Starting phenix.real_space_refine on Fri Aug 7 21:19:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i62_52646/08_2026/9i62_52646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i62_52646/08_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_52646/08_2026/9i62_52646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i62_52646/08_2026/9i62_52646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i62_52646/08_2026/9i62_52646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i62_52646/08_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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/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, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' CA': 2, 'ATP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 5.39, per 1000 atoms: 0.22 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: 2.14 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 3.20 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: 6.40 Time building geometry restraints manager: 2.86 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: 32023 1.02 - 2.03: 1500 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 2.510 nonbonded pdb="CA CA G 403 " pdb=" O3G ATP G 402 " model vdw 2.128 2.510 nonbonded pdb="CA CA C 403 " pdb=" O3G ATP C 402 " model vdw 2.138 2.510 nonbonded pdb="CA CA D 403 " pdb=" O3G ATP D 402 " model vdw 2.140 2.510 nonbonded pdb="CA CA E 403 " pdb=" O3G ATP E 402 " model vdw 2.145 2.510 ... (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: 7.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.750 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 27.200 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:10.090 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.430 ------------------------------------------------------------------------------- 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 : 0.527 5.083 33980 Z= 0.388 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 0.52748 / 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 : 0.942 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: 0.7921 (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: 0.8160 (p0) REVERT: D 39 LYS cc_start: 0.8832 (mttt) cc_final: 0.8616 (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: 0.8361 (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: 0.9318 time to fit residues: 317.8062 Evaluate side-chains 219 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 216 time to evaluate : 0.944 ------------------------------------------------------------------------------- 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: 0.7980 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: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 242 GLN D 36 ASN E 62 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.107353 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.059558 restraints weight = 89080.309| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 3.54 r_work: 0.2533 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2576 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2576 r_free = 0.2576 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2576 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 24785 Z= 0.150 Angle : 0.547 8.269 33980 Z= 0.316 Chirality : 0.040 0.170 3861 Planarity : 0.004 0.068 3992 Dihedral : 18.172 89.931 4584 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.29 % Allowed : 7.81 % Favored : 90.90 % 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: 1.18 (0.14), residues: 1303 sheet: 0.31 (0.25), residues: 500 loop : 0.52 (0.21), residues: 1000 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG H 235 TYR 0.027 0.001 TYR I 191 PHE 0.016 0.001 PHE A 126 HIS 0.003 0.001 HIS H 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (24785) covalent geometry : angle 0.54672 / 0.32 (33980) hydrogen bonds : bond 0.04838 / 3.22 ( 1295) hydrogen bonds : angle 5.09529 / 3.60 ( 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 274 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8756 (mp0) REVERT: A 178 TYR cc_start: 0.8201 (m-80) cc_final: 0.7766 (m-80) REVERT: A 188 ASN cc_start: 0.8627 (m-40) cc_final: 0.8401 (m-40) REVERT: A 205 TYR cc_start: 0.9440 (m-80) cc_final: 0.9133 (m-80) REVERT: A 210 MET cc_start: 0.9095 (mtm) cc_final: 0.8869 (mtm) REVERT: A 229 ARG cc_start: 0.8851 (OUTLIER) cc_final: 0.8530 (ttm170) REVERT: A 243 MET cc_start: 0.8508 (tpt) cc_final: 0.8299 (tpt) REVERT: A 290 ASN cc_start: 0.8051 (m-40) cc_final: 0.7745 (m110) REVERT: B 34 ASN cc_start: 0.7208 (t0) cc_final: 0.6921 (t0) REVERT: B 68 GLU cc_start: 0.9035 (mt-10) cc_final: 0.8780 (tm-30) REVERT: B 202 GLN cc_start: 0.9217 (tt0) cc_final: 0.9007 (tp-100) REVERT: B 235 ARG cc_start: 0.8525 (ttp-170) cc_final: 0.8015 (ttm170) REVERT: C 213 GLU cc_start: 0.8440 (mp0) cc_final: 0.8183 (mp0) REVERT: D 39 LYS cc_start: 0.8648 (mttt) cc_final: 0.8441 (mmpt) REVERT: D 67 SER cc_start: 0.8255 (t) cc_final: 0.7823 (p) REVERT: D 68 GLU cc_start: 0.8666 (mt-10) cc_final: 0.8353 (tm-30) REVERT: D 72 ASP cc_start: 0.8832 (m-30) cc_final: 0.8562 (m-30) REVERT: D 202 GLN cc_start: 0.9108 (tt0) cc_final: 0.8610 (tm-30) REVERT: E 30 GLN cc_start: 0.8817 (mt0) cc_final: 0.8338 (tm130) REVERT: E 43 GLU cc_start: 0.8572 (OUTLIER) cc_final: 0.8174 (pp20) REVERT: E 68 GLU cc_start: 0.8583 (mp0) cc_final: 0.8328 (tm-30) REVERT: E 72 ASP cc_start: 0.8548 (p0) cc_final: 0.7947 (p0) REVERT: F 27 ARG cc_start: 0.8656 (mtp180) cc_final: 0.8237 (tpp-160) REVERT: F 30 GLN cc_start: 0.8031 (mp10) cc_final: 0.7831 (mp10) REVERT: F 202 GLN cc_start: 0.8763 (tt0) cc_final: 0.8526 (tm-30) REVERT: F 247 ARG cc_start: 0.8812 (mtp85) cc_final: 0.8329 (ttp80) REVERT: F 306 ARG cc_start: 0.8583 (ttt180) cc_final: 0.8212 (ttp-110) REVERT: G 68 GLU cc_start: 0.9036 (mt-10) cc_final: 0.8730 (mp0) REVERT: G 202 GLN cc_start: 0.8861 (tt0) cc_final: 0.8346 (tm-30) REVERT: G 210 MET cc_start: 0.9233 (mtm) cc_final: 0.8973 (mtp) REVERT: H 62 ASN cc_start: 0.8906 (m-40) cc_final: 0.8677 (m-40) REVERT: H 163 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8357 (mt-10) REVERT: H 243 MET cc_start: 0.8815 (tpp) cc_final: 0.8614 (mpp) REVERT: H 274 ASP cc_start: 0.8888 (m-30) cc_final: 0.8199 (p0) REVERT: I 96 ARG cc_start: 0.6899 (mtp85) cc_final: 0.5300 (mtm180) REVERT: I 124 GLU cc_start: 0.8733 (OUTLIER) cc_final: 0.8428 (tt0) REVERT: I 163 GLU cc_start: 0.8649 (mt-10) cc_final: 0.8383 (mt-10) REVERT: I 191 TYR cc_start: 0.8081 (t80) cc_final: 0.7817 (t80) REVERT: I 216 TYR cc_start: 0.8486 (m-80) cc_final: 0.7790 (m-80) REVERT: I 251 MET cc_start: 0.8747 (mpp) cc_final: 0.8390 (mpp) outliers start: 29 outliers final: 4 residues processed: 263 average time/residue: 0.7412 time to fit residues: 218.1159 Evaluate side-chains 218 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 211 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 144 CYS 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 Chi-restraints excluded: chain I residue 326 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 252 optimal weight: 0.5980 chunk 256 optimal weight: 5.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 0.8980 chunk 159 optimal weight: 0.4980 chunk 58 optimal weight: 5.9990 chunk 242 optimal weight: 9.9990 chunk 162 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 187 optimal weight: 20.0000 chunk 62 optimal weight: 8.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 ASN E 62 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 242 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.106496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.058392 restraints weight = 89907.342| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.57 r_work: 0.2511 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2511 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2553 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2553 r_free = 0.2553 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2553 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 24785 Z= 0.199 Angle : 0.512 8.239 33980 Z= 0.292 Chirality : 0.040 0.178 3861 Planarity : 0.003 0.048 3992 Dihedral : 18.360 89.909 4581 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 1.51 % Allowed : 9.37 % Favored : 89.13 % 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: 1.09 (0.16), residues: 2803 helix: 1.30 (0.14), residues: 1314 sheet: 0.14 (0.24), residues: 536 loop : 0.48 (0.21), residues: 953 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 306 TYR 0.020 0.001 TYR I 232 PHE 0.010 0.001 PHE A 166 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00434 / 0.20 (24785) covalent geometry : angle 0.51189 / 0.29 (33980) hydrogen bonds : bond 0.04213 / 2.82 ( 1295) hydrogen bonds : angle 4.69903 / 3.32 ( 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 259 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 225 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9200 (mt-10) cc_final: 0.8727 (mp0) REVERT: A 178 TYR cc_start: 0.8173 (m-80) cc_final: 0.7728 (m-80) REVERT: A 188 ASN cc_start: 0.8666 (m-40) cc_final: 0.8435 (m-40) REVERT: A 205 TYR cc_start: 0.9476 (m-80) cc_final: 0.9145 (m-80) REVERT: A 229 ARG cc_start: 0.8846 (OUTLIER) cc_final: 0.8515 (ttm170) REVERT: A 290 ASN cc_start: 0.8101 (m-40) cc_final: 0.7787 (m110) REVERT: B 68 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8698 (tm-30) REVERT: B 202 GLN cc_start: 0.9213 (tt0) cc_final: 0.8972 (tp-100) REVERT: B 235 ARG cc_start: 0.8522 (ttp-170) cc_final: 0.8021 (ttm170) REVERT: C 68 GLU cc_start: 0.7832 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 72 ASP cc_start: 0.7934 (p0) cc_final: 0.7585 (p0) REVERT: C 130 ARG cc_start: 0.8811 (OUTLIER) cc_final: 0.8579 (ttp-170) REVERT: D 39 LYS cc_start: 0.8667 (mttt) cc_final: 0.8457 (mmpt) REVERT: D 68 GLU cc_start: 0.8646 (mt-10) cc_final: 0.8339 (tm-30) REVERT: D 72 ASP cc_start: 0.8866 (m-30) cc_final: 0.8568 (m-30) REVERT: D 202 GLN cc_start: 0.9119 (tt0) cc_final: 0.8627 (tm-30) REVERT: E 30 GLN cc_start: 0.8770 (mt0) cc_final: 0.8354 (tm130) REVERT: E 43 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8169 (pp20) REVERT: F 27 ARG cc_start: 0.8661 (mtp180) cc_final: 0.8293 (mmm160) REVERT: F 30 GLN cc_start: 0.8097 (mp10) cc_final: 0.7690 (mp10) REVERT: F 202 GLN cc_start: 0.8794 (tt0) cc_final: 0.8546 (tm-30) REVERT: F 247 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8301 (ttp80) REVERT: F 306 ARG cc_start: 0.8605 (ttt180) cc_final: 0.8275 (ttp-170) REVERT: G 34 ASN cc_start: 0.8099 (t0) cc_final: 0.7879 (t0) REVERT: G 68 GLU cc_start: 0.9049 (mt-10) cc_final: 0.8774 (mp0) REVERT: G 202 GLN cc_start: 0.8857 (tt0) cc_final: 0.8334 (tm-30) REVERT: G 210 MET cc_start: 0.9210 (mtm) cc_final: 0.8985 (mtp) REVERT: H 274 ASP cc_start: 0.8881 (m-30) cc_final: 0.8187 (p0) REVERT: I 25 ILE cc_start: 0.7276 (tt) cc_final: 0.6954 (tp) REVERT: I 96 ARG cc_start: 0.6852 (mtp85) cc_final: 0.5284 (mtm180) REVERT: I 124 GLU cc_start: 0.8761 (OUTLIER) cc_final: 0.8520 (tt0) REVERT: I 163 GLU cc_start: 0.8695 (mt-10) cc_final: 0.8442 (mt-10) REVERT: I 191 TYR cc_start: 0.8238 (t80) cc_final: 0.8016 (t80) REVERT: I 216 TYR cc_start: 0.8520 (m-80) cc_final: 0.8049 (m-80) outliers start: 34 outliers final: 9 residues processed: 247 average time/residue: 0.7554 time to fit residues: 209.6129 Evaluate side-chains 219 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.783 ------------------------------------------------------------------------------- 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 270 VAL 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 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 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: 7.9990 chunk 244 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 chunk 175 optimal weight: 4.9990 chunk 72 optimal weight: 4.9990 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: 0.