Starting phenix.real_space_refine on Fri Sep 19 07:18:00 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9i62_52646/09_2025/9i62_52646.cif Found real_map, /net/cci-nas-00/data/ceres_data/9i62_52646/09_2025/9i62_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_52646/09_2025/9i62_52646.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9i62_52646/09_2025/9i62_52646.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9i62_52646/09_2025/9i62_52646.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9i62_52646/09_2025/9i62_52646.map" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 18 9.91 5 P 137 5.49 5 S 121 5.16 5 C 14728 2.51 5 N 4257 2.21 5 O 4944 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/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: 6.26, per 1000 atoms: 0.26 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: 2.13 Conformation dependent library (CDL) restraints added in 1.1 seconds Enol-peptide restraints added in 476.8 nanoseconds 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: 3.25 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: 5.24 Time building geometry restraints manager: 2.82 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=" 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=" 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 bond pdb=" N ILE E 63 " pdb=" CA ILE E 63 " ideal model delta sigma weight residual 1.458 1.494 -0.036 1.24e-02 6.50e+03 8.33e+00 bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 7.66e+00 bond pdb=" N ILE G 63 " pdb=" CA ILE G 63 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.17e-02 7.31e+03 6.99e+00 ... (remaining 24780 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.02: 32520 1.02 - 2.03: 1133 2.03 - 3.05: 259 3.05 - 4.07: 53 4.07 - 5.08: 15 Bond angle restraints: 33980 Sorted by residual: angle pdb=" N GLY A 65 " pdb=" CA GLY A 65 " pdb=" C GLY A 65 " ideal model delta sigma weight residual 115.36 110.28 5.08 1.33e+00 5.65e-01 1.46e+01 angle pdb=" N VAL B 273 " pdb=" CA VAL B 273 " pdb=" C VAL B 273 " ideal model delta sigma weight residual 111.91 108.81 3.10 8.90e-01 1.26e+00 1.21e+01 angle pdb=" N GLY E 65 " pdb=" CA GLY E 65 " pdb=" C GLY E 65 " ideal model delta sigma weight residual 115.36 111.12 4.24 1.33e+00 5.65e-01 1.02e+01 angle pdb=" N GLY B 65 " pdb=" CA GLY B 65 " pdb=" C GLY B 65 " ideal model delta sigma weight residual 115.36 111.36 4.00 1.33e+00 5.65e-01 9.06e+00 angle pdb=" N GLY G 65 " pdb=" CA GLY G 65 " pdb=" C GLY G 65 " ideal model delta sigma weight residual 115.36 111.37 3.99 1.33e+00 5.65e-01 9.01e+00 ... (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: 3050 0.047 - 0.094: 643 0.094 - 0.141: 147 0.141 - 0.188: 11 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: 5.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.570 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 26.610 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 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 : 0.006 0.039 24785 Z= 0.287 Angle : 0.480 5.083 33980 Z= 0.280 Chirality : 0.042 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 aren 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 covalent geometry : bond 0.00631 (24785) covalent geometry : angle 0.47977 (33980) hydrogen bonds : bond 0.21981 ( 1295) hydrogen bonds : angle 7.18759 ( 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 : 0.841 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: 0.8617 (mmpt) REVERT: D 67 SER cc_start: 0.8630 (t) cc_final: 0.8226 (p) REVERT: D 68 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8603 (tm-30) REVERT: D 72 ASP cc_start: 0.8891 (m-30) cc_final: 0.8523 (m-30) REVERT: D 202 GLN cc_start: 0.9148 (tt0) cc_final: 0.8617 (tm-30) REVERT: E 30 GLN cc_start: 0.8897 (mt0) cc_final: 0.8317 (tm130) REVERT: E 36 ASN cc_start: 0.8804 (m-40) cc_final: 0.8495 (t0) REVERT: F 27 ARG cc_start: 0.8769 (mtp180) cc_final: 0.8256 (tpp-160) REVERT: F 202 GLN cc_start: 0.8847 (tt0) cc_final: 0.8630 (tm-30) REVERT: F 306 ARG cc_start: 0.8627 (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: 0.9800 time to fit residues: 332.0441 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 : 0.813 ------------------------------------------------------------------------------- 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... Flipped N/Q/H residues before XYZ refinement: A 242 GLN D 272 GLN 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 = 0.3679 r_free = 0.3679 target = 0.108449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.060768 restraints weight = 86530.630| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.54 r_work: 0.2566 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 24785 Z= 0.128 Angle : 0.485 5.703 33980 Z= 0.277 Chirality : 0.038 0.146 3861 Planarity : 0.003 0.035 3992 Dihedral : 18.176 89.872 4584 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.15 % Allowed : 7.94 % 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 aren not related in a simple way. whole: 1.24 (0.17), residues: 2803 helix: 1.30 (0.14), residues: 1311 sheet: 0.24 (0.24), residues: 535 loop : 0.75 (0.22), residues: 957 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 247 TYR 0.024 0.001 TYR I 191 PHE 0.012 0.001 PHE A 126 HIS 0.002 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00267 (24785) covalent geometry : angle 0.48494 (33980) hydrogen bonds : bond 0.03618 ( 1295) hydrogen bonds : angle 4.71379 ( 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 280 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.929 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: symmetry clash REVERT: A 91 GLU cc_start: 0.8580 (mp0) cc_final: 0.8344 (mp0) REVERT: A 178 TYR cc_start: 0.8101 (m-80) cc_final: 0.7651 (m-80) REVERT: A 188 ASN cc_start: 0.8759 (m-40) cc_final: 0.8541 (m-40) REVERT: A 205 TYR cc_start: 0.9442 (m-80) cc_final: 0.9159 (m-80) REVERT: A 229 ARG cc_start: 0.8854 (OUTLIER) cc_final: 0.8550 (ttm170) REVERT: A 267 ASN cc_start: 0.8950 (t0) cc_final: 0.8600 (t0) REVERT: A 290 ASN cc_start: 0.8092 (m-40) cc_final: 0.7808 (m110) REVERT: B 34 ASN cc_start: 0.7188 (t0) cc_final: 0.6918 (t0) REVERT: B 68 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8648 (tm-30) REVERT: B 202 GLN cc_start: 0.9188 (tt0) cc_final: 0.8930 (tp-100) REVERT: B 235 ARG cc_start: 0.8493 (ttp-170) cc_final: 0.7998 (ttm170) REVERT: B 285 LYS cc_start: 0.7958 (ptpt) cc_final: 0.7754 (ptmt) REVERT: C 68 GLU cc_start: 0.7350 (tm-30) cc_final: 0.7086 (tm-30) REVERT: C 72 ASP cc_start: 0.8035 (m-30) cc_final: 0.7590 (m-30) REVERT: D 67 SER cc_start: 0.8131 (t) cc_final: 0.7679 (p) REVERT: D 68 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8206 (tm-30) REVERT: D 72 ASP cc_start: 0.8854 (m-30) cc_final: 0.8584 (m-30) REVERT: D 176 GLU cc_start: 0.8318 (mm-30) cc_final: 0.8097 (mm-30) REVERT: D 202 GLN cc_start: 0.9105 (tt0) cc_final: 0.8633 (tm-30) REVERT: E 30 GLN cc_start: 0.8691 (mt0) cc_final: 0.8322 (tm130) REVERT: E 43 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8130 (pp20) REVERT: E 272 GLN cc_start: 0.8910 (mt0) cc_final: 0.8697 (mt0) REVERT: F 27 ARG cc_start: 0.8703 (mtp180) cc_final: 0.8242 (tpp-160) REVERT: F 30 GLN cc_start: 0.8139 (mp10) cc_final: 0.7932 (mp10) REVERT: F 95 ARG cc_start: 0.8429 (mtm-85) cc_final: 0.8112 (mtm-85) REVERT: F 202 GLN cc_start: 0.8764 (tt0) cc_final: 0.8534 (tm-30) REVERT: F 247 ARG cc_start: 0.8804 (mtp85) cc_final: 0.8313 (ttp80) REVERT: F 306 ARG cc_start: 0.8570 (ttt180) cc_final: 0.8194 (ttp-110) REVERT: G 68 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8747 (mp0) REVERT: G 202 GLN cc_start: 0.8860 (tt0) cc_final: 0.8332 (tm-30) REVERT: G 210 MET cc_start: 0.9221 (mtm) cc_final: 0.8984 (mtp) REVERT: H 163 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8350 (mt-10) REVERT: H 274 ASP cc_start: 0.8839 (m-30) cc_final: 0.8143 (p0) REVERT: I 25 ILE cc_start: 0.7344 (tt) cc_final: 0.7026 (tp) REVERT: I 96 ARG cc_start: 0.6774 (mtp85) cc_final: 0.5248 (mtm180) REVERT: I 124 GLU cc_start: 0.8753 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: I 163 GLU cc_start: 0.8708 (mt-10) cc_final: 0.8444 (mt-10) REVERT: I 191 TYR cc_start: 0.8171 (t80) cc_final: 0.7895 (t80) REVERT: I 216 TYR cc_start: 0.8547 (m-80) cc_final: 0.7916 (m-80) outliers start: 26 outliers final: 4 residues processed: 267 average time/residue: 0.8380 time to fit residues: 249.8394 Evaluate side-chains 223 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 216 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 GLU 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 61 ILE Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain I residue 124 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 252 optimal weight: 40.0000 chunk 256 optimal weight: 7.9990 chunk 124 optimal weight: 8.9990 chunk 76 optimal weight: 1.9990 chunk 159 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 242 optimal weight: 0.3980 chunk 162 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 187 optimal weight: 6.9990 chunk 62 optimal weight: 8.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN ** E 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 62 ASN H 62 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.106614 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.058595 restraints weight = 84129.901| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.47 r_work: 0.2518 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.2518 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 24785 Z= 0.213 Angle : 0.487 6.105 33980 Z= 0.274 Chirality : 0.039 0.138 3861 Planarity : 0.003 0.033 3992 Dihedral : 18.256 96.083 4581 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Rotamer: Outliers : 1.24 % Allowed : 9.50 % Favored : 89.26 % 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 aren not related in a simple way. whole: 1.27 (0.16), residues: 2803 helix: 1.46 (0.14), residues: 1314 sheet: 0.21 (0.25), residues: 499 loop : 0.53 (0.21), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 306 TYR 0.016 0.001 TYR I 191 PHE 0.013 0.001 PHE A 327 HIS 0.003 0.001 HIS E 294 Details of bonding type rmsd covalent geometry : bond 0.00483 (24785) covalent geometry : angle 0.48740 (33980) hydrogen bonds : bond 0.03703 ( 1295) hydrogen bonds : angle 4.48140 ( 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 256 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 228 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9240 (mt-10) cc_final: 0.8779 (mp0) REVERT: A 178 TYR cc_start: 0.8170 (m-80) cc_final: 0.7693 (m-80) REVERT: A 188 ASN cc_start: 0.8775 (m-40) cc_final: 0.8546 (m-40) REVERT: A 229 ARG cc_start: 0.8865 (OUTLIER) cc_final: 0.8552 (ttm170) REVERT: A 290 ASN cc_start: 0.8168 (m-40) cc_final: 0.7892 (m110) REVERT: B 43 GLU cc_start: 0.8981 (pt0) cc_final: 0.8648 (pp20) REVERT: B 68 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8635 (tm-30) REVERT: B 202 GLN cc_start: 0.9178 (tt0) cc_final: 0.8881 (tp-100) REVERT: B 213 GLU cc_start: 0.8252 (OUTLIER) cc_final: 0.7775 (mt-10) REVERT: B 235 ARG cc_start: 0.8533 (ttp-170) cc_final: 0.7997 (ttm170) REVERT: C 68 GLU cc_start: 0.7411 (tm-30) cc_final: 0.7067 (tm-30) REVERT: C 72 ASP cc_start: 0.8045 (m-30) cc_final: 0.7328 (m-30) REVERT: C 130 ARG cc_start: 0.8814 (OUTLIER) cc_final: 0.8573 (ttp-170) REVERT: D 39 LYS cc_start: 0.8672 (mttt) cc_final: 0.8453 (mmpt) REVERT: D 67 SER cc_start: 0.8198 (t) cc_final: 0.7774 (p) REVERT: D 68 GLU cc_start: 0.8686 (mt-10) cc_final: 0.8273 (tm-30) REVERT: D 72 ASP cc_start: 0.8877 (m-30) cc_final: 0.8587 (m-30) REVERT: D 176 GLU cc_start: 0.8403 (mm-30) cc_final: 0.8088 (mm-30) REVERT: D 202 GLN cc_start: 0.9106 (tt0) cc_final: 0.8633 (tm-30) REVERT: E 30 GLN cc_start: 0.8701 (mt0) cc_final: 0.8324 (tm130) REVERT: E 43 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8236 (pp20) REVERT: F 27 ARG cc_start: 0.8670 (mtp180) cc_final: 0.8138 (tpp-160) REVERT: F 30 GLN cc_start: 0.8234 (mp10) cc_final: 0.7961 (mp10) REVERT: F 202 GLN cc_start: 0.8796 (tt0) cc_final: 0.8556 (tm-30) REVERT: F 247 ARG cc_start: 0.8787 (mtp85) cc_final: 0.8296 (ttp80) REVERT: F 306 ARG cc_start: 0.8581 (ttt180) cc_final: 0.8224 (ttp-110) REVERT: G 68 GLU cc_start: 0.9053 (mt-10) cc_final: 0.8822 (mp0) REVERT: G 202 GLN cc_start: 0.8863 (tt0) cc_final: 0.8326 (tm-30) REVERT: G 210 MET cc_start: 0.9240 (mtm) cc_final: 0.8964 (mtp) REVERT: H 274 ASP cc_start: 0.8849 (m-30) cc_final: 0.8199 (p0) REVERT: I 96 ARG cc_start: 0.6716 (mtp85) cc_final: 0.5233 (mtm180) REVERT: I 124 GLU cc_start: 0.8629 (OUTLIER) cc_final: 0.8412 (tt0) REVERT: I 163 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8553 (mt-10) REVERT: I 216 TYR cc_start: 0.8597 (m-80) cc_final: 0.7912 (m-80) outliers start: 28 outliers final: 8 residues processed: 248 average time/residue: 0.8926 time to fit residues: 246.0605 Evaluate side-chains 222 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 209 time to evaluate : 0.894 ------------------------------------------------------------------------------- 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 213 GLU Chi-restraints excluded: chain C residue 130 ARG 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 84 MET Chi-restraints excluded: chain G residue 61 ILE Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 277 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 244 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 72 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 30 optimal weight: 0.9980 chunk 285 optimal weight: 20.0000 chunk 163 optimal weight: 4.9990 chunk 182 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 HIS A 267 ASN E 62 ASN F 62 ASN H 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.106969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.058928 restraints weight = 88868.425| |-----------------------------------------------------------------------------| r_work (start): 0.2714 rms_B_bonded: 3.58 r_work: 0.2524 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 24785 Z= 0.186 Angle : 0.471 6.416 33980 Z= 0.265 Chirality : 0.038 0.141 3861 Planarity : 0.003 0.036 3992 Dihedral : 18.284 97.141 4581 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.38 % Allowed : 10.61 % 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 aren not related in a simple way. whole: 1.27 (0.16), residues: 2803 helix: 1.52 (0.14), residues: 1318 sheet: 0.05 (0.24), residues: 507 loop : 0.55 (0.21), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.026 0.001 TYR I 191 PHE 0.015 0.001 PHE A 166 HIS 0.003 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00419 (24785) covalent geometry : angle 0.47136 (33980) hydrogen bonds : bond 0.03236 ( 1295) hydrogen bonds : angle 4.29388 ( 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 253 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 222 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8416 (mp0) cc_final: 0.8214 (mp0) REVERT: A 178 TYR cc_start: 0.8208 (m-80) cc_final: 0.7712 (m-80) REVERT: A 188 ASN cc_start: 0.8775 (m-40) cc_final: 0.8545 (m-40) REVERT: A 229 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8556 (ttm170) REVERT: A 290 ASN cc_start: 0.8139 (m-40) cc_final: 0.7878 (m110) REVERT: B 43 GLU cc_start: 0.9015 (pt0) cc_final: 0.8688 (pp20) REVERT: B 62 ASN cc_start: 0.9113 (m-40) cc_final: 0.8722 (t0) REVERT: B 68 GLU cc_start: 0.8937 (mt-10) cc_final: 0.8656 (tm-30) REVERT: B 202 GLN cc_start: 0.9181 (tt0) cc_final: 0.8870 (tp-100) REVERT: B 235 ARG cc_start: 0.8488 (ttp-170) cc_final: 0.8002 (ttm170) REVERT: C 130 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8571 (ttp-170) REVERT: D 39 LYS cc_start: 0.8669 (mttt) cc_final: 0.8442 (mmpt) REVERT: D 67 SER cc_start: 0.8198 (t) cc_final: 0.7789 (p) REVERT: D 68 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8251 (tm-30) REVERT: D 72 ASP cc_start: 0.8879 (m-30) cc_final: 0.8545 (m-30) REVERT: D 176 GLU cc_start: 0.8425 (mm-30) cc_final: 0.8071 (mm-30) REVERT: D 202 GLN cc_start: 0.9111 (tt0) cc_final: 0.8632 (tm-30) REVERT: E 30 GLN cc_start: 0.8658 (mt0) cc_final: 0.8318 (tm130) REVERT: E 43 