Starting phenix.real_space_refine on Sun May 3 22:14:21 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9srz_55166/05_2026/9srz_55166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9srz_55166/05_2026/9srz_55166.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.61 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9srz_55166/05_2026/9srz_55166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9srz_55166/05_2026/9srz_55166.map" model { file = "/net/cci-nas-00/data/ceres_data/9srz_55166/05_2026/9srz_55166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9srz_55166/05_2026/9srz_55166.cif" } resolution = 2.61 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.133 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 12 9.91 5 P 36 5.49 5 S 84 5.16 5 C 9795 2.51 5 N 2809 2.21 5 O 3067 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc2-6044/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 15803 Number of models: 1 Model: "" Number of chains: 19 Chain: "A" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 139 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "E" Number of atoms: 143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 143 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "F" Number of atoms: 139 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 139 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 149 Unusual residues: {'ACE': 1} Classifications: {'peptide': 19, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 4, 'TRANS': 14} Chain breaks: 1 Chain: "I" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2395 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "J" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2395 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "K" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2395 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "L" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2395 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "M" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2395 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "N" Number of atoms: 2395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 312, 2395 Classifications: {'peptide': 312} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 300} Chain breaks: 1 Chain: "O" Number of atoms: 367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 367 Classifications: {'DNA': 18} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 17} Chain: "I" Number of atoms: 34 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 34 Unusual residues: {' CA': 3, 'ATP': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' CA': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.14, per 1000 atoms: 0.26 Number of scatterers: 15803 At special positions: 0 Unit cell: (120.12, 119.28, 163.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Ca 12 19.99 S 84 16.00 P 36 15.00 O 3067 8.00 N 2809 7.00 C 9795 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=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 761.1 milliseconds 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3636 Finding SS restraints... Secondary structure from input PDB file: 100 helices and 18 sheets defined 51.0% alpha, 15.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 2 through 6 Processing helix chain 'B' and resid 2 through 6 Processing helix chain 'E' and resid 2 through 6 Processing helix chain 'C' and resid 2 through 6 Processing helix chain 'F' and resid 2 through 6 Processing helix chain 'D' and resid 2 through 10 Proline residue: D 7 - end of helix Processing helix chain 'I' and resid 24 through 32 removed outlier: 3.510A pdb=" N GLY I 32 " --> pdb=" O GLU I 29 " (cutoff:3.500A) Processing helix chain 'I' and resid 34 through 43 Processing helix chain 'I' and resid 48 through 54 Processing helix chain 'I' and resid 56 through 62 Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.577A pdb=" N LYS I 80 " --> pdb=" O ALA I 76 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 89 through 98 removed outlier: 3.911A pdb=" N GLU I 98 " --> pdb=" O GLN I 94 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.764A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 removed outlier: 3.575A pdb=" N VAL I 185 " --> pdb=" O SER I 181 " (cutoff:3.500A) Processing helix chain 'I' and resid 196 through 212 removed outlier: 4.029A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN I 206 " --> pdb=" O GLN I 202 " (cutoff:3.500A) Processing helix chain 'I' and resid 225 through 232 removed outlier: 3.962A pdb=" N THR I 230 " --> pdb=" O ALA I 226 " (cutoff:3.500A) Processing helix chain 'I' and resid 234 through 236 No H-bonds generated for 'chain 'I' and resid 234 through 236' Processing helix chain 'I' and resid 237 through 260 Processing helix chain 'I' and resid 288 through 296 removed outlier: 3.846A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing helix chain 'J' and resid 24 through 32 removed outlier: 3.613A pdb=" N GLY J 32 " --> pdb=" O GLU J 29 " (cutoff:3.500A) Processing helix chain 'J' and resid 34 through 45 Processing helix chain 'J' and resid 48 through 54 removed outlier: 3.534A pdb=" N VAL J 52 " --> pdb=" O THR J 48 " (cutoff:3.500A) Processing helix chain 'J' and resid 56 through 61 Processing helix chain 'J' and resid 67 through 82 removed outlier: 3.619A pdb=" N LYS J 80 " --> pdb=" O ALA J 76 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N LEU J 81 " --> pdb=" O GLU J 77 " (cutoff:3.500A) Processing helix chain 'J' and resid 89 through 97 Processing helix chain 'J' and resid 106 through 113 Processing helix chain 'J' and resid 132 through 144 removed outlier: 3.698A pdb=" N VAL J 142 " --> pdb=" O HIS J 138 " (cutoff:3.500A) Processing helix chain 'J' and resid 145 through 146 No H-bonds generated for 'chain 'J' and resid 145 through 146' Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 167 through 178 removed outlier: 3.810A pdb=" N LEU J 171 " --> pdb=" O ARG J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 181 through 188 Processing helix chain 'J' and resid 196 through 214 removed outlier: 3.806A pdb=" N LEU J 204 " --> pdb=" O GLN J 200 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N TYR J 205 " --> pdb=" O THR J 201 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN J 206 " --> pdb=" O GLN J 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER J 208 " --> pdb=" O LEU J 204 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N ALA J 209 " --> pdb=" O TYR J 205 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLU J 213 " --> pdb=" O ALA J 209 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 232 Processing helix chain 'J' and resid 234 through 236 No H-bonds generated for 'chain 'J' and resid 234 through 236' Processing helix chain 'J' and resid 237 through 260 Processing helix chain 'J' and resid 288 through 296 removed outlier: 3.752A pdb=" N ILE J 292 " --> pdb=" O GLY J 288 " (cutoff:3.500A) Processing helix chain 'K' and resid 24 through 32 removed outlier: 3.720A pdb=" N GLY K 32 " --> pdb=" O GLU K 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 34 through 44 Processing helix chain 'K' and resid 48 through 54 Processing helix chain 'K' and resid 56 through 62 Processing helix chain 'K' and resid 67 through 80 Processing helix chain 'K' and resid 89 through 97 Processing helix chain 'K' and resid 106 through 113 Processing helix chain 'K' and resid 132 through 144 removed outlier: 3.733A pdb=" N VAL K 142 " --> pdb=" O HIS K 138 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 178 removed outlier: 3.800A pdb=" N LEU K 171 " --> pdb=" O ARG K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 181 through 188 Processing helix chain 'K' and resid 196 through 214 removed outlier: 3.870A pdb=" N LEU K 204 " --> pdb=" O GLN K 200 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N TYR K 205 " --> pdb=" O THR K 201 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN K 206 " --> pdb=" O GLN K 202 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ALA K 209 " --> pdb=" O TYR K 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL K 212 " --> pdb=" O SER K 208 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLU K 213 " --> pdb=" O ALA K 209 " (cutoff:3.500A) Processing helix chain 'K' and resid 227 through 232 removed outlier: 3.536A pdb=" N TYR K 232 " --> pdb=" O TYR K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 234 through 236 No H-bonds generated