j 15 Details of bonding type rmsd hydrogen bonds : bond 0.04438 ( 1317) hydrogen bonds : angle 4.02669 ( 3735) covalent geometry : bond 0.00433 (28087) covalent geometry : angle 0.84863 (38824) Misc. bond : bond 0.13158 ( 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 314 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 295 time to evaluate : 4.448 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7437 (ptm160) REVERT: C 214 ASP cc_start: 0.8665 (m-30) cc_final: 0.8288 (m-30) REVERT: D 19 LYS cc_start: 0.8141 (ttmt) cc_final: 0.7915 (tttt) REVERT: E 1 MET cc_start: 0.7316 (ttm) cc_final: 0.6848 (mtp) REVERT: F 27 GLN cc_start: 0.8503 (mt0) cc_final: 0.8282 (mt0) REVERT: F 54 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.7630 (pp20) REVERT: U 27 GLN cc_start: 0.8238 (mt0) cc_final: 0.7942 (mt0) REVERT: f 11 MET cc_start: 0.8504 (OUTLIER) cc_final: 0.8092 (ttm) REVERT: i 19 LYS cc_start: 0.8045 (tttt) cc_final: 0.7772 (tttp) outliers start: 19 outliers final: 6 residues processed: 305 average time/residue: 2.6647 time to fit residues: 924.6789 Evaluate side-chains 279 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 270 time to evaluate : 3.016 ------------------------------------------------------------------------------- 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 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 J residue 18 LEU Chi-restraints excluded: chain P residue 52 THR 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 182 optimal weight: 0.6980 chunk 254 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 chunk 34 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 198 optimal weight: 0.8980 chunk 152 optimal weight: 1.9990 chunk 136 optimal weight: 3.9990 chunk 6 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3255 r_free = 0.3255 target = 0.111715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.093995 restraints weight = 31432.889| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.19 r_work: 0.2911 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2810 rms_B_bonded: 2.88 restraints_weight: 0.2500 r_work (final): 0.2810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.1279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.398 28150 Z= 0.200 Angle : 0.808 15.609 38824 Z= 0.314 Chirality : 0.039 0.145 3780 Planarity : 0.005 0.062 4704 Dihedral : 19.206 179.497 5265 Min Nonbonded Distance : 1.997 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 1.46 % Allowed : 8.11 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.15), residues: 2698 helix: 2.15 (0.12), residues: 1495 sheet: 0.47 (1.05), residues: 26 loop : -0.04 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 265 HIS 0.009 0.002 HIS M 183 PHE 0.028 0.002 PHE L 218 TYR 0.027 0.002 TYR M 194 ARG 0.004 0.000 ARG M 248 Details of bonding type rmsd hydrogen bonds : bond 0.04561 ( 1317) hydrogen bonds : angle 3.98981 ( 3735) covalent geometry : bond 0.00489 (28087) covalent geometry : angle 0.80841 (38824) Misc. bond : bond 0.12231 ( 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 318 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 286 time to evaluate : 2.664 Fit side-chains revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8764 (OUTLIER) cc_final: 0.7422 (ptm-80) REVERT: L 79 PHE cc_start: 0.8401 (m-80) cc_final: 0.8023 (m-80) REVERT: D 19 LYS cc_start: 0.8096 (ttmt) cc_final: 0.7840 (tttt) REVERT: Q 15 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.7378 (tt0) REVERT: V 15 ARG cc_start: 0.8168 (OUTLIER) cc_final: 0.7137 (ttp-110) REVERT: b 7 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8402 (mtpm) REVERT: f 11 MET cc_start: 0.8515 (OUTLIER) cc_final: 0.8084 (ttm) REVERT: i 19 LYS cc_start: 0.8098 (tttt) cc_final: 0.7846 (tttm) outliers start: 32 outliers final: 15 residues processed: 300 average time/residue: 1.7755 time to fit residues: 611.5465 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 : 2.