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8251 (pp20) REVERT: F 27 ARG cc_start: 0.8666 (mtp180) cc_final: 0.8122 (tpp-160) REVERT: F 30 GLN cc_start: 0.8320 (mp10) cc_final: 0.8030 (mp10) REVERT: F 202 GLN cc_start: 0.8794 (tt0) cc_final: 0.8530 (tm-30) REVERT: F 247 ARG cc_start: 0.8781 (mtp85) cc_final: 0.8294 (ttp80) REVERT: F 306 ARG cc_start: 0.8560 (ttt180) cc_final: 0.8203 (ttp-110) REVERT: G 202 GLN cc_start: 0.8871 (tt0) cc_final: 0.8322 (tm-30) REVERT: G 210 MET cc_start: 0.9237 (mtm) cc_final: 0.8921 (mtp) REVERT: G 306 ARG cc_start: 0.7586 (tpp-160) cc_final: 0.7293 (tpp-160) REVERT: H 274 ASP cc_start: 0.8879 (m-30) cc_final: 0.8219 (p0) REVERT: I 49 VAL cc_start: 0.8828 (p) cc_final: 0.8487 (p) REVERT: I 96 ARG cc_start: 0.6705 (mtp85) cc_final: 0.5280 (mtm180) REVERT: I 124 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.8406 (tt0) REVERT: I 163 GLU cc_start: 0.8796 (mt-10) cc_final: 0.8519 (mt-10) REVERT: I 216 TYR cc_start: 0.8611 (m-80) cc_final: 0.8028 (m-80) REVERT: I 243 MET cc_start: 0.9136 (mmm) cc_final: 0.8926 (tmm) outliers start: 31 outliers final: 11 residues processed: 244 average time/residue: 0.8147 time to fit residues: 222.8823 Evaluate side-chains 226 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 211 time to evaluate : 0.905 ------------------------------------------------------------------------------- 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 130 ARG 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 84 MET 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 284 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 275 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 20.0000 chunk 95 optimal weight: 0.7980 chunk 216 optimal weight: 2.9990 chunk 72 optimal weight: 5.9990 chunk 104 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 267 optimal weight: 7.9990 chunk 230 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 62 ASN F 62 ASN ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.106819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.059526 restraints weight = 65865.744| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 3.12 r_work: 0.2551 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2593 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2593 r_free = 0.2593 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2593 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 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 : 0.004 0.030 24785 Z= 0.184 Angle : 0.470 7.182 33980 Z= 0.265 Chirality : 0.038 0.139 3861 Planarity : 0.003 0.042 3992 Dihedral : 18.276 99.177 4581 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer: Outliers : 1.60 % Allowed : 10.87 % Favored : 87.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.27 (0.16), residues: 2803 helix: 1.53 (0.14), residues: 1323 sheet: 0.01 (0.24), residues: 507 loop : 0.55 (0.21), residues: 973 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 306 TYR 0.027 0.001 TYR I 191 PHE 0.012 0.001 PHE A 327 HIS 0.002 0.001 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00414 (24785) covalent geometry : angle 0.47043 (33980) hydrogen bonds : bond 0.03197 ( 1295) hydrogen bonds : angle 4.24146 ( 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 255 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 219 time to evaluate : 0.898 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8451 (mp0) cc_final: 0.8210 (mp0) REVERT: A 178 TYR cc_start: 0.8254 (m-80) cc_final: 0.7818 (m-80) REVERT: A 188 ASN cc_start: 0.8760 (m-40) cc_final: 0.8463 (m-40) REVERT: A 229 ARG cc_start: 0.8864 (OUTLIER) cc_final: 0.8547 (ttm170) REVERT: A 290 ASN cc_start: 0.8157 (m-40) cc_final: 0.7846 (m110) REVERT: B 43 GLU cc_start: 0.9041 (pt0) cc_final: 0.8739 (pp20) REVERT: B 62 ASN cc_start: 0.9102 (m-40) cc_final: 0.8705 (t0) REVERT: B 68 GLU cc_start: 0.8922 (mt-10) cc_final: 0.8659 (tm-30) REVERT: B 202 GLN cc_start: 0.9160 (tt0) cc_final: 0.8847 (tp-100) REVERT: B 229 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.8713 (ttp-170) REVERT: B 235 ARG cc_start: 0.8458 (ttp-170) cc_final: 0.7967 (ttm170) REVERT: C 68 GLU cc_start: 0.7541 (tm-30) cc_final: 0.7300 (tm-30) REVERT: C 130 ARG cc_start: 0.8806 (OUTLIER) cc_final: 0.8576 (ttp-170) REVERT: C 213 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8097 (tm-30) REVERT: D 39 LYS cc_start: 0.8674 (mttt) cc_final: 0.8469 (mmpt) REVERT: D 67 SER cc_start: 0.8173 (t) cc_final: 0.7789 (p) REVERT: D 68 GLU cc_start: 0.8656 (mt-10) cc_final: 0.8260 (tm-30) REVERT: D 72 ASP cc_start: 0.8859 (m-30) cc_final: 0.8509 (m-30) REVERT: D 176 GLU cc_start: 0.8420 (mm-30) cc_final: 0.8048 (mm-30) REVERT: D 202 GLN cc_start: 0.9091 (tt0) cc_final: 0.8618 (tm-30) REVERT: E 30 GLN cc_start: 0.8648 (mt0) cc_final: 0.8321 (tm130) REVERT: E 43 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8262 (pp20) REVERT: F 27 ARG cc_start: 0.8673 (mtp180) cc_final: 0.8095 (tpp-160) REVERT: F 30 GLN cc_start: 0.8345 (mp10) cc_final: 0.8026 (mp10) REVERT: F 202 GLN cc_start: 0.8767 (tt0) cc_final: 0.8505 (tm-30) REVERT: F 247 ARG cc_start: 0.8762 (mtp85) cc_final: 0.8277 (ttp80) REVERT: F 306 ARG cc_start: 0.8548 (ttt180) cc_final: 0.8195 (ttp-110) REVERT: G 163 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8508 (mt-10) REVERT: G 202 GLN cc_start: 0.8864 (tt0) cc_final: 0.8309 (tm-30) REVERT: G 210 