for 'chain 'K' and resid 234 through 236' Processing helix chain 'K' and resid 237 through 260 Processing helix chain 'K' and resid 288 through 296 removed outlier: 3.820A pdb=" N ILE K 292 " --> pdb=" O GLY K 288 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA K 293 " --> pdb=" O GLY K 289 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 31 Processing helix chain 'L' and resid 34 through 44 Processing helix chain 'L' and resid 48 through 54 Processing helix chain 'L' and resid 56 through 62 removed outlier: 3.580A pdb=" N LEU L 60 " --> pdb=" O PRO L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 80 Processing helix chain 'L' and resid 89 through 97 Processing helix chain 'L' and resid 106 through 113 Processing helix chain 'L' and resid 132 through 144 removed outlier: 3.747A pdb=" N VAL L 142 " --> pdb=" O HIS L 138 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 178 removed outlier: 3.835A pdb=" N LEU L 171 " --> pdb=" O ARG L 167 " (cutoff:3.500A) Processing helix chain 'L' and resid 181 through 188 Processing helix chain 'L' and resid 196 through 214 removed outlier: 3.891A pdb=" N LEU L 204 " --> pdb=" O GLN L 200 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR L 205 " --> pdb=" O THR L 201 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N GLN L 206 " --> pdb=" O GLN L 202 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER L 208 " --> pdb=" O LEU L 204 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ALA L 209 " --> pdb=" O TYR L 205 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLU L 213 " --> pdb=" O ALA L 209 " (cutoff:3.500A) Processing helix chain 'L' and resid 227 through 232 removed outlier: 3.559A pdb=" N TYR L 232 " --> pdb=" O TYR L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 234 through 236 No H-bonds generated for 'chain 'L' and resid 234 through 236' Processing helix chain 'L' and resid 237 through 260 Processing helix chain 'L' and resid 288 through 296 removed outlier: 3.746A pdb=" N ILE L 292 " --> pdb=" O GLY L 288 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ALA L 293 " --> pdb=" O GLY L 289 " (cutoff:3.500A) Processing helix chain 'M' and resid 24 through 31 Processing helix chain 'M' and resid 34 through 44 Processing helix chain 'M' and resid 48 through 54 Processing helix chain 'M' and resid 56 through 62 Processing helix chain 'M' and resid 67 through 82 removed outlier: 3.528A pdb=" N LYS M 80 " --> pdb=" O ALA M 76 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU M 81 " --> pdb=" O GLU M 77 " (cutoff:3.500A) Processing helix chain 'M' and resid 89 through 97 Processing helix chain 'M' and resid 106 through 114 Processing helix chain 'M' and resid 132 through 144 removed outlier: 3.735A pdb=" N VAL M 142 " --> pdb=" O HIS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 145 through 146 No H-bonds generated for 'chain 'M' and resid 145 through 146' Processing helix chain 'M' and resid 147 through 151 Processing helix chain 'M' and resid 167 through 178 removed outlier: 3.828A pdb=" N LEU M 171 " --> pdb=" O ARG M 167 " (cutoff:3.500A) Processing helix chain 'M' and resid 181 through 188 Processing helix chain 'M' and resid 196 through 214 removed outlier: 3.885A pdb=" N LEU M 204 " --> pdb=" O GLN M 200 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N TYR M 205 " --> pdb=" O THR M 201 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLN M 206 " --> pdb=" O GLN M 202 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N ALA M 209 " --> pdb=" O TYR M 205 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N VAL M 212 " --> pdb=" O SER M 208 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU M 213 " --> pdb=" O ALA M 209 " (cutoff:3.500A) Processing helix chain 'M' and resid 225 through 232 removed outlier: 4.059A pdb=" N THR M 230 " --> pdb=" O ALA M 226 " (cutoff:3.500A) Processing helix chain 'M' and resid 234 through 236 No H-bonds generated for 'chain 'M' and resid 234 through 236' Processing helix chain 'M' and resid 237 through 260 Processing helix chain 'M' and resid 288 through 296 removed outlier: 3.701A pdb=" N ILE M 292 " --> pdb=" O GLY M 288 " (cutoff:3.500A) Processing helix chain 'N' and resid 24 through 32 Processing helix chain 'N' and resid 34 through 44 Processing helix chain 'N' and resid 48 through 54 Processing helix chain 'N' and resid 56 through 62 removed outlier: 3.564A pdb=" N LEU N 60 " --> pdb=" O PRO N 56 " (cutoff:3.500A) Processing helix chain 'N' and resid 67 through 80 removed outlier: 3.583A pdb=" N LYS N 80 " --> pdb=" O ALA N 76 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 97 Processing helix chain 'N' and resid 106 through 113 Processing helix chain 'N' and resid 132 through 144 removed outlier: 3.741A pdb=" N VAL N 142 " --> pdb=" O HIS N 138 " (cutoff:3.500A) Processing helix chain 'N' and resid 167 through 178 removed outlier: 3.797A pdb=" N LEU N 171 " --> pdb=" O ARG N 167 " (cutoff:3.500A) Processing helix chain 'N' and resid 181 through 188 Processing helix chain 'N' and resid 196 through 214 removed outlier: 3.950A pdb=" N LEU N 204 " --> pdb=" O GLN N 200 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR N 205 " --> pdb=" O THR N 201 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N GLN N 206 " --> pdb=" O GLN N 202 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N VAL N 212 " --> pdb=" O SER N 208 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N GLU N 213 " --> pdb=" O ALA N 209 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 232 removed outlier: 4.057A pdb=" N THR N 230 " --> pdb=" O ALA N 226 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 236 No H-bonds generated for 'chain 'N' and resid 234 through 236' Processing helix chain 'N' and resid 237 through 260 Processing helix chain 'N' and resid 288 through 296 removed outlier: 3.790A pdb=" N ILE N 292 " --> pdb=" O GLY N 288 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA N 293 " --> pdb=" O GLY N 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'I' and resid 86 through 88 removed outlier: 6.554A pdb=" N LYS J 156 " --> pdb=" O LEU J 218 " (cutoff:3.500A) removed outlier: 8.139A pdb=" N ILE J 220 " --> pdb=" O LYS J 156 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N MET J 158 " --> pdb=" O ILE J 220 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N ASP J 222 " --> pdb=" O MET J 158 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ILE J 160 " --> pdb=" O ASP J 222 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY J 127 " --> pdb=" O ASN J 267 " (cutoff:3.500A) removed outlier: 6.149A pdb=" N ARG J 299 " --> pdb=" O TYR J 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'I' and resid 189 through 193 removed outlier: 6.615A pdb=" N ALA I 157 " --> pdb=" O ALA I 190 " (cutoff:3.500A) removed outlier: 8.202A pdb=" N ALA I 192 " --> pdb=" O ALA I 157 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR I 159 " --> pdb=" O ALA I 192 " (cutoff:3.500A) removed outlier: 5.298A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N ALA I 217 " --> pdb=" O ALA I 262 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N VAL I 264 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 6.370A pdb=" N LEU I 219 " --> pdb=" O VAL I 264 " (cutoff:3.500A) removed outlier: 8.287A pdb=" N THR I 266 " --> pdb=" O LEU I 219 " (cutoff:3.500A) removed outlier: 7.557A pdb=" N VAL I 221 " --> pdb=" O THR I 266 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'I' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'J' and resid 87 through 88 removed outlier: 6.522A pdb=" N LYS K 156 " --> pdb=" O LEU K 218 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ILE K 220 " --> pdb=" O LYS K 156 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N MET K 158 " --> pdb=" O ILE K 220 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ASP K 222 " --> pdb=" O MET K 158 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N ILE K 160 " --> pdb=" O ASP K 222 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLY K 127 " --> pdb=" O ASN K 267 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE K 122 " --> pdb=" O THR K 298 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU K 300 " --> pdb=" O ILE K 122 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N GLU K 124 " --> pdb=" O LEU K 300 " (cutoff:3.500A) removed outlier: 7.809A pdb=" N LEU K 302 " --> pdb=" O GLU K 124 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N PHE K 126 " --> pdb=" O