Starting phenix.real_space_refine on Fri Jul 3 20:56:45 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9srz_55166/07_2026/9srz_55166.cif Found real_map, /net/cci-nas-00/data/ceres_data/9srz_55166/07_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_55166/07_2026/9srz_55166.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9srz_55166/07_2026/9srz_55166.map" model { file = "/net/cci-nas-00/data/ceres_data/9srz_55166/07_2026/9srz_55166.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9srz_55166/07_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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, 31 Ad-hoc single atom residues: {' CA': 3} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 3 Chain: "J" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "K" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "L" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "M" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 31 Ad-hoc single atom residues: {' CA': 2} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 2 Chain: "N" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 31 Ad-hoc single atom residues: {' CA': 1} Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain breaks: 1 Time building chain proxies: 3.18, per 1000 atoms: 0.20 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: 1.07 Conformation dependent library (CDL) restraints added in 638.9 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: 0.47 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: 2.61 Time building geometry restraints manager: 1.48 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: 21433 1.68 - 3.36: 291 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: 1530 0.029 - 0.057: 600 0.057 - 0.086: 172 0.086 - 0.115: 137 0.115 - 0.143: 21 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 3.250 nonbonded pdb=" O SER M 296 " pdb="CA CA M 403 " model vdw 2.306 3.250 nonbonded pdb=" O SER K 296 " pdb="CA CA K 403 " model vdw 2.316 3.250 nonbonded pdb="CA CA M 403 " pdb=" O1G ATP N 401 " model vdw 2.324 3.250 nonbonded pdb=" O1G ATP I 401 " pdb="CA CA I 403 " model vdw 2.325 3.250 ... (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: 3.010 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: 0.340 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 14.100 Find NCS groups from input model: 0.410 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:6.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 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= 0.179 Angle : 0.511 8.399 21780 Z= 0.276 Chirality : 0.040 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/Z covalent geometry : bond 0.00316 / 0.18 (16078) covalent geometry : angle 0.51129 / 0.28 (21780) hydrogen bonds : bond 0.17959 / 11.28 ( 754) hydrogen bonds : angle 6.40196 / 4.56 ( 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 : 0.501 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: 0.8336 time to fit residues: 232.1630 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 : 0.563 ------------------------------------------------------------------------------- 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... J 36 ASN J 202 GLN K 272 GLN L 34 ASN M 94 GLN N 114 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.137643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.110540 restraints weight = 15781.075| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.16 r_work: 0.2997 rms_B_bonded: 1.68 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.0882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 16078 Z= 0.109 Angle : 0.455 5.669 21780 Z= 0.250 Chirality : 0.039 0.132 2460 Planarity : 0.004 0.040 2739 Dihedral : 11.468 82.964 2619 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.45 % Allowed : 19.11 % 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: 0.64 (0.19), residues: 1938 helix: 1.02 (0.18), residues: 870 sheet: 1.63 (0.31), residues: 288 loop : -0.68 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 27 TYR 0.009 0.001 TYR M 315 PHE 0.012 0.001 PHE K 129 HIS 0.002 0.001 HIS J 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00214 / 0.11 (16078) covalent geometry : angle 0.45474 / 0.25 (21780) hydrogen bonds : bond 0.04548 / 2.99 ( 754) hydrogen bonds : angle 4.81231 / 3.46 ( 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 263 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 224 time to evaluate : 0.527 Fit side-chains REVERT: I 27 ARG cc_start: 0.7381 (tmt170) cc_final: 0.7162 (tpt90) REVERT: I 39 LYS cc_start: 0.7753 (tptt) cc_final: 0.6912 (mmmt) REVERT: I 130 ARG cc_start: 0.8275 (OUTLIER) cc_final: 0.6755 (ptp-170) REVERT: I 247 ARG cc_start: 0.8447 (mtt-85) cc_final: 0.8057 (mtm110) REVERT: I 251 MET cc_start: 0.8551 (mtp) cc_final: 0.7984 (tpt) REVERT: J 39 LYS cc_start: 0.7657 (mmtt) cc_final: 0.7237 (mmmt) REVERT: K 39 LYS cc_start: 0.7970 (mtpp) cc_final: 0.7460 (ttpt) REVERT: K 72 ASP cc_start: 0.7827 (m-30) cc_final: 0.7479 (m-30) REVERT: K 108 GLU cc_start: 0.8599 (mm-30) cc_final: 0.8344 (mm-30) REVERT: K 213 GLU cc_start: 0.8137 (mm-30) cc_final: 0.7739 (mp0) REVERT: K 247 ARG cc_start: 0.8620 (mtt-85) cc_final: 0.8278 (mtt180) REVERT: L 20 PHE cc_start: 0.6211 (OUTLIER) cc_final: 0.4816 (m-80) REVERT: L 87 THR cc_start: 0.8717 (p) cc_final: 0.8515 (t) REVERT: L 176 GLU cc_start: 0.8291 (tp30) cc_final: 0.7981 (tm-30) REVERT: L 202 GLN cc_start: 0.8712 (tp-100) cc_final: 0.8496 (mm-40) REVERT: L 247 ARG cc_start: 0.8484 (ttm-80) cc_final: 0.8282 (mtm110) REVERT: M 68 GLU cc_start: 0.7497 (OUTLIER) cc_final: 0.6897 (mp0) REVERT: M 99 ILE cc_start: 0.7824 (mm) cc_final: 0.7505 (tt) REVERT: M 107 LYS cc_start: 0.8289 (mtpp) cc_final: 0.7896 (mttm) REVERT: M 202 GLN cc_start: 0.8451 (tp40) cc_final: 0.8209 (mm110) REVERT: M 247 ARG cc_start: 0.8762 (mtt180) cc_final: 0.8440 (mtm110) REVERT: N 64 LYS cc_start: 0.8293 (ttmm) cc_final: 0.7782 (ttpt) REVERT: N 107 LYS cc_start: 0.8165 (mtmm) cc_final: 0.7832 (mttm) REVERT: N 176 GLU cc_start: 0.8168 (tt0) cc_final: 0.7845 (tp30) REVERT: N 247 ARG cc_start: 0.8415 (ttm-80) cc_final: 0.8104 (mtt180) REVERT: N 251 MET cc_start: 0.8463 (ttm) cc_final: 0.8122 (mtm) outliers start: 39 outliers final: 21 residues processed: 250 average time/residue: 0.8068 time to fit residues: 216.8692 Evaluate side-chains 241 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 217 time to evaluate : 0.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 1 MET Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain I residue 48 THR 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 230 THR 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 20 PHE 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 L residue 233 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 68 GLU Chi-restraints excluded: chain M residue 87 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 52 VAL Chi-restraints excluded: chain N residue 230 THR 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: 0.0020 chunk 95 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 122 optimal weight: 3.9990 chunk 121 optimal weight: 4.9990 chunk 140 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 overall best weight: 3.7996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3420 r_free = 0.3420 target = 0.130585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.100861 restraints weight = 16207.342| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 1.44 r_work: 0.2891 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 3.01 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9067 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.079 16078 Z= 0.281 Angle : 0.661 7.629 21780 Z= 0.356 Chirality : 0.048 0.167 2460 Planarity : 0.006 0.122 2739 Dihedral : 12.010 88.261 2613 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 2.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Rotamer: Outliers : 4.27 % Allowed : 17.16 % 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: 0.13 (0.18), residues: 1938 helix: 0.51 (0.17), residues: 864 sheet: 1.33 (0.29), residues: 288 loop : -0.80 (0.20), residues: 786 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 229 TYR 0.015 0.002 TYR M 159 PHE 0.015 0.002 PHE K 195 HIS 0.008 0.002 HIS J 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00674 / 0.28 (16078) covalent geometry : angle 0.66071 / 0.36 (21780) hydrogen bonds : bond 0.06988 / 4.68 ( 754) hydrogen bonds : angle 5.26206 / 3.75 ( 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 : 0.624 Fit side-chains REVERT: I 27 ARG cc_start: 0.7514 (tmt170) cc_final: 0.7311 (tpt90) REVERT: I 36 ASN cc_start: 0.7435 (OUTLIER) cc_final: 0.7132 (m110) REVERT: I 39 LYS cc_start: 0.7795 (tptt) cc_final: 0.7140 (mmmt) REVERT: I 247 ARG cc_start: 0.8589 (mtt-85) cc_final: 0.8156 (mtm110) REVERT: I 251 MET cc_start: 0.8616 (mtp) cc_final: 0.8015 (tpt) REVERT: K 20 PHE cc_start: 0.5207 (OUTLIER) cc_final: 0.4570 (p90) REVERT: K 39 LYS cc_start: 0.8068 (mtpp) cc_final: 0.7544 (ttpt) REVERT: K 72 ASP cc_start: 0.7909 (m-30) cc_final: 0.7549 (m-30) REVERT: K 213 GLU cc_start: 0.8265 (mm-30) cc_final: 0.7872 (mp0) REVERT: K 247 ARG cc_start: 0.8668 (mtt-85) cc_final: 0.8343 (mtm180) REVERT: K 284 LYS cc_start: 0.8563 (OUTLIER) cc_final: 0.7984 (mttt) REVERT: K 306 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7776 (mmt180) REVERT: L 20 PHE cc_start: 0.6061 (OUTLIER) cc_final: 0.4844 (m-80) REVERT: L 40 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7763 (mtpt) REVERT: L 70 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7610 (ttpt) REVERT: L 94 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.8117 (tm-30) REVERT: L 202 GLN cc_start: 0.8802 (tp-100) cc_final: 0.8590 (mm-40) REVERT: L 247 ARG cc_start: 0.8637 (ttm-80) cc_final: 0.8397 (mtm110) REVERT: M 68 GLU cc_start: 0.7472 (OUTLIER) cc_final: 0.6922 (mp0) REVERT: M 107 LYS cc_start: 0.8384 (mtpp) cc_final: 0.7948 (mttm) REVERT: M 202 GLN cc_start: 0.8570 (tp40) cc_final: 0.8303 (mm110) REVERT: M 247 ARG cc_start: 0.8878 (mtt180) cc_final: 0.8523 (mtm110) REVERT: M 284 LYS cc_start: 0.8611 (OUTLIER) cc_final: 0.7988 (mttt) REVERT: N 27 ARG cc_start: 0.7966 (OUTLIER) cc_final: 0.7124 (mtp180) REVERT: N 64 LYS cc_start: 0.8331 (ttmm) cc_final: 0.7848 (ttpt) REVERT: N 247 ARG cc_start: 0.8490 (ttm-80) cc_final: 0.8097 (mtt90) REVERT: N 251 MET cc_start: 0.8667 (ttm) cc_final: 0.8367 (mtm) REVERT: N 284 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7557 (mttt) outliers start: 68 outliers final: 31 residues processed: 251 average time/residue: 0.7969 time to fit residues: 214.9888 Evaluate side-chains 249 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 206 time to evaluate : 0.512 ------------------------------------------------------------------------------- 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 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 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 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 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 68 GLU 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 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 213 GLU Chi-restraints excluded: chain N residue 230 THR 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: 8.