Starting phenix.real_space_refine on Sat Jul 4 23:07:05 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i62_52646/07_2026/9i62_52646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i62_52646/07_2026/9i62_52646.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9i62_52646/07_2026/9i62_52646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i62_52646/07_2026/9i62_52646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i62_52646/07_2026/9i62_52646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i62_52646/07_2026/9i62_52646.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 18 9.91 5 P 137 5.49 5 S 121 5.16 5 C 14728 2.51 5 N 4257 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s 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: 24205 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "B" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "C" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "D" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "E" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "F" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "G" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "H" Number of atoms: 2435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 319, 2435 Classifications: {'peptide': 319} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 307} Chain: "I" Number of atoms: 2384 Number of conformers: 1 Conformer: "" Number of residues, atoms: 311, 2384 Classifications: {'peptide': 311} Modifications used: {'COO': 1} Link IDs: {'CIS': 1, 'PTRANS': 10, 'TRANS': 299} Chain breaks: 1 Chain: "J" Number of atoms: 527 Number of conformers: 1 Conformer: "" Number of residues, atoms: 26, 527 Classifications: {'DNA': 26} Link IDs: {'rna3p': 25} Chain: "K" Number of atoms: 881 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 41, 837 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Conformer: "B" Number of residues, atoms: 41, 837 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} bond proxies already assigned to first conformer: 888 Chain: "L" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 840 Classifications: {'DNA': 41} Link IDs: {'rna3p': 40} Chain: "A" 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: "B" 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: "C" 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: "D" 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: "E" 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: "F" 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: "G" 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: "H" 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: "I" 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 Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" P A DG K 26 " occ=0.62 ... (42 atoms not shown) pdb=" C4 B DG K 26 " occ=0.38 residue: pdb=" P A DG K 27 " occ=0.21 ... (42 atoms not shown) pdb=" C4 B DG K 27 " occ=0.79 Time building chain proxies: 5.13, per 1000 atoms: 0.21 Number of scatterers: 24205 At special positions: 0 Unit cell: (144.744, 113.448, 193.644, 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 18 19.99 S 121 16.00 P 137 15.00 O 4944 8.00 N 4257 7.00 C 14728 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: 1.79 Conformation dependent library (CDL) restraints added in 872.6 milliseconds 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5168 Finding SS restraints... Secondary structure from input PDB file: 152 helices and 27 sheets defined 54.4% alpha, 16.8% beta 37 base pairs and 75 stacking pairs defined. Time for finding SS restraints: 2.98 Creating SS restraints... Processing helix chain 'A' and resid 24 through 32 removed outlier: 3.594A pdb=" N GLU A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 45 removed outlier: 3.514A pdb=" N LYS A 40 " --> pdb=" O ASN A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 48 through 55 Processing helix chain 'A' and resid 56 through 63 removed outlier: 3.795A pdb=" N LEU A 60 " --> pdb=" O PRO A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 82 Processing helix chain 'A' and resid 89 through 97 Processing helix chain 'A' and resid 106 through 114 Processing helix chain 'A' and resid 132 through 144 Processing helix chain 'A' and resid 145 through 146 No H-bonds generated for 'chain 'A' and resid 145 through 146' Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 167 through 178 removed outlier: 3.807A pdb=" N LEU A 171 " --> pdb=" O ARG A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 188 Processing helix chain 'A' and resid 196 through 214 removed outlier: 4.104A pdb=" N LEU A 204 " --> pdb=" O GLN A 200 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N TYR A 205 " --> pdb=" O THR A 201 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLN A 206 " --> pdb=" O GLN A 202 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 213 " --> pdb=" O ALA A 209 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 232 removed outlier: 3.810A pdb=" N TYR A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 237 through 260 Processing helix chain 'A' and resid 288 through 296 removed outlier: 4.134A pdb=" N ILE A 292 " --> pdb=" O GLY A 288 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ALA A 293 " --> pdb=" O GLY A 289 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 32 removed outlier: 3.503A pdb=" N GLN B 30 " --> pdb=" O ARG B 27 " (cutoff:3.500A) Processing helix chain 'B' and resid 34 through 45 Processing helix chain 'B' and resid 48 through 55 Processing helix chain 'B' and resid 56 through 62 removed outlier: 3.742A pdb=" N LEU B 60 " --> pdb=" O PRO B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 67 through 82 Processing helix chain 'B' and resid 89 through 97 Processing helix chain 'B' and resid 106 through 114 Processing helix chain 'B' and resid 132 through 144 Processing helix chain 'B' and resid 145 through 146 No H-bonds generated for 'chain 'B' and resid 145 through 146' Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 167 through 178 removed outlier: 3.761A pdb=" N LEU B 171 " --> pdb=" O ARG B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 181 through 188 Processing helix chain 'B' and resid 196 through 214 removed outlier: 3.931A pdb=" N LEU B 204 " --> pdb=" O GLN B 200 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N TYR B 205 " --> pdb=" O THR B 201 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA B 209 " --> pdb=" O TYR B 205 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU B 213 " --> pdb=" O ALA B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 232 removed outlier: 3.690A pdb=" N TYR B 232 " --> pdb=" O TYR B 228 " (cutoff:3.500A) Processing helix chain 'B' and resid 234 through 236 No H-bonds generated for 'chain 'B' and resid 234 through 236' Processing helix chain 'B' and resid 237 through 260 Processing helix chain 'B' and resid 288 through 296 removed outlier: 3.832A pdb=" N ILE B 292 " --> pdb=" O GLY B 288 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 293 " --> pdb=" O GLY B 289 " (cutoff:3.500A) Processing helix chain 'C' and resid 24 through 32 removed outlier: 3.533A pdb=" N GLN C 30 " --> pdb=" O ARG C 27 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N GLY C 32 " --> pdb=" O GLU C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 34 through 44 Processing helix chain 'C' and resid 48 through 55 Processing helix chain 'C' and resid 56 through 63 removed outlier: 3.736A pdb=" N LEU C 60 " --> pdb=" O PRO C 56 " (cutoff:3.500A) Processing helix chain 'C' and resid 67 through 82 removed outlier: 3.550A pdb=" N LEU C 81 " --> pdb=" O GLU C 77 " (cutoff:3.500A) Processing helix chain 'C' and resid 89 through 97 Processing helix chain 'C' and resid 106 through 114 Processing helix chain 'C' and resid 132 through 144 removed outlier: 3.520A pdb=" N VAL C 142 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 through 146 No H-bonds generated for 'chain 'C' and resid 145 through 146' Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 167 through 178 removed outlier: 3.671A pdb=" N LEU C 171 " --> pdb=" O ARG C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 181 through 188 Processing helix chain 'C' and resid 196 through 214 removed outlier: 3.930A pdb=" N LEU C 204 " --> pdb=" O GLN C 200 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N TYR C 205 " --> pdb=" O THR C 201 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ALA C 209 " --> pdb=" O TYR C 205 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLU C 213 " --> pdb=" O ALA C 209 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 232 removed outlier: 3.721A pdb=" N TYR C 232 " --> pdb=" O TYR C 228 " (cutoff:3.500A) Processing helix chain 'C' and resid 234 through 236 No H-bonds generated for 'chain 'C' and resid 234 through 236' Processing helix chain 'C' and resid 237 through 260 Processing helix chain 'C' and resid 288 through 296 removed outlier: 3.884A pdb=" N ILE C 292 " --> pdb=" O GLY C 288 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA C 293 " --> pdb=" O GLY C 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 24 through 32 removed outlier: 3.599A pdb=" N GLU D 29 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY D 32 " --> pdb=" O GLU D 29 " (cutoff:3.500A) Processing helix chain 'D' and resid 34 through 44 Processing helix chain 'D' and resid 48 through 55 Processing helix chain 'D' and resid 56 through 62 removed outlier: 3.682A pdb=" N LEU D 60 " --> pdb=" O PRO D 56 " (cutoff:3.500A) Processing helix chain 'D' and resid 67 through 82 removed outlier: 3.588A pdb=" N LEU D 81 " --> pdb=" O GLU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 97 Processing helix chain 'D' and resid 106 through 114 Processing helix chain 'D' and