LEU K 302 " (cutoff:3.500A) removed outlier: 8.867A pdb=" N LYS K 304 " --> pdb=" O PHE K 126 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ARG K 299 " --> pdb=" O TYR K 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'J' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'J' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'K' and resid 87 through 88 removed outlier: 6.989A pdb=" N LYS L 156 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 5.937A pdb=" N LEU L 219 " --> pdb=" O LYS L 156 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N MET L 158 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 5.532A pdb=" N VAL L 221 " --> pdb=" O MET L 158 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N ILE L 160 " --> pdb=" O VAL L 221 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N ALA L 217 " --> pdb=" O ALA L 262 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N VAL L 264 " --> pdb=" O ALA L 217 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N LEU L 219 " --> pdb=" O VAL L 264 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N THR L 266 " --> pdb=" O LEU L 219 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N VAL L 221 " --> pdb=" O THR L 266 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLY L 127 " --> pdb=" O ASN L 267 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG L 299 " --> pdb=" O TYR L 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'K' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'L' and resid 87 through 88 removed outlier: 7.037A pdb=" N LYS M 156 " --> pdb=" O ALA M 217 " (cutoff:3.500A) removed outlier: 5.964A pdb=" N LEU M 219 " --> pdb=" O LYS M 156 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N MET M 158 " --> pdb=" O LEU M 219 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N VAL M 221 " --> pdb=" O MET M 158 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ILE M 160 " --> pdb=" O VAL M 221 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N GLY M 127 " --> pdb=" O ASN M 267 " (cutoff:3.500A) removed outlier: 6.728A pdb=" N ILE M 122 " --> pdb=" O THR M 298 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N LEU M 300 " --> pdb=" O ILE M 122 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N GLU M 124 " --> pdb=" O LEU M 300 " (cutoff:3.500A) removed outlier: 7.637A pdb=" N LEU M 302 " --> pdb=" O GLU M 124 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE M 126 " --> pdb=" O LEU M 302 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N LYS M 304 " --> pdb=" O PHE M 126 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ARG M 299 " --> pdb=" O TYR M 315 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE M 311 " --> pdb=" O ARG M 303 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'L' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'M' and resid 87 through 88 removed outlier: 6.722A pdb=" N LYS N 156 " --> pdb=" O LEU N 218 " (cutoff:3.500A) removed outlier: 8.237A pdb=" N ILE N 220 " --> pdb=" O LYS N 156 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N MET N 158 " --> pdb=" O ILE N 220 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N ASP N 222 " --> pdb=" O MET N 158 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N ILE N 160 " --> pdb=" O ASP N 222 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA N 217 " --> pdb=" O ALA N 262 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N VAL N 264 " --> pdb=" O ALA N 217 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N LEU N 219 " --> pdb=" O VAL N 264 " (cutoff:3.500A) removed outlier: 8.071A pdb=" N THR N 266 " --> pdb=" O LEU N 219 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N VAL N 221 " --> pdb=" O THR N 266 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N GLY N 127 " --> pdb=" O ASN N 267 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N ARG N 299 " --> pdb=" O TYR N 315 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'M' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'M' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'N' and resid 101 through 102 Processing sheet with id=AB9, first strand: chain 'N' and resid 269 through 271 754 hydrogen bonds defined for protein. 2046 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: 2.70 Time building geometry restraints manager: 2.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4209 1.33 - 1.45: 2687 1.45 - 1.57: 8979 1.57 - 1.69: 65 1.69 - 1.81: 138 Bond restraints: 16078 Sorted by residual: bond pdb=" C ACE F 0 " pdb=" N MET F 1 " ideal model delta sigma weight residual 1.329 1.422 -0.093 2.00e-02 2.50e+03 2.15e+01 bond pdb=" C ACE A 0 " pdb=" N MET A 1 " ideal model delta sigma weight residual 1.329 1.419 -0.090 2.00e-02 2.50e+03 2.04e+01 bond pdb=" C ACE B 0 " pdb=" N MET B 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.97e+01 bond pdb=" C ACE E 0 " pdb=" N MET E 1 " ideal model delta sigma weight residual 1.329 1.418 -0.089 2.00e-02 2.50e+03 1.96e+01 bond pdb=" C ACE C 0 " pdb=" N MET C 1 " ideal model delta sigma weight residual 1.329 1.417 -0.088 2.00e-02 2.50e+03 1.95e+01 ... (remaining 16073 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.68: 21457 1.68 - 3.36: 267 3.36 - 5.04: 45 5.04 - 6.72: 5 6.72 - 8.40: 6 Bond angle restraints: 21780 Sorted by residual: angle pdb=" CG MET B 1 " pdb=" SD MET B 1 " pdb=" CE MET B 1 " ideal model delta sigma weight residual 100.90 109.30 -8.40 2.20e+00 2.07e-01 1.46e+01 angle pdb=" CG MET A 1 " pdb=" SD MET A 1 " pdb=" CE MET A 1 " ideal model delta sigma weight residual 100.90 109.23 -8.33 2.20e+00 2.07e-01 1.44e+01 angle pdb=" CG MET C 1 " pdb=" SD MET C 1 " pdb=" CE MET C 1 " ideal model delta sigma weight residual 100.90 109.20 -8.30 2.20e+00 2.07e-01 1.42e+01 angle pdb=" CG MET D 1 " pdb=" SD MET D 1 " pdb=" CE MET D 1 " ideal model delta sigma weight residual 100.90 109.10 -8.20 2.20e+00 2.07e-01 1.39e+01 angle pdb=" CG MET E 1 " pdb=" SD MET E 1 " pdb=" CE MET E 1 " ideal model delta sigma weight residual 100.90 109.05 -8.15 2.20e+00 2.07e-01 1.37e+01 ... (remaining 21775 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 8483 17.99 - 35.98: 973 35.98 - 53.97: 327 53.97 - 71.96: 93 71.96 - 89.95: 22 Dihedral angle restraints: 9898 sinusoidal: 4240 harmonic: 5658 Sorted by residual: dihedral pdb=" CA ASP N 187 " pdb=" CB ASP N 187 " pdb=" CG ASP N 187 " pdb=" OD1 ASP N 187 " ideal model delta sinusoidal sigma weight residual -30.00 -88.82 58.82 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA THR I 103 " pdb=" C THR I 103 " pdb=" N THR I 104 " pdb=" CA THR I 104 " ideal model delta harmonic sigma weight residual 180.00 163.48 16.52 0 5.00e+00 4.00e-02 1.09e+01 dihedral pdb=" CG ARG K 170 " pdb=" CD ARG K 170 " pdb=" NE ARG K 170 " pdb=" CZ ARG K 170 " ideal model delta sinusoidal sigma weight residual 180.00 135.63 44.37 2 1.50e+01 4.44e-03 1.04e+01 ... (remaining 9895 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1559 0.029 - 0.057: 589 0.057 - 0.086: 156 0.086 - 0.115: 136 0.115 - 0.143: 20 Chirality restraints: 2460 Sorted by residual: chirality pdb=" CA MET F 1 " pdb=" N MET F 1 " pdb=" C MET F 1 " pdb=" CB MET F 1 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.15e-01 chirality pdb=" CA ARG K 130 " pdb=" N ARG K 130 " pdb=" C ARG K 130 " pdb=" CB ARG K 130 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.46e-01 chirality pdb=" CA VAL M 82 " pdb=" N VAL M 82 " pdb=" C VAL M 82 " pdb=" CB VAL M 82 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 2457 not shown) Planarity restraints: 2739 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG I 130 " 0.007 2.00e-02 2.50e+03 1.43e-02 2.06e+00 pdb=" C ARG I 130 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG I 130 " 0.009 2.00e-02 2.50e+03 pdb=" N THR I 131 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG M 130 " -0.006 2.00e-02 2.50e+03 1.27e-02 1.61e+00 pdb=" C ARG M 130 " 0.022 2.00e-02 2.50e+03 pdb=" O ARG M 130 " -0.008 2.00e-02 2.50e+03 pdb=" N THR M 131 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU I 146 " 0.021 5.00e-02 4.00e+02 3.17e-02 1.61e+00 pdb=" N PRO I 147 " -0.055 5.00e-02 4.00e+02 pdb=" CA PRO I 147 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO I 147 " 0.018 5.00e-02 4.00e+02 ... (remaining 2736 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 4311 2.82 - 3.34: 13304 3.34 - 3.86: 25788 3.86 - 4.38: 33057 4.38 - 4.90: 53725 Nonbonded interactions: 130185 Sorted by model distance: nonbonded pdb=" O SER L 296 " pdb="CA CA L 403 " model vdw 2.296 2.510 nonbonded pdb=" O SER M 296 " pdb="CA CA M 403 " model vdw 2.306 2.510 nonbonded pdb=" O SER K 296 " pdb="CA CA K 403 " model vdw 2.316 2.510 nonbonded pdb="CA CA M 403 " pdb=" O1G ATP N 401 " model vdw 2.324 2.510 nonbonded pdb=" O1G ATP I 401 " pdb="CA CA I 403 " model vdw 2.325 2.510 ... (remaining 130180 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' selection = (chain 'B' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'C' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'D' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 24 or (resid 25 and (name N or name \ CA or name C or name O or name CB )) or resid 26)) selection = (chain 'E' and (resid 0 through 18 or (resid 19 and (name N or name CA or name C \ or name O or name CB )) or resid 20 through 26)) selection = chain 'F' } ncs_group { reference = (chain 'I' and resid 20 through 402) selection = (chain 'J' and resid 20 through 402) selection = (chain 'K' and resid 20 through 402) selection = (chain 'L' and resid 20 through 402) selection = (chain 'M' and resid 20 through 402) selection = chain 'N' } 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: 3.