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 52 THR Chi-restraints excluded: chain C residue 57 ARG Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain F residue 54 GLU Chi-restraints excluded: chain J residue 18 LEU 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 Q residue 15 GLU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER 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 213 optimal weight: 3.9990 chunk 244 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 229 optimal weight: 0.5980 chunk 71 optimal weight: 1.9990 chunk 106 optimal weight: 1.9990 chunk 208 optimal weight: 4.9990 chunk 199 optimal weight: 0.9980 chunk 116 optimal weight: 2.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3280 r_free = 0.3280 target = 0.113653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.096216 restraints weight = 31619.123| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.16 r_work: 0.2941 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.85 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.1383 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= 0.144 Angle : 0.726 11.888 38824 Z= 0.280 Chirality : 0.037 0.137 3780 Planarity : 0.005 0.058 4704 Dihedral : 18.809 179.846 5265 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.69 % Allowed : 9.25 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.15), residues: 2698 helix: 2.41 (0.12), residues: 1495 sheet: 0.53 (1.06), residues: 26 loop : 0.04 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 253 HIS 0.007 0.001 HIS M 183 PHE 0.027 0.002 PHE L 218 TYR 0.023 0.001 TYR M 194 ARG 0.004 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04182 ( 1317) hydrogen bonds : angle 3.83931 ( 3735) covalent geometry : bond 0.00342 (28087) covalent geometry : angle 0.72615 (38824) Misc. bond : bond 0.11675 ( 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 323 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 286 time to evaluate : 2.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8743 (OUTLIER) cc_final: 0.7356 (ptm160) REVERT: L 79 PHE cc_start: 0.8408 (m-80) cc_final: 0.8010 (m-80) REVERT: M 80 ASP cc_start: 0.8182 (m-30) cc_final: 0.7889 (m-30) REVERT: F 27 GLN cc_start: 0.8345 (OUTLIER) cc_final: 0.8133 (mt0) REVERT: V 15 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.7136 (ttp-110) REVERT: c 15 GLU cc_start: 0.7554 (OUTLIER) cc_final: 0.6605 (tm-30) REVERT: f 11 MET cc_start: 0.8475 (OUTLIER) cc_final: 0.8069 (ttm) REVERT: i 19 LYS cc_start: 0.8128 (tttt) cc_final: 0.7885 (tttm) outliers start: 37 outliers final: 19 residues processed: 306 average time/residue: 1.6307 time to fit residues: 575.2724 Evaluate side-chains 296 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 272 time to evaluate : 2.545 ------------------------------------------------------------------------------- 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 168 HIS Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain A residue 11 MET 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 V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER 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 179 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 154 optimal weight: 0.7980 chunk 75 optimal weight: 2.9990 chunk 166 optimal weight: 2.9990 chunk 196 optimal weight: 3.9990 chunk 228 optimal weight: 4.9990 chunk 238 optimal weight: 8.9990 chunk 255 optimal weight: 0.0570 chunk 55 optimal weight: 0.9990 chunk 112 optimal weight: 5.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3302 r_free = 0.3302 target = 0.114798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.098392 restraints weight = 31582.236| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.09 r_work: 0.2963 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2862 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.392 28150 Z= 0.202 Angle : 0.799 13.029 38824 Z= 0.309 Chirality : 0.039 0.145 3780 Planarity : 0.005 0.058 4704 Dihedral : 18.972 179.926 5265 Min Nonbonded Distance : 1.988 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 1.91 % Allowed : 9.48 % Favored : 88.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.15), residues: 2698 helix: 2.23 (0.12), residues: 1495 sheet: 0.31 (0.96), residues: 36 loop : 0.01 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 253 HIS 0.008 0.002 HIS M 183 PHE 0.029 0.002 PHE L 218 TYR 0.027 0.002 TYR M 194 ARG 0.004 0.000 ARG M 248 Details of bonding type rmsd hydrogen bonds : bond 0.04523 ( 1317) hydrogen bonds : angle 3.96399 ( 3735) covalent geometry : bond 0.00495 (28087) covalent geometry : angle 0.79887 (38824) Misc. bond : bond 0.12178 ( 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 322 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 280 time to evaluate : 2.