resid 132 through 144 removed outlier: 3.666A pdb=" N VAL D 142 " --> pdb=" O HIS D 138 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 146 No H-bonds generated for 'chain 'D' and resid 145 through 146' Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 167 through 179 removed outlier: 3.745A pdb=" N LEU D 171 " --> pdb=" O ARG D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 181 through 188 Processing helix chain 'D' and resid 196 through 214 removed outlier: 3.893A pdb=" N LEU D 204 " --> pdb=" O GLN D 200 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N TYR D 205 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN D 206 " --> pdb=" O GLN D 202 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N GLU D 213 " --> pdb=" O ALA D 209 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 232 removed outlier: 3.514A pdb=" N TYR D 232 " --> pdb=" O TYR D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 234 through 236 No H-bonds generated for 'chain 'D' and resid 234 through 236' Processing helix chain 'D' and resid 237 through 260 Processing helix chain 'D' and resid 288 through 296 removed outlier: 3.824A pdb=" N ILE D 292 " --> pdb=" O GLY D 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 24 through 32 Processing helix chain 'E' and resid 34 through 44 Processing helix chain 'E' and resid 48 through 54 Processing helix chain 'E' and resid 56 through 63 removed outlier: 3.631A pdb=" N LEU E 60 " --> pdb=" O PRO E 56 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ILE E 63 " --> pdb=" O GLU E 59 " (cutoff:3.500A) Processing helix chain 'E' and resid 67 through 82 Processing helix chain 'E' and resid 89 through 97 Processing helix chain 'E' and resid 106 through 113 Processing helix chain 'E' and resid 132 through 144 removed outlier: 3.613A pdb=" N VAL E 142 " --> pdb=" O HIS E 138 " (cutoff:3.500A) Processing helix chain 'E' and resid 145 through 146 No H-bonds generated for 'chain 'E' and resid 145 through 146' Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 167 through 178 removed outlier: 3.726A pdb=" N LEU E 171 " --> pdb=" O ARG E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 188 Processing helix chain 'E' and resid 196 through 214 removed outlier: 3.925A pdb=" N LEU E 204 " --> pdb=" O GLN E 200 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N TYR E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLN E 206 " --> pdb=" O GLN E 202 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA E 209 " --> pdb=" O TYR E 205 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N GLU E 213 " --> pdb=" O ALA E 209 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 232 removed outlier: 3.622A pdb=" N TYR E 232 " --> pdb=" O TYR E 228 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 236 No H-bonds generated for 'chain 'E' and resid 234 through 236' Processing helix chain 'E' and resid 237 through 260 Processing helix chain 'E' and resid 288 through 296 removed outlier: 3.725A pdb=" N ILE E 292 " --> pdb=" O GLY E 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 32 Processing helix chain 'F' and resid 34 through 44 Processing helix chain 'F' and resid 48 through 55 Processing helix chain 'F' and resid 56 through 63 removed outlier: 3.687A pdb=" N LEU F 60 " --> pdb=" O PRO F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 82 removed outlier: 3.592A pdb=" N LEU F 81 " --> pdb=" O GLU F 77 " (cutoff:3.500A) Processing helix chain 'F' and resid 89 through 97 Processing helix chain 'F' and resid 106 through 114 Processing helix chain 'F' and resid 132 through 144 removed outlier: 3.657A pdb=" N VAL F 142 " --> pdb=" O HIS F 138 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 146 No H-bonds generated for 'chain 'F' and resid 145 through 146' Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 167 through 178 removed outlier: 3.695A pdb=" N LEU F 171 " --> pdb=" O ARG F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 181 through 188 Processing helix chain 'F' and resid 196 through 214 removed outlier: 3.892A pdb=" N LEU F 204 " --> pdb=" O GLN F 200 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N TYR F 205 " --> pdb=" O THR F 201 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLN F 206 " --> pdb=" O GLN F 202 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA F 209 " --> pdb=" O TYR F 205 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLU F 213 " --> pdb=" O ALA F 209 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 232 removed outlier: 3.680A pdb=" N TYR F 232 " --> pdb=" O TYR F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 236 No H-bonds generated for 'chain 'F' and resid 234 through 236' Processing helix chain 'F' and resid 237 through 260 Processing helix chain 'F' and resid 288 through 296 removed outlier: 3.839A pdb=" N ILE F 292 " --> pdb=" O GLY F 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 24 through 32 Processing helix chain 'G' and resid 34 through 44 Processing helix chain 'G' and resid 48 through 55 Processing helix chain 'G' and resid 56 through 63 removed outlier: 3.729A pdb=" N LEU G 60 " --> pdb=" O PRO G 56 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ILE G 63 " --> pdb=" O GLU G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 67 through 82 removed outlier: 3.517A pdb=" N LEU G 81 " --> pdb=" O GLU G 77 " (cutoff:3.500A) Processing helix chain 'G' and resid 89 through 97 Processing helix chain 'G' and resid 106 through 114 Processing helix chain 'G' and resid 132 through 144 removed outlier: 3.608A pdb=" N VAL G 142 " --> pdb=" O HIS G 138 " (cutoff:3.500A) Processing helix chain 'G' and resid 145 through 146 No H-bonds generated for 'chain 'G' and resid 145 through 146' Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 167 through 179 removed outlier: 3.726A pdb=" N LEU G 171 " --> pdb=" O ARG G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 181 through 188 Processing helix chain 'G' and resid 196 through 214 removed outlier: 3.898A pdb=" N LEU G 204 " --> pdb=" O GLN G 200 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N TYR G 205 " --> pdb=" O THR G 201 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLN G 206 " --> pdb=" O GLN G 202 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ALA G 209 " --> pdb=" O TYR G 205 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLU G 213 " --> pdb=" O ALA G 209 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 232 removed outlier: 3.626A pdb=" N TYR G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 237 through 260 Processing helix chain 'G' and resid 288 through 296 removed outlier: 3.825A pdb=" N ILE G 292 " --> pdb=" O GLY G 288 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N ALA G 293 " --> pdb=" O GLY G 289 " (cutoff:3.500A) Processing helix chain 'H' and resid 24 through 32 Processing helix chain 'H' and resid 34 through 44 removed outlier: 3.513A pdb=" N LYS H 39 " --> pdb=" O ALA H 35 " (cutoff:3.500A) Processing helix chain 'H' and resid 48 through 55 Processing helix chain 'H' and resid 56 through 63 removed outlier: 3.927A pdb=" N LEU H 60 " --> pdb=" O PRO H 56 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ILE H 63 " --> pdb=" O GLU H 59 " (cutoff:3.500A) Processing helix chain 'H' and resid 67 through 82 Processing helix chain 'H' and resid 89 through 97 Processing helix chain 'H' and resid 106 through 114 Processing helix chain 'H' and resid 132 through 144 removed outlier: 3.500A pdb=" N VAL H 142 " --> pdb=" O HIS H 138 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 146 No H-bonds generated for 'chain 'H' and resid 145 through 146' Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 167 through 178 removed outlier: 3.751A pdb=" N LEU H 171 " --> pdb=" O ARG H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 181 through 188 Processing helix chain 'H' and resid 196 through 214 removed outlier: 3.918A pdb=" N LEU H 204 " --> pdb=" O GLN H 200 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N TYR H 205 " --> pdb=" O THR H 201 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN H 206 " --> pdb=" O GLN H 202 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA H 209 " --> pdb=" O TYR H 205 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLU H 213 " --> pdb=" O ALA H 209 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 232 removed outlier: 3.524A pdb=" N TYR H 232 " --> pdb=" O TYR H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 234 through 236 No H-bonds generated for 'chain 'H' and resid 234 through 236' Processing helix chain 'H' and resid 237 through 260 Processing helix chain 'H' and resid 274 through 278 removed outlier: 3.683A pdb=" N ALA H 277 " --> pdb=" O ASP H 274 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET H 278 " --> pdb=" O GLY H 275 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 274 through 278' Processing helix chain 'H' and resid 288 through 296 removed outlier: 3.840A pdb=" N ILE H 292 " --> pdb=" O GLY H 288 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ALA H 293 " --> pdb=" O GLY H 289 " (cutoff:3.500A) Processing helix chain 'I' and resid 24 through 32 Processing helix chain 'I' and resid 34 through 44 removed outlier: 3.522A pdb=" N LYS I 40 " --> pdb=" O ASN I 36 " (cutoff:3.500A) Processing helix chain 'I' and resid 48 through 55 Processing helix chain 'I' and resid 56 through 63 removed outlier: 3.521A pdb=" N LEU I 60 " --> pdb=" O PRO I 56 " (cutoff:3.500A) Processing helix chain 'I' and resid 67 through 82 removed outlier: 3.517A pdb=" N ASP I 72 " --> pdb=" O GLU I 68 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LEU I 81 " --> pdb=" O GLU I 77 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 97 Processing helix chain 'I' and resid 106 through 