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 15.660 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8492 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.093 16078 Z= 0.147 Angle : 0.504 8.399 21780 Z= 0.262 Chirality : 0.039 0.143 2460 Planarity : 0.004 0.037 2739 Dihedral : 17.919 89.955 6262 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.01 % Allowed : 20.43 % Favored : 78.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.37 (0.18), residues: 1938 helix: 0.77 (0.18), residues: 852 sheet: 1.49 (0.30), residues: 288 loop : -0.74 (0.19), residues: 798 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG M 27 TYR 0.008 0.001 TYR K 205 PHE 0.013 0.001 PHE L 327 HIS 0.003 0.001 HIS J 138 Details of bonding type rmsd covalent geometry : bond 0.00301 (16078) covalent geometry : angle 0.50388 (21780) hydrogen bonds : bond 0.17959 ( 754) hydrogen bonds : angle 6.40196 ( 2046) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 248 time to evaluate : 0.422 Fit side-chains REVERT: C 1 MET cc_start: 0.9042 (mtp) cc_final: 0.8776 (mtp) REVERT: D 1 MET cc_start: 0.9270 (mtp) cc_final: 0.9030 (mtp) REVERT: I 198 ASP cc_start: 0.8398 (m-30) cc_final: 0.8160 (m-30) REVERT: I 247 ARG cc_start: 0.8163 (mtt-85) cc_final: 0.7754 (mtm110) REVERT: I 251 MET cc_start: 0.8250 (mtp) cc_final: 0.7722 (tpt) REVERT: J 247 ARG cc_start: 0.8286 (mtt90) cc_final: 0.7977 (mtm180) REVERT: K 39 LYS cc_start: 0.8036 (mtpp) cc_final: 0.7727 (ttpt) REVERT: K 72 ASP cc_start: 0.7922 (m-30) cc_final: 0.7696 (m-30) REVERT: K 108 GLU cc_start: 0.8537 (mm-30) cc_final: 0.8306 (mm-30) REVERT: K 114 GLN cc_start: 0.8507 (mt0) cc_final: 0.8305 (mt0) REVERT: K 213 GLU cc_start: 0.8447 (mm-30) cc_final: 0.7996 (mp0) REVERT: K 247 ARG cc_start: 0.8296 (mtt-85) cc_final: 0.7768 (mtt180) REVERT: L 59 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8163 (mt-10) REVERT: L 70 LYS cc_start: 0.8050 (OUTLIER) cc_final: 0.7843 (ttpt) REVERT: L 176 GLU cc_start: 0.8139 (tp30) cc_final: 0.7915 (tm-30) REVERT: L 202 GLN cc_start: 0.8468 (tp-100) cc_final: 0.8195 (mm-40) REVERT: L 247 ARG cc_start: 0.8028 (ttm-80) cc_final: 0.7775 (mtm110) REVERT: M 99 ILE cc_start: 0.7901 (mm) cc_final: 0.7650 (tt) REVERT: M 107 LYS cc_start: 0.8310 (mtpp) cc_final: 0.7842 (mmpt) REVERT: M 184 ASP cc_start: 0.8329 (m-30) cc_final: 0.8031 (m-30) REVERT: M 202 GLN cc_start: 0.8383 (tp40) cc_final: 0.8084 (mm110) REVERT: M 247 ARG cc_start: 0.8424 (mtt180) cc_final: 0.8017 (mtm110) REVERT: M 306 ARG cc_start: 0.8295 (ttp80) cc_final: 0.8028 (ttp80) REVERT: N 64 LYS cc_start: 0.8289 (ttmm) cc_final: 0.7985 (ttpt) REVERT: N 107 LYS cc_start: 0.8302 (mtmm) cc_final: 0.8064 (mttm) REVERT: N 108 GLU cc_start: 0.8231 (mm-30) cc_final: 0.8003 (tp30) REVERT: N 176 GLU cc_start: 0.8018 (tt0) cc_final: 0.7798 (tp30) REVERT: N 247 ARG cc_start: 0.8258 (ttm-80) cc_final: 0.7934 (mtt180) REVERT: N 251 MET cc_start: 0.8347 (ttm) cc_final: 0.8022 (mtm) outliers start: 16 outliers final: 6 residues processed: 260 average time/residue: 0.9553 time to fit residues: 265.0255 Evaluate side-chains 227 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 109 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 98 optimal weight: 0.9980 chunk 194 optimal weight: 6.9990 chunk 107 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 7.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 3.9990 chunk 103 optimal weight: 0.0670 chunk 77 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 91 optimal weight: 3.9990 overall best weight: 0.6920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 36 ASN J 202 GLN K 272 GLN ** L 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 94 GLN N 114 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.138756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.111738 restraints weight = 15676.220| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.13 r_work: 0.3005 rms_B_bonded: 1.69 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.0986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 16078 Z= 0.102 Angle : 0.437 5.595 21780 Z= 0.239 Chirality : 0.039 0.131 2460 Planarity : 0.004 0.035 2739 Dihedral : 11.619 84.522 2619 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Rotamer: Outliers : 2.70 % Allowed : 18.35 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.19), residues: 1938 helix: 1.03 (0.18), residues: 870 sheet: 1.61 (0.31), residues: 288 loop : -0.65 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 3 TYR 0.008 0.001 TYR K 315 PHE 0.009 0.001 PHE K 129 HIS 0.002 0.001 HIS J 93 Details of bonding type rmsd covalent geometry : bond 0.00206 (16078) covalent geometry : angle 0.43671 (21780) hydrogen bonds : bond 0.04082 ( 754) hydrogen bonds : angle 4.65261 ( 2046) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 232 time to evaluate : 0.599 Fit side-chains REVERT: I 27 ARG cc_start: 0.7483 (tmt170) cc_final: 0.7189 (tpt90) REVERT: I 39 LYS cc_start: 0.7765 (tptt) cc_final: 0.6918 (mmmt) REVERT: I 130 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.6807 (ptp-170) REVERT: I 247 ARG cc_start: 0.8477 (mtt-85) cc_final: 0.8074 (mtm110) REVERT: I 251 MET cc_start: 0.8526 (mtp) cc_final: 0.7979 (tpt) REVERT: J 37 ASP cc_start: 0.8333 (m-30) cc_final: 0.8130 (m-30) REVERT: J 39 LYS cc_start: 0.7737 (mmtt) cc_final: 0.7328 (mmmt) REVERT: K 39 LYS cc_start: 0.7968 (mtpp) cc_final: 0.7456 (ttpt) REVERT: K 72 ASP cc_start: 0.7896 (m-30) cc_final: 0.7576 (m-30) REVERT: K 108 GLU cc_start: 0.8616 (mm-30) cc_final: 0.8368 (mm-30) REVERT: K 213 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7678 (mp0) REVERT: K 247 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8265 (mtt180) REVERT: K 284 LYS cc_start: 0.8470 (OUTLIER) cc_final: 0.7948 (mttt) REVERT: L 87 THR cc_start: 0.8740 (p) cc_final: 0.8528 (t) REVERT: L 176 GLU cc_start: 0.8294 (tp30) cc_final: 0.7977 (tm-30) REVERT: L 202 GLN cc_start: 0.8677 (tp-100) cc_final: 0.8460 (mm-40) REVERT: L 247 ARG cc_start: 0.8497 (ttm-80) cc_final: 0.8288 (mtm110) REVERT: M 99 ILE cc_start: 0.7837 (mm) cc_final: 0.7512 (tt) REVERT: M 107 LYS cc_start: 0.8288 (mtpp) cc_final: 0.7914 (mttm) REVERT: M 202 GLN cc_start: 0.8437 (tp40) cc_final: 0.8206 (mm110) REVERT: M 247 ARG cc_start: 0.8754 (mtt180) cc_final: 0.8433 (mtm110) REVERT: N 64 LYS cc_start: 0.8243 (ttmm) cc_final: 0.7776 (ttpt) REVERT: N 107 LYS cc_start: 0.8186 (mtmm) cc_final: 0.7871 (mttm) REVERT: N 176 GLU cc_start: 0.8190 (OUTLIER) cc_final: 0.7866 (tp30) REVERT: N 184 ASP cc_start: 0.7810 (OUTLIER) cc_final: 0.7256 (m-30) REVERT: N 247 ARG cc_start: 0.8428 (ttm-80) cc_final: 0.8094 (mtt90) REVERT: N 251 MET cc_start: 0.8445 (ttm) cc_final: 0.8085 (mtm) REVERT: N 284 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7527 (mttt) outliers start: 43 outliers final: 23 residues processed: 260 average time/residue: 0.8898 time to fit residues: 247.9157 Evaluate side-chains 248 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 220 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 230 THR Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 148 optimal weight: 4.9990 chunk 114 optimal weight: 4.9990 chunk 123 optimal weight: 6.9990 chunk 80 optimal weight: 6.9990 chunk 95 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 122 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 overall best weight: 3.