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 134 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 156 optimal weight: 0.7980 overall best weight: 0.7460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... J 202 GLN K 272 GLN M 94 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3493 r_free = 0.3493 target = 0.136344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.109234 restraints weight = 15919.334| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 1.00 r_work: 0.2998 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2894 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 16078 Z= 0.109 Angle : 0.447 6.014 21780 Z= 0.245 Chirality : 0.039 0.135 2460 Planarity : 0.004 0.045 2739 Dihedral : 11.758 86.393 2612 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 3.08 % Allowed : 18.73 % 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: 0.50 (0.19), residues: 1938 helix: 0.91 (0.18), residues: 870 sheet: 1.42 (0.30), residues: 288 loop : -0.69 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 27 TYR 0.009 0.001 TYR M 315 PHE 0.009 0.001 PHE K 129 HIS 0.002 0.001 HIS J 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.11 (16078) covalent geometry : angle 0.44666 / 0.24 (21780) hydrogen bonds : bond 0.04168 / 2.77 ( 754) hydrogen bonds : angle 4.55401 / 3.27 ( 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 267 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 218 time to evaluate : 0.611 Fit side-chains REVERT: I 27 ARG cc_start: 0.7543 (tmt170) cc_final: 0.7230 (tpt90) REVERT: I 39 LYS cc_start: 0.7687 (tptt) cc_final: 0.6930 (mmmt) REVERT: I 130 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.6600 (ptp-170) REVERT: I 247 ARG cc_start: 0.8439 (mtt-85) cc_final: 0.8070 (mtm110) REVERT: I 251 MET cc_start: 0.8484 (mtp) cc_final: 0.7995 (tpt) REVERT: J 39 LYS cc_start: 0.7832 (mmtt) cc_final: 0.7435 (mmmt) REVERT: K 39 LYS cc_start: 0.8031 (mtpp) cc_final: 0.7510 (ttpt) REVERT: K 72 ASP cc_start: 0.7852 (m-30) cc_final: 0.7512 (m-30) REVERT: K 213 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7702 (mp0) REVERT: K 247 ARG cc_start: 0.8555 (mtt-85) cc_final: 0.8286 (mtm180) REVERT: K 284 LYS cc_start: 0.8492 (OUTLIER) cc_final: 0.7957 (mttt) REVERT: L 70 LYS cc_start: 0.7950 (OUTLIER) cc_final: 0.7581 (ttpt) REVERT: L 87 THR cc_start: 0.8827 (p) cc_final: 0.8497 (t) REVERT: L 94 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7980 (tm-30) REVERT: M 68 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.6953 (mp0) REVERT: M 107 LYS cc_start: 0.8303 (mtpp) cc_final: 0.7906 (mttm) REVERT: M 247 ARG cc_start: 0.8739 (mtt180) cc_final: 0.8454 (mtm110) REVERT: N 27 ARG cc_start: 0.8005 (OUTLIER) cc_final: 0.7114 (mtp180) REVERT: N 64 LYS cc_start: 0.8292 (ttmm) cc_final: 0.7835 (ttpt) REVERT: N 184 ASP cc_start: 0.7868 (m-30) cc_final: 0.7386 (m-30) REVERT: N 247 ARG cc_start: 0.8371 (ttm-80) cc_final: 0.8068 (mtt90) REVERT: N 251 MET cc_start: 0.8453 (OUTLIER) cc_final: 0.8080 (mtm) REVERT: N 284 LYS cc_start: 0.8154 (OUTLIER) cc_final: 0.7474 (mttt) outliers start: 49 outliers final: 26 residues processed: 249 average time/residue: 0.8369 time to fit residues: 223.6731 Evaluate side-chains 245 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 211 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER 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 230 THR Chi-restraints excluded: chain K residue 61 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 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 158 MET Chi-restraints excluded: chain L residue 230 THR 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 68 GLU 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 27 ARG Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 176 GLU Chi-restraints excluded: chain N residue 213 GLU 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 79 optimal weight: 10.0000 chunk 30 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 58 optimal weight: 1.9990 chunk 169 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 64 optimal weight: 6.9990 chunk 147 optimal weight: 3.9990 chunk 141 optimal weight: 9.9990 chunk 103 optimal weight: 0.7980 chunk 188 optimal weight: 0.7980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3476 r_free = 0.3476 target = 0.134870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.107676 restraints weight = 15928.944| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.00 r_work: 0.2963 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2859 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9008 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 : 0.003 0.042 16078 Z= 0.151 Angle : 0.495 6.131 21780 Z= 0.268 Chirality : 0.041 0.146 2460 Planarity : 0.004 0.071 2739 Dihedral : 11.798 87.894 2612 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 3.90 % Allowed : 17.79 % 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: 0.51 (0.19), residues: 1938 helix: 0.93 (0.18), residues: 870 sheet: 1.37 (0.30), residues: 288 loop : -0.68 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG A 3 TYR 0.010 0.001 TYR M 315 PHE 0.011 0.002 PHE K 195 HIS 0.004 0.001 HIS J 138 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.15 (16078) covalent geometry : angle 0.49467 / 0.27 (21780) hydrogen bonds : bond 0.04779 / 3.20 ( 754) hydrogen bonds : angle 4.64899 / 3.33 ( 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 272 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 210 time to evaluate : 0.453 Fit side-chains REVERT: C 19 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.6912 (tppp) REVERT: I 27 ARG cc_start: 0.7509 (tmt170) cc_final: 0.7247 (tpt90) REVERT: I 36 ASN cc_start: 0.7475 (OUTLIER) cc_final: 0.7189 (m110) REVERT: I 39 LYS cc_start: 0.7661 (tptt) cc_final: 0.6922 (mmmt) REVERT: I 247 ARG cc_start: 0.8444 (mtt-85) cc_final: 0.8069 (mtm110) REVERT: I 251 MET cc_start: 0.8494 (mtp) cc_final: 0.8010 (tpt) REVERT: J 39 LYS cc_start: 0.7869 (mmtt) cc_final: 0.7472 (mmmt) REVERT: J 84 MET cc_start: 0.8407 (mmm) cc_final: 0.7211 (mtm) REVERT: J 284 LYS cc_start: 0.8592 (OUTLIER) cc_final: 0.8361 (mtmt) REVERT: K 20 PHE cc_start: 0.5258 (OUTLIER) cc_final: 0.4622 (p90) REVERT: K 39 LYS cc_start: 0.8062 (mtpp) cc_final: 0.7543 (ttpt) REVERT: K 62 ASN cc_start: 0.7927 (OUTLIER) cc_final: 0.7379 (t0) REVERT: K 72 ASP cc_start: 0.7839 (m-30) cc_final: 0.7481 (m-30) REVERT: K 247 ARG cc_start: 0.8573 (mtt-85) cc_final: 0.8299 (mtm180) REVERT: K 284 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.7963 (mttt) REVERT: L 40 LYS cc_start: 0.8163 (OUTLIER) cc_final: 0.7720 (mtpt) REVERT: L 70 LYS cc_start: 0.7964 (OUTLIER) cc_final: 0.7613 (ttpt) REVERT: L 94 GLN cc_start: 0.8317 (OUTLIER) cc_final: 0.7970 (tm-30) REVERT: M 68 GLU cc_start: 0.7387 (OUTLIER) cc_final: 0.6875 (mp0) REVERT: M 107 LYS cc_start: 0.8305 (mtpp) cc_final: 0.7912 (mttm) REVERT: M 247 ARG cc_start: 0.8757 (mtt180) cc_final: 0.8472 (mtm110) REVERT: N 27 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7111 (mtp180) REVERT: N 64 LYS cc_start: 0.8244 (ttmm) cc_final: 0.7815 (ttpt) REVERT: N 184 ASP cc_start: 0.7886 (m-30) cc_final: 0.7377 (m-30) REVERT: N 247 ARG cc_start: 0.8351 (ttm-80) cc_final: 0.8047 (mtt90) REVERT: N 251 MET cc_start: 0.8452 (OUTLIER) cc_final: 0.8067 (mtm) REVERT: N 284 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7484 (mttt) outliers start: 62 outliers final: 30 residues processed: 252 average time/residue: 0.8263 time to fit residues: 223.8067 Evaluate side-chains 253 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 8 SER Chi-restraints excluded: chain E residue 4 SER Chi-restraints excluded: chain C residue 19 LYS 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 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 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 230 THR Chi-restraints excluded: chain K residue 284 LYS Chi-restraints excluded: chain L residue 40 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 26 SER Chi-restraints excluded: chain M residue 68 GLU 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 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 213 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 71 optimal weight: 6.9990 chunk 16 optimal weight: 0.5980 chunk 106 optimal weight: 2.9990 chunk 182 optimal weight: 6.9990 chunk 42 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 110 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 133 optimal weight: 7.9990 chunk 126 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3434 r_free = 0.3434 target = 0.131525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.103981 restraints weight = 15966.273| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 1.01 r_work: 0.2948 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2844 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9042 moved from start: 0.1514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.073 16078 Z= 0.272 Angle : 0.632 7.077 21780 Z= 0.340 Chirality : 0.047 0.166 2460 Planarity : 0.006 0.122 2739 Dihedral : 12.181 89.705 2612 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer: Outliers : 3.90 % Allowed : 17.98 % Favored : 78.13 % 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: 0.17 (0.18), residues: 1938 helix: 0.58 (0.17), residues: 870 sheet: 1.23 (0.29), residues: 288 loop : -0.79 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 3 TYR 0.014 0.002 TYR J 228 PHE 0.015 0.002 PHE K 195 HIS 0.006 0.001 HIS K 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00658 / 0.27 (16078) covalent geometry : angle 0.63155 / 0.34 (21780) hydrogen bonds : bond 0.06411 / 4.31 ( 754) hydrogen bonds : angle 5.04389 / 3.60 ( 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 266 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 204 time to evaluate : 0.633 Fit side-chains REVERT: C 19 LYS cc_start: 0.7995 (OUTLIER) cc_final: 0.6932 (tppp) REVERT: I 36 ASN cc_start: 0.7416 (OUTLIER) cc_final: 0.7120 (m110) REVERT: I 247 ARG cc_start: 0.8508 (mtt-85) cc_final: 0.8110 (mtm110) REVERT: I 251 MET cc_start: 0.8502 (mtp) cc_final: 0.7981 (tpt) REVERT: J 39 LYS cc_start: 0.7985 (mmtt) cc_final: 0.7578 (mmmt) REVERT: J 84 MET cc_start: 0.8398 (mmm) cc_final: 0.7256 (mtm) REVERT: J 284 LYS cc_start: 0.8636 (OUTLIER) cc_final: 0.8383 (mtmt) REVERT: K 20 PHE cc_start: 0.5296 (OUTLIER) cc_final: 0.4617 (p90) REVERT: K 39 LYS cc_start: 0.8078 (mtpp) cc_final: 0.7573 (ttpt) REVERT: K 62 ASN cc_start: 0.7958 (OUTLIER) cc_final: 0.7554 (t0) REVERT: K 72 ASP cc_start: 0.7859 (m-30) cc_final: 0.7491 (m-30) REVERT: K 94 GLN cc_start: 0.8406 (OUTLIER) cc_final: 0.8135 (tt0) REVERT: K 109 LEU cc_start: 0.9003 (OUTLIER) cc_final: 0.8460 (mp) REVERT: K 247 ARG cc_start: 0.8572 (mtt-85) cc_final: 0.8305 (mtm180) REVERT: K 284 LYS cc_start: 0.8571 (OUTLIER) cc_final: 0.7975 (mttt) REVERT: K 306 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7678 (mmt180) REVERT: L 40 LYS cc_start: 0.8231 (OUTLIER) cc_final: 0.7784 (mtpt) REVERT: L 70 LYS cc_start: 0.7998 (OUTLIER) cc_final: 0.7603 (ttpt) REVERT: L 94 GLN cc_start: 0.8376 (OUTLIER) cc_final: 0.8040 (tm-30) REVERT: L 284 LYS cc_start: 0.8718 (OUTLIER) cc_final: 0.8327 (mtpt) REVERT: M 107 LYS cc_start: 0.8362 (mtpp) cc_final: 0.7930 (mttm) REVERT: M 247 ARG cc_start: 0.8773 (mtt180) cc_final: 0.8481 (mtm110) REVERT: M 284 LYS cc_start: 0.8581 (OUTLIER) cc_final: 0.7998 (mttt) REVERT: N 27 ARG cc_start: 0.7920 (OUTLIER) cc_final: 0.7220 (mtp180) REVERT: N 64 LYS cc_start: 0.8339 (ttmm) cc_final: 0.7903 (ttpt) REVERT: N 184 ASP cc_start: 0.7979 (OUTLIER) cc_final: 0.7454 (m-30) REVERT: N 247 ARG cc_start: 0.8380 (ttm-80) cc_final: 0.8063 (mtt90) REVERT: N 251 MET cc_start: 0.8540 (OUTLIER) cc_final: 0.8260 (mtm) REVERT: N 284 LYS cc_start: 0.8182 (OUTLIER) cc_final: 0.7524 (mttt) outliers start: 62 outliers final: 31 residues processed: 248 average time/residue: 0.8683 time to fit residues: 231.6005 Evaluate side-chains 251 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 202 time to evaluate : 0.596 ------------------------------------------------------------------------------- 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 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 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 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 284 LYS 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 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 284 LYS 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 213 GLU 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: 0.9990 chunk 130 optimal weight: 0.0770 chunk 100 optimal weight: 0.7980 chunk 128 optimal weight: 0.9980 chunk 31 optimal weight: 3.9990 chunk 178 optimal weight: 1.9990 chunk 107 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 74 optimal weight: 0.0060 chunk 60 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 overall best weight: 0.5354 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3482 r_free = 0.3482 target = 0.135632 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.105693 restraints weight = 15957.805| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.16 r_work: 0.2994 rms_B_bonded: 1.74 restraints_weight: 0.5000 r_work: 0.2887 rms_B_bonded: 2.84 restraints_weight: 0.2500 r_work (final): 0.2887 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.1523 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= 0.098 Angle : 0.430 6.040 21780 Z= 0.236 Chirality : 0.039 0.136 2460 Planarity : 0.004 0.044 2739 Dihedral : 11.838 86.330 2612 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % 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: 0.60 (0.19), residues: 1938 helix: 1.02 (0.18), residues: 870 sheet: 1.32 (0.30), residues: 288 loop : -0.62 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 27 TYR 0.008 0.001 TYR M 315 PHE 0.010 0.001 PHE K 129 HIS 0.003 0.001 HIS K 244 Details of bonding type rmsd/Z covalent geometry : bond 0.00197 / 0.10 (16078) covalent geometry : angle 0.42992 / 0.24 (21780) hydrogen bonds : bond 0.03682 / 2.45 ( 754) hydrogen bonds : angle 4.37912 / 3.14 ( 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: 42 poor density : 214 time to evaluate : 0.585 Fit side-chains REVERT: I 27 ARG cc_start: 0.7557 (tmt170) cc_final: 0.7264 (tpt90) REVERT: I 247 ARG cc_start: 0.8517 (mtt-85) cc_final: 0.8098 (mtm110) REVERT: I 251 MET cc_start: 0.8517 (mtp) cc_final: 0.8005 (tpt) REVERT: J 39 LYS cc_start: 0.7879 (mmtt) cc_final: 0.7460 (mmmt) REVERT: J 70 LYS cc_start: 0.7904 (OUTLIER) cc_final: 0.7648 (ttpt) REVERT: J 84 MET cc_start: 0.8358 (mmm) cc_final: 0.7166 (mtm) REVERT: K 20 PHE cc_start: 0.5221 (OUTLIER) cc_final: 0.4552 (p90) REVERT: K 39 LYS cc_start: 0.8019 (mtpp) cc_final: 0.7474 (ttpt) REVERT: K 62 ASN cc_start: 0.7901 (OUTLIER) cc_final: 0.7380 (t0) REVERT: K 64 LYS cc_start: 0.7837 (tmtt) cc_final: 0.7589 (tttp) REVERT: K 72 ASP cc_start: 0.7836 (m-30) cc_final: 0.7454 (m-30) REVERT: K 213 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7621 (mp0) REVERT: K 247 ARG cc_start: 0.8610 (mtt-85) cc_final: 0.8304 (mtm180) REVERT: K 284 LYS cc_start: 0.8488 (OUTLIER) cc_final: 0.8014 (mttt) REVERT: L 70 LYS cc_start: 0.7918 (OUTLIER) cc_final: 0.7498 (ttpt) REVERT: L 87 THR cc_start: 0.8857 (p) cc_final: 0.8535 (t) REVERT: L 94 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.8031 (tm-30) REVERT: M 26 SER cc_start: 0.8268 (OUTLIER) cc_final: 0.7864 (p) REVERT: M 68 GLU