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.7487 (ptm-80) REVERT: C 326 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.7902 (mm-30) REVERT: L 79 PHE cc_start: 0.8456 (m-80) cc_final: 0.8041 (m-80) REVERT: M 80 ASP cc_start: 0.8158 (m-30) cc_final: 0.7858 (m-30) REVERT: B 20 GLU cc_start: 0.7240 (tt0) cc_final: 0.6895 (pt0) REVERT: D 19 LYS cc_start: 0.8219 (ttmt) cc_final: 0.7950 (tttt) REVERT: K 14 THR cc_start: 0.8040 (OUTLIER) cc_final: 0.7820 (p) REVERT: S 45 MET cc_start: 0.8808 (mtm) cc_final: 0.8548 (mtm) REVERT: V 15 ARG cc_start: 0.8261 (OUTLIER) cc_final: 0.7179 (ttp-110) REVERT: c 15 GLU cc_start: 0.7672 (OUTLIER) cc_final: 0.6696 (tm-30) REVERT: f 11 MET cc_start: 0.8507 (ttp) cc_final: 0.8138 (ttm) REVERT: i 19 LYS cc_start: 0.8193 (tttt) cc_final: 0.7956 (tttm) outliers start: 42 outliers final: 21 residues processed: 305 average time/residue: 1.5024 time to fit residues: 528.9072 Evaluate side-chains 302 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 276 time to evaluate : 2.762 ------------------------------------------------------------------------------- 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 326 GLU Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 217 PHE Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain A residue 11 MET Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 33 LEU Chi-restraints excluded: chain N residue 52 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 36 optimal weight: 1.9990 chunk 93 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 206 optimal weight: 0.8980 chunk 250 optimal weight: 1.9990 chunk 249 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 11 optimal weight: 10.0000 chunk 144 optimal weight: 2.9990 chunk 35 optimal weight: 0.0870 chunk 220 optimal weight: 8.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3320 r_free = 0.3320 target = 0.116269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.099741 restraints weight = 31275.430| |-----------------------------------------------------------------------------| r_work (start): 0.3110 rms_B_bonded: 1.02 r_work: 0.2986 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 2.70 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.347 28150 Z= 0.149 Angle : 0.729 12.426 38824 Z= 0.283 Chirality : 0.037 0.138 3780 Planarity : 0.005 0.056 4704 Dihedral : 18.688 179.623 5265 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 10.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.73 % Allowed : 9.85 % Favored : 88.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.15), residues: 2698 helix: 2.41 (0.12), residues: 1495 sheet: 0.36 (0.97), residues: 36 loop : 0.06 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP f 9 HIS 0.007 0.001 HIS M 183 PHE 0.026 0.002 PHE L 218 TYR 0.024 0.001 TYR M 194 ARG 0.004 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04199 ( 1317) hydrogen bonds : angle 3.83697 ( 3735) covalent geometry : bond 0.00357 (28087) covalent geometry : angle 0.72918 (38824) Misc. bond : bond 0.11758 ( 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 312 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 274 time to evaluate : 2.559 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8821 (OUTLIER) cc_final: 0.7476 (ptm-80) REVERT: L 191 MET cc_start: 0.8883 (OUTLIER) cc_final: 0.8604 (mtp) REVERT: M 80 ASP cc_start: 0.8191 (m-30) cc_final: 0.7921 (m-30) REVERT: H 84 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7677 (mttt) REVERT: H 126 ARG cc_start: 0.8031 (ptm-80) cc_final: 0.7627 (ptt180) REVERT: H 221 PHE cc_start: 0.9035 (OUTLIER) cc_final: 0.8774 (m-80) REVERT: B 20 GLU cc_start: 0.7254 (tt0) cc_final: 0.6940 (pt0) REVERT: K 14 THR cc_start: 0.8059 (OUTLIER) cc_final: 0.7844 (p) REVERT: V 15 ARG cc_start: 0.8272 (OUTLIER) cc_final: 0.7255 (ttp-110) REVERT: c 15 GLU cc_start: 0.7624 (OUTLIER) cc_final: 0.6667 (tm-30) REVERT: f 11 MET cc_start: 0.8497 (ttp) cc_final: 0.8110 (ttm) REVERT: i 19 LYS cc_start: 0.8230 (tttt) cc_final: 0.7983 (tttp) outliers start: 38 outliers final: 20 residues processed: 297 average time/residue: 1.5666 time to fit residues: 533.1679 Evaluate side-chains 296 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 269 time to evaluate : 2.441 ------------------------------------------------------------------------------- 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 191 MET Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 96 optimal weight: 0.5980 chunk 106 optimal weight: 1.9990 chunk 231 optimal weight: 6.9990 chunk 118 optimal weight: 2.9990 chunk 255 optimal weight: 0.7980 chunk 82 optimal weight: 0.7980 chunk 160 optimal weight: 1.9990 chunk 162 optimal weight: 40.0000 chunk 201 optimal weight: 3.9990 chunk 181 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3281 r_free = 0.3281 target = 0.113718 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.096392 restraints weight = 31493.779| |-----------------------------------------------------------------------------| r_work (start): 0.3066 rms_B_bonded: 1.14 r_work: 0.2944 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.81 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.341 28150 Z= 0.141 Angle : 0.715 12.456 38824 Z= 0.278 Chirality : 0.036 0.146 3780 Planarity : 0.005 0.056 4704 Dihedral : 18.461 179.780 5265 Min Nonbonded Distance : 2.018 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.64 % Allowed : 10.35 % Favored : 88.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.15), residues: 2698 helix: 2.51 (0.12), residues: 1495 sheet: 0.37 (0.98), residues: 36 loop : 0.10 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 253 HIS 0.006 0.001 HIS M 183 PHE 0.025 0.002 PHE L 218 TYR 0.023 0.001 TYR M 194 ARG 0.004 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 1317) hydrogen bonds : angle 3.78680 ( 3735) covalent geometry : bond 0.00336 (28087) covalent geometry : angle 0.71457 (38824) Misc. bond : bond 0.11121 ( 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 312 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 276 time to evaluate : 2.526 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8729 (OUTLIER) cc_final: 0.7338 (ptm160) REVERT: C 326 GLU cc_start: 0.8536 (OUTLIER) cc_final: 0.7903 (mm-30) REVERT: M 80 ASP cc_start: 0.8101 (m-30) cc_final: 0.7846 (m-30) REVERT: H 1 MET cc_start: 0.7508 (mpt) cc_final: 0.7256 (mpt) REVERT: H 84 LYS cc_start: 0.8088 (OUTLIER) cc_final: 0.7551 (mttt) REVERT: H 126 ARG cc_start: 0.7953 (ptm-80) cc_final: 0.7558 (ptt180) REVERT: H 221 PHE cc_start: 0.8936 (OUTLIER) cc_final: 0.8676 (m-80) REVERT: B 20 GLU cc_start: 0.7254 (tt0) cc_final: 0.6873 (pt0) REVERT: F 27 GLN cc_start: 0.8316 (mt0) cc_final: 0.8040 (mt0) REVERT: K 14 THR cc_start: 0.7997 (OUTLIER) cc_final: 0.7737 (p) REVERT: V 15 ARG cc_start: 0.8093 (OUTLIER) cc_final: 0.7033 (ttp-110) REVERT: b 7 LYS cc_start: 0.8817 (OUTLIER) cc_final: 0.8344 (mtpm) REVERT: c 15 GLU cc_start: 0.7471 (OUTLIER) cc_final: 0.6481 (tm-30) REVERT: f 11 MET cc_start: 0.8379 (ttp) cc_final: 0.7983 (ttm) REVERT: i 19 LYS cc_start: 0.8051 (tttt) cc_final: 0.7805 (tttp) outliers start: 36 outliers final: 20 residues processed: 298 average time/residue: 1.5834 time to fit residues: 540.5648 Evaluate side-chains 298 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 270 time to evaluate : 2.619 ------------------------------------------------------------------------------- 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 C residue 326 GLU Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 100 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 111 optimal weight: 1.9990 chunk 62 optimal weight: 7.9990 chunk 204 optimal weight: 5.9990 chunk 107 optimal weight: 0.5980 chunk 121 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 239 optimal weight: 4.9990 chunk 248 optimal weight: 4.9990 chunk 224 optimal weight: 50.