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.130111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.100442 restraints weight = 16198.172| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.32 r_work: 0.2876 rms_B_bonded: 1.70 restraints_weight: 0.5000 r_work: 0.2768 rms_B_bonded: 2.78 restraints_weight: 0.2500 r_work (final): 0.2768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8857 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 16078 Z= 0.298 Angle : 0.666 7.586 21780 Z= 0.358 Chirality : 0.049 0.171 2460 Planarity : 0.006 0.130 2739 Dihedral : 12.419 89.914 2613 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 2.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.27 % Allowed : 17.41 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.10 (0.18), residues: 1938 helix: 0.47 (0.17), residues: 864 sheet: 1.33 (0.30), residues: 288 loop : -0.81 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 241 TYR 0.016 0.003 TYR J 228 PHE 0.017 0.003 PHE K 195 HIS 0.009 0.002 HIS J 138 Details of bonding type rmsd covalent geometry : bond 0.00717 (16078) covalent geometry : angle 0.66598 (21780) hydrogen bonds : bond 0.07028 ( 754) hydrogen bonds : angle 5.25153 ( 2046) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 205 time to evaluate : 0.594 Fit side-chains REVERT: I 36 ASN cc_start: 0.7370 (OUTLIER) cc_final: 0.7066 (m110) REVERT: I 39 LYS cc_start: 0.7693 (tptt) cc_final: 0.7034 (mmmt) REVERT: I 247 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8108 (mtm110) REVERT: I 251 MET cc_start: 0.8555 (mtp) cc_final: 0.7989 (tpt) REVERT: J 284 LYS cc_start: 0.8660 (OUTLIER) cc_final: 0.8384 (mtmt) REVERT: K 20 PHE cc_start: 0.5239 (OUTLIER) cc_final: 0.4605 (p90) REVERT: K 39 LYS cc_start: 0.8105 (mtpp) cc_final: 0.7531 (ttpt) REVERT: K 72 ASP cc_start: 0.7881 (m-30) cc_final: 0.7535 (m-30) REVERT: K 247 ARG cc_start: 0.8633 (mtt-85) cc_final: 0.8319 (mtm180) REVERT: K 284 LYS cc_start: 0.8622 (OUTLIER) cc_final: 0.7995 (mttt) REVERT: K 306 ARG cc_start: 0.8152 (OUTLIER) cc_final: 0.7717 (mmt180) REVERT: L 20 PHE cc_start: 0.6004 (OUTLIER) cc_final: 0.4831 (m-80) REVERT: L 40 LYS cc_start: 0.8280 (OUTLIER) cc_final: 0.7848 (mtpt) REVERT: L 94 GLN cc_start: 0.8437 (OUTLIER) cc_final: 0.8092 (tm-30) REVERT: L 202 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8526 (mm-40) REVERT: L 247 ARG cc_start: 0.8631 (ttm-80) cc_final: 0.8390 (mtm110) REVERT: M 107 LYS cc_start: 0.8359 (mtpp) cc_final: 0.7919 (mttm) REVERT: M 202 GLN cc_start: 0.8540 (tp40) cc_final: 0.8255 (mm110) REVERT: M 247 ARG cc_start: 0.8847 (mtt180) cc_final: 0.8495 (mtm110) REVERT: M 284 LYS cc_start: 0.8600 (OUTLIER) cc_final: 0.7982 (mttt) REVERT: N 27 ARG cc_start: 0.7925 (OUTLIER) cc_final: 0.7160 (mtp180) REVERT: N 64 LYS cc_start: 0.8321 (ttmm) cc_final: 0.7817 (ttpt) REVERT: N 247 ARG cc_start: 0.8459 (ttm-80) cc_final: 0.8082 (mtt90) REVERT: N 251 MET cc_start: 0.8603 (OUTLIER) cc_final: 0.8333 (mtm) REVERT: N 284 LYS cc_start: 0.8204 (OUTLIER) cc_final: 0.7541 (mttt) outliers start: 68 outliers final: 28 residues processed: 255 average time/residue: 0.8662 time to fit residues: 237.2795 Evaluate side-chains 241 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 201 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 284 LYS Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 20 PHE Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 284 LYS Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 163 optimal weight: 4.9990 chunk 171 optimal weight: 0.0370 chunk 158 optimal weight: 3.9990 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 156 optimal weight: 0.9980 overall best weight: 0.7060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN L 34 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.110265 restraints weight = 15899.661| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 1.01 r_work: 0.2989 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2888 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2888 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 16078 Z= 0.098 Angle : 0.426 5.555 21780 Z= 0.232 Chirality : 0.039 0.135 2460 Planarity : 0.004 0.045 2739 Dihedral : 11.993 86.688 2612 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 2.64 % Allowed : 18.92 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.57 (0.19), residues: 1938 helix: 1.00 (0.18), residues: 870 sheet: 1.43 (0.30), residues: 288 loop : -0.69 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG I 247 TYR 0.008 0.001 TYR M 315 PHE 0.009 0.001 PHE N 126 HIS 0.002 0.001 HIS J 93 Details of bonding type rmsd covalent geometry : bond 0.00203 (16078) covalent geometry : angle 0.42641 (21780) hydrogen bonds : bond 0.03683 ( 754) hydrogen bonds : angle 4.42818 ( 2046) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 219 time to evaluate : 0.653 Fit side-chains REVERT: I 27 ARG cc_start: 0.7590 (tmt170) cc_final: 0.7259 (tpt90) REVERT: I 36 ASN cc_start: 0.7496 (OUTLIER) cc_final: 0.7207 (m110) REVERT: I 130 ARG cc_start: 0.8284 (OUTLIER) cc_final: 0.7396 (ptt180) REVERT: I 247 ARG cc_start: 0.8456 (mtt-85) cc_final: 0.8071 (mtm110) REVERT: I 251 MET cc_start: 0.8496 (mtp) cc_final: 0.8009 (tpt) REVERT: J 39 LYS cc_start: 0.7915 (mmtt) cc_final: 0.7529 (mmmt) REVERT: J 84 MET cc_start: 0.8392 (mmm) cc_final: 0.7202 (mtm) REVERT: K 39 LYS cc_start: 0.8072 (mtpp) cc_final: 0.7543 (ttpt) REVERT: K 62 ASN cc_start: 0.7917 (OUTLIER) cc_final: 0.7417 (t0) REVERT: K 64 LYS cc_start: 0.7816 (tmtt) cc_final: 0.7542 (tttp) REVERT: K 72 ASP cc_start: 0.7851 (m-30) cc_final: 0.7512 (m-30) REVERT: K 247 ARG cc_start: 0.8571 (mtt-85) cc_final: 0.8208 (mtt180) REVERT: K 284 LYS cc_start: 0.8463 (OUTLIER) cc_final: 0.7903 (mttt) REVERT: L 70 LYS cc_start: 0.8010 (OUTLIER) cc_final: 0.7636 (ttpt) REVERT: L 87 THR cc_start: 0.8862 (p) cc_final: 0.8517 (t) REVERT: L 94 GLN cc_start: 0.8321 (OUTLIER) cc_final: 0.8024 (tm-30) REVERT: M 107 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7912 (mttm) REVERT: M 202 GLN cc_start: 0.8428 (tp40) cc_final: 0.8191 (mm110) REVERT: M 247 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8458 (mtm110) REVERT: N 27 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7079 (mtp180) REVERT: N 64 LYS cc_start: 0.8222 (ttmm) cc_final: 0.7814 (ttpt) REVERT: N 128 GLU cc_start: 0.8002 (tt0) cc_final: 0.7613 (tt0) REVERT: N 184 ASP cc_start: 0.7708 (m-30) cc_final: 0.7249 (m-30) REVERT: N 247 ARG cc_start: 0.8358 (ttm-80) cc_final: 0.8047 (mtt90) REVERT: N 251 MET cc_start: 0.8451 (ttm) cc_final: 0.8125 (mtm) outliers start: 42 outliers final: 23 residues processed: 248 average time/residue: 0.9063 time to fit residues: 240.5545 Evaluate side-chains 242 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 212 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain L residue 61 ILE Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 230 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 79 optimal weight: 9.9990 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 1.9990 chunk 58 optimal weight: 0.7980 chunk 169 optimal weight: 6.9990 chunk 91 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 147 optimal weight: 2.9990 chunk 141 optimal weight: 10.0000 chunk 103 optimal weight: 0.8980 chunk 188 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.134359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.107011 restraints weight = 15939.769| |-----------------------------------------------------------------------------| r_work (start): 0.3091 rms_B_bonded: 1.01 r_work: 0.2958 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2854 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 16078 Z= 0.141 Angle : 0.480 5.871 21780 Z= 0.259 Chirality : 0.041 0.146 2460 Planarity : 0.004 0.065 2739 Dihedral : 12.085 86.086 2612 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.65 % Allowed : 17.85 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.19), residues: 1938 helix: 1.00 (0.18), residues: 870 sheet: 1.40 (0.30), residues: 288 loop : -0.66 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 27 TYR 0.010 0.001 TYR M 315 PHE 0.011 0.001 PHE K 195 HIS 0.003 0.001 HIS J 138 Details of bonding type rmsd covalent geometry : bond 0.00321 (16078) covalent geometry : angle 0.47994 (21780) hydrogen bonds : bond 0.04608 ( 754) hydrogen bonds : angle 4.56593 ( 2046) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 