cc_start: 0.7199 (OUTLIER) cc_final: 0.6815 (mp0) REVERT: M 107 LYS cc_start: 0.8254 (mtpp) cc_final: 0.7873 (mttm) REVERT: M 247 ARG cc_start: 0.8812 (mtt180) cc_final: 0.8479 (mtm110) REVERT: N 27 ARG cc_start: 0.7914 (OUTLIER) cc_final: 0.7068 (mtp180) REVERT: N 64 LYS cc_start: 0.8306 (ttmm) cc_final: 0.7885 (ttpt) REVERT: N 184 ASP cc_start: 0.7881 (m-30) cc_final: 0.7374 (m-30) REVERT: N 247 ARG cc_start: 0.8419 (ttm-80) cc_final: 0.8074 (mtt90) REVERT: N 251 MET cc_start: 0.8492 (OUTLIER) cc_final: 0.8193 (mtm) REVERT: N 284 LYS cc_start: 0.8172 (OUTLIER) cc_final: 0.7555 (mttt) outliers start: 42 outliers final: 22 residues processed: 241 average time/residue: 0.8600 time to fit residues: 222.2272 Evaluate side-chains 245 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 212 time to evaluate : 0.569 ------------------------------------------------------------------------------- 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 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 70 LYS 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 149 ASP 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 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 M residue 26 SER Chi-restraints excluded: chain M residue 61 ILE Chi-restraints excluded: chain M residue 68 GLU 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 M residue 233 SER Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 213 GLU 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=2.00 ------------------------------------------------------------------------------- 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: 0.9980 chunk 151 optimal weight: 0.0370 chunk 117 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 160 optimal weight: 2.9990 chunk 48 optimal weight: 9.9990 chunk 145 optimal weight: 5.9990 chunk 30 optimal weight: 9.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3472 r_free = 0.3472 target = 0.134680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.107329 restraints weight = 16027.618| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 1.00 r_work: 0.2964 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2860 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.1534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16078 Z= 0.132 Angle : 0.471 6.018 21780 Z= 0.256 Chirality : 0.040 0.144 2460 Planarity : 0.004 0.062 2739 Dihedral : 11.814 86.000 2612 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Rotamer: Outliers : 2.70 % Allowed : 19.04 % 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: 0.63 (0.19), residues: 1938 helix: 1.05 (0.18), residues: 870 sheet: 1.34 (0.30), residues: 288 loop : -0.62 (0.21), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 3 TYR 0.009 0.001 TYR M 315 PHE 0.010 0.001 PHE K 195 HIS 0.003 0.001 HIS K 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 (16078) covalent geometry : angle 0.47115 / 0.26 (21780) hydrogen bonds : bond 0.04328 / 2.91 ( 754) hydrogen bonds : angle 4.49225 / 3.21 ( 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 253 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 210 time to evaluate : 0.584 Fit side-chains REVERT: I 27 ARG cc_start: 0.7587 (tmt170) cc_final: 0.7323 (tpt90) REVERT: I 247 ARG cc_start: 0.8478 (mtt-85) cc_final: 0.8076 (mtm110) REVERT: I 251 MET cc_start: 0.8470 (mtp) cc_final: 0.8001 (tpt) REVERT: J 39 LYS cc_start: 0.7916 (mmtt) cc_final: 0.7523 (mmmt) REVERT: J 84 MET cc_start: 0.8356 (mmm) cc_final: 0.7216 (mtm) REVERT: K 20 PHE cc_start: 0.5260 (OUTLIER) cc_final: 0.4580 (p90) REVERT: K 39 LYS cc_start: 0.8028 (mtpp) cc_final: 0.7514 (ttpt) REVERT: K 62 ASN cc_start: 0.7897 (OUTLIER) cc_final: 0.7391 (t0) REVERT: K 64 LYS cc_start: 0.7858 (tmtt) cc_final: 0.7592 (tttp) REVERT: K 72 ASP cc_start: 0.7832 (m-30) cc_final: 0.7437 (m-30) REVERT: K 213 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7633 (mp0) REVERT: K 247 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8221 (mtt180) REVERT: K 284 LYS cc_start: 0.8483 (OUTLIER) cc_final: 0.7938 (mttt) REVERT: L 70 LYS cc_start: 0.7935 (OUTLIER) cc_final: 0.7535 (ttpt) REVERT: L 94 GLN cc_start: 0.8346 (OUTLIER) cc_final: 0.8012 (tm-30) REVERT: M 26 SER cc_start: 0.8296 (OUTLIER) cc_final: 0.7896 (p) REVERT: M 68 GLU cc_start: 0.7168 (OUTLIER) cc_final: 0.6819 (mp0) REVERT: M 107 LYS cc_start: 0.8313 (mtpp) cc_final: 0.7911 (mttm) REVERT: M 247 ARG cc_start: 0.8761 (mtt180) cc_final: 0.8472 (mtm110) REVERT: N 27 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7080 (mtp180) REVERT: N 64 LYS cc_start: 0.8353 (ttmm) cc_final: 0.7919 (ttpt) REVERT: N 184 ASP cc_start: 0.7868 (m-30) cc_final: 0.7367 (m-30) REVERT: N 247 ARG cc_start: 0.8345 (ttm-80) cc_final: 0.8049 (mtt90) REVERT: N 251 MET cc_start: 0.8446 (OUTLIER) cc_final: 0.8150 (mtm) REVERT: N 284 LYS cc_start: 0.8137 (OUTLIER) cc_final: 0.7544 (mttt) outliers start: 43 outliers final: 28 residues processed: 239 average time/residue: 0.8263 time to fit residues: 212.3554 Evaluate side-chains 248 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 210 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 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 183 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 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 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 68 GLU 