MET cc_start: 0.9205 (mtm) cc_final: 0.8930 (mtp) REVERT: G 306 ARG cc_start: 0.7545 (tpp-160) cc_final: 0.7279 (tpp-160) REVERT: H 274 ASP cc_start: 0.8880 (m-30) cc_final: 0.8246 (p0) REVERT: I 23 GLN cc_start: 0.5913 (OUTLIER) cc_final: 0.5689 (pp30) REVERT: I 96 ARG cc_start: 0.6828 (mtp85) cc_final: 0.5302 (mtm180) REVERT: I 124 GLU cc_start: 0.8619 (OUTLIER) cc_final: 0.8384 (tt0) REVERT: I 163 GLU cc_start: 0.8797 (mt-10) cc_final: 0.8529 (mt-10) REVERT: I 216 TYR cc_start: 0.8658 (m-80) cc_final: 0.8166 (m-80) outliers start: 36 outliers final: 13 residues processed: 246 average time/residue: 0.7896 time to fit residues: 217.8683 Evaluate side-chains 225 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 205 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 B residue 229 ARG Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 213 GLU 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 84 MET 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 103 THR Chi-restraints excluded: chain I residue 23 GLN Chi-restraints excluded: chain I residue 124 GLU Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 224 optimal weight: 4.9990 chunk 210 optimal weight: 3.9990 chunk 195 optimal weight: 3.9990 chunk 205 optimal weight: 0.7980 chunk 138 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 151 optimal weight: 4.9990 chunk 102 optimal weight: 0.8980 chunk 287 optimal weight: 10.0000 chunk 226 optimal weight: 2.9990 chunk 95 optimal weight: 0.8980 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN E 62 ASN F 62 ASN ** I 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.107895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.060300 restraints weight = 80575.126| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.44 r_work: 0.2562 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2602 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2602 r_free = 0.2602 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2602 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.2538 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= 0.131 Angle : 0.451 7.790 33980 Z= 0.253 Chirality : 0.037 0.137 3861 Planarity : 0.003 0.049 3992 Dihedral : 18.170 100.701 4581 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 1.29 % Allowed : 11.54 % Favored : 87.17 % 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 aren not related in a simple way. whole: 1.35 (0.17), residues: 2803 helix: 1.59 (0.14), residues: 1323 sheet: 0.05 (0.23), residues: 539 loop : 0.61 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 250 TYR 0.029 0.001 TYR I 191 PHE 0.014 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00287 (24785) covalent geometry : angle 0.45148 (33980) hydrogen bonds : bond 0.02774 ( 1295) hydrogen bonds : angle 4.06318 ( 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 260 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8477 (mp0) cc_final: 0.8234 (mp0) REVERT: A 178 TYR cc_start: 0.8282 (m-80) cc_final: 0.7807 (m-80) REVERT: A 290 ASN cc_start: 0.8203 (m-40) cc_final: 0.7945 (m110) REVERT: B 43 GLU cc_start: 0.9062 (pt0) cc_final: 0.8771 (pp20) REVERT: B 62 ASN cc_start: 0.9094 (m-40) cc_final: 0.8703 (t0) REVERT: B 68 GLU cc_start: 0.8932 (mt-10) cc_final: 0.8614 (tm-30) REVERT: B 202 GLN cc_start: 0.9137 (tt0) cc_final: 0.8820 (tp-100) REVERT: B 235 ARG cc_start: 0.8398 (ttp-170) cc_final: 0.7905 (ttm170) REVERT: C 57 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8483 (tttt) REVERT: C 68 GLU cc_start: 0.7528 (tm-30) cc_final: 0.7318 (tm-30) REVERT: C 130 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8546 (ttp-170) REVERT: D 39 LYS cc_start: 0.8669 (mttt) cc_final: 0.8454 (mmpt) REVERT: D 67 SER cc_start: 0.8193 (t) cc_final: 0.7825 (p) REVERT: D 68 GLU cc_start: 0.8673 (mt-10) cc_final: 0.8287 (tm-30) REVERT: D 72 ASP cc_start: 0.8854 (m-30) cc_final: 0.8542 (m-30) REVERT: D 176 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8087 (mm-30) REVERT: D 202 GLN cc_start: 0.9113 (tt0) cc_final: 0.8633 (tm-30) REVERT: D 250 ARG cc_start: 0.9388 (OUTLIER) cc_final: 0.9158 (tpt-90) REVERT: E 30 GLN cc_start: 0.8593 (mt0) cc_final: 0.8319 (tm130) REVERT: E 43 GLU cc_start: 0.8646 (OUTLIER) cc_final: 0.8291 (pp20) REVERT: F 27 ARG cc_start: 0.8678 (mtp180) cc_final: 0.8409 (tpp-160) REVERT: F 43 GLU cc_start: 0.8935 (mm-30) cc_final: 0.8730 (mm-30) REVERT: F 202 GLN cc_start: 0.8779 (tt0) cc_final: 0.8500 (tm-30) REVERT: F 247 ARG cc_start: 0.8768 (mtp85) cc_final: 0.8289 (ttp80) REVERT: F 306 ARG cc_start: 0.8542 (ttt180) cc_final: 0.8153 (ttp-110) REVERT: G 202 GLN cc_start: 0.8874 (tt0) cc_final: 0.8320 (tm-30) REVERT: H 88 THR cc_start: 0.8786 (m) cc_final: 0.8445 (t) REVERT: H 274 ASP cc_start: 0.8863 (m-30) cc_final: 0.8258 (p0) REVERT: I 96 ARG cc_start: 0.6811 (mtp85) cc_final: 0.5300 (mtm180) REVERT: I 163 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8540 (mt-10) REVERT: I 216 TYR cc_start: 0.8648 (m-80) cc_final: 0.8042 (m-80) outliers start: 29 outliers final: 12 residues processed: 254 average time/residue: 0.8067 time to fit residues: 229.9429 Evaluate side-chains 229 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 214 time to evaluate : 0.873 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 266 THR 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 E 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 72 ASP Chi-restraints excluded: chain H residue 103 THR 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: 5.9990 chunk 92 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 198 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 180 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 229 optimal weight: 6.9990 chunk 256 optimal weight: 7.