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 36 ASN A 244 HIS B 62 ASN E 62 ASN F 62 ASN I 267 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.105474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.057252 restraints weight = 91930.810| |-----------------------------------------------------------------------------| r_work (start): 0.2676 rms_B_bonded: 3.57 r_work: 0.2484 rms_B_bonded: 3.76 restraints_weight: 0.5000 r_work (final): 0.2484 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2526 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2526 r_free = 0.2526 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2526 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 24785 Z= 0.297 Angle : 0.549 8.218 33980 Z= 0.308 Chirality : 0.042 0.162 3861 Planarity : 0.004 0.050 3992 Dihedral : 18.510 97.891 4581 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Rotamer: Outliers : 1.73 % Allowed : 10.25 % Favored : 88.02 % 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: 1.00 (0.16), residues: 2803 helix: 1.32 (0.14), residues: 1314 sheet: -0.02 (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 0.024 0.002 TYR B 216 PHE 0.020 0.001 PHE A 327 HIS 0.003 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.30 (24785) covalent geometry : angle 0.54906 / 0.31 (33980) hydrogen bonds : bond 0.04173 / 2.80 ( 1295) hydrogen bonds : angle 4.63549 / 3.27 ( 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 248 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 209 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8826 (mp0) REVERT: A 178 TYR cc_start: 0.8172 (m-80) cc_final: 0.7744 (m-80) REVERT: A 188 ASN cc_start: 0.8719 (m-40) cc_final: 0.8474 (m-40) REVERT: A 229 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8546 (ttm170) REVERT: A 290 ASN cc_start: 0.8162 (m-40) cc_final: 0.7864 (m110) REVERT: B 68 GLU cc_start: 0.9034 (mt-10) cc_final: 0.8664 (tm-30) REVERT: B 202 GLN cc_start: 0.9211 (tt0) cc_final: 0.8943 (tp-100) REVERT: B 235 ARG cc_start: 0.8587 (ttp-170) cc_final: 0.8023 (ttm170) REVERT: C 68 GLU cc_start: 0.7853 (tm-30) cc_final: 0.7590 (tm-30) REVERT: C 72 ASP cc_start: 0.7908 (p0) cc_final: 0.7462 (p0) REVERT: D 39 LYS cc_start: 0.8670 (mttt) cc_final: 0.8458 (mmpt) REVERT: D 68 GLU cc_start: 0.8697 (mt-10) cc_final: 0.8339 (tm-30) REVERT: D 72 ASP cc_start: 0.8907 (m-30) cc_final: 0.8586 (m-30) REVERT: D 202 GLN cc_start: 0.9130 (tt0) cc_final: 0.8622 (tm-30) REVERT: E 30 GLN cc_start: 0.8763 (mt0) cc_final: 0.8336 (tm130) REVERT: E 43 GLU cc_start: 0.8606 (OUTLIER) cc_final: 0.8223 (pp20) REVERT: F 27 ARG cc_start: 0.8681 (mtp180) cc_final: 0.8308 (mmm160) REVERT: F 30 GLN cc_start: 0.8178 (mp10) cc_final: 0.7756 (mp10) REVERT: F 202 GLN cc_start: 0.8828 (tt0) cc_final: 0.8555 (tm-30) REVERT: F 247 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8319 (ttp80) REVERT: F 306 ARG cc_start: 0.8600 (ttt180) cc_final: 0.8300 (ttp-170) REVERT: G 34 ASN cc_start: 0.8137 (t0) cc_final: 0.7886 (t0) REVERT: G 202 GLN cc_start: 0.8875 (tt0) cc_final: 0.8341 (tm-30) REVERT: G 210 MET cc_start: 0.9273 (mtm) cc_final: 0.8998 (mtp) REVERT: H 274 ASP cc_start: 0.8918 (m-30) cc_final: 0.8238 (p0) REVERT: I 96 ARG cc_start: 0.6787 (mtp85) cc_final: 0.5251 (mtm180) REVERT: I 124 GLU cc_start: 0.8717 (OUTLIER) cc_final: 0.8441 (tt0) REVERT: I 163 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8518 (mt-10) outliers start: 39 outliers final: 15 residues processed: 236 average time/residue: 0.7128 time to fit residues: 190.1103 Evaluate side-chains 217 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 199 time to evaluate : 0.533 ------------------------------------------------------------------------------- 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 270 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain E residue 43 GLU 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 I residue 124 GLU Chi-restraints excluded: chain I residue 270 VAL Chi-restraints excluded: chain I residue 284 LYS 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: 3.9990 chunk 19 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 216 optimal weight: 4.9990 chunk 72 optimal weight: 0.9980 chunk 104 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 267 optimal weight: 8.9990 chunk 230 optimal weight: 0.8980 chunk 117 optimal weight: 0.8980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 62 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 = 0.3658 r_free = 0.3658 target = 0.107197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.059527 restraints weight = 75265.164| |-----------------------------------------------------------------------------| r_work (start): 0.2728 rms_B_bonded: 3.32 r_work: 0.2544 rms_B_bonded: 3.62 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2589 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2589 r_free = 0.2589 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2589 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2150 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 : 0.481 9.223 33980 Z= 0.274 Chirality : 0.039 0.185 3861 Planarity : 0.003 0.039 3992 Dihedral : 18.493 104.401 4581 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.29 % Allowed : 10.87 % Favored : 87.84 % 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: 1.39 (0.14), residues: 1314 sheet: -0.07 (0.24), residues: 507 loop : 0.43 (0.21), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.027 0.001 TYR I 191 PHE 0.030 0.001 PHE A 166 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.15 (24785) covalent geometry : angle 0.48105 / 0.27 (33980) hydrogen bonds : bond 0.03328 / 2.22 ( 1295) hydrogen bonds : angle 4.35600 / 3.07 ( 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 243 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 214 time to evaluate : 0.864 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9199 (mt-10) cc_final: 0.8839 (mp0) REVERT: A 178 TYR cc_start: 0.8175 (m-80) cc_final: 0.7698 (m-80) REVERT: A 188 ASN cc_start: 0.8754 (m-40) cc_final: 0.8504 (m-40) REVERT: A 290 ASN cc_start: 0.8158 (m-40) cc_final: 0.7861 (m110) REVERT: B 62 ASN cc_start: 0.9096 (m-40) cc_final: 0.8691 (t0) REVERT: B 68 GLU cc_start: 0.8968 (mt-10) cc_final: 0.8659 (tm-30) REVERT: B 202 GLN cc_start: 0.9181 (tt0) cc_final: 0.8884 (tp-100) REVERT: B 235 ARG cc_start: 0.8541 (ttp-170) cc_final: 0.8047 (ttm170) REVERT: C 68 GLU cc_start: 0.7837 (tm-30) cc_final: 0.7550 (tm-30) REVERT: C 72 ASP cc_start: 0.7955 (p0) cc_final: 0.7411 (p0) REVERT: D 39 LYS cc_start: 0.8660 (mttt) cc_final: 0.8445 (mmpt) REVERT: D 68 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8287 (tm-30) REVERT: D 72 ASP cc_start: 0.8869 (m-30) cc_final: 0.8541 (m-30) REVERT: D 176 GLU cc_start: 0.8334 (mm-30) cc_final: 0.8032 (mm-30) REVERT: D 202 GLN cc_start: 0.9108 (tt0) cc_final: 0.8626 (tm-30) REVERT: E 30 GLN cc_start: 0.8717 (mt0) cc_final: 0.8346 (tm130) REVERT: E 43 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8206 (pp20) REVERT: F 27 ARG cc_start: 0.8693 (mtp180) cc_final: 0.8149 (tpp-160) REVERT: F 30 GLN cc_start: 0.8265 (mp10) cc_final: 0.7975 (mp10) REVERT: F 202 GLN cc_start: 0.8792 (tt0) cc_final: 0.8523 (tm-30) REVERT: F 247 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8285 (ttp80) REVERT: F 306 ARG cc_start: 0.8569 (ttt180) cc_final: 0.8244 (ttp-170) REVERT: G 34 ASN cc_start: 0.8171 (t0) cc_final: 0.7917 (t0) REVERT: G 202 GLN cc_start: 0.8849 (tt0) cc_final: 0.8321 (tm-30) REVERT: G 210 MET cc_start: 0.9238 (mtm) cc_final: 0.8927 (mtp) REVERT: H 274 ASP cc_start: 0.8884 (m-30) cc_final: 0.8219 (p0) REVERT: I 96 ARG cc_start: 0.6765 (mtp85) cc_final: 0.5264 (mtm180) REVERT: I 124 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8510 (tt0) REVERT: I 163 GLU cc_start: 0.8715 (mt-10) cc_final: 0.8431 (mt-10) REVERT: I 191 TYR cc_start: 0.8112 (t80) cc_final: 0.7795 (t80) REVERT: I 210 MET cc_start: 0.8455 (mtm) cc_final: 0.8243 (mpt) REVERT: I 216 TYR cc_start: 0.8584 (m-80) cc_final: 0.7935 (m-80) REVERT: I 243 MET cc_start: 0.9150 (mmm) cc_final: 0.8946 (mmm) outliers start: 29 outliers final: 15 residues processed: 239 average time/residue: 0.7044 time to fit residues: 190.7510 Evaluate side-chains 218 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.572 ------------------------------------------------------------------------------- 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 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 F residue 297 THR Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 144 CYS 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 Chi-restraints excluded: chain I residue 290 ASN 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: 0.9980 chunk 195 optimal weight: 2.9990 chunk 205 optimal weight: 0.9990 chunk 138 optimal weight: 0.5980 chunk 121 optimal weight: 4.9990 chunk 151 optimal weight: 5.9990 chunk 102 optimal weight: 1.9990 chunk 287 optimal weight: 40.0000 chunk 226 optimal weight: 0.9980 chunk 95 optimal weight: 0.5980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 272 GLN E 62 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN I 267 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.108105 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.060242 restraints weight = 88900.328| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 3.59 r_work: 0.2555 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2600 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2600 r_free = 0.2600 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: 0.2600 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2340 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= 0.117 Angle : 0.463 7.390 33980 Z= 0.265 Chirality : 0.038 0.192 3861 Planarity : 0.003 0.047 3992 Dihedral : 18.438 111.170 4581 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.33 % Allowed : 11.54 % Favored : 87.13 % 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: 1.17 (0.16), residues: 2803 helix: 1.43 (0.14), residues: 1319 sheet: 0.03 (0.23), residues: 525 loop : 0.51 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG G 306 TYR 0.024 0.001 TYR B 216 PHE 0.014 0.001 PHE A 327 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (24785) covalent geometry : angle 0.46310 / 0.26 (33980) hydrogen bonds : bond 0.02954 / 1.97 ( 1295) hydrogen bonds : angle 4.19123 / 2.95 ( 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 249 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 219 time to evaluate : 0.