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 M residue 233 SER Chi-restraints excluded: chain N residue 27 ARG Chi-restraints excluded: chain N residue 109 LEU Chi-restraints excluded: chain N residue 213 GLU 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=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: 5.9990 chunk 145 optimal weight: 5.9990 chunk 197 optimal weight: 8.9990 chunk 165 optimal weight: 2.9990 chunk 99 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 21 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 146 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3452 r_free = 0.3452 target = 0.132791 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.105280 restraints weight = 15943.608| |-----------------------------------------------------------------------------| r_work (start): 0.3103 rms_B_bonded: 1.02 r_work: 0.2968 rms_B_bonded: 1.54 restraints_weight: 0.5000 r_work: 0.2864 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9032 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 16078 Z= 0.233 Angle : 0.592 6.649 21780 Z= 0.319 Chirality : 0.046 0.162 2460 Planarity : 0.005 0.112 2739 Dihedral : 12.167 87.308 2612 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 3.39 % Allowed : 18.42 % 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: 0.31 (0.18), residues: 1938 helix: 0.75 (0.18), residues: 870 sheet: 1.21 (0.30), residues: 288 loop : -0.74 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG J 229 TYR 0.013 0.002 TYR M 159 PHE 0.014 0.002 PHE K 195 HIS 0.005 0.001 HIS K 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00556 / 0.23 (16078) covalent geometry : angle 0.59226 / 0.32 (21780) hydrogen bonds : bond 0.05872 / 3.96 ( 754) hydrogen bonds : angle 4.89406 / 3.49 ( 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 262 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 208 time to evaluate : 0.633 Fit side-chains REVERT: I 27 ARG cc_start: 0.7602 (tmt170) cc_final: 0.7365 (tpt90) REVERT: I 36 ASN cc_start: 0.7467 (OUTLIER) cc_final: 0.7204 (m110) REVERT: I 247 ARG cc_start: 0.8503 (mtt-85) cc_final: 0.8097 (mtm110) REVERT: I 251 MET cc_start: 0.8480 (mtp) cc_final: 0.7974 (tpt) REVERT: J 39 LYS cc_start: 0.7993 (mmtt) cc_final: 0.7587 (mmmt) REVERT: J 70 LYS cc_start: 0.7976 (OUTLIER) cc_final: 0.7738 (ttpt) REVERT: J 84 MET cc_start: 0.8375 (mmm) cc_final: 0.7233 (mtm) REVERT: J 284 LYS cc_start: 0.8641 (OUTLIER) cc_final: 0.8408 (mtmt) REVERT: K 20 PHE cc_start: 0.5269 (OUTLIER) cc_final: 0.4584 (p90) REVERT: K 39 LYS cc_start: 0.8057 (mtpp) cc_final: 0.7513 (ttpt) REVERT: K 62 ASN cc_start: 0.7932 (OUTLIER) cc_final: 0.7548 (t0) REVERT: K 64 LYS cc_start: 0.7915 (tmtt) cc_final: 0.7679 (tttp) REVERT: K 72 ASP cc_start: 0.7832 (m-30) cc_final: 0.7443 (m-30) REVERT: K 109 LEU cc_start: 0.8993 (OUTLIER) cc_final: 0.8627 (mp) REVERT: K 247 ARG cc_start: 0.8561 (mtt-85) cc_final: 0.8304 (mtm180) REVERT: K 284 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7926 (mttt) REVERT: K 306 ARG cc_start: 0.8086 (OUTLIER) cc_final: 0.7642 (mmt-90) REVERT: L 70 LYS cc_start: 0.7992 (OUTLIER) cc_final: 0.7587 (ttpt) REVERT: L 94 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.8048 (tm-30) REVERT: M 107 LYS cc_start: 0.8358 (mtpp) cc_final: 0.7937 (mttm) REVERT: M 247 ARG cc_start: 0.8765 (mtt180) cc_final: 0.8484 (mtm110) REVERT: M 284 LYS cc_start: 0.8602 (OUTLIER) cc_final: 0.8131 (mttt) REVERT: N 27 ARG cc_start: 0.7908 (OUTLIER) cc_final: 0.7212 (mtp180) REVERT: N 64 LYS cc_start: 0.8400 (ttmm) cc_final: 0.7961 (ttpt) REVERT: N 184 ASP cc_start: 0.7969 (m-30) cc_final: 0.7458 (m-30) REVERT: N 247 ARG cc_start: 0.8379 (ttm-80) cc_final: 0.8057 (mtt90) REVERT: N 251 MET cc_start: 0.8520 (OUTLIER) cc_final: 0.8240 (mtm) REVERT: N 284 LYS cc_start: 0.8157 (OUTLIER) cc_final: 0.7441 (mttt) outliers start: 54 outliers final: 28 residues processed: 246 average time/residue: 0.8135 time to fit residues: 215.3552 Evaluate side-chains 250 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.581 ------------------------------------------------------------------------------- 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 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 70 LYS 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 62 ASN Chi-restraints excluded: chain K residue 109 LEU 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 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 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 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 109 LEU Chi-restraints excluded: chain N residue 213 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 173 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 148 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 135 optimal weight: 2.9990 chunk 170 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 chunk 188 optimal weight: 7.