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 ASN E 62 ASN E 272 GLN F 62 ASN H 62 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.107395 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.059993 restraints weight = 68633.396| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.19 r_work: 0.2560 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2601 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2601 r_free = 0.2601 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2601 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2532 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= 0.162 Angle : 0.469 8.032 33980 Z= 0.262 Chirality : 0.038 0.130 3861 Planarity : 0.003 0.044 3992 Dihedral : 18.203 101.521 4581 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.07 % Allowed : 12.34 % Favored : 86.60 % 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 aren not related in a simple way. whole: 1.36 (0.17), residues: 2803 helix: 1.64 (0.15), residues: 1323 sheet: 0.01 (0.23), residues: 539 loop : 0.60 (0.22), residues: 941 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 306 TYR 0.031 0.001 TYR I 191 PHE 0.012 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00364 (24785) covalent geometry : angle 0.46868 (33980) hydrogen bonds : bond 0.02958 ( 1295) hydrogen bonds : angle 4.09104 ( 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 245 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 221 time to evaluate : 0.959 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: 0.9266 (mt-10) cc_final: 0.8836 (mp0) REVERT: A 46 PHE cc_start: 0.8626 (m-10) cc_final: 0.8380 (m-80) REVERT: A 59 GLU cc_start: 0.8491 (mp0) cc_final: 0.8223 (mp0) REVERT: A 178 TYR cc_start: 0.8321 (m-80) cc_final: 0.7818 (m-80) REVERT: A 188 ASN cc_start: 0.8518 (m110) cc_final: 0.8198 (m110) REVERT: A 199 HIS cc_start: 0.8632 (t-90) cc_final: 0.8240 (t-90) REVERT: A 290 ASN cc_start: 0.8208 (m-40) cc_final: 0.7946 (m110) REVERT: B 43 GLU cc_start: 0.9072 (pt0) cc_final: 0.8779 (pp20) REVERT: B 62 ASN cc_start: 0.9089 (m-40) cc_final: 0.8688 (t0) REVERT: B 68 GLU cc_start: 0.8918 (mt-10) cc_final: 0.8625 (tm-30) REVERT: B 202 GLN cc_start: 0.9141 (tt0) cc_final: 0.8821 (tp-100) REVERT: B 235 ARG cc_start: 0.8397 (ttp-170) cc_final: 0.7913 (ttm170) REVERT: C 57 LYS cc_start: 0.8772 (ttmt) cc_final: 0.8519 (tttt) REVERT: C 68 GLU cc_start: 0.7553 (tm-30) cc_final: 0.7258 (tm-30) REVERT: C 130 ARG cc_start: 0.8803 (OUTLIER) cc_final: 0.8571 (ttp-170) REVERT: C 213 GLU cc_start: 0.8477 (OUTLIER) cc_final: 0.8095 (tm-30) REVERT: D 39 LYS cc_start: 0.8677 (mttt) cc_final: 0.8459 (mmpt) REVERT: D 67 SER cc_start: 0.8194 (t) cc_final: 0.7817 (p) REVERT: D 68 GLU cc_start: 0.8676 (mt-10) cc_final: 0.8294 (tm-30) REVERT: D 72 ASP cc_start: 0.8858 (m-30) cc_final: 0.8518 (m-30) REVERT: D 176 GLU cc_start: 0.8487 (mm-30) cc_final: 0.8067 (mm-30) REVERT: D 202 GLN cc_start: 0.9091 (tt0) cc_final: 0.8614 (tm-30) REVERT: D 250 ARG cc_start: 0.9375 (OUTLIER) cc_final: 0.9152 (tpt-90) REVERT: D 306 ARG cc_start: 0.8350 (ttm110) cc_final: 0.8085 (tpt-90) REVERT: E 30 GLN cc_start: 0.8604 (mt0) cc_final: 0.8325 (tm130) REVERT: E 43 GLU cc_start: 0.8658 (OUTLIER) cc_final: 0.8299 (pp20) REVERT: E 210 MET cc_start: 0.9167 (mtp) cc_final: 0.8934 (mtm) REVERT: E 272 GLN cc_start: 0.8996 (mt0) cc_final: 0.8790 (mt0) REVERT: F 27 ARG cc_start: 0.8844 (mtp180) cc_final: 0.8448 (tpp-160) REVERT: F 43 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8713 (mm-30) REVERT: F 202 GLN cc_start: 0.8776 (tt0) cc_final: 0.8495 (tm-30) REVERT: F 247 ARG cc_start: 0.8761 (mtp85) cc_final: 0.8286 (ttp80) REVERT: F 306 ARG cc_start: 0.8554 (ttt180) cc_final: 0.8170 (ttp-110) REVERT: G 202 GLN cc_start: 0.8861 (tt0) cc_final: 0.8301 (tm-30) REVERT: G 210 MET cc_start: 0.9164 (mtp) cc_final: 0.8952 (mtp) REVERT: G 306 ARG cc_start: 0.7807 (tpp-160) cc_final: 0.7560 (tpp-160) REVERT: H 23 GLN cc_start: 0.9115 (mt0) cc_final: 0.8885 (mt0) REVERT: H 88 THR cc_start: 0.8809 (m) cc_final: 0.8464 (t) REVERT: H 274 ASP cc_start: 0.8865 (m-30) cc_final: 0.8248 (p0) REVERT: I 50 GLU cc_start: 0.8074 (mp0) cc_final: 0.7745 (tt0) REVERT: I 96 ARG cc_start: 0.6807 (mtp85) cc_final: 0.5288 (mtm180) REVERT: I 163 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8536 (mt-10) REVERT: I 216 TYR cc_start: 0.8689 (m-80) cc_final: 0.8090 (m-80) outliers start: 24 outliers final: 12 residues processed: 240 average time/residue: 0.8261 time to fit residues: 222.4932 Evaluate side-chains 227 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 211 time to evaluate : 0.884 ------------------------------------------------------------------------------- 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 99 ILE Chi-restraints excluded: chain C residue 130 ARG Chi-restraints excluded: chain C residue 213 GLU Chi-restraints excluded: chain C residue 266 THR 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 E 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 72 ASP Chi-restraints