114 Processing helix chain 'I' and resid 132 through 144 removed outlier: 3.548A pdb=" N CYS I 137 " --> pdb=" O LYS I 133 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N VAL I 142 " --> pdb=" O HIS I 138 " (cutoff:3.500A) Processing helix chain 'I' and resid 145 through 146 No H-bonds generated for 'chain 'I' and resid 145 through 146' Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 167 through 178 removed outlier: 3.821A pdb=" N LEU I 171 " --> pdb=" O ARG I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 181 through 188 Processing helix chain 'I' and resid 196 through 214 removed outlier: 3.831A pdb=" N LEU I 204 " --> pdb=" O GLN I 200 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N TYR I 205 " --> pdb=" O THR I 201 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ALA I 209 " --> pdb=" O TYR I 205 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N GLU I 213 " --> pdb=" O ALA I 209 " (cutoff:3.500A) Processing helix chain 'I' and resid 227 through 232 removed outlier: 3.852A pdb=" N TYR I 232 " --> pdb=" O TYR I 228 " (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: 3.937A pdb=" N ILE I 292 " --> pdb=" O GLY I 288 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA I 293 " --> pdb=" O GLY I 289 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 87 through 88 removed outlier: 7.078A pdb=" N LYS B 156 " --> pdb=" O ALA B 217 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N LEU B 219 " --> pdb=" O LYS B 156 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N MET B 158 " --> pdb=" O LEU B 219 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N VAL B 221 " --> pdb=" O MET B 158 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N ILE B 160 " --> pdb=" O VAL B 221 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY B 127 " --> pdb=" O ASN B 267 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ARG B 299 " --> pdb=" O TYR B 315 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 101 through 102 Processing sheet with id=AA3, first strand: chain 'A' and resid 189 through 193 removed outlier: 7.448A pdb=" N ALA A 157 " --> pdb=" O ALA A 190 " (cutoff:3.500A) removed outlier: 8.035A pdb=" N ALA A 192 " --> pdb=" O ALA A 157 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N TYR A 159 " --> pdb=" O ALA A 192 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LYS A 156 " --> pdb=" O ALA A 217 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N LEU A 219 " --> pdb=" O LYS A 156 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N MET A 158 " --> pdb=" O LEU A 219 " (cutoff:3.500A) removed outlier: 5.814A pdb=" N VAL A 221 " --> pdb=" O MET A 158 " (cutoff:3.500A) removed outlier: 6.905A pdb=" N ILE A 160 " --> pdb=" O VAL A 221 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLY A 127 " --> pdb=" O ASN A 267 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N ARG A 299 " --> pdb=" O TYR A 315 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N ILE A 311 " --> pdb=" O ARG A 303 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 269 through 271 Processing sheet with id=AA5, first strand: chain 'B' and resid 87 through 88 removed outlier: 5.441A pdb=" N LYS C 156 " --> pdb=" O TYR C 216 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N LEU C 218 " --> pdb=" O LYS C 156 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N GLY C 127 " --> pdb=" O ASN C 267 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ARG C 299 " --> pdb=" O TYR C 315 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 101 through 102 Processing sheet with id=AA7, first strand: chain 'B' and resid 269 through 271 Processing sheet with id=AA8, first strand: chain 'C' and resid 87 through 88 removed outlier: 5.469A pdb=" N LYS D 156 " --> pdb=" O TYR D 216 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N LEU D 218 " --> pdb=" O LYS D 156 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY D 127 " --> pdb=" O ASN D 267 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N ARG D 299 " --> pdb=" O TYR D 315 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 101 through 102 Processing sheet with id=AB1, first strand: chain 'C' and resid 269 through 271 Processing sheet with id=AB2, first strand: chain 'D' and resid 87 through 88 removed outlier: 5.492A pdb=" N LYS E 156 " --> pdb=" O TYR E 216 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LEU E 218 " --> pdb=" O LYS E 156 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ILE E 122 " --> pdb=" O THR E 298 " (cutoff:3.500A) removed outlier: 8.100A pdb=" N LEU E 300 " --> pdb=" O ILE E 122 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N GLU E 124 " --> pdb=" O LEU E 300 " (cutoff:3.500A) removed outlier: 7.437A pdb=" N LEU E 302 " --> pdb=" O GLU E 124 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N PHE E 126 " --> pdb=" O LEU E 302 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N LYS E 304 " --> pdb=" O PHE E 126 " (cutoff:3.500A) removed outlier: 6.158A pdb=" N ARG E 299 " --> pdb=" O TYR E 315 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 101 through 102 Processing sheet with id=AB4, first strand: chain 'D' and resid 269 through 271 Processing sheet with id=AB5, first strand: chain 'E' and resid 87 through 88 removed outlier: 5.539A pdb=" N LYS F 156 " --> pdb=" O TYR F 216 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU F 218 " --> pdb=" O LYS F 156 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ILE F 122 " --> pdb=" O THR F 298 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU F 300 " --> pdb=" O ILE F 122 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N GLU F 124 " --> pdb=" O LEU F 300 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N LEU F 302 " --> pdb=" O GLU F 124 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N PHE F 126 " --> pdb=" O LEU F 302 " (cutoff:3.500A) removed outlier: 8.453A pdb=" N LYS F 304 " --> pdb=" O PHE F 126 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG F 299 " --> pdb=" O TYR F 315 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY F 333 " --> pdb=" O ASN F 330 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 101 through 102 Processing sheet with id=AB7, first strand: chain 'E' and resid 269 through 271 Processing sheet with id=AB8, first strand: chain 'F' and resid 87 through 88 removed outlier: 5.469A pdb=" N LYS G 156 " --> pdb=" O TYR G 216 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N LEU G 218 " --> pdb=" O LYS G 156 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ILE G 122 " --> pdb=" O THR G 298 " (cutoff:3.500A) removed outlier: 8.142A pdb=" N LEU G 300 " --> pdb=" O ILE G 122 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU G 124 " --> pdb=" O LEU G 300 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU G 302 " --> pdb=" O GLU G 124 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N PHE G 126 " --> pdb=" O LEU G 302 " (cutoff:3.500A) removed outlier: 8.469A pdb=" N LYS G 304 " --> pdb=" O PHE G 126 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N ARG G 299 " --> pdb=" O TYR G 315 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 101 through 102 Processing sheet with id=AC1, first strand: chain 'F' and resid 269 through 271 Processing sheet with id=AC2, first strand: chain 'G' and resid 87 through 88 removed outlier: 5.399A pdb=" N LYS H 156 " --> pdb=" O TYR H 216 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LEU H 218 " --> pdb=" O LYS H 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N THR H 298 " --> pdb=" O ILE H 122 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG H 299 " --> pdb=" O TYR H 315 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 101 through 102 Processing sheet with id=AC4, first strand: chain 'G' and resid 269 through 271 Processing sheet with id=AC5, first strand: chain 'H' and resid 87 through 88 removed outlier: 5.630A pdb=" N LYS I 156 " --> pdb=" O TYR I 216 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA I 262 " --> pdb=" O ALA I 217 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY I 127 " --> pdb=" O ASN I 267 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ARG I 299 " --> pdb=" O TYR I 315 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 101 through 102 Processing sheet with id=AC7, first strand: chain 'H' and resid 269 through 271 Processing sheet with id=AC8, first strand: chain 'I' and resid 101 through 102 Processing sheet with id=AC9, first strand: chain 'I' and resid 269 through 271 1202 hydrogen bonds defined for protein. 