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3274 r_free = 0.3274 target = 0.113144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.095844 restraints weight = 31464.326| |-----------------------------------------------------------------------------| r_work (start): 0.3060 rms_B_bonded: 1.12 r_work: 0.2939 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2839 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.1609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.344 28150 Z= 0.152 Angle : 0.727 12.777 38824 Z= 0.283 Chirality : 0.037 0.149 3780 Planarity : 0.005 0.054 4704 Dihedral : 18.417 179.805 5265 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.82 % Allowed : 10.26 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.15), residues: 2698 helix: 2.48 (0.12), residues: 1495 sheet: 0.35 (0.98), residues: 36 loop : 0.11 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP f 9 HIS 0.007 0.001 HIS M 183 PHE 0.027 0.002 PHE L 218 TYR 0.024 0.001 TYR M 194 ARG 0.005 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04170 ( 1317) hydrogen bonds : angle 3.80641 ( 3735) covalent geometry : bond 0.00365 (28087) covalent geometry : angle 0.72665 (38824) Misc. bond : bond 0.11039 ( 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 314 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 274 time to evaluate : 2.620 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7345 (ptm160) REVERT: C 326 GLU cc_start: 0.8638 (OUTLIER) cc_final: 0.8014 (mm-30) REVERT: M 80 ASP cc_start: 0.8119 (m-30) cc_final: 0.7873 (m-30) REVERT: H 84 LYS cc_start: 0.8082 (OUTLIER) cc_final: 0.7544 (mttt) REVERT: H 126 ARG cc_start: 0.7943 (ptm-80) cc_final: 0.7603 (ptt180) REVERT: H 221 PHE cc_start: 0.8899 (OUTLIER) cc_final: 0.8622 (m-80) REVERT: H 231 GLU cc_start: 0.8024 (OUTLIER) cc_final: 0.7033 (pp20) REVERT: B 20 GLU cc_start: 0.7258 (tt0) cc_final: 0.6883 (pt0) REVERT: F 27 GLN cc_start: 0.8316 (OUTLIER) cc_final: 0.8040 (mt0) REVERT: K 14 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7724 (p) REVERT: P 46 GLU cc_start: 0.8313 (tp30) cc_final: 0.8012 (mm-30) REVERT: V 15 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7033 (ttp-110) REVERT: b 7 LYS cc_start: 0.8849 (OUTLIER) cc_final: 0.8420 (mtpm) REVERT: c 15 GLU cc_start: 0.7438 (OUTLIER) cc_final: 0.6426 (tm-30) REVERT: f 11 MET cc_start: 0.8374 (ttp) cc_final: 0.7976 (ttm) REVERT: i 19 LYS cc_start: 0.8057 (tttt) cc_final: 0.7811 (tttm) outliers start: 40 outliers final: 22 residues processed: 298 average time/residue: 1.5523 time to fit residues: 529.9808 Evaluate side-chains 302 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 270 time to evaluate : 2.444 ------------------------------------------------------------------------------- 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 C residue 326 GLU Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 84 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 18 LEU Chi-restraints excluded: chain S residue 27 GLN Chi-restraints excluded: chain V residue 15 ARG Chi-restraints excluded: chain W residue 13 LEU Chi-restraints excluded: chain X residue 11 MET Chi-restraints excluded: chain b residue 7 LYS Chi-restraints excluded: chain b residue 16 SER Chi-restraints excluded: chain c residue 15 GLU Chi-restraints excluded: chain d residue 4 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 40 optimal weight: 0.9980 chunk 164 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 141 optimal weight: 0.7980 chunk 87 optimal weight: 0.6980 chunk 218 optimal weight: 3.9990 chunk 11 optimal weight: 10.0000 chunk 44 optimal weight: 2.9990 chunk 116 optimal weight: 3.9990 chunk 210 optimal weight: 2.9990 chunk 228 optimal weight: 1.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 168 HIS H 90 ASN W 27 GLN i 27 GLN j 39 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.115180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.098595 restraints weight = 31696.656| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 1.02 r_work: 0.2972 rms_B_bonded: 1.59 restraints_weight: 0.5000 r_work: 0.2872 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8401 moved from start: 0.1623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.379 28150 Z= 0.195 Angle : 0.783 13.273 38824 Z= 0.305 Chirality : 0.039 0.148 3780 Planarity : 0.005 0.054 4704 Dihedral : 18.639 179.678 5265 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.82 % Allowed : 10.53 % Favored : 87.