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9207 (mt-10) cc_final: 0.8771 (mp0) REVERT: A 178 TYR cc_start: 0.8196 (m-80) cc_final: 0.7732 (m-80) REVERT: A 229 ARG cc_start: 0.8860 (OUTLIER) cc_final: 0.8547 (ttm170) REVERT: A 290 ASN cc_start: 0.8154 (m-40) cc_final: 0.7873 (m110) REVERT: B 43 GLU cc_start: 0.9005 (pt0) cc_final: 0.8659 (pp20) REVERT: B 62 ASN cc_start: 0.9098 (m-40) cc_final: 0.8697 (t0) REVERT: B 68 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8657 (tm-30) REVERT: B 202 GLN cc_start: 0.9173 (tt0) cc_final: 0.8867 (tp-100) REVERT: B 235 ARG cc_start: 0.8514 (ttp-170) cc_final: 0.8028 (ttm170) REVERT: C 68 GLU cc_start: 0.7801 (tm-30) cc_final: 0.7481 (tm-30) REVERT: C 72 ASP cc_start: 0.7993 (p0) cc_final: 0.7394 (p0) REVERT: D 39 LYS cc_start: 0.8652 (mttt) cc_final: 0.8426 (mmpt) REVERT: D 67 SER cc_start: 0.8217 (OUTLIER) cc_final: 0.7759 (p) REVERT: D 68 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8209 (tm-30) REVERT: D 72 ASP cc_start: 0.8861 (m-30) cc_final: 0.8528 (m-30) REVERT: D 176 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7997 (mm-30) REVERT: D 202 GLN cc_start: 0.9125 (tt0) cc_final: 0.8641 (tm-30) REVERT: D 250 ARG cc_start: 0.9381 (OUTLIER) cc_final: 0.9154 (tpt-90) REVERT: E 30 GLN cc_start: 0.8643 (mt0) cc_final: 0.8316 (tm130) REVERT: E 43 GLU cc_start: 0.8586 (OUTLIER) cc_final: 0.8214 (pp20) REVERT: E 272 GLN cc_start: 0.9023 (mt0) cc_final: 0.8743 (mt0) REVERT: F 27 ARG cc_start: 0.8687 (mtp180) cc_final: 0.8151 (tpp-160) REVERT: F 30 GLN cc_start: 0.8310 (mp10) cc_final: 0.7996 (mp10) REVERT: F 202 GLN cc_start: 0.8793 (tt0) cc_final: 0.8509 (tm-30) REVERT: F 247 ARG cc_start: 0.8780 (mtp85) cc_final: 0.8300 (ttp80) REVERT: F 306 ARG cc_start: 0.8561 (ttt180) cc_final: 0.8169 (ttp-110) REVERT: G 34 ASN cc_start: 0.8189 (t0) cc_final: 0.7932 (t0) REVERT: G 202 GLN cc_start: 0.8885 (tt0) cc_final: 0.8337 (tm-30) REVERT: H 274 ASP cc_start: 0.8876 (m-30) cc_final: 0.8228 (p0) REVERT: I 96 ARG cc_start: 0.6711 (mtp85) cc_final: 0.5219 (mtm180) REVERT: I 124 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8480 (tt0) REVERT: I 163 GLU cc_start: 0.8752 (mt-10) cc_final: 0.8460 (mt-10) REVERT: I 191 TYR cc_start: 0.8190 (t80) cc_final: 0.7873 (t80) REVERT: I 216 TYR cc_start: 0.8608 (m-80) cc_final: 0.7996 (m-80) REVERT: I 243 MET cc_start: 0.9148 (mmm) cc_final: 0.8932 (mmm) outliers start: 30 outliers final: 14 residues processed: 244 average time/residue: 0.6797 time to fit residues: 188.1445 Evaluate side-chains 225 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 206 time to evaluate : 0.821 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 229 ARG 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 D residue 67 SER Chi-restraints excluded: chain D residue 250 ARG 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 103 THR Chi-restraints excluded: chain H residue 130 ARG Chi-restraints excluded: chain H residue 270 VAL 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: 4.9990 chunk 92 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 198 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 180 optimal weight: 2.9990 chunk 46 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 60 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 256 optimal weight: 0.1980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN A 188 ASN E 62 ASN F 62 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.107694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.060169 restraints weight = 72121.416| |-----------------------------------------------------------------------------| r_work (start): 0.2745 rms_B_bonded: 3.28 r_work: 0.2563 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2604 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2604 r_free = 0.2604 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: 0.2604 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8708 moved from start: 0.2378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 24785 Z= 0.140 Angle : 0.466 7.695 33980 Z= 0.265 Chirality : 0.038 0.195 3861 Planarity : 0.003 0.039 3992 Dihedral : 18.447 114.777 4581 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.51 % Allowed : 11.58 % Favored : 86.91 % 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: 1.19 (0.16), residues: 2803 helix: 1.48 (0.14), residues: 1319 sheet: -0.07 (0.23), residues: 535 loop : 0.55 (0.22), residues: 949 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 306 TYR 0.018 0.001 TYR B 216 PHE 0.018 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.14 (24785) covalent geometry : angle 0.46579 / 0.26 (33980) hydrogen bonds : bond 0.03033 / 2.03 ( 1295) hydrogen bonds : angle 4.17697 / 2.94 ( 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 249 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 215 time to evaluate : 0.888 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 TYR cc_start: 0.8219 (m-80) cc_final: 0.7714 (m-80) REVERT: A 188 ASN cc_start: 0.8388 (m110) cc_final: 0.8174 (m110) REVERT: A 229 ARG cc_start: 0.8868 (OUTLIER) cc_final: 0.8549 (ttm170) REVERT: A 290 ASN cc_start: 0.8189 (m-40) cc_final: 0.7908 (m110) REVERT: B 43 GLU cc_start: 0.9022 (pt0) cc_final: 0.8692 (pp20) REVERT: B 68 GLU cc_start: 0.8966 (mt-10) cc_final: 0.8654 (tm-30) REVERT: B 202 GLN cc_start: 0.9153 (tt0) cc_final: 0.8844 (tp-100) REVERT: B 235 ARG cc_start: 0.8496 (ttp-170) cc_final: 0.7988 (ttm170) REVERT: C 68 GLU cc_start: 0.7813 (tm-30) cc_final: 0.7469 (tm-30) REVERT: C 72 ASP cc_start: 0.8000 (p0) cc_final: 0.7371 (p0) REVERT: D 39 LYS cc_start: 0.8663 (mttt) cc_final: 0.8442 (mmpt) REVERT: D 67 SER cc_start: 0.8222 (OUTLIER) cc_final: 0.7788 (p) REVERT: D 68 GLU cc_start: 0.8661 (mt-10) cc_final: 0.8214 (tm-30) REVERT: D 72 ASP cc_start: 0.8853 (m-30) cc_final: 0.8477 (m-30) REVERT: D 176 GLU cc_start: 0.8364 (mm-30) cc_final: 0.7990 (mm-30) REVERT: D 202 GLN cc_start: 0.9105 (tt0) cc_final: 0.8620 (tm-30) REVERT: D 250 ARG cc_start: 0.9377 (OUTLIER) cc_final: 0.9173 (tpt-90) REVERT: E 30 GLN cc_start: 0.8632 (mt0) cc_final: 0.8320 (tm130) REVERT: E 43 GLU cc_start: 0.8584 (OUTLIER) cc_final: 0.8228 (pp20) REVERT: E 