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3448 r_free = 0.3448 target = 0.132740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.103062 restraints weight = 16050.177| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.13 r_work: 0.2930 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2822 rms_B_bonded: 2.83 restraints_weight: 0.2500 r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9024 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16078 Z= 0.153 Angle : 0.504 6.253 21780 Z= 0.274 Chirality : 0.041 0.145 2460 Planarity : 0.004 0.067 2739 Dihedral : 12.083 88.871 2612 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 2.83 % Allowed : 19.17 % Favored : 78.00 % 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: 0.39 (0.18), residues: 1938 helix: 0.84 (0.18), residues: 870 sheet: 1.22 (0.30), residues: 288 loop : -0.71 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 3 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/Z covalent geometry : bond 0.00349 / 0.15 (16078) covalent geometry : angle 0.50416 / 0.27 (21780) hydrogen bonds : bond 0.04848 / 3.27 ( 754) hydrogen bonds : angle 4.68269 / 3.35 ( 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 255 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 210 time to evaluate : 0.609 Fit side-chains REVERT: I 27 ARG cc_start: 0.7577 (tmt170) cc_final: 0.7333 (tpt90) REVERT: I 247 ARG cc_start: 0.8549 (mtt-85) cc_final: 0.8118 (mtm110) REVERT: I 251 MET cc_start: 0.8558 (mtp) cc_final: 0.8034 (tpt) REVERT: J 39 LYS cc_start: 0.7945 (mmtt) cc_final: 0.7542 (mmmt) REVERT: J 70 LYS cc_start: 0.7958 (OUTLIER) cc_final: 0.7687 (ttpt) REVERT: J 84 MET cc_start: 0.8373 (mmm) cc_final: 0.7221 (mtm) REVERT: J 284 LYS cc_start: 0.8613 (OUTLIER) cc_final: 0.8383 (mtmt) REVERT: K 20 PHE cc_start: 0.5204 (OUTLIER) cc_final: 0.4511 (p90) REVERT: K 39 LYS cc_start: 0.8039 (mtpp) cc_final: 0.7486 (ttpt) REVERT: K 62 ASN cc_start: 0.7911 (OUTLIER) cc_final: 0.7491 (t0) REVERT: K 64 LYS cc_start: 0.7888 (tmtt) cc_final: 0.7626 (tttp) REVERT: K 72 ASP cc_start: 0.7860 (m-30) cc_final: 0.7469 (m-30) REVERT: K 109 LEU cc_start: 0.8961 (OUTLIER) cc_final: 0.8666 (mp) REVERT: K 213 GLU cc_start: 0.8131 (mm-30) cc_final: 0.7648 (mp0) REVERT: K 247 ARG cc_start: 0.8634 (mtt-85) cc_final: 0.8334 (mtm180) REVERT: K 284 LYS cc_start: 0.8520 (OUTLIER) cc_final: 0.7932 (mttt) REVERT: K 306 ARG cc_start: 0.8114 (OUTLIER) cc_final: 0.7641 (mmt180) REVERT: L 70 LYS cc_start: 0.7947 (OUTLIER) cc_final: 0.7536 (ttpt) REVERT: L 94 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.8069 (tm-30) REVERT: M 107 LYS cc_start: 0.8320 (mtpp) cc_final: 0.7897 (mttm) REVERT: M 247 ARG cc_start: 0.8815 (mtt180) cc_final: 0.8491 (mtm110) REVERT: M 284 LYS cc_start: 0.8589 (OUTLIER) cc_final: 0.8090 (mttt) REVERT: N 27 ARG cc_start: 0.7886 (OUTLIER) cc_final: 0.7195 (mtp180) REVERT: N 64 LYS cc_start: 0.8381 (ttmm) cc_final: 0.7937 (ttpt) REVERT: N 184 ASP cc_start: 0.7942 (m-30) cc_final: 0.7420 (m-30) REVERT: N 247 ARG cc_start: 0.8418 (ttm-80) cc_final: 0.8090 (mtt90) REVERT: N 251 MET cc_start: 0.8530 (OUTLIER) cc_final: 0.8266 (mtm) REVERT: N 284 LYS cc_start: 0.8193 (OUTLIER) cc_final: 0.7568 (mttt) outliers start: 45 outliers final: 29 residues processed: 241 average time/residue: 0.8524 time to fit residues: 220.2485 Evaluate side-chains 250 residues out of total 1596 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 208 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 4 SER 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 70 LYS Chi-restraints excluded: chain J residue 183 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 109 LEU 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 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 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 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 213 GLU 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 199 random chunks: chunk 122 optimal weight: 2.9990 chunk 95 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 73 optimal weight: 0.0170 chunk 146 optimal weight: 1.9990 chunk 144 optimal weight: 0.5980 chunk 112 optimal weight: 0.9980 chunk 193 optimal weight: 2.9990 chunk 156 optimal weight: 3.9990 chunk 120 optimal weight: 0.7980 chunk 79 optimal weight: 10.0000 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3516 r_free = 0.3516 target = 0.138067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3185 r_free = 0.3185 target = 0.111032 restraints weight = 15775.772| |-----------------------------------------------------------------------------| r_work (start): 0.3138 rms_B_bonded: 1.00 r_work: 0.3003 rms_B_bonded: 1.56 restraints_weight: 0.5000 r_work: 0.2900 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2900 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8970 moved from start: 0.1624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 16078 Z= 0.097 Angle : 0.426 5.937 21780 Z= 0.233 Chirality : 0.039 0.138 2460 Planarity : 0.004 0.044 2739 Dihedral : 11.735 84.879 2612 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.36 % Favored : 99.64 % Rotamer: Outliers : 2.39 % Allowed : 19.55 % Favored : 78.06 % 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: 0.69 (0.19), residues: 1938 helix: 1.09 (0.18), residues: 870 sheet: 1.60 (0.31), residues: 276 loop : -0.64 (0.21), residues: 792 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 130 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/Z covalent geometry : bond 0.00198 / 0.10 (16078) covalent geometry : angle 0.42640 / 0.23 (21780) hydrogen bonds : bond 0.03516 / 2.35 ( 754) hydrogen bonds : angle 4.29958 / 3.09 ( 2046) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6542.83 seconds wall clock time: 111 minutes 48.87 seconds (6708.87 seconds total)