excluded: chain H residue 103 THR 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: 5.9990 chunk 282 optimal weight: 8.9990 chunk 207 optimal weight: 0.9980 chunk 198 optimal weight: 1.9990 chunk 78 optimal weight: 0.6980 chunk 209 optimal weight: 2.9990 chunk 216 optimal weight: 2.9990 chunk 184 optimal weight: 0.9980 chunk 159 optimal weight: 0.9990 chunk 175 optimal weight: 0.7980 chunk 102 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 138 HIS ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 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 = 0.3684 r_free = 0.3684 target = 0.108715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.061286 restraints weight = 79214.415| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 3.41 r_work: 0.2584 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.2584 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2625 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2625 r_free = 0.2625 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2625 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.2740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 24785 Z= 0.113 Angle : 0.453 8.510 33980 Z= 0.254 Chirality : 0.037 0.126 3861 Planarity : 0.002 0.039 3992 Dihedral : 18.097 103.395 4581 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Rotamer: Outliers : 0.93 % Allowed : 12.78 % Favored : 86.28 % 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 aren not related in a simple way. whole: 1.41 (0.17), residues: 2803 helix: 1.64 (0.15), residues: 1327 sheet: 0.09 (0.24), residues: 525 loop : 0.62 (0.22), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 306 TYR 0.033 0.001 TYR I 191 PHE 0.013 0.001 PHE A 126 HIS 0.002 0.000 HIS D 294 Details of bonding type rmsd covalent geometry : bond 0.00245 (24785) covalent geometry : angle 0.45284 (33980) hydrogen bonds : bond 0.02575 ( 1295) hydrogen bonds : angle 3.96009 ( 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 252 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 231 time to evaluate : 0.796 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8904 (mp0) REVERT: A 59 GLU cc_start: 0.8505 (mp0) cc_final: 0.8234 (mp0) REVERT: A 73 LYS cc_start: 0.9279 (tttt) cc_final: 0.9001 (tptm) REVERT: A 178 TYR cc_start: 0.8333 (m-80) cc_final: 0.7824 (m-80) REVERT: A 188 ASN cc_start: 0.8506 (m110) cc_final: 0.8242 (m-40) REVERT: A 199 HIS cc_start: 0.8568 (t-90) cc_final: 0.8111 (t-90) REVERT: A 290 ASN cc_start: 0.8204 (m-40) cc_final: 0.7824 (m-40) REVERT: B 43 GLU cc_start: 0.9066 (pt0) cc_final: 0.8780 (pp20) REVERT: B 62 ASN cc_start: 0.9078 (m-40) cc_final: 0.8686 (t0) REVERT: B 68 GLU cc_start: 0.8926 (mt-10) cc_final: 0.8613 (tm-30) REVERT: B 202 GLN cc_start: 0.9124 (tt0) cc_final: 0.8796 (tp-100) REVERT: B 235 ARG cc_start: 0.8332 (ttp-170) cc_final: 0.7889 (ttm170) REVERT: C 57 LYS cc_start: 0.8762 (ttmt) cc_final: 0.8498 (tttt) REVERT: C 68 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7291 (tm-30) REVERT: C 213 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8103 (tm-30) REVERT: D 67 SER cc_start: 0.8196 (t) cc_final: 0.7824 (p) REVERT: D 68 GLU cc_start: 0.8663 (mt-10) cc_final: 0.8292 (tm-30) REVERT: D 72 ASP cc_start: 0.8861 (m-30) cc_final: 0.8560 (m-30) REVERT: D 176 GLU cc_start: 0.8518 (mm-30) cc_final: 0.8095 (mm-30) REVERT: D 202 GLN cc_start: 0.9116 (tt0) cc_final: 0.8646 (tm-30) REVERT: D 306 ARG cc_start: 0.8393 (ttm110) cc_final: 0.8134 (tpt-90) REVERT: E 30 GLN cc_start: 0.8549 (mt0) cc_final: 0.8295 (tm130) REVERT: E 43 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.8383 (pp20) REVERT: E 210 MET cc_start: 0.9163 (mtp) cc_final: 0.8904 (mtm) REVERT: E 278 MET cc_start: 0.7980 (OUTLIER) cc_final: 0.7634 (ppp) REVERT: F 27 ARG cc_start: 0.8823 (mtp180) cc_final: 0.8052 (tpp-160) REVERT: F 30 GLN cc_start: 0.8861 (tm-30) cc_final: 0.8594 (mp10) REVERT: F 43 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8719 (mm-30) REVERT: F 202 GLN cc_start: 0.8776 (tt0) cc_final: 0.8483 (tm-30) REVERT: F 247 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8287 (ttp80) REVERT: F 306 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8123 (ttp-110) REVERT: G 202 GLN cc_start: 0.8856 (tt0) cc_final: 0.8301 (tm-30) REVERT: G 210 MET cc_start: 0.9162 (mtp) cc_final: 0.8958 (mtp) REVERT: G 306 ARG cc_start: 0.7836 (tpp-160) cc_final: 0.7572 (tpp-160) REVERT: H 23 GLN cc_start: 0.9141 (mt0) cc_final: 0.8910 (mt0) REVERT: H 88 THR cc_start: 0.8801 (m) cc_final: 0.8469 (t) REVERT: H 274 ASP cc_start: 0.8871 (m-30) cc_final: 0.8209 (p0) REVERT: I 50 GLU cc_start: 0.8060 (mp0) cc_final: 0.7755 (tt0) REVERT: I 96 ARG cc_start: 0.6734 (mtp85) cc_final: 0.5196 (mtm180) REVERT: I 163 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8539 (mt-10) REVERT: I 216 TYR cc_start: 0.8672 (m-80) cc_final: 0.8085 (m-80) outliers start: 21 outliers final: 11 residues processed: 247 average time/residue: 0.7873 time to fit residues: 218.5314 Evaluate side-chains 231 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 217 time to evaluate : 0.913 ------------------------------------------------------------------------------- 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 213 GLU 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 E residue 278 MET 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 H residue 72 