210 time to evaluate : 0.561 Fit side-chains REVERT: I 36 ASN cc_start: 0.7533 (OUTLIER) cc_final: 0.7216 (m110) REVERT: I 247 ARG cc_start: 0.8472 (mtt-85) cc_final: 0.8062 (mtm110) REVERT: I 251 MET cc_start: 0.8473 (mtp) cc_final: 0.7978 (tpt) REVERT: J 39 LYS cc_start: 0.7913 (mmtt) cc_final: 0.7494 (mmmt) REVERT: J 84 MET cc_start: 0.8354 (mmm) cc_final: 0.7202 (mtm) REVERT: K 20 PHE cc_start: 0.5238 (OUTLIER) cc_final: 0.4575 (p90) REVERT: K 39 LYS cc_start: 0.8030 (mtpp) cc_final: 0.7489 (ttpt) REVERT: K 62 ASN cc_start: 0.7880 (m-40) cc_final: 0.7396 (t0) REVERT: K 64 LYS cc_start: 0.7849 (tmtt) cc_final: 0.7565 (tttp) REVERT: K 72 ASP cc_start: 0.7798 (m-30) cc_final: 0.7387 (m-30) REVERT: K 247 ARG cc_start: 0.8548 (mtt-85) cc_final: 0.8276 (mtm180) REVERT: L 40 LYS cc_start: 0.8134 (OUTLIER) cc_final: 0.7679 (mtpt) REVERT: L 70 LYS cc_start: 0.7968 (OUTLIER) cc_final: 0.7548 (ttpt) REVERT: L 94 GLN cc_start: 0.8381 (OUTLIER) cc_final: 0.8038 (tm-30) REVERT: M 26 SER cc_start: 0.8270 (OUTLIER) cc_final: 0.7858 (p) REVERT: M 107 LYS cc_start: 0.8298 (mtpp) cc_final: 0.7898 (mttm) REVERT: M 247 ARG cc_start: 0.8741 (mtt180) cc_final: 0.8452 (mtm110) REVERT: N 27 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7052 (mtp180) REVERT: N 64 LYS cc_start: 0.8302 (ttmm) cc_final: 0.7872 (ttpt) REVERT: N 184 ASP cc_start: 0.7728 (m-30) cc_final: 0.7215 (m-30) REVERT: N 247 ARG cc_start: 0.8339 (ttm-80) cc_final: 0.8021 (mtt90) REVERT: N 251 MET cc_start: 0.8444 (ttm) cc_final: 0.8111 (mtm) outliers start: 58 outliers final: 32 residues processed: 252 average time/residue: 0.8743 time to fit residues: 236.3090 Evaluate side-chains 249 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 210 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 48 THR Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 230 THR Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 87 THR Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 230 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 71 optimal weight: 7.9990 chunk 16 optimal weight: 7.9990 chunk 106 optimal weight: 0.9990 chunk 182 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 133 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 8.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.130663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.102929 restraints weight = 15971.090| |-----------------------------------------------------------------------------| r_work (start): 0.3071 rms_B_bonded: 1.04 r_work: 0.2935 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2831 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2831 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8847 moved from start: 0.1603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16078 Z= 0.302 Angle : 0.663 7.553 21780 Z= 0.355 Chirality : 0.049 0.171 2460 Planarity : 0.006 0.123 2739 Dihedral : 12.602 89.200 2612 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 4.34 % Allowed : 17.35 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.18), residues: 1938 helix: 0.54 (0.17), residues: 858 sheet: 1.35 (0.30), residues: 294 loop : -0.84 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 130 TYR 0.016 0.003 TYR J 228 PHE 0.017 0.003 PHE K 195 HIS 0.006 0.002 HIS K 294 Details of bonding type rmsd covalent geometry : bond 0.00731 (16078) covalent geometry : angle 0.66297 (21780) hydrogen bonds : bond 0.06865 ( 754) hydrogen bonds : angle 5.13184 ( 2046) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 204 time to evaluate : 0.558 Fit side-chains REVERT: I 36 ASN cc_start: 0.7543 (OUTLIER) cc_final: 0.7191 (m110) REVERT: I 247 ARG cc_start: 0.8545 (mtt-85) cc_final: 0.8134 (mtm110) REVERT: I 251 MET cc_start: 0.8526 (mtp) cc_final: 0.8004 (tpt) REVERT: J 84 MET cc_start: 0.8393 (mmm) cc_final: 0.7259 (mtm) REVERT: J 284 LYS cc_start: 0.8594 (OUTLIER) cc_final: 0.8346 (mtmt) REVERT: K 20 PHE cc_start: 0.5257 (OUTLIER) cc_final: 0.4553 (p90) REVERT: K 39 LYS cc_start: 0.8084 (mtpp) cc_final: 0.7547 (ttpt) REVERT: K 62 ASN cc_start: 0.7973 (OUTLIER) cc_final: 0.7574 (t0) REVERT: K 72 ASP cc_start: 0.7879 (m-30) cc_final: 0.7540 (m-30) REVERT: K 94 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8200 (tt0) REVERT: K 109 LEU cc_start: 0.8994 (OUTLIER) cc_final: 0.8532 (mp) REVERT: K 247 ARG cc_start: 0.8587 (mtt-85) cc_final: 0.8315 (mtm180) REVERT: K 306 ARG cc_start: 0.8126 (OUTLIER) cc_final: 0.7677 (mmt-90) REVERT: L 40 LYS cc_start: 0.8278 (OUTLIER) cc_final: 0.7844 (mtpt) REVERT: L 70 LYS cc_start: 0.8029 (OUTLIER) cc_final: 0.7611 (ttpt) REVERT: L 80 LYS cc_start: 0.9228 (OUTLIER) cc_final: 0.8949 (mtpt) REVERT: L 94 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8091 (tm-30) REVERT: L 284 LYS cc_start: 0.8750 (OUTLIER) cc_final: 0.8357 (mtpt) REVERT: M 107 LYS cc_start: 0.8390 (mtpp) cc_final: 0.7957 (mttm) REVERT: M 247 ARG cc_start: 0.8774 (mtt180) cc_final: 0.8478 (mtm110) REVERT: M 284 LYS cc_start: 0.8601 (OUTLIER) cc_final: 0.8016 (mttt) REVERT: N 27 ARG cc_start: 0.7944 (OUTLIER) cc_final: 0.7363 (mtp180) REVERT: N 64 LYS cc_start: 0.8421 (ttmm) cc_final: 0.8012 (ttpt) REVERT: N 108 GLU cc_start: 0.7992 (mm-30) cc_final: 0.7738 (tp30) REVERT: N 184 ASP cc_start: 0.7996 (OUTLIER) cc_final: 0.7483 (m-30) REVERT: N 247 ARG cc_start: 0.8446 (ttm-80) cc_final: 0.8090 (mtt90) REVERT: N 251 MET cc_start: 0.8553 (OUTLIER) cc_final: 0.8281 (mtm) REVERT: N 284 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7521 (mttt) outliers start: 69 outliers final: 34 residues processed: 252 average time/residue: 0.8683 time to fit residues: 234.8051 Evaluate side-chains 253 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 202 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 60 LEU Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 148 ILE Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain J residue 284 LYS Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 GLN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 109 LEU Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 40 LYS Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 80 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain L residue 284 LYS Chi-restraints excluded: chain L residue 339 ASP Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 284 LYS Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 184 ASP Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 251 MET Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 85 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 128 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 178 optimal weight: 0.8980 chunk 107 optimal weight: 0.9980 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 0.3980 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 114 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.137115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.109836 restraints weight = 15749.570| |-----------------------------------------------------------------------------| r_work (start): 0.3131 rms_B_bonded: 1.14 r_work: 0.2986 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2882 rms_B_bonded: 2.68 restraints_weight: 0.2500 r_work (final): 0.2882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8777 moved from start: 0.1607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 16078 Z= 0.102 Angle : 0.434 5.664 21780 Z= 0.236 Chirality : 0.039 0.137 2460 Planarity : 0.004 0.047 2739 Dihedral : 12.033 85.670 2612 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.21 % Favored : 99.79 % Rotamer: Outliers : 2.70 % Allowed : 18.92 % Favored : 78.