272 GLN cc_start: 0.9012 (mt0) cc_final: 0.8731 (mt0) REVERT: F 27 ARG cc_start: 0.8699 (mtp180) cc_final: 0.8144 (tpp-160) REVERT: F 30 GLN cc_start: 0.8331 (mp10) cc_final: 0.8007 (mp10) REVERT: F 202 GLN cc_start: 0.8782 (tt0) cc_final: 0.8505 (tm-30) REVERT: F 247 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8291 (ttp80) REVERT: F 306 ARG cc_start: 0.8558 (ttt180) cc_final: 0.8177 (ttp-110) REVERT: G 34 ASN cc_start: 0.8235 (t0) cc_final: 0.7988 (t0) REVERT: G 202 GLN cc_start: 0.8853 (tt0) cc_final: 0.8308 (tm-30) REVERT: H 274 ASP cc_start: 0.8852 (m-30) cc_final: 0.8209 (p0) REVERT: I 96 ARG cc_start: 0.6640 (mtp85) cc_final: 0.5154 (mtm180) REVERT: I 124 GLU cc_start: 0.8711 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: I 163 GLU cc_start: 0.8755 (mt-10) cc_final: 0.8465 (mt-10) REVERT: I 191 TYR cc_start: 0.8204 (t80) cc_final: 0.7861 (t80) REVERT: I 216 TYR cc_start: 0.8617 (m-80) cc_final: 0.8082 (m-80) REVERT: I 243 MET cc_start: 0.9145 (mmm) cc_final: 0.8924 (mmm) outliers start: 34 outliers final: 14 residues processed: 242 average time/residue: 0.7593 time to fit residues: 207.6404 Evaluate side-chains 223 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 125 MET Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 229 ARG 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 D residue 67 SER Chi-restraints excluded: chain D residue 250 ARG 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 103 THR Chi-restraints excluded: chain H residue 270 VAL 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: 0.9980 chunk 282 optimal weight: 30.0000 chunk 207 optimal weight: 0.5980 chunk 198 optimal weight: 0.8980 chunk 78 optimal weight: 8.9990 chunk 209 optimal weight: 0.8980 chunk 216 optimal weight: 5.9990 chunk 184 optimal weight: 0.7980 chunk 159 optimal weight: 6.9990 chunk 175 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 145 GLN 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 = 0.3679 r_free = 0.3679 target = 0.108414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.060831 restraints weight = 81745.924| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.47 r_work: 0.2572 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2614 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2614 r_free = 0.2614 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2614 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8701 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 24785 Z= 0.111 Angle : 0.464 8.720 33980 Z= 0.263 Chirality : 0.038 0.203 3861 Planarity : 0.003 0.046 3992 Dihedral : 18.394 118.833 4581 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.15 % Allowed : 12.29 % Favored : 86.55 % 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: 1.26 (0.16), residues: 2803 helix: 1.50 (0.14), residues: 1319 sheet: 0.07 (0.23), residues: 525 loop : 0.57 (0.21), residues: 959 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG G 306 TYR 0.017 0.001 TYR I 191 PHE 0.016 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00221 / 0.11 (24785) covalent geometry : angle 0.46379 / 0.26 (33980) hydrogen bonds : bond 0.02804 / 1.86 ( 1295) hydrogen bonds : angle 4.06609 / 2.86 ( 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 245 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9228 (mt-10) cc_final: 0.8739 (mp0) REVERT: A 178 TYR cc_start: 0.8215 (m-80) cc_final: 0.7750 (m-80) REVERT: A 188 ASN cc_start: 0.8550 (m-40) cc_final: 0.8310 (m110) REVERT: A 229 ARG cc_start: 0.8887 (OUTLIER) cc_final: 0.8576 (ttm170) REVERT: A 290 ASN cc_start: 0.8190 (m-40) cc_final: 0.7937 (m110) REVERT: B 43 GLU cc_start: 0.9035 (pt0) cc_final: 0.8704 (pp20) REVERT: B 68 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8655 (tm-30) REVERT: B 202 GLN cc_start: 0.9139 (tt0) cc_final: 0.8822 (tp-100) REVERT: B 213 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7705 (mp0) REVERT: B 235 ARG cc_start: 0.8471 (ttp-170) cc_final: 0.7960 (ttm170) REVERT: C 68 GLU cc_start: 0.7795 (tm-30) cc_final: 0.7436 (tm-30) REVERT: C 72 ASP cc_start: 0.8017 (p0) cc_final: 0.7363 (p0) REVERT: D 39 LYS cc_start: 0.8659 (mttt) cc_final: 0.8435 (mmpt) REVERT: D 67 SER cc_start: 0.8212 (OUTLIER) cc_final: 0.7769 (p) REVERT: D 68 GLU cc_start: 0.8653 (mt-10) cc_final: 0.8187 (tm-30) REVERT: D 72 ASP cc_start: 0.8845 (m-30) cc_final: 0.8499 (m-30) REVERT: D 176 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7985 (mm-30) REVERT: D 202 GLN cc_start: 0.9122 (tt0) cc_final: 0.8644 (tm-30) REVERT: D 250 ARG cc_start: 0.9378 (OUTLIER) cc_final: 0.9151 (tpt-90) REVERT: D 306 ARG cc_start: 0.8343 (mmm-85) cc_final: 0.8095 (tpt-90) REVERT: E 30 GLN cc_start: 0.8592 (mt0) cc_final: 0.8299 (tm130) REVERT: E 43 GLU cc_start: 0.8605 (OUTLIER) cc_final: 0.8251 (pp20) REVERT: F 27 ARG cc_start: 0.8701 (mtp180) cc_final: 0.8135 (tpp-160) REVERT: F 30 GLN cc_start: 0.8364 (mp10) cc_final: 0.8026 (mp10) REVERT: F 202 GLN cc_start: 0.8778 (tt0) cc_final: 0.8504 (tm-30) REVERT: F 247 ARG cc_start: 0.8773 (mtp85) cc_final: 0.8295 (ttp80) REVERT: F 306 ARG cc_start: 0.8549 (ttt180) cc_final: 0.8140 (ttp-110) REVERT: G 34 ASN cc_start: 0.8248 (t0) cc_final: 0.8013 (t0) REVERT: G 202 GLN cc_start: 0.8870 (tt0) cc_final: 0.8326 (tm-30) REVERT: H 88 THR cc_start: 0.8764 (m) cc_final: 0.8432 (t) REVERT: H 274 ASP cc_start: 0.8860 (m-30) cc_final: 0.8226 (p0) REVERT: I 96 ARG cc_start: 0.6628 (mtp85) cc_final: 0.5148 (mtm180) REVERT: I 163 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8494 (mt-10) REVERT: I 191 TYR cc_start: 0.8232 (t80) cc_final: 0.7829 (t80) REVERT: I 216 TYR cc_start: 0.8622 (m-80) cc_final: 0.7890 (m-80) REVERT: I 243 MET cc_start: 0.9140 (mmm) cc_final: 0.8887 (tmm) outliers start: 26 outliers final: 12 residues processed: 240 average time/residue: 0.7227 time to fit residues: 196.8590 Evaluate side-chains 230 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 213 time to evaluate : 0.