3294 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 93 hydrogen bonds 186 hydrogen bond angles 0 basepair planarities 37 basepair parallelities 76 stacking parallelities Total time for adding SS restraints: 4.62 Time building geometry restraints manager: 2.44 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: 5761 1.33 - 1.45: 5099 1.45 - 1.57: 13479 1.57 - 1.69: 249 1.69 - 1.81: 197 Bond restraints: 24785 Sorted by residual: bond pdb=" C3' DT K 33 " pdb=" C2' DT K 33 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.02e+01 bond pdb=" C3'A DG K 26 " pdb=" C2'A DG K 26 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" N ILE I 63 " pdb=" CA ILE I 63 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.19e-02 7.06e+03 9.97e+00 bond pdb=" C3' DG L 33 " pdb=" C2' DG L 33 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.60e+00 bond pdb=" N ILE H 63 " pdb=" CA ILE H 63 " ideal model delta sigma weight residual 1.458 1.496 -0.037 1.20e-02 6.94e+03 9.59e+00 ... (remaining 24780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 32039 1.02 - 2.03: 1484 2.03 - 3.05: 386 3.05 - 4.07: 56 4.07 - 5.08: 15 Bond angle restraints: 33980 Sorted by residual: angle pdb=" N3 DT K 8 " pdb=" C4 DT K 8 " pdb=" O4 DT K 8 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" N3 DT L 2 " pdb=" C4 DT L 2 " pdb=" O4 DT L 2 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" O4' DC K 21 " pdb=" C4' DC K 21 " pdb=" C3' DC K 21 " ideal model delta sigma weight residual 106.00 103.43 2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT J 20 " pdb=" C4 DT J 20 " pdb=" O4 DT J 20 " ideal model delta sigma weight residual 119.90 122.40 -2.50 6.00e-01 2.78e+00 1.73e+01 angle pdb=" N3 DT L 38 " pdb=" C4 DT L 38 " pdb=" O4 DT L 38 " ideal model delta sigma weight residual 119.90 122.39 -2.49 6.00e-01 2.78e+00 1.72e+01 ... (remaining 33975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.88: 13555 17.88 - 35.77: 785 35.77 - 53.65: 421 53.65 - 71.54: 110 71.54 - 89.42: 17 Dihedral angle restraints: 14888 sinusoidal: 6813 harmonic: 8075 Sorted by residual: dihedral pdb=" CA ARG E 27 " pdb=" CB ARG E 27 " pdb=" CG ARG E 27 " pdb=" CD ARG E 27 " ideal model delta sinusoidal sigma weight residual -180.00 -120.19 -59.81 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG G 247 " pdb=" CB ARG G 247 " pdb=" CG ARG G 247 " pdb=" CD ARG G 247 " ideal model delta sinusoidal sigma weight residual -180.00 -121.17 -58.83 3 1.50e+01 4.44e-03 9.47e+00 dihedral pdb=" CB ARG H 229 " pdb=" CG ARG H 229 " pdb=" CD ARG H 229 " pdb=" NE ARG H 229 " ideal model delta sinusoidal sigma weight residual -60.00 -114.56 54.56 3 1.50e+01 4.44e-03 9.29e+00 ... (remaining 14885 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 2958 0.047 - 0.094: 690 0.094 - 0.141: 190 0.141 - 0.188: 13 0.188 - 0.234: 10 Chirality restraints: 3861 Sorted by residual: chirality pdb=" CA ILE C 63 " pdb=" N ILE C 63 " pdb=" C ILE C 63 " pdb=" CB ILE C 63 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE F 63 " pdb=" N ILE F 63 " pdb=" C ILE F 63 " pdb=" CB ILE F 63 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CA LYS G 64 " pdb=" N LYS G 64 " pdb=" C LYS G 64 " pdb=" CB LYS G 64 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.32e+00 ... (remaining 3858 not shown) Planarity restraints: 3992 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN A 62 " 0.012 2.00e-02 2.50e+03 2.45e-02 6.02e+00 pdb=" C ASN A 62 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN A 62 " 0.016 2.00e-02 2.50e+03 pdb=" N ILE A 63 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN F 62 " 0.011 2.00e-02 2.50e+03 2.33e-02 5.41e+00 pdb=" C ASN F 62 " -0.040 2.00e-02 2.50e+03 pdb=" O ASN F 62 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE F 63 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN C 62 " 0.010 2.00e-02 2.50e+03 1.97e-02 3.88e+00 pdb=" C ASN C 62 " -0.034 2.00e-02 2.50e+03 pdb=" O ASN C 62 " 0.013 2.00e-02 2.50e+03 pdb=" N ILE C 63 " 0.012 2.00e-02 2.50e+03 ... (remaining 3989 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 583 2.67 - 3.23: 22463 3.23 - 3.78: 38437 3.78 - 4.34: 57224 4.34 - 4.90: 88635 Nonbonded interactions: 207342 Sorted by model distance: nonbonded pdb="CA CA H 403 " pdb=" O3G ATP H 402 " model vdw 2.112 3.250 nonbonded pdb="CA CA G 403 " pdb=" O3G ATP G 402 " model vdw 2.128 3.250 nonbonded pdb="CA CA C 403 " pdb=" O3G ATP C 402 " model vdw 2.138 3.250 nonbonded pdb="CA CA D 403 " pdb=" O3G ATP D 402 " model vdw 2.140 3.250 nonbonded pdb="CA CA E 403 " pdb=" O3G ATP E 402 " model vdw 2.145 3.250 ... (remaining 207337 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' selection = chain 'C' selection = chain 'D' selection = (chain 'E' and (resid 21 through 274 or resid 283 through 402)) selection = (chain 'F' and (resid 21 through 274 or resid 283 through 402)) selection = (chain 'G' and (resid 21 through 274 or resid 283 through 402)) selection = (chain 'H' and (resid 21 through 274 or resid 283 through 402)) selection = chain 'I' } 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=0.21 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: 5.120 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: 0.010 Extract box with map and model: 0.620 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 22.150 Find NCS groups from input model: 0.570 Set up NCS constraints: 0.060 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:6.330 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8916 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 : 0.007 0.039 24785 Z= 0.370 Angle : 0.526 5.083 33980 Z= 0.387 Chirality : 0.044 0.234 3861 Planarity : 0.003 0.034 3992 Dihedral : 14.929 89.422 9720 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 0.49 % Allowed : 3.11 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 0.74 (0.16), residues: 2803 helix: 0.69 (0.14), residues: 1322 sheet: 0.43 (0.26), residues: 495 loop : 0.53 (0.21), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 310 TYR 0.012 0.001 TYR H 315 PHE 0.009 0.001 PHE G 248 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00654 / 0.37 (24785) covalent geometry : angle 0.52628 / 0.39 (33980) hydrogen bonds : bond 0.21981 / 14.58 ( 1295) hydrogen bonds : angle 7.18759 / 5.13 ( 3480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 298 time to evaluate : 0.939 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8824 (mp0) REVERT: A 178 TYR cc_start: 0.8473 (m-80) cc_final: 0.8069 (m-80) REVERT: A 188 ASN cc_start: 0.8574 (m-40) cc_final: 0.7924 (m110) REVERT: A 290 ASN cc_start: 0.8565 (m-40) cc_final: 0.8213 (m110) REVERT: A 327 PHE cc_start: 0.9185 (p90) cc_final: 0.8709 (p90) REVERT: B 66 ILE cc_start: 0.8695 (OUTLIER) cc_final: 0.8464 (mt) REVERT: B 68 GLU cc_start: 0.9150 (mt-10) cc_final: 0.8946 (tm-30) REVERT: B 202 GLN cc_start: 0.9272 (tt0) cc_final: 0.8901 (tm-30) REVERT: B 213 GLU cc_start: 0.8971 (mt-10) cc_final: 0.8767 (mp0) REVERT: B 235 ARG cc_start: 0.8550 (ttp-170) cc_final: 0.7994 (ttm110) REVERT: B 285 LYS cc_start: 0.8330 (ptpt) cc_final: 0.8100 (ptmt) REVERT: C 72 ASP cc_start: 0.8679 (m-30) cc_final: 0.8165 (p0) REVERT: D 39 LYS cc_start: 0.8832 (mttt) cc_final: 0.8617 (mmpt) REVERT: D 67 SER cc_start: 0.8630 (t) cc_final: 0.8226 (p) REVERT: D 68 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8603 (tm-30) REVERT: D 72 ASP cc_start: 0.8891 (m-30) cc_final: 0.8523 (m-30) REVERT: D 202 GLN cc_start: 0.9148 (tt0) cc_final: 0.8617 (tm-30) REVERT: E 30 GLN cc_start: 0.8897 (mt0) cc_final: 0.8317 (tm130) REVERT: E 36 ASN cc_start: 0.8804 (m-40) cc_final: 0.8495 (t0) REVERT: F 27 ARG cc_start: 0.8769 (mtp180) cc_final: 0.8256 (tpp-160) REVERT: F 202 GLN cc_start: 0.8847 (tt0) cc_final: 0.8630 (tm-30) REVERT: F 306 ARG cc_start: 0.8628 (ttt180) cc_final: 0.8377 (ttp-170) REVERT: G 68 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8721 (mp0) REVERT: G 202 GLN cc_start: 0.8917 (tt0) cc_final: 0.8368 (tm-30) REVERT: H 163 GLU cc_start: 0.8612 (mt-10) cc_final: 0.8359 (mt-10) REVERT: H 274 ASP cc_start: 0.8729 (m-30) cc_final: 0.8233 (p0) REVERT: I 96 ARG cc_start: 0.7374 (mtp85) cc_final: 0.5714 (mtt180) REVERT: I 163 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8436 (mt-10) outliers start: 11 outliers final: 2 residues processed: 308 average time/residue: 0.8894 time to fit residues: 303.2504 Evaluate side-chains 217 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 214 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 ILE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 270 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 197 optimal weight: 0.6980 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 50.0000 chunk 207 optimal weight: 0.7980 chunk 155 optimal weight: 8.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 242 GLN E 62 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.060116 restraints weight = 89843.638| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.58 r_work: 0.2546 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 moved from start: 0.1608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.098 24785 Z= 0.154 Angle : 0.536 7.167 33980 Z= 0.312 Chirality : 0.040 0.174 3861 Planarity : 0.004 0.055 3992 Dihedral : 18.057 87.546 4584 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Rotamer: Outliers : 1.15 % Allowed : 8.21 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 2803 helix: 1.19 (0.14), residues: 1303 sheet: 0.30 (0.25), residues: 500 loop : 0.54 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 235 TYR 0.026 0.001 TYR I 191 PHE 0.014 0.001 PHE A 126 HIS 0.003 0.001 HIS H 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.15 (24785) covalent geometry : angle 0.53616 / 0.31 (33980) hydrogen bonds : bond 0.05340 / 3.55 ( 1295) hydrogen bonds : angle 5.14426 / 3.64 ( 3480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 245 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9214 (mt-10) cc_final: 0.8835 (mp0) REVERT: A 178 TYR cc_start: 0.8219 (m-80) cc_final: 0.7725 (m-80) REVERT: A 188 ASN cc_start: 0.8644 (m-40) cc_final: 0.8421 (m-40) REVERT: A 205 TYR cc_start: 0.9443 (m-80) cc_final: 0.9176 (m-80) REVERT: A 210 MET cc_start: 0.9097 (mtm) cc_final: 0.8830 (mtm) REVERT: A 229 ARG cc_start: 0.8858 (OUTLIER) cc_final: 0.8538 (ttm170) REVERT: B 34 ASN cc_start: 0.7216 (t0) cc_final: 0.6932 (t0) REVERT: B 68 GLU cc_start: 0.9044 (mt-10) cc_final: 0.8801 (tm-30) REVERT: B 163 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8833 (mt-10) REVERT: B 202 GLN cc_start: 0.9230 (tt0) cc_final: 0.9023 (tp-100) REVERT: B 235 ARG cc_start: 0.8501 (ttp-170) cc_final: 0.8006 (ttm170) REVERT: D 39 LYS cc_start: 0.8643 (mttt) cc_final: 0.8437 (mmpt) REVERT: D 67 SER cc_start: 0.8249 (t) cc_final: 0.7816 (p) REVERT: D 68 GLU cc_start: 0.8665 (mt-10) cc_final: 0.8353 (tm-30) REVERT: D 72 ASP cc_start: 0.8829 (m-30) cc_final: 0.8572 (m-30) REVERT: D 202 GLN cc_start: 0.9100 (tt0) cc_final: 0.8599 (tm-30) REVERT: E 30 GLN cc_start: 0.8822 (mt0) cc_final: 0.8341 (tm130) REVERT: E 43 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8178 (pp20) REVERT: F 27 ARG cc_start: 0.8651 (mtp180) cc_final: 0.8238 (tpp-160) REVERT: F 34 ASN cc_start: 0.7741 (t0) cc_final: 0.7533 (t0) REVERT: F 202 GLN cc_start: 0.8771 (tt0) cc_final: 0.8534 (tm-30) REVERT: F 247 ARG cc_start: 0.8816 (mtp85) cc_final: 0.8339 (ttp80) REVERT: F 279 PHE cc_start: 0.8585 (m-80) cc_final: 0.8358 (m-80) REVERT: F 306 ARG cc_start: 0.8586 (ttt180) cc_final: 0.8215 (ttp-110) REVERT: G 34 ASN cc_start: 0.8129 (t0) cc_final: 0.7914 (t0) REVERT: G 68 GLU cc_start: 0.9043 (mt-10) cc_final: 0.8733 (mp0) REVERT: G 202 GLN cc_start: 0.8861 (tt0) cc_final: 0.8341 (tm-30) REVERT: G 210 MET cc_start: 0.9243 (mtm) cc_final: 0.8997 (mtp) REVERT: H 62 ASN cc_start: 0.8913 (m-40) cc_final: 0.8678 (m-40) REVERT: H 243 MET cc_start: 0.8824 (tpp) cc_final: 0.8619 (mpp) REVERT: H 274 ASP cc_start: 0.8882 (m-30) cc_final: 0.8205 (p0) REVERT: I 96 ARG cc_start: 0.6932 (mtp85) cc_final: 0.5369 (mtm180) REVERT: I 124 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8457 (tt0) REVERT: I 163 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8513 (mt-10) REVERT: I 191 TYR cc_start: 0.8121 (t80) cc_final: 0.7886 (t80) REVERT: I 216 TYR cc_start: 0.8507 (m-80) cc_final: 0.7805 (m-80) REVERT: I 251 MET cc_start: 0.8753 (mpp) cc_final: 0.8396 (mpp) outliers start: 26 outliers final: 4 residues processed: 263 average time/residue: 0.7921 time to fit residues: 233.0285 Evaluate side-chains 217 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 210 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 290 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 252 optimal weight: 2.9990 chunk 256 optimal weight: 0.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 0.0970 chunk 159 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 242 optimal weight: 7.9990 chunk 162 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 62 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 ASN D 272 GLN E 62 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.060425 restraints weight = 88727.200| |-----------------------------------------------------------------------------| r_work (start): 0.2749 rms_B_bonded: 3.58 r_work: 0.2558 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24785 Z= 0.141 Angle : 0.493 7.831 33980 Z= 0.284 Chirality : 0.039 0.167 3861 Planarity : 0.003 0.044 3992 Dihedral : 18.243 91.828 4582 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.51 % Allowed : 8.97 % Favored : 89.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.16), residues: 2803 helix: 1.24 (0.14), residues: 1314 sheet: 0.13 (0.23), residues: 544 loop : 0.55 (0.21), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 306 TYR 0.019 0.001 TYR I 232 PHE 0.011 0.001 PHE A 166 HIS 0.003 0.001 HIS G 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.14 (24785) covalent geometry : angle 0.49272 / 0.28 (33980) hydrogen bonds : bond 0.03842 / 2.58 ( 1295) hydrogen bonds : angle 4.63280 / 3.27 ( 3480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 236 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLU cc_start: 0.8551 (mp0) cc_final: 0.8322 (mp0) REVERT: A 178 TYR cc_start: 0.8174 (m-80) cc_final: 0.7750 (m-80) REVERT: A 188 ASN cc_start: 0.8682 (m-40) cc_final: 0.8465 (m-40) REVERT: A 244 HIS cc_start: 0.9142 (t-90) cc_final: 0.8865 (t-90) REVERT: B 68 GLU cc_start: 0.9023 (mt-10) cc_final: 0.8696 (tm-30) REVERT: B 202 GLN cc_start: 0.9215 (tt0) cc_final: 0.8973 (tp-100) REVERT: B 235 ARG cc_start: 0.8466 (ttp-170) cc_final: 0.7979 (ttm170) REVERT: C 130 ARG cc_start: 0.8777 (OUTLIER) cc_final: 0.8543 (ttp-170) REVERT: D 39 LYS cc_start: 0.8649 (mttt) cc_final: 0.8440 (mmpt) REVERT: D 67 SER cc_start: 0.8141 (t) cc_final: 0.7699 (p) REVERT: D 68 GLU cc_start: 0.8609 (mt-10) cc_final: 0.8247 (tm-30) REVERT: D 72 ASP cc_start: 0.8857 (m-30) cc_final: 0.8553 (m-30) REVERT: D 202 GLN cc_start: 0.9103 (tt0) cc_final: 0.8620 (tm-30) REVERT: E 30 GLN cc_start: 0.8755 (mt0) cc_final: 0.8361 (tm130) REVERT: E 43 GLU cc_start: 0.8577 (OUTLIER) cc_final: 0.8165 (pp20) REVERT: F 27 ARG cc_start: 0.8690 (mtp180) cc_final: 0.8415 (mmm160) REVERT: F 30 GLN cc_start: 0.8076 (mp10) cc_final: 0.7676 (mp10) REVERT: F 34 ASN cc_start: 0.7747 (t0) cc_final: 0.7532 (t0) REVERT: F 202 GLN cc_start: 0.8786 (tt0) cc_final: 0.8550 (tm-30) REVERT: F 247 ARG cc_start: 0.8820 (mtp85) cc_final: 0.8310 (ttp80) REVERT: F 279 PHE cc_start: 0.8533 (m-80) cc_final: 0.8288 (m-80) REVERT: F 306 ARG cc_start: 0.8598 (ttt180) cc_final: 0.8216 (ttp-110) REVERT: G 34 ASN cc_start: 0.8128 (t0) cc_final: 0.7889 (t0) REVERT: G 68 GLU cc_start: 0.9037 (mt-10) cc_final: 0.8775 (mp0) REVERT: G 202 GLN cc_start: 0.8860 (tt0) cc_final: 0.8308 (tm-30) REVERT: H 62 ASN cc_start: 0.8917 (m-40) cc_final: 0.8706 (m-40) REVERT: H 274 ASP cc_start: 0.8852 (m-30) cc_final: 0.8178 (p0) REVERT: I 25 ILE cc_start: 0.7314 (tt) cc_final: 0.7018 (tp) REVERT: I 96 ARG cc_start: 0.6816 (mtp85) cc_final: 0.5260 (mtm180) REVERT: I 124 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8511 (tt0) REVERT: I 163 GLU cc_start: 0.8860 (mt-10) cc_final: 0.8553 (mt-10) REVERT: I 191 TYR cc_start: 0.8200 (t80) cc_final: 0.7969 (t80) REVERT: I 216 TYR cc_start: 0.8544 (m-80) cc_final: 0.7983 (m-80) outliers start: 34 outliers final: 7 residues processed: 259 average time/residue: 0.7324 time to fit residues: 212.7565 Evaluate side-chains 225 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 215 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 66 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 251 MET Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain I residue 124 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 277 optimal weight: 20.0000 chunk 24 optimal weight: 6.9990 chunk 244 optimal weight: 1.9990 chunk 10 optimal weight: 7.9990 chunk 175 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 21 optimal weight: 20.0000 chunk 30 optimal weight: 40.0000 chunk 285 optimal weight: 50.0000 chunk 163 optimal weight: 3.9990 chunk 182 optimal weight: 5.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN B 62 ASN E 62 ASN F 62 ASN I 242 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.105327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.057047 restraints weight = 94533.463| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.62 r_work: 0.2478 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2478 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8770 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.060 24785 Z= 0.361 Angle : 0.586 7.613 33980 Z= 0.326 Chirality : 0.043 0.184 3861 Planarity : 0.004 0.061 3992 Dihedral : 18.425 99.421 4581 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.91 % Allowed : 10.12 % Favored : 87.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % 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: 0.91 (0.16), residues: 2803 helix: 1.21 (0.14), residues: 1314 sheet: -0.03 (0.24), residues: 499 loop : 0.33 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.023 0.002 TYR B 216 PHE 0.026 0.002 PHE A 166 HIS 0.004 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00819 / 0.36 (24785) covalent geometry : angle 0.58564 / 0.33 (33980) hydrogen bonds : bond 0.04542 / 3.06 ( 1295) hydrogen bonds : angle 4.74011 / 3.35 ( 3480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 211 time to evaluate : 0.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9165 (mt-10) cc_final: 0.8788 (mp0) REVERT: A 178 TYR cc_start: 0.8188 (m-80) cc_final: 0.7704 (m-80) REVERT: A 188 ASN cc_start: 0.8723 (m-40) cc_final: 0.8500 (m-40) REVERT: A 229 ARG cc_start: 0.8834 (OUTLIER) cc_final: 0.8477 (ttm170) REVERT: B 68 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8676 (tm-30) REVERT: B 202 GLN cc_start: 0.9232 (tt0) cc_final: 0.8963 (tp-100) REVERT: B 229 ARG cc_start: 0.9030 (OUTLIER) cc_final: 0.8815 (ttp-170) REVERT: B 235 ARG cc_start: 0.8584 (ttp-170) cc_final: 0.8062 (ttm170) REVERT: C 68 GLU cc_start: 0.7851 (tm-30) cc_final: 0.7600 (tm-30) REVERT: C 72 ASP cc_start: 0.7958 (p0) cc_final: 0.7582 (p0) REVERT: D 39 LYS cc_start: 0.8670 (mttt) cc_final: 0.8463 (mmpt) REVERT: D 67 SER cc_start: 0.8222 (t) cc_final: 0.7790 (p) REVERT: D 68 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8310 (tm-30) REVERT: D 72 ASP cc_start: 0.8901 (m-30) cc_final: 0.8587 (m-30) REVERT: D 202 GLN cc_start: 0.9148 (tt0) cc_final: 0.8638 (tm-30) REVERT: E 30 GLN cc_start: 0.8753 (mt0) cc_final: 0.8325 (tm130) REVERT: E 43 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: E 68 GLU cc_start: 0.8617 (mp0) cc_final: 0.8224 (tm-30) REVERT: E 72 ASP cc_start: 0.8768 (p0) cc_final: 0.8254 (p0) REVERT: F 27 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8267 (mmm160) REVERT: F 30 GLN cc_start: 0.8081 (mp10) cc_final: 0.7678 (mp10) REVERT: F 34 ASN cc_start: 0.7895 (t0) cc_final: 0.7630 (t0) REVERT: F 202 GLN cc_start: 0.8853 (tt0) cc_final: 0.8575 (tm-30) REVERT: F 247 ARG cc_start: 0.8828 (mtp85) cc_final: 0.8347 (ttp80) REVERT: F 279 PHE cc_start: 0.8510 (m-80) cc_final: 0.8253 (m-80) REVERT: F 306 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8320 (ttp-170) REVERT: G 34 ASN cc_start: 0.8265 (t0) cc_final: 0.8022 (t0) REVERT: G 202 GLN cc_start: 0.8890 (tt0) cc_final: 0.8349 (tm-30) REVERT: H 274 ASP cc_start: 0.8922 (m-30) cc_final: 0.8238 (p0) REVERT: I 96 ARG cc_start: 0.6764 (mtp85) cc_final: 0.5208 (mtm180) REVERT: I 124 GLU cc_start: 0.8757 (OUTLIER) cc_final: 0.8533 (tt0) REVERT: I 163 GLU cc_start: 0.8828 (mt-10) cc_final: 0.8578 (mt-10) REVERT: I 210 MET cc_start: 0.8443 (OUTLIER) cc_final: 0.8217 (mpt) REVERT: I 216 TYR cc_start: 0.8540 (m-80) cc_final: 0.8120 (m-80) REVERT: I 243 MET cc_start: 0.9155 (mmm) cc_final: 0.8938 (tmm) outliers start: 43 outliers final: 15 residues processed: 242 average time/residue: 0.7281 time to fit residues: 197.9970 Evaluate side-chains 221 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 201 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 229 ARG Chi-restraints excluded: chain B residue 270 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 61 ILE Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain E residue 297 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 210 MET Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 326 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 275 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 95 optimal weight: 0.8980 chunk 216 optimal weight: 2.9990 chunk 72 optimal weight: 0.8980 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 7.9990 chunk 267 optimal weight: 5.9990 chunk 230 optimal weight: 0.7980 chunk 117 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 244 HIS B 62 ASN E 62 ASN F 62 ASN I 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.108251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.060849 restraints weight = 74407.992| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.31 r_work: 0.2576 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2619 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2619 r_free = 0.2619 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2619 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 24785 Z= 0.124 Angle : 0.484 9.558 33980 Z= 0.277 Chirality : 0.039 0.179 3861 Planarity : 0.003 0.037 3992 Dihedral : 18.362 105.890 4581 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.11 % Allowed : 11.01 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.02 (0.16), residues: 2803 helix: 1.26 (0.14), residues: 1319 sheet: 0.03 (0.23), residues: 531 loop : 0.47 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.022 0.001 TYR B 216 PHE 0.017 0.001 PHE A 166 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00248 / 0.12 (24785) covalent geometry : angle 0.48423 / 0.28 (33980) hydrogen bonds : bond 0.03297 / 2.21 ( 1295) hydrogen bonds : angle 4.38952 / 3.09 ( 3480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 217 time to evaluate : 0.870 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9145 (mt-10) cc_final: 0.8897 (mt-10) REVERT: A 178 TYR cc_start: 0.8168 (m-80) cc_final: 0.7700 (m-80) REVERT: A 188 ASN cc_start: 0.8793 (m-40) cc_final: 0.8557 (m-40) REVERT: B 62 ASN cc_start: 0.9092 (m-40) cc_final: 0.8694 (t0) REVERT: B 68 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8673 (tm-30) REVERT: B 202 GLN cc_start: 0.9205 (tt0) cc_final: 0.8907 (tp-100) REVERT: B 235 ARG cc_start: 0.8536 (ttp-170) cc_final: 0.8039 (ttm170) REVERT: C 68 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7562 (tm-30) REVERT: C 72 ASP cc_start: 0.7967 (p0) cc_final: 0.7471 (p0) REVERT: D 39 LYS cc_start: 0.8651 (mttt) cc_final: 0.8439 (mmpt) REVERT: D 67 SER cc_start: 0.8149 (t) cc_final: 0.7719 (p) REVERT: D 68 GLU cc_start: 0.8629 (mt-10) cc_final: 0.8255 (tm-30) REVERT: D 72 ASP cc_start: 0.8865 (m-30) cc_final: 0.8547 (m-30) REVERT: D 176 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8008 (mm-30) REVERT: D 202 GLN cc_start: 0.9102 (tt0) cc_final: 0.8631 (tm-30) REVERT: E 30 GLN cc_start: 0.8702 (mt0) cc_final: 0.8342 (tm130) REVERT: E 43 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8199 (pp20) REVERT: F 27 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8278 (mmm160) REVERT: F 30 GLN cc_start: 0.8170 (mp10) cc_final: 0.7737 (mp10) REVERT: F 34 ASN cc_start: 0.7932 (t0) cc_final: 0.7684 (t0) REVERT: F 202 GLN cc_start: 0.8799 (tt0) cc_final: 0.8551 (tm-30) REVERT: F 247 ARG cc_start: 0.8801 (mtp85) cc_final: 0.8315 (ttp80) REVERT: F 279 PHE cc_start: 0.8514 (m-80) cc_final: 0.8226 (m-80) REVERT: F 306 ARG cc_start: 0.8589 (ttt180) cc_final: 0.8213 (ttp-110) REVERT: G 34 ASN cc_start: 0.8271 (t0) cc_final: 0.8041 (t0) REVERT: G 202 GLN cc_start: 0.8849 (tt0) cc_final: 0.8316 (tm-30) REVERT: G 306 ARG cc_start: 0.7595 (tpp-160) cc_final: 0.7277 (tpp-160) REVERT: H 62 ASN cc_start: 0.8902 (m-40) cc_final: 0.8587 (m-40) REVERT: H 274 ASP cc_start: 0.8876 (m-30) cc_final: 0.8239 (p0) REVERT: I 96 ARG cc_start: 0.6723 (mtp85) cc_final: 0.5175 (mtm180) REVERT: I 124 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.8294 (tt0) REVERT: I 163 GLU cc_start: 0.8859 (mt-10) cc_final: 0.8627 (mt-10) REVERT: I 191 TYR cc_start: 0.8034 (t80) cc_final: 0.7826 (t80) REVERT: I 216 TYR cc_start: 0.8599 (m-80) cc_final: 0.7843 (m-80) REVERT: I 243 MET cc_start: 0.9149 (mmm) cc_final: 0.8947 (mmm) outliers start: 25 outliers final: 8 residues processed: 237 average time/residue: 0.7139 time to fit residues: 191.2774 Evaluate side-chains 217 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 207 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 36 ASN Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 124 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 224 optimal weight: 3.9990 chunk 210 optimal weight: 0.8980 chunk 195 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 121 optimal weight: 2.9990 chunk 151 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 287 optimal weight: 50.0000 chunk 226 optimal weight: 9.9990 chunk 95 optimal weight: 2.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN F 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.107859 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.060147 restraints weight = 89107.518| |-----------------------------------------------------------------------------| r_work (start): 0.2746 rms_B_bonded: 3.57 r_work: 0.2555 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2599 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2599 r_free = 0.2599 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2599 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 24785 Z= 0.148 Angle : 0.483 9.450 33980 Z= 0.275 Chirality : 0.039 0.180 3861 Planarity : 0.003 0.039 3992 Dihedral : 18.376 110.918 4581 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 1.51 % Allowed : 11.14 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.16), residues: 2803 helix: 1.32 (0.15), residues: 1319 sheet: 0.01 (0.23), residues: 531 loop : 0.50 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.023 0.001 TYR B 216 PHE 0.020 0.001 PHE I 126 HIS 0.003 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.15 (24785) covalent geometry : angle 0.48304 / 0.27 (33980) hydrogen bonds : bond 0.03259 / 2.19 ( 1295) hydrogen bonds : angle 4.32795 / 3.06 ( 3480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 212 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.8203 (m-80) cc_final: 0.7754 (m-80) REVERT: A 188 ASN cc_start: 0.8783 (m-40) cc_final: 0.8477 (m-40) REVERT: A 290 ASN cc_start: 0.8252 (m110) cc_final: 0.7933 (m110) REVERT: B 68 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8702 (tm-30) REVERT: B 202 GLN cc_start: 0.9202 (tt0) cc_final: 0.8897 (tp-100) REVERT: B 235 ARG cc_start: 0.8516 (ttp-170) cc_final: 0.7972 (ttm170) REVERT: C 68 GLU cc_start: 0.7847 (tm-30) cc_final: 0.7510 (tm-30) REVERT: C 72 ASP cc_start: 0.8023 (p0) cc_final: 0.7448 (p0) REVERT: D 39 LYS cc_start: 0.8653 (mttt) cc_final: 0.8432 (mmpt) REVERT: D 67 SER cc_start: 0.8154 (t) cc_final: 0.7741 (p) REVERT: D 68 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8260 (tm-30) REVERT: D 72 ASP cc_start: 0.8868 (m-30) cc_final: 0.8553 (m-30) REVERT: D 176 GLU cc_start: 0.8345 (mm-30) cc_final: 0.8019 (mm-30) REVERT: D 202 GLN cc_start: 0.9120 (tt0) cc_final: 0.8641 (tm-30) REVERT: E 30 GLN cc_start: 0.8665 (mt0) cc_final: 0.8321 (tm130) REVERT: E 43 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.8252 (pp20) REVERT: E 210 MET cc_start: 0.9135 (mtp) cc_final: 0.8888 (mtm) REVERT: E 272 GLN cc_start: 0.8985 (mt0) cc_final: 0.8699 (mt0) REVERT: F 27 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8149 (tpp-160) REVERT: F 30 GLN cc_start: 0.8204 (mp10) cc_final: 0.7918 (mp10) REVERT: F 34 ASN cc_start: 0.7912 (t0) cc_final: 0.7635 (t0) REVERT: F 202 GLN cc_start: 0.8824 (tt0) cc_final: 0.8545 (tm-30) REVERT: F 247 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8314 (ttp80) REVERT: F 279 PHE cc_start: 0.8532 (m-80) cc_final: 0.8221 (m-80) REVERT: F 306 ARG cc_start: 0.8577 (ttt180) cc_final: 0.8237 (ttp-170) REVERT: G 34 ASN cc_start: 0.8280 (t0) cc_final: 0.8047 (t0) REVERT: G 107 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8423 (mtmm) REVERT: G 202 GLN cc_start: 0.8891 (tt0) cc_final: 0.8337 (tm-30) REVERT: G 306 ARG cc_start: 0.7611 (tpp-160) cc_final: 0.7277 (tpp-160) REVERT: H 62 ASN cc_start: 0.8907 (m-40) cc_final: 0.8660 (m-40) REVERT: H 163 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8034 (pt0) REVERT: H 274 ASP cc_start: 0.8869 (m-30) cc_final: 0.8213 (p0) REVERT: I 96 ARG cc_start: 0.6703 (mtp85) cc_final: 0.5132 (mtm180) REVERT: I 124 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8393 (tt0) REVERT: I 163 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8626 (mt-10) REVERT: I 191 TYR cc_start: 0.8103 (t80) cc_final: 0.7898 (t80) REVERT: I 216 TYR cc_start: 0.8645 (m-80) cc_final: 0.8085 (m-80) REVERT: I 243 MET cc_start: 0.9147 (mmm) cc_final: 0.8940 (mmm) outliers start: 34 outliers final: 12 residues processed: 240 average time/residue: 0.6926 time to fit residues: 187.8833 Evaluate side-chains 220 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 204 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 163 GLU Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 90 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 198 optimal weight: 