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.19), residues: 1938 helix: 0.99 (0.18), residues: 870 sheet: 1.31 (0.30), residues: 288 loop : -0.69 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 27 TYR 0.008 0.001 TYR M 315 PHE 0.011 0.001 PHE N 126 HIS 0.002 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00218 (16078) covalent geometry : angle 0.43390 (21780) hydrogen bonds : bond 0.03629 ( 754) hydrogen bonds : angle 4.36598 ( 2046) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 213 time to evaluate : 0.752 Fit side-chains REVERT: C 19 LYS cc_start: 0.7859 (OUTLIER) cc_final: 0.6800 (tppp) REVERT: I 27 ARG cc_start: 0.7607 (OUTLIER) cc_final: 0.7340 (tpt90) REVERT: I 247 ARG cc_start: 0.8473 (mtt-85) cc_final: 0.8065 (mtm110) REVERT: I 251 MET cc_start: 0.8521 (mtp) cc_final: 0.8015 (tpt) REVERT: J 39 LYS cc_start: 0.7922 (mmtt) cc_final: 0.7527 (mmmt) REVERT: J 84 MET cc_start: 0.8357 (mmm) cc_final: 0.7200 (mtm) REVERT: K 20 PHE cc_start: 0.5147 (OUTLIER) cc_final: 0.4497 (p90) REVERT: K 39 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7485 (ttpt) REVERT: K 62 ASN cc_start: 0.7878 (OUTLIER) cc_final: 0.7414 (t0) REVERT: K 64 LYS cc_start: 0.7871 (tmtt) cc_final: 0.7571 (tttp) REVERT: K 72 ASP cc_start: 0.7820 (m-30) cc_final: 0.7428 (m-30) REVERT: K 213 GLU cc_start: 0.8033 (mm-30) cc_final: 0.7621 (mp0) REVERT: K 247 ARG cc_start: 0.8619 (mtt-85) cc_final: 0.8231 (mtt180) REVERT: K 306 ARG cc_start: 0.8079 (OUTLIER) cc_final: 0.7541 (mmt180) REVERT: L 70 LYS cc_start: 0.7977 (OUTLIER) cc_final: 0.7573 (ttpt) REVERT: L 94 GLN cc_start: 0.8400 (OUTLIER) cc_final: 0.8060 (tm-30) REVERT: M 107 LYS cc_start: 0.8290 (mtpp) cc_final: 0.7890 (mttm) REVERT: M 247 ARG cc_start: 0.8764 (mtt180) cc_final: 0.8463 (mtm110) REVERT: N 27 ARG cc_start: 0.7888 (OUTLIER) cc_final: 0.7099 (mtp180) REVERT: N 64 LYS cc_start: 0.8373 (ttmm) cc_final: 0.7963 (ttpt) REVERT: N 108 GLU cc_start: 0.7955 (mm-30) cc_final: 0.7704 (tp30) REVERT: N 128 GLU cc_start: 0.8007 (tt0) cc_final: 0.7556 (tt0) REVERT: N 184 ASP cc_start: 0.7704 (m-30) cc_final: 0.7214 (m-30) REVERT: N 247 ARG cc_start: 0.8416 (ttm-80) cc_final: 0.8076 (mtt90) REVERT: N 251 MET cc_start: 0.8459 (ttm) cc_final: 0.8140 (mtm) REVERT: N 284 LYS cc_start: 0.8177 (OUTLIER) cc_final: 0.7432 (mttt) outliers start: 43 outliers final: 27 residues processed: 244 average time/residue: 0.9116 time to fit residues: 237.9470 Evaluate side-chains 249 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 213 time to evaluate : 0.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 114 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 51 optimal weight: 8.9990 chunk 63 optimal weight: 2.9990 chunk 151 optimal weight: 0.0770 chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 145 optimal weight: 4.9990 chunk 30 optimal weight: 10.0000 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.134377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.107038 restraints weight = 15867.477| |-----------------------------------------------------------------------------| r_work (start): 0.3080 rms_B_bonded: 1.02 r_work: 0.2945 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2841 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 16078 Z= 0.170 Angle : 0.520 6.134 21780 Z= 0.280 Chirality : 0.042 0.153 2460 Planarity : 0.005 0.078 2739 Dihedral : 12.253 87.840 2612 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 3.21 % Allowed : 18.54 % Favored : 78.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.43 (0.19), residues: 1938 helix: 0.88 (0.18), residues: 870 sheet: 1.26 (0.30), residues: 288 loop : -0.71 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 130 TYR 0.011 0.002 TYR M 315 PHE 0.012 0.002 PHE K 195 HIS 0.003 0.001 HIS K 294 Details of bonding type rmsd covalent geometry : bond 0.00397 (16078) covalent geometry : angle 0.52004 (21780) hydrogen bonds : bond 0.05065 ( 754) hydrogen bonds : angle 4.69006 ( 2046) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 208 time to evaluate : 0.711 Fit side-chains REVERT: C 19 LYS cc_start: 0.7893 (OUTLIER) cc_final: 0.6891 (tppt) REVERT: I 27 ARG cc_start: 0.7608 (OUTLIER) cc_final: 0.7382 (tmt170) REVERT: I 36 ASN cc_start: 0.7526 (OUTLIER) cc_final: 0.7258 (m110) REVERT: I 247 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8090 (mtm110) REVERT: I 251 MET cc_start: 0.8505 (mtp) cc_final: 0.8020 (tpt) REVERT: J 39 LYS cc_start: 0.7999 (mmtt) cc_final: 0.7602 (mmmt) REVERT: J 84 MET cc_start: 0.8356 (mmm) cc_final: 0.7219 (mtm) REVERT: K 20 PHE cc_start: 0.5181 (OUTLIER) cc_final: 0.4487 (p90) REVERT: K 39 LYS cc_start: 0.8035 (mtpp) cc_final: 0.7511 (ttpt) REVERT: K 62 ASN cc_start: 0.7870 (OUTLIER) cc_final: 0.7397 (t0) REVERT: K 64 LYS cc_start: 0.7901 (tmtt) cc_final: 0.7615 (tttp) REVERT: K 72 ASP cc_start: 0.7807 (m-30) cc_final: 0.7406 (m-30) REVERT: K 213 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7630 (mp0) REVERT: K 247 ARG cc_start: 0.8600 (mtt-85) cc_final: 0.8326 (mtm180) REVERT: K 306 ARG cc_start: 0.8098 (OUTLIER) cc_final: 0.7769 (mmt-90) REVERT: L 70 LYS cc_start: 0.7982 (OUTLIER) cc_final: 0.7580 (ttpt) REVERT: L 94 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.8067 (tm-30) REVERT: M 107 LYS cc_start: 0.8328 (mtpp) cc_final: 0.7927 (mttm) REVERT: M 247 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8490 (mtm110) REVERT: M 284 LYS cc_start: 0.8567 (OUTLIER) cc_final: 0.8106 (mttt) REVERT: N 27 ARG cc_start: 0.7897 (OUTLIER) cc_final: 0.7195 (mtp180) REVERT: N 64 LYS cc_start: 0.8376 (ttmm) cc_final: 0.7970 (ttpt) REVERT: N 108 GLU cc_start: 0.7954 (mm-30) cc_final: 0.7699 (tp30) REVERT: N 184 ASP cc_start: 0.7808 (m-30) cc_final: 0.7297 (m-30) REVERT: N 247 ARG cc_start: 0.8376 (ttm-80) cc_final: 0.8066 (mtt90) REVERT: N 251 MET cc_start: 0.8478 (ttm) cc_final: 0.8199 (mtm) REVERT: N 284 LYS cc_start: 0.8167 (OUTLIER) cc_final: 0.7537 (mttt) outliers start: 51 outliers final: 30 residues processed: 243 average time/residue: 0.8976 time to fit residues: 233.6153 Evaluate side-chains 250 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 209 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 284 LYS Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 65 optimal weight: 7.9990 chunk 124 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 145 optimal weight: 4.9990 chunk 197 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 21 optimal weight: 5.9990 chunk 6 optimal weight: 10.0000 chunk 146 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.135196 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.108103 restraints weight = 15856.258| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 1.01 r_work: 0.2983 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2879 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2879 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 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 : 0.003 0.027 16078 Z= 0.142 Angle : 0.485 5.974 21780 Z= 0.263 Chirality : 0.041 0.147 2460 Planarity : 0.004 0.065 2739 Dihedral : 12.163 86.512 2612 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 2.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Rotamer: Outliers : 3.27 % Allowed : 18.54 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.19), residues: 1938 helix: 0.95 (0.18), residues: 870 sheet: 1.27 (0.30), residues: 288 loop : -0.69 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 27 TYR 0.010 0.001 TYR M 315 PHE 0.011 0.002 PHE K 195 HIS 0.003 0.001 HIS K 294 Details of bonding type rmsd covalent geometry : bond 0.00323 (16078) covalent geometry : angle 0.48539 (21780) hydrogen bonds : bond 0.04540 ( 754) hydrogen bonds : angle 4.58176 ( 2046) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 209 time to evaluate : 0.632 Fit side-chains REVERT: C 19 LYS cc_start: 0.7874 (OUTLIER) cc_final: 0.6872 (tppt) REVERT: I 27 ARG cc_start: 0.7625 (OUTLIER) cc_final: 0.7398 (tmt170) REVERT: I 247 ARG cc_start: 0.8454 (mtt-85) cc_final: 0.8067 (mtm110) REVERT: I 251 MET cc_start: 0.8492 (mtp) cc_final: 0.8005 (tpt) REVERT: J 39 LYS cc_start: 0.7998 (mmtt) cc_final: 0.7609 (mmmt) REVERT: K 20 PHE cc_start: 0.5201 (OUTLIER) cc_final: 0.4510 (p90) REVERT: K 39 LYS cc_start: 0.8049 (mtpp) cc_final: 0.7522 (ttpt) REVERT: K 62 ASN cc_start: 0.7860 (OUTLIER) cc_final: 0.7415 (t0) REVERT: K 64 LYS cc_start: 0.7869 (tmtt) cc_final: 0.7601 (tttp) REVERT: K 72 ASP cc_start: 0.7826 (m-30) cc_final: 0.7413 (m-30) REVERT: K 213 GLU cc_start: 0.8051 (mm-30) cc_final: 0.7592 (mp0) REVERT: K 247 ARG cc_start: 0.8609 (mtt-85) cc_final: 0.8324 (mtm180) REVERT: K 306 ARG cc_start: 0.8096 (OUTLIER) cc_final: 0.7587 (mmt-90) REVERT: L 70 LYS cc_start: 0.7983 (OUTLIER) cc_final: 0.7587 (ttpt) REVERT: L 94 GLN cc_start: 0.8391 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: M 26 SER cc_start: 0.8306 (OUTLIER) cc_final: 0.7961 (p) REVERT: M 107 LYS cc_start: 0.8308 (mtpp) cc_final: 0.7912 (mttm) REVERT: M 247 ARG cc_start: 0.8758 (mtt180) cc_final: 0.8479 (mtm110) REVERT: M 284 LYS cc_start: 0.8530 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: N 27 ARG cc_start: 0.7912 (OUTLIER) cc_final: 0.7176 (mtp180) REVERT: N 64 LYS cc_start: 0.8382 (ttmm) cc_final: 0.7992 (ttpt) REVERT: N 108 GLU cc_start: 0.7975 (mm-30) cc_final: 0.7721 (tp30) REVERT: N 184 ASP cc_start: 0.7744 (m-30) cc_final: 0.7248 (m-30) REVERT: N 247 ARG cc_start: 0.8365 (ttm-80) cc_final: 0.8049 (mtt90) REVERT: N 251 MET cc_start: 0.8462 (ttm) cc_final: 0.8135 (mtm) REVERT: N 284 LYS cc_start: 0.8178 (OUTLIER) cc_final: 0.7541 (mttt) outliers start: 52 outliers final: 33 residues processed: 245 average time/residue: 0.9114 time to fit residues: 238.9957 Evaluate side-chains 253 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 209 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 284 LYS Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 233 SER Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 173 optimal weight: 9.9990 chunk 85 optimal weight: 0.7980 chunk 148 optimal weight: 0.7980 chunk 84 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 135 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 157 optimal weight: 6.9990 chunk 188 optimal weight: 2.