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.15), residues: 2698 helix: 2.31 (0.12), residues: 1495 sheet: 0.28 (0.98), residues: 36 loop : 0.06 (0.18), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP L 265 HIS 0.008 0.001 HIS M 183 PHE 0.030 0.002 PHE L 218 TYR 0.026 0.002 TYR M 194 ARG 0.005 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 1317) hydrogen bonds : angle 3.91584 ( 3735) covalent geometry : bond 0.00477 (28087) covalent geometry : angle 0.78273 (38824) Misc. bond : bond 0.11498 ( 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 317 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 4.616 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8831 (OUTLIER) cc_final: 0.7488 (ptm-80) REVERT: C 326 GLU cc_start: 0.8640 (OUTLIER) cc_final: 0.8013 (mm-30) REVERT: L 191 MET cc_start: 0.8917 (OUTLIER) cc_final: 0.8692 (mtp) REVERT: M 80 ASP cc_start: 0.8247 (m-30) cc_final: 0.7973 (m-30) REVERT: M 139 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.8328 (mmpt) REVERT: H 1 MET cc_start: 0.7636 (mpt) cc_final: 0.7330 (mpt) REVERT: H 84 LYS cc_start: 0.8171 (OUTLIER) cc_final: 0.7890 (mttp) REVERT: H 126 ARG cc_start: 0.8055 (ptm-80) cc_final: 0.7725 (ptt180) REVERT: H 221 PHE cc_start: 0.9014 (OUTLIER) cc_final: 0.8711 (m-80) REVERT: H 231 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.7064 (pp20) REVERT: B 20 GLU cc_start: 0.7330 (tt0) cc_final: 0.6984 (pt0) REVERT: F 27 GLN cc_start: 0.8390 (OUTLIER) cc_final: 0.8139 (mt0) REVERT: K 14 THR cc_start: 0.8078 (OUTLIER) cc_final: 0.7851 (p) REVERT: P 46 GLU cc_start: 0.8356 (tp30) cc_final: 0.8051 (mm-30) REVERT: V 15 ARG cc_start: 0.8269 (OUTLIER) cc_final: 0.7210 (ttp-110) REVERT: c 15 GLU cc_start: 0.7655 (OUTLIER) cc_final: 0.6668 (tm-30) REVERT: f 11 MET cc_start: 0.8501 (ttp) cc_final: 0.8083 (ttm) REVERT: i 19 LYS cc_start: 0.8206 (tttt) cc_final: 0.7976 (tttm) outliers start: 40 outliers final: 23 residues processed: 297 average time/residue: 1.8325 time to fit residues: 629.7092 Evaluate side-chains 313 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 279 time to evaluate : 2.975 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain L residue 191 MET Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 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 84 LYS Chi-restraints excluded: chain H residue 219 LYS Chi-restraints excluded: chain H residue 221 PHE Chi-restraints excluded: chain H residue 231 GLU Chi-restraints excluded: chain H residue 239 ASP Chi-restraints excluded: chain F residue 27 GLN Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain J residue 52 THR Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain P residue 35 LEU Chi-restraints excluded: chain P residue 52 THR Chi-restraints excluded: chain Q residue 57 VAL Chi-restraints excluded: chain R residue 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 28 optimal weight: 0.6980 chunk 202 optimal weight: 0.5980 chunk 176 optimal weight: 6.9990 chunk 44 optimal weight: 1.9990 chunk 86 optimal weight: 0.8980 chunk 134 optimal weight: 2.9990 chunk 82 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 151 optimal weight: 7.9990 chunk 206 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3286 r_free = 0.3286 target = 0.114092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3066 r_free = 0.3066 target = 0.096761 restraints weight = 31283.457| |-----------------------------------------------------------------------------| r_work (start): 0.3073 rms_B_bonded: 1.15 r_work: 0.2951 rms_B_bonded: 1.66 restraints_weight: 0.5000 r_work: 0.2851 rms_B_bonded: 2.82 restraints_weight: 0.2500 r_work (final): 0.2851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.344 28150 Z= 0.134 Angle : 0.707 12.071 38824 Z= 0.277 Chirality : 0.036 0.142 3780 Planarity : 0.004 0.054 4704 Dihedral : 18.301 179.512 5265 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 1.46 % Allowed : 10.98 % Favored : 87.