1.9990 chunk 77 optimal weight: 0.9980 chunk 180 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 85 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 229 optimal weight: 0.8980 chunk 256 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN E 62 ASN F 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.108894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.061654 restraints weight = 72071.451| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.28 r_work: 0.2599 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.066 24785 Z= 0.116 Angle : 0.466 10.336 33980 Z= 0.266 Chirality : 0.038 0.190 3861 Planarity : 0.003 0.042 3992 Dihedral : 18.325 116.779 4581 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.15 % Allowed : 11.54 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.10 (0.16), residues: 2803 helix: 1.36 (0.15), residues: 1319 sheet: -0.10 (0.23), residues: 535 loop : 0.57 (0.22), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 306 TYR 0.019 0.001 TYR B 216 PHE 0.014 0.001 PHE A 126 HIS 0.003 0.000 HIS A 47 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (24785) covalent geometry : angle 0.46566 / 0.27 (33980) hydrogen bonds : bond 0.02985 / 2.00 ( 1295) hydrogen bonds : angle 4.18708 / 2.96 ( 3480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 221 time to evaluate : 1.007 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.6819 (OUTLIER) cc_final: 0.6314 (t80) REVERT: A 178 TYR cc_start: 0.8202 (m-80) cc_final: 0.7708 (m-80) REVERT: A 290 ASN cc_start: 0.8253 (m110) cc_final: 0.7936 (m110) REVERT: B 43 GLU cc_start: 0.8998 (pt0) cc_final: 0.8661 (pp20) REVERT: B 68 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8651 (tm-30) REVERT: B 202 GLN cc_start: 0.9179 (tt0) cc_final: 0.8867 (tp-100) REVERT: B 235 ARG cc_start: 0.8479 (ttp-170) cc_final: 0.7999 (ttm170) REVERT: C 68 GLU cc_start: 0.7849 (tm-30) cc_final: 0.7482 (tm-30) REVERT: C 72 ASP cc_start: 0.8067 (p0) cc_final: 0.7438 (p0) REVERT: C 176 GLU cc_start: 0.8943 (tp30) cc_final: 0.8741 (tp30) REVERT: D 39 LYS cc_start: 0.8650 (mttt) cc_final: 0.8430 (mmpt) REVERT: D 67 SER cc_start: 0.8150 (t) cc_final: 0.7755 (p) REVERT: D 68 GLU cc_start: 0.8634 (mt-10) cc_final: 0.8252 (tm-30) REVERT: D 72 ASP cc_start: 0.8849 (m-30) cc_final: 0.8551 (m-30) REVERT: D 176 GLU cc_start: 0.8349 (mm-30) cc_final: 0.7986 (mm-30) REVERT: D 202 GLN cc_start: 0.9096 (tt0) cc_final: 0.8616 (tm-30) REVERT: D 306 ARG cc_start: 0.8316 (mmm-85) cc_final: 0.8064 (tpt-90) REVERT: E 30 GLN cc_start: 0.8627 (mt0) cc_final: 0.8333 (tm130) REVERT: E 43 GLU cc_start: 0.8608 (OUTLIER) cc_final: 0.8219 (pp20) REVERT: E 210 MET cc_start: 0.9114 (mtp) cc_final: 0.8881 (mtm) REVERT: E 272 GLN cc_start: 0.8994 (mt0) cc_final: 0.8694 (mt0) REVERT: F 27 ARG cc_start: 0.8695 (mtp180) cc_final: 0.8154 (tpp-160) REVERT: F 30 GLN cc_start: 0.8291 (mp10) cc_final: 0.7993 (mp10) REVERT: F 34 ASN cc_start: 0.7948 (t0) cc_final: 0.7664 (t0) REVERT: F 202 GLN cc_start: 0.8788 (tt0) cc_final: 0.8516 (tm-30) REVERT: F 247 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8284 (ttp80) REVERT: F 279 PHE cc_start: 0.8536 (m-80) cc_final: 0.8229 (m-80) REVERT: F 306 ARG cc_start: 0.8554 (ttt180) cc_final: 0.8168 (ttp-110) REVERT: G 34 ASN cc_start: 0.8296 (t0) cc_final: 0.8064 (t0) REVERT: G 107 LYS cc_start: 0.8643 (OUTLIER) cc_final: 0.8422 (mtmm) REVERT: G 202 GLN cc_start: 0.8855 (tt0) cc_final: 0.8308 (tm-30) REVERT: G 306 ARG cc_start: 0.7624 (tpp-160) cc_final: 0.7399 (tpp-160) REVERT: H 62 ASN cc_start: 0.8907 (m-40) cc_final: 0.8696 (m-40) REVERT: H 274 ASP cc_start: 0.8850 (m-30) cc_final: 0.8238 (p0) REVERT: I 96 ARG cc_start: 0.6658 (mtp85) cc_final: 0.5121 (mtm180) REVERT: I 124 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8339 (tt0) REVERT: I 163 GLU cc_start: 0.8904 (mt-10) cc_final: 0.8651 (mt-10) REVERT: I 191 TYR cc_start: 0.8136 (t80) cc_final: 0.7846 (t80) REVERT: I 216 TYR cc_start: 0.8635 (m-80) cc_final: 0.8004 (m-80) REVERT: I 243 MET cc_start: 0.9148 (mmm) cc_final: 0.8932 (mmm) outliers start: 26 outliers final: 11 residues processed: 243 average time/residue: 0.7256 time to fit residues: 200.2110 Evaluate side-chains 224 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 209 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 243 optimal weight: 8.9990 chunk 282 optimal weight: 30.0000 chunk 207 optimal weight: 0.5980 chunk 198 optimal weight: 0.0020 chunk 78 optimal weight: 6.9990 chunk 209 optimal weight: 0.8980 chunk 216 optimal weight: 3.9990 chunk 184 optimal weight: 0.4980 chunk 159 optimal weight: 5.9990 chunk 175 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 overall best weight: 1.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 188 ASN A 267 ASN E 62 ASN F 62 ASN I 242 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.061080 restraints weight = 81895.190| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.45 r_work: 0.2583 rms_B_bonded: 3.73 restraints_weight: 0.5000 r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.2497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 24785 Z= 0.130 Angle : 0.469 8.582 33980 Z= 0.267 Chirality : 0.038 0.192 3861 Planarity : 0.003 0.043 3992 Dihedral : 18.307 120.658 4581 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.93 % Allowed : 12.21 % Favored : 86.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2803 helix: 1.40 (0.15), residues: 1319 sheet: 0.01 (0.23), residues: 525 loop : 0.60 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.015 0.001 TYR B 216 PHE 0.015 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.13 (24785) covalent geometry : angle 0.46905 / 0.27 (33980) hydrogen bonds : bond 0.03009 / 2.01 ( 1295) hydrogen bonds : angle 4.16888 / 2.95 ( 3480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 223 time to evaluate : 0.860 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.6766 (OUTLIER) cc_final: 0.6281 (t80) REVERT: A 178 TYR cc_start: 0.8213 (m-80) cc_final: 0.7756 (m-80) REVERT: A 199 HIS cc_start: 0.8599 (t-90) cc_final: 0.8291 (t-90) REVERT: A 290 ASN cc_start: 0.8292 (m110) cc_final: 0.7960 (m110) REVERT: B 68 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8667 (tm-30) REVERT: B 202 GLN cc_start: 0.9167 (tt0) cc_final: 0.8849 (tp-100) REVERT: B 235 ARG cc_start: 0.8439 (ttp-170) cc_final: 0.7973 (ttm170) REVERT: C 68 GLU cc_start: 0.7866 (tm-30) cc_final: 0.7480 (tm-30) REVERT: C 72 ASP cc_start: 0.8094 (p0) cc_final: 0.7451 (p0) REVERT: D 39 LYS cc_start: 0.8654 (mttt) cc_final: 0.8433 (mmpt) REVERT: D 67 SER cc_start: 0.8154 (t) cc_final: 0.7775 (p) REVERT: D 68 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8272 (tm-30) REVERT: D 72 ASP cc_start: 0.8854 (m-30) cc_final: 0.8561 (m-30) REVERT: D 176 GLU cc_start: 0.8379 (mm-30) cc_final: 0.8005 (mm-30) REVERT: D 202 GLN cc_start: 0.9116 (tt0) cc_final: 0.8628 (tm-30) REVERT: D 306 ARG cc_start: 0.8337 (mmm-85) cc_final: 0.8085 (tpt-90) REVERT: E 30 GLN cc_start: 0.8618 (mt0) cc_final: 0.8328 (tm130) REVERT: E 43 GLU cc_start: 0.8634 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: F 27 ARG cc_start: 0.8689 (mtp180) cc_final: 0.8149 (tpp-160) REVERT: F 30 GLN cc_start: 0.8314 (mp10) cc_final: 0.8014 (mp10) REVERT: F 34 ASN cc_start: 0.7949 (t0) cc_final: 0.7672 (t0) REVERT: F 202 GLN cc_start: 0.8788 (tt0) cc_final: 0.8514 (tm-30) REVERT: F 247 ARG cc_start: 0.8789 (mtp85) cc_final: 0.8308 (ttp80) REVERT: F 279 PHE cc_start: 0.8534 (m-80) cc_final: 0.8218 (m-80) REVERT: F 306 ARG cc_start: 0.8565 (ttt180) cc_final: 0.8168 (ttp-110) REVERT: G 34 ASN cc_start: 0.8309 (t0) cc_final: 0.8083 (t0) REVERT: G 107 LYS cc_start: 0.8646 (OUTLIER) cc_final: 0.8429 (mtmm) REVERT: G 202 GLN cc_start: 0.8873 (tt0) cc_final: 0.8323 (tm-30) REVERT: G 306 ARG cc_start: 0.7638 (tpp-160) cc_final: 0.7406 (tpp-160) REVERT: H 62 ASN cc_start: 0.8909 (m-40) cc_final: 0.8676 (m-40) REVERT: H 88 THR cc_start: 0.8839 (m) cc_final: 0.8388 (t) REVERT: H 274 ASP cc_start: 0.8866 (m-30) cc_final: 0.8238 (p0) REVERT: I 96 ARG cc_start: 0.6656 (mtp85) cc_final: 0.5119 (mtm180) REVERT: I 124 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8338 (tt0) REVERT: I 163 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8670 (mt-10) REVERT: I 191 TYR cc_start: 0.8205 (t80) cc_final: 0.7916 (t80) REVERT: I 216 TYR cc_start: 0.8654 (m-80) cc_final: 0.8037 (m-80) REVERT: I 243 MET cc_start: 0.9148 (mmm) cc_final: 0.8930 (mmm) outliers start: 21 outliers final: 13 residues processed: 240 average time/residue: 0.6873 time to fit residues: 187.3303 Evaluate side-chains 232 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 215 time to evaluate : 0.817 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 107 LYS Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 224 optimal weight: 6.9990 chunk 26 optimal weight: 0.7980 chunk 195 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 285 optimal weight: 50.0000 chunk 266 optimal weight: 9.9990 chunk 156 optimal weight: 3.9990 chunk 44 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 186 optimal weight: 10.0000 chunk 277 optimal weight: 4.