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 ILE Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain B residue 213 GLU Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 266 THR Chi-restraints excluded: chain D residue 67 SER Chi-restraints excluded: chain D residue 250 ARG 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 103 THR Chi-restraints excluded: chain H residue 130 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 224 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 195 optimal weight: 3.9990 chunk 47 optimal weight: 10.0000 chunk 285 optimal weight: 50.0000 chunk 266 optimal weight: 10.0000 chunk 156 optimal weight: 0.4980 chunk 44 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 186 optimal weight: 10.0000 chunk 277 optimal weight: 8.9990 overall best weight: 4.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 62 ASN F 62 ASN ** G 36 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.105601 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.058112 restraints weight = 65692.822| |-----------------------------------------------------------------------------| r_work (start): 0.2696 rms_B_bonded: 3.14 r_work: 0.2514 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2514 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2559 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2559 r_free = 0.2559 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2559 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 24785 Z= 0.320 Angle : 0.554 9.227 33980 Z= 0.306 Chirality : 0.042 0.190 3861 Planarity : 0.004 0.058 3992 Dihedral : 18.559 120.135 4581 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 1.07 % Allowed : 12.78 % Favored : 86.15 % 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: 1.15 (0.16), residues: 2803 helix: 1.45 (0.15), residues: 1319 sheet: -0.01 (0.24), residues: 489 loop : 0.42 (0.21), residues: 995 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG G 306 TYR 0.024 0.002 TYR B 216 PHE 0.013 0.002 PHE A 126 HIS 0.003 0.001 HIS C 93 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.32 (24785) covalent geometry : angle 0.55403 / 0.31 (33980) hydrogen bonds : bond 0.03805 / 2.56 ( 1295) hydrogen bonds : angle 4.36078 / 3.07 ( 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 234 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 210 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8780 (mp0) REVERT: A 74 ILE cc_start: 0.9188 (pt) cc_final: 0.8980 (pp) REVERT: A 178 TYR cc_start: 0.8262 (m-80) cc_final: 0.7783 (m-80) REVERT: A 199 HIS cc_start: 0.8675 (t-90) cc_final: 0.8412 (t-90) REVERT: A 229 ARG cc_start: 0.8867 (OUTLIER) cc_final: 0.8551 (ttm170) REVERT: A 290 ASN cc_start: 0.8258 (m-40) cc_final: 0.7960 (m110) REVERT: B 68 GLU cc_start: 0.8972 (mt-10) cc_final: 0.8655 (tm-30) REVERT: B 202 GLN cc_start: 0.9176 (tt0) cc_final: 0.8863 (tp-100) REVERT: B 235 ARG cc_start: 0.8540 (ttp-170) cc_final: 0.8016 (ttm170) REVERT: C 68 GLU cc_start: 0.7870 (tm-30) cc_final: 0.7531 (tm-30) REVERT: C 72 ASP cc_start: 0.8058 (p0) cc_final: 0.7429 (p0) REVERT: D 39 LYS cc_start: 0.8679 (mttt) cc_final: 0.8462 (mmpt) REVERT: D 67 SER cc_start: 0.8279 (OUTLIER) cc_final: 0.7865 (p) REVERT: D 68 GLU cc_start: 0.8709 (mt-10) cc_final: 0.8268 (tm-30) REVERT: D 72 ASP cc_start: 0.8877 (m-30) cc_final: 0.8527 (m-30) REVERT: D 176 GLU cc_start: 0.8418 (mm-30) cc_final: 0.8036 (mm-30) REVERT: D 202 GLN cc_start: 0.9110 (tt0) cc_final: 0.8615 (tm-30) REVERT: E 30 GLN cc_start: 0.8656 (mt0) cc_final: 0.8314 (tm130) REVERT: E 43 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.8290 (pp20) REVERT: F 27 ARG cc_start: 0.8708 (mtp180) cc_final: 0.8148 (tpp-160) REVERT: F 30 GLN cc_start: 0.8352 (mp10) cc_final: 0.8030 (mp10) REVERT: F 202 GLN cc_start: 0.8795 (tt0) cc_final: 0.8526 (tm-30) REVERT: F 247 ARG cc_start: 0.8797 (mtp85) cc_final: 0.8320 (ttp80) REVERT: F 306 ARG cc_start: 0.8575 (ttt180) cc_final: 0.8277 (ttp-170) REVERT: G 34 ASN cc_start: 0.8368 (t0) cc_final: 0.8138 (t0) REVERT: G 202 GLN cc_start: 0.8855 (tt0) cc_final: 0.8295 (tm-30) REVERT: H 24 PRO cc_start: 0.8461 (Cg_exo) cc_final: 0.8223 (Cg_endo) REVERT: H 274 ASP cc_start: 0.8874 (m-30) cc_final: 0.8207 (p0) REVERT: I 96 ARG cc_start: 0.6714 (mtp85) cc_final: 0.5208 (mtm180) REVERT: I 163 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8522 (mt-10) REVERT: I 191 TYR cc_start: 0.8361 (t80) cc_final: 0.8083 (t80) REVERT: I 216 TYR cc_start: 0.8663 (m-80) cc_final: 0.8037 (m-80) REVERT: I 243 MET cc_start: 0.9160 (mmm) cc_final: 0.8936 (mmm) outliers start: 24 outliers final: 14 residues processed: 230 average time/residue: 0.7387 time to fit residues: 191.9720 Evaluate side-chains 218 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 201 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 THR Chi-restraints excluded: chain A residue 129 PHE Chi-restraints excluded: chain A residue 229 ARG Chi-restraints excluded: chain B residue 144 CYS Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain D residue 67 SER 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 297 THR Chi-restraints excluded: chain I residue 23 GLN 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: 0.9990 chunk 264 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 9.9990 chunk 206 optimal weight: 0.9990 chunk 84 optimal weight: 0.7980 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 6.