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.15), residues: 2698 helix: 2.53 (0.12), residues: 1495 sheet: -0.30 (1.22), residues: 25 loop : 0.18 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP Z 9 HIS 0.006 0.001 HIS M 183 PHE 0.029 0.002 PHE L 218 TYR 0.022 0.001 TYR M 194 ARG 0.006 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04074 ( 1317) hydrogen bonds : angle 3.77110 ( 3735) covalent geometry : bond 0.00318 (28087) covalent geometry : angle 0.70656 (38824) Misc. bond : bond 0.10843 ( 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 307 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 275 time to evaluate : 2.796 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 57 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.7367 (ptm160) REVERT: C 214 ASP cc_start: 0.8752 (m-30) cc_final: 0.8363 (m-30) REVERT: C 326 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.7975 (mm-30) REVERT: M 80 ASP cc_start: 0.8108 (m-30) cc_final: 0.7857 (m-30) REVERT: M 139 LYS cc_start: 0.8576 (OUTLIER) cc_final: 0.8212 (mmpt) REVERT: H 1 MET cc_start: 0.7565 (mpt) cc_final: 0.7069 (mpt) REVERT: H 84 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7567 (mttt) REVERT: H 126 ARG cc_start: 0.7956 (ptm-80) cc_final: 0.7687 (ptt180) REVERT: H 221 PHE cc_start: 0.8942 (OUTLIER) cc_final: 0.8657 (m-80) REVERT: B 20 GLU cc_start: 0.7271 (tt0) cc_final: 0.6913 (pt0) REVERT: F 27 GLN cc_start: 0.8349 (OUTLIER) cc_final: 0.8073 (mt0) REVERT: K 14 THR cc_start: 0.7963 (OUTLIER) cc_final: 0.7737 (p) REVERT: P 46 GLU cc_start: 0.8331 (tp30) cc_final: 0.8037 (mm-30) REVERT: V 15 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7114 (ttp-110) REVERT: c 15 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.6440 (tm-30) REVERT: i 19 LYS cc_start: 0.8096 (tttt) cc_final: 0.7853 (tttp) outliers start: 32 outliers final: 20 residues processed: 291 average time/residue: 1.6123 time to fit residues: 536.9801 Evaluate side-chains 300 residues out of total 2194 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 271 time to evaluate : 2.729 ------------------------------------------------------------------------------- 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 61 MET Chi-restraints excluded: chain C residue 104 VAL Chi-restraints excluded: chain C residue 264 PHE Chi-restraints excluded: chain C residue 326 GLU Chi-restraints excluded: chain L residue 259 LYS Chi-restraints excluded: chain M residue 51 ILE Chi-restraints excluded: chain M residue 56 THR Chi-restraints excluded: chain M residue 139 LYS Chi-restraints excluded: chain M residue 307 THR Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain H residue 84 LYS 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 K residue 14 THR Chi-restraints excluded: chain N residue 8 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 32 optimal weight: 0.8980 chunk 225 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 142 optimal weight: 8.9990 chunk 198 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 246 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 166 optimal weight: 0.7980 chunk 232 optimal weight: 1.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3279 r_free = 0.3279 target = 0.113590 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.096341 restraints weight = 31323.200| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 1.12 r_work: 0.2944 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.77 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.342 28150 Z= 0.145 Angle : 0.718 12.440 38824 Z= 0.281 Chirality : 0.036 0.142 3780 Planarity : 0.005 0.054 4704 Dihedral : 18.243 179.544 5265 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.15 % Favored : 97.85 % Rotamer: Outliers : 1.64 % Allowed : 11.26 % Favored : 87.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.22 (0.15), residues: 2698 helix: 2.51 (0.12), residues: 1495 sheet: -0.26 (1.22), residues: 25 loop : 0.19 (0.18), residues: 1178 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 253 HIS 0.006 0.001 HIS M 183 PHE 0.030 0.002 PHE L 218 TYR 0.023 0.001 TYR M 194 ARG 0.005 0.000 ARG L 13 Details of bonding type rmsd hydrogen bonds : bond 0.04119 ( 1317) hydrogen bonds : angle 3.78342 ( 3735) covalent geometry : bond 0.00348 (28087) covalent geometry : angle 0.71818 (38824) Misc. bond : bond 0.10915 ( 63) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 19163.45 seconds wall clock time: 336 minutes 9.14 seconds (20169.14 seconds total)