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.134789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.106969 restraints weight = 15773.530| |-----------------------------------------------------------------------------| r_work (start): 0.3062 rms_B_bonded: 1.18 r_work: 0.2919 rms_B_bonded: 1.64 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8809 moved from start: 0.1627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16078 Z= 0.153 Angle : 0.502 6.011 21780 Z= 0.271 Chirality : 0.041 0.148 2460 Planarity : 0.004 0.070 2739 Dihedral : 12.198 87.291 2612 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 2.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 3.14 % Allowed : 18.54 % Favored : 78.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.45 (0.19), residues: 1938 helix: 0.90 (0.18), residues: 870 sheet: 1.25 (0.30), residues: 288 loop : -0.71 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 130 TYR 0.011 0.001 TYR M 315 PHE 0.012 0.002 PHE K 195 HIS 0.003 0.001 HIS K 294 Details of bonding type rmsd covalent geometry : bond 0.00351 (16078) covalent geometry : angle 0.50181 (21780) hydrogen bonds : bond 0.04762 ( 754) hydrogen bonds : angle 4.64511 ( 2046) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3876 Ramachandran restraints generated. 1938 Oldfield, 0 Emsley, 1938 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 208 time to evaluate : 0.636 Fit side-chains REVERT: C 19 LYS cc_start: 0.7887 (OUTLIER) cc_final: 0.6857 (tppt) REVERT: I 27 ARG cc_start: 0.7591 (OUTLIER) cc_final: 0.7360 (tmt170) REVERT: I 36 ASN cc_start: 0.7523 (OUTLIER) cc_final: 0.7248 (m-40) REVERT: I 58 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7434 (ptmt) REVERT: I 247 ARG cc_start: 0.8485 (mtt-85) cc_final: 0.8068 (mtm110) REVERT: I 251 MET cc_start: 0.8521 (mtp) cc_final: 0.8000 (tpt) REVERT: J 39 LYS cc_start: 0.7970 (mmtt) cc_final: 0.7558 (mmmt) REVERT: J 84 MET cc_start: 0.8382 (mmm) cc_final: 0.7287 (mtm) REVERT: K 20 PHE cc_start: 0.5213 (OUTLIER) cc_final: 0.4526 (p90) REVERT: K 39 LYS cc_start: 0.8041 (mtpp) cc_final: 0.7485 (ttpt) REVERT: K 62 ASN cc_start: 0.7846 (OUTLIER) cc_final: 0.7398 (t0) REVERT: K 64 LYS cc_start: 0.7912 (tmtt) cc_final: 0.7614 (tttp) REVERT: K 72 ASP cc_start: 0.7814 (m-30) cc_final: 0.7384 (m-30) REVERT: K 94 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: K 213 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7576 (mp0) REVERT: K 247 ARG cc_start: 0.8649 (mtt-85) cc_final: 0.8333 (mtm180) REVERT: K 306 ARG cc_start: 0.8110 (OUTLIER) cc_final: 0.7779 (mmt-90) REVERT: L 70 LYS cc_start: 0.7963 (OUTLIER) cc_final: 0.7537 (ttpt) REVERT: L 94 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.8078 (tm-30) REVERT: M 26 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7909 (p) REVERT: M 107 LYS cc_start: 0.8312 (mtpp) cc_final: 0.7896 (mttm) REVERT: M 247 ARG cc_start: 0.8795 (mtt180) cc_final: 0.8475 (mtm110) REVERT: M 284 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.8072 (mttt) REVERT: N 27 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7194 (mtp180) REVERT: N 64 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7978 (ttpt) REVERT: N 108 GLU cc_start: 0.7941 (mm-30) cc_final: 0.7684 (tp30) REVERT: N 184 ASP cc_start: 0.7741 (m-30) cc_final: 0.7218 (m-30) REVERT: N 247 ARG cc_start: 0.8390 (ttm-80) cc_final: 0.8039 (mtt90) REVERT: N 251 MET cc_start: 0.8490 (ttm) cc_final: 0.8154 (mtm) REVERT: N 284 LYS cc_start: 0.8217 (OUTLIER) cc_final: 0.7567 (mttt) outliers start: 50 outliers final: 33 residues processed: 244 average time/residue: 0.9052 time to fit residues: 236.3141 Evaluate side-chains 255 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 208 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain C residue 19 LYS Chi-restraints excluded: chain I residue 27 ARG Chi-restraints excluded: chain I residue 36 ASN Chi-restraints excluded: chain I residue 58 LYS Chi-restraints excluded: chain I residue 88 THR Chi-restraints excluded: chain I residue 99 ILE Chi-restraints excluded: chain I residue 130 ARG Chi-restraints excluded: chain I residue 148 ILE Chi-restraints excluded: chain I residue 233 SER Chi-restraints excluded: chain J residue 87 THR Chi-restraints excluded: chain J residue 183 SER Chi-restraints excluded: chain J residue 208 SER Chi-restraints excluded: chain J residue 223 SER Chi-restraints excluded: chain J residue 230 THR Chi-restraints excluded: chain K residue 20 PHE Chi-restraints excluded: chain K residue 61 ILE Chi-restraints excluded: chain K residue 62 ASN Chi-restraints excluded: chain K residue 87 THR Chi-restraints excluded: chain K residue 94 GLN Chi-restraints excluded: chain K residue 99 ILE Chi-restraints excluded: chain K residue 149 ASP Chi-restraints excluded: chain K residue 306 ARG Chi-restraints excluded: chain L residue 70 LYS Chi-restraints excluded: chain L residue 88 THR Chi-restraints excluded: chain L residue 94 GLN Chi-restraints excluded: chain L residue 99 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 149 ASP Chi-restraints excluded: chain L residue 233 SER Chi-restraints excluded: chain L residue 239 SER Chi-restraints excluded: chain M residue 26 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 88 THR Chi-restraints excluded: chain M residue 109 LEU Chi-restraints excluded: chain M residue 130 ARG Chi-restraints excluded: chain M residue 230 THR Chi-restraints excluded: chain M residue 233 SER Chi-restraints excluded: chain M residue 284 LYS Chi-restraints excluded: chain M residue 334 VAL Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 52 VAL Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 230 THR Chi-restraints excluded: chain N residue 233 SER Chi-restraints excluded: chain N residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 122 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 0.0670 chunk 146 optimal weight: 0.9990 chunk 144 optimal weight: 7.9990 chunk 112 optimal weight: 1.9990 chunk 193 optimal weight: 0.7980 chunk 156 optimal weight: 2.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 9.9990 overall best weight: 0.7120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 202 GLN K 272 GLN N 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.137615 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.110823 restraints weight = 15762.499| |-----------------------------------------------------------------------------| r_work (start): 0.3146 rms_B_bonded: 1.08 r_work: 0.2996 rms_B_bonded: 1.63 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.1666 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 16078 Z= 0.095 Angle : 0.425 5.663 21780 Z= 0.231 Chirality : 0.039 0.135 2460 Planarity : 0.004 0.042 2739 Dihedral : 11.894 87.752 2612 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Rotamer: Outliers : 2.64 % Allowed : 19.17 % Favored : 78.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.32 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.16 (0.19), residues: 1938 helix: 1.45 (0.18), residues: 828 sheet: 1.63 (0.30), residues: 276 loop : -0.17 (0.21), residues: 834 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 27 TYR 0.008 0.001 TYR M 315 PHE 0.009 0.001 PHE N 126 HIS 0.002 0.001 HIS K 93 Details of bonding type rmsd covalent geometry : bond 0.00198 (16078) covalent geometry : angle 0.42532 (21780) hydrogen bonds : bond 0.03442 ( 754) hydrogen bonds : angle 4.28353 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6975.82 seconds wall clock time: 119 minutes 3.77 seconds (7143.77 seconds total)