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 62 ASN F 62 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.106187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058895 restraints weight = 66031.887| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.12 r_work: 0.2539 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2582 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2582 r_free = 0.2582 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2582 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.2356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 24785 Z= 0.284 Angle : 0.545 9.161 33980 Z= 0.303 Chirality : 0.041 0.183 3861 Planarity : 0.004 0.044 3992 Dihedral : 18.411 122.834 4581 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.11 % Allowed : 12.16 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.08 (0.17), residues: 2803 helix: 1.38 (0.15), residues: 1319 sheet: -0.16 (0.24), residues: 507 loop : 0.51 (0.21), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.025 0.002 TYR B 216 PHE 0.013 0.002 PHE I 126 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00642 / 0.28 (24785) covalent geometry : angle 0.54481 / 0.30 (33980) hydrogen bonds : bond 0.03796 / 2.55 ( 1295) hydrogen bonds : angle 4.40707 / 3.12 ( 3480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 208 time to evaluate : 0.884 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.6733 (OUTLIER) cc_final: 0.6209 (t80) REVERT: A 178 TYR cc_start: 0.8254 (m-80) cc_final: 0.7789 (m-80) REVERT: A 290 ASN cc_start: 0.8332 (m110) cc_final: 0.8006 (m110) REVERT: B 68 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8680 (tm-30) REVERT: B 202 GLN cc_start: 0.9187 (tt0) cc_final: 0.8866 (tp-100) REVERT: B 235 ARG cc_start: 0.8516 (ttp-170) cc_final: 0.8026 (ttm170) REVERT: C 68 GLU cc_start: 0.7899 (tm-30) cc_final: 0.7500 (tm-30) REVERT: C 72 ASP cc_start: 0.8101 (p0) cc_final: 0.7445 (p0) REVERT: D 39 LYS cc_start: 0.8663 (mttt) cc_final: 0.8446 (mmpt) REVERT: D 67 SER cc_start: 0.8181 (t) cc_final: 0.7812 (p) REVERT: D 68 GLU cc_start: 0.8683 (mt-10) cc_final: 0.8296 (tm-30) REVERT: D 72 ASP cc_start: 0.8870 (m-30) cc_final: 0.8548 (m-30) REVERT: D 176 GLU cc_start: 0.8393 (mm-30) cc_final: 0.8018 (mm-30) REVERT: D 202 GLN cc_start: 0.9100 (tt0) cc_final: 0.8605 (tm-30) REVERT: E 30 GLN cc_start: 0.8648 (mt0) cc_final: 0.8312 (tm130) REVERT: E 43 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.8269 (pp20) REVERT: F 27 ARG cc_start: 0.8709 (mtp180) cc_final: 0.8156 (tpp-160) REVERT: F 30 GLN cc_start: 0.8321 (mp10) cc_final: 0.8031 (mp10) REVERT: F 34 ASN cc_start: 0.8013 (t0) cc_final: 0.7710 (t0) REVERT: F 202 GLN cc_start: 0.8806 (tt0) cc_final: 0.8526 (tm-30) REVERT: F 247 ARG cc_start: 0.8793 (mtp85) cc_final: 0.8315 (ttp80) REVERT: F 306 ARG cc_start: 0.8582 (ttt180) cc_final: 0.8272 (ttp-170) REVERT: G 34 ASN cc_start: 0.8419 (t0) cc_final: 0.8210 (t0) REVERT: G 202 GLN cc_start: 0.8853 (tt0) cc_final: 0.8296 (tm-30) REVERT: G 306 ARG cc_start: 0.7582 (tpp-160) cc_final: 0.7354 (tpp-160) REVERT: H 62 ASN cc_start: 0.8880 (m-40) cc_final: 0.8637 (m-40) REVERT: H 274 ASP cc_start: 0.8891 (m-30) cc_final: 0.8205 (p0) REVERT: I 96 ARG cc_start: 0.6713 (mtp85) cc_final: 0.5173 (mtm180) REVERT: I 124 GLU cc_start: 0.8622 (OUTLIER) cc_final: 0.8417 (tt0) REVERT: I 163 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8610 (mt-10) REVERT: I 216 TYR cc_start: 0.8676 (m-80) cc_final: 0.8076 (m-80) REVERT: I 243 MET cc_start: 0.9160 (mmm) cc_final: 0.8939 (mmm) outliers start: 25 outliers final: 14 residues processed: 230 average time/residue: 0.7347 time to fit residues: 191.7198 Evaluate side-chains 220 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 203 time to evaluate : 0.949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 297 THR Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 253 optimal weight: 10.0000 chunk 108 optimal weight: 0.7980 chunk 264 optimal weight: 3.9990 chunk 60 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 chunk 10 optimal weight: 10.0000 chunk 206 optimal weight: 0.9980 chunk 84 optimal weight: 0.6980 chunk 80 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 8.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 267 ASN E 62 ASN E 272 GLN F 62 ASN ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.108582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.061591 restraints weight = 65544.729| |-----------------------------------------------------------------------------| r_work (start): 0.2780 rms_B_bonded: 3.12 r_work: 0.2601 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2601 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8679 moved from start: 0.2536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 24785 Z= 0.121 Angle : 0.483 9.607 33980 Z= 0.274 Chirality : 0.038 0.199 3861 Planarity : 0.003 0.052 3992 Dihedral : 18.313 124.702 4581 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.58 % Allowed : 13.05 % Favored : 86.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.14 (0.17), residues: 2803 helix: 1.38 (0.15), residues: 1323 sheet: -0.11 (0.23), residues: 539 loop : 0.63 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 247 TYR 0.012 0.001 TYR B 216 PHE 0.012 0.001 PHE I 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00242 / 0.12 (24785) covalent geometry : angle 0.48256 / 0.27 (33980) hydrogen bonds : bond 0.03018 / 2.02 ( 1295) hydrogen bonds : angle 4.21957 / 2.97 ( 3480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5606 Ramachandran restraints generated. 2803 Oldfield, 0 Emsley, 2803 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 214 time to evaluate : 1.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 129 PHE cc_start: 0.6745 (OUTLIER) cc_final: 0.6246 (t80) REVERT: A 178 TYR cc_start: 0.8253 (m-80) cc_final: 0.7791 (m-80) REVERT: A 199 HIS cc_start: 0.8533 (t-90) cc_final: 0.8213 (t-90) REVERT: A 290 ASN cc_start: 0.8267 (m110) cc_final: 0.7940 (m110) REVERT: B 68 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8642 (tm-30) REVERT: B 202 GLN cc_start: 0.9154 (tt0) cc_final: 0.8831 (tp-100) REVERT: B 235 ARG cc_start: 0.8423 (ttp-170) cc_final: 0.7904 (ttm170) REVERT: C 68 GLU cc_start: 0.7865 (tm-30) cc_final: 0.7482 (tm-30) REVERT: C 72 ASP cc_start: 0.8103 (p0) cc_final: 0.7437 (p0) REVERT: D 39 LYS cc_start: 0.8647 (mttt) cc_final: 0.8424 (mmpt) REVERT: D 67 SER cc_start: 0.8141 (t) cc_final: 0.7752 (p) REVERT: D 68 GLU cc_start: 0.8628 (mt-10) cc_final: 0.8261 (tm-30) REVERT: D 72 ASP cc_start: 0.8835 (m-30) cc_final: 0.8513 (m-30) REVERT: D 176 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7981 (mm-30) REVERT: D 202 GLN cc_start: 0.9085 (tt0) cc_final: 0.8601 (tm-30) REVERT: D 306 ARG cc_start: 0.8278 (ttm110) cc_final: 0.8057 (tpt-90) REVERT: E 30 GLN cc_start: 0.8627 (mt0) cc_final: 0.8327 (tm130) REVERT: E 43 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8249 (pp20) REVERT: F 27 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8129 (tpp-160) REVERT: F 30 GLN cc_start: 0.8320 (mp10) cc_final: 0.8002 (mp10) REVERT: F 34 ASN cc_start: 0.8008 (t0) cc_final: 0.7725 (t0) REVERT: F 202 GLN cc_start: 0.8769 (tt0) cc_final: 0.8488 (tm-30) REVERT: F 247 ARG cc_start: 0.8767 (mtp85) cc_final: 0.8283 (ttp80) REVERT: F 306 ARG cc_start: 0.8545 (ttt180) cc_final: 0.8148 (ttp-110) REVERT: G 34 ASN cc_start: 0.8357 (t0) cc_final: 0.8154 (t0) REVERT: G 202 GLN cc_start: 0.8844 (tt0) cc_final: 0.8291 (tm-30) REVERT: G 306 ARG cc_start: 0.7595 (tpp-160) cc_final: 0.7375 (tpp-160) REVERT: H 62 ASN cc_start: 0.8860 (m-40) cc_final: 0.8624 (m-40) REVERT: H 88 THR cc_start: 0.8766 (m) cc_final: 0.8438 (t) REVERT: H 274 ASP cc_start: 0.8880 (m-30) cc_final: 0.8232 (p0) REVERT: I 73 LYS cc_start: 0.7943 (tptm) cc_final: 0.7469 (ptmm) REVERT: I 96 ARG cc_start: 0.6698 (mtp85) cc_final: 0.5233 (mtm180) REVERT: I 124 GLU cc_start: 0.8612 (OUTLIER) cc_final: 0.8340 (tt0) REVERT: I 163 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8608 (mt-10) REVERT: I 216 TYR cc_start: 0.8673 (m-80) cc_final: 0.8003 (m-80) REVERT: I 243 MET cc_start: 0.9155 (mmm) cc_final: 0.8905 (tmm) outliers start: 13 outliers final: 7 residues processed: 225 average time/residue: 0.7524 time to fit residues: 192.4609 Evaluate side-chains 220 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 210 time to evaluate : 1.074 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 144 CYS Chi-restraints excluded: chain H residue 72 ASP Chi-restraints excluded: chain H residue 297 THR Chi-restraints excluded: chain I residue 124 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 35 optimal weight: 9.9990 chunk 228 optimal weight: 5.9990 chunk 204 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 chunk 130 optimal weight: 1.9990 chunk 193 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 121 optimal weight: 2.9990 chunk 278 optimal weight: 7.9990 chunk 104 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN E 62 ASN F 62 ASN ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.108144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.060708 restraints weight = 77918.076| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.36 r_work: 0.2575 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2575 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2617 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2617 r_free = 0.2617 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2617 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 24785 Z= 0.151 Angle : 0.488 9.924 33980 Z= 0.276 Chirality : 0.039 0.199 3861 Planarity : 0.003 0.062 3992 Dihedral : 18.311 127.975 4581 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.62 % Allowed : 13.45 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.17), residues: 2803 helix: 1.43 (0.15), residues: 1319 sheet: -0.13 (0.23), residues: 539 loop : 0.64 (0.22), residues: 945 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 247 TYR 0.038 0.001 TYR I 191 PHE 0.013 0.001 PHE I 126 HIS 0.002 0.000 HIS A 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.15 (24785) covalent geometry : angle 0.48765 / 0.28 (33980) hydrogen bonds : bond 0.03100 / 2.07 ( 1295) hydrogen bonds : angle 4.22462 / 2.98 ( 3480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9753.01 seconds wall clock time: 166 minutes 31.35 seconds (9991.35 seconds total)