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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** I 267 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107926 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.060727 restraints weight = 64453.953| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.11 r_work: 0.2579 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2579 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2621 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2621 r_free = 0.2621 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2621 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 24785 Z= 0.116 Angle : 0.486 9.779 33980 Z= 0.274 Chirality : 0.038 0.207 3861 Planarity : 0.003 0.059 3992 Dihedral : 18.479 121.594 4581 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Rotamer: Outliers : 0.58 % Allowed : 13.45 % Favored : 85.97 % 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: 1.27 (0.16), residues: 2803 helix: 1.52 (0.14), residues: 1318 sheet: 0.02 (0.23), residues: 529 loop : 0.59 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 306 TYR 0.017 0.001 TYR I 191 PHE 0.016 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00230 / 0.12 (24785) covalent geometry : angle 0.48586 / 0.27 (33980) hydrogen bonds : bond 0.02946 / 1.96 ( 1295) hydrogen bonds : angle 4.16042 / 2.92 ( 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 224 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 211 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9250 (mt-10) cc_final: 0.8759 (mp0) REVERT: A 178 TYR cc_start: 0.8256 (m-80) cc_final: 0.7774 (m-80) REVERT: A 199 HIS cc_start: 0.8611 (t-90) cc_final: 0.8263 (t-90) REVERT: A 267 ASN cc_start: 0.8963 (t0) cc_final: 0.8760 (t0) REVERT: A 290 ASN cc_start: 0.8183 (m-40) cc_final: 0.7912 (m110) REVERT: B 43 GLU cc_start: 0.9033 (pt0) cc_final: 0.8722 (pp20) REVERT: B 68 GLU cc_start: 0.8962 (mt-10) cc_final: 0.8646 (tm-30) REVERT: B 202 GLN cc_start: 0.9135 (tt0) cc_final: 0.8813 (tp-100) REVERT: B 235 ARG cc_start: 0.8500 (ttp-170) cc_final: 0.7980 (ttm170) REVERT: C 68 GLU cc_start: 0.7805 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 72 ASP cc_start: 0.8017 (p0) cc_final: 0.7386 (p0) REVERT: D 39 LYS cc_start: 0.8652 (mttt) cc_final: 0.8425 (mmpt) REVERT: D 68 GLU cc_start: 0.8642 (mt-10) cc_final: 0.8247 (tm-30) REVERT: D 72 ASP cc_start: 0.8837 (m-30) cc_final: 0.8477 (m-30) REVERT: D 176 GLU cc_start: 0.8377 (mm-30) cc_final: 0.7983 (mm-30) REVERT: D 202 GLN cc_start: 0.9102 (tt0) cc_final: 0.8613 (tm-30) REVERT: E 30 GLN cc_start: 0.8625 (mt0) cc_final: 0.8336 (tm130) REVERT: E 43 GLU cc_start: 0.8613 (OUTLIER) cc_final: 0.8239 (pp20) REVERT: F 27 ARG cc_start: 0.8683 (mtp180) cc_final: 0.8107 (tpp-160) REVERT: F 30 GLN cc_start: 0.8342 (mp10) cc_final: 0.7996 (mp10) REVERT: F 202 GLN cc_start: 0.8758 (tt0) cc_final: 0.8480 (tm-30) REVERT: F 247 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8275 (ttp80) REVERT: F 306 ARG cc_start: 0.8542 (ttt180) cc_final: 0.8135 (ttp-110) REVERT: G 34 ASN cc_start: 0.8313 (t0) cc_final: 0.8096 (t0) REVERT: G 202 GLN cc_start: 0.8841 (tt0) cc_final: 0.8294 (tm-30) REVERT: H 274 ASP cc_start: 0.8875 (m-30) cc_final: 0.8216 (p0) REVERT: I 96 ARG cc_start: 0.6683 (mtp85) cc_final: 0.5184 (mtm180) REVERT: I 142 VAL cc_start: 0.9074 (t) cc_final: 0.8786 (m) REVERT: I 163 GLU cc_start: 0.8778 (mt-10) cc_final: 0.8485 (mt-10) REVERT: I 191 TYR cc_start: 0.8287 (t80) cc_final: 0.7958 (t80) REVERT: I 216 TYR cc_start: 0.8659 (m-80) cc_final: 0.7975 (m-80) REVERT: I 243 MET cc_start: 0.9152 (mmm) cc_final: 0.8897 (tmm) outliers start: 13 outliers final: 9 residues processed: 222 average time/residue: 0.7337 time to fit residues: 185.0203 Evaluate side-chains 219 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 209 time to evaluate : 0.866 ------------------------------------------------------------------------------- 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 87 THR Chi-restraints excluded: chain H residue 297 THR 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: 6.9990 chunk 204 optimal weight: 0.9990 chunk 188 optimal weight: 0.9990 chunk 130 optimal weight: 4.9990 chunk 193 optimal weight: 2.9990 chunk 21 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 121 optimal weight: 7.9990 chunk 278 optimal weight: 6.9990 chunk 104 optimal weight: 1.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 36 ASN F 62 ASN ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.107267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.059746 restraints weight = 76873.889| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 3.33 r_work: 0.2548 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.2548 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2590 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2590 r_free = 0.2590 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2590 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24785 Z= 0.161 Angle : 0.493 10.184 33980 Z= 0.276 Chirality : 0.039 0.206 3861 Planarity : 0.003 0.057 3992 Dihedral : 18.497 124.348 4581 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.71 % Allowed : 13.27 % Favored : 86.02 % 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: 1.29 (0.16), residues: 2803 helix: 1.54 (0.14), residues: 1318 sheet: 0.01 (0.23), residues: 529 loop : 0.61 (0.21), residues: 956 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG G 306 TYR 0.016 0.001 TYR B 216 PHE 0.014 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.16 (24785) covalent geometry : angle 0.49275 / 0.28 (33980) hydrogen bonds : bond 0.03094 / 2.07 ( 1295) hydrogen bonds : angle 4.16582 / 2.93 ( 3480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9754.47 seconds wall clock time: 166 minutes 24.96 seconds (9984.96 seconds total)