ASP Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain I residue 284 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 224 optimal weight: 2.9990 chunk 26 optimal weight: 9.9990 chunk 195 optimal weight: 1.9990 chunk 47 optimal weight: 7.9990 chunk 285 optimal weight: 20.0000 chunk 266 optimal weight: 10.0000 chunk 156 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 186 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 188 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 267 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 = 0.3637 r_free = 0.3637 target = 0.105948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.058683 restraints weight = 58156.973| |-----------------------------------------------------------------------------| r_work (start): 0.2710 rms_B_bonded: 2.93 r_work: 0.2531 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2577 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2577 r_free = 0.2577 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2577 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 24785 Z= 0.278 Angle : 0.536 9.304 33980 Z= 0.295 Chirality : 0.040 0.136 3861 Planarity : 0.003 0.030 3992 Dihedral : 18.394 101.793 4581 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Rotamer: Outliers : 1.24 % Allowed : 12.87 % Favored : 85.89 % 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 aren not related in a simple way. whole: 1.30 (0.17), residues: 2803 helix: 1.58 (0.15), residues: 1323 sheet: 0.02 (0.23), residues: 529 loop : 0.54 (0.22), residues: 951 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 247 TYR 0.037 0.002 TYR I 191 PHE 0.013 0.001 PHE A 126 HIS 0.008 0.001 HIS I 199 Details of bonding type rmsd covalent geometry : bond 0.00635 (24785) covalent geometry : angle 0.53626 (33980) hydrogen bonds : bond 0.03608 ( 1295) hydrogen bonds : angle 4.31335 ( 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 242 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 214 time to evaluate : 0.698 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8881 (mp0) REVERT: A 59 GLU cc_start: 0.8528 (mp0) cc_final: 0.8242 (mp0) REVERT: A 178 TYR cc_start: 0.8339 (m-80) cc_final: 0.7852 (m-80) REVERT: A 199 HIS cc_start: 0.8612 (t-90) cc_final: 0.8228 (t-90) REVERT: A 229 ARG cc_start: 0.8870 (OUTLIER) cc_final: 0.8539 (ttm170) REVERT: A 290 ASN cc_start: 0.8185 (m-40) cc_final: 0.7907 (m110) REVERT: B 43 GLU cc_start: 0.9104 (pt0) cc_final: 0.8820 (pp20) REVERT: B 62 ASN cc_start: 0.9056 (m-40) cc_final: 0.8652 (t0) REVERT: B 68 GLU cc_start: 0.8910 (mt-10) cc_final: 0.8617 (tm-30) REVERT: B 202 GLN cc_start: 0.9153 (tt0) cc_final: 0.8829 (tp-100) REVERT: B 235 ARG cc_start: 0.8497 (ttp-170) cc_final: 0.7979 (ttm170) REVERT: C 57 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8603 (tttt) REVERT: C 68 GLU cc_start: 0.7660 (tm-30) cc_final: 0.7280 (tm-30) REVERT: C 213 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8064 (tm-30) REVERT: D 67 SER cc_start: 0.8217 (t) cc_final: 0.7847 (p) REVERT: D 68 GLU cc_start: 0.8734 (mt-10) cc_final: 0.8373 (tm-30) REVERT: D 72 ASP cc_start: 0.8905 (m-30) cc_final: 0.8592 (m-30) REVERT: D 176 GLU cc_start: 0.8517 (mm-30) cc_final: 0.8093 (mm-30) REVERT: D 202 GLN cc_start: 0.9085 (tt0) cc_final: 0.8593 (tm-30) REVERT: E 30 GLN cc_start: 0.8671 (mt0) cc_final: 0.8338 (tm130) REVERT: E 43 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8408 (pp20) REVERT: E 278 MET cc_start: 0.8001 (OUTLIER) cc_final: 0.7708 (ppp) REVERT: F 27 ARG cc_start: 0.8850 (mtp180) cc_final: 0.8081 (tpp-160) REVERT: F 30 GLN cc_start: 0.8869 (tm-30) cc_final: 0.8574 (mp10) REVERT: F 43 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8734 (mm-30) REVERT: F 202 GLN cc_start: 0.8778 (tt0) cc_final: 0.8493 (tm-30) REVERT: F 247 ARG cc_start: 0.8754 (mtp85) cc_final: 0.8269 (ttp80) REVERT: F 306 ARG cc_start: 0.8573 (ttt180) cc_final: 0.8245 (ttp-110) REVERT: G 202 GLN cc_start: 0.8841 (tt0) cc_final: 0.8284 (tm-30) REVERT: G 306 ARG cc_start: 0.7744 (tpp-160) cc_final: 0.7476 (tpp-160) REVERT: H 23 GLN cc_start: 0.9188 (mt0) cc_final: 0.8961 (mt0) REVERT: H 88 THR cc_start: 0.8798 (m) cc_final: 0.8441 (t) REVERT: H 274 ASP cc_start: 0.8920 (m-30) cc_final: 0.8192 (p0) REVERT: I 50 GLU cc_start: 0.8066 (mp0) cc_final: 0.7729 (tt0) REVERT: I 96 ARG cc_start: 0.6870 (mtp85) cc_final: 0.5324 (mtm180) REVERT: I 163 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8522 (mt-10) REVERT: I 216 TYR cc_start: 0.8683 (m-80) cc_final: 0.8123 (m-80) outliers start: 28 outliers final: 12 residues processed: 233 average time/residue: 0.8268 time to fit residues: 216.0669 Evaluate side-chains 222 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 206 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 213 GLU Chi-restraints excluded: chain E residue 43 GLU Chi-restraints excluded: chain E residue 130 ARG Chi-restraints excluded: chain E residue 278 MET 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 163 GLU Chi-restraints excluded: chain G residue 266 THR Chi-restraints excluded: chain H residue 103 THR Chi-restraints excluded: chain I residue 103 THR 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: 20.0000 chunk 108 optimal weight: 0.9980 chunk 264 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 104 optimal weight: 1.9990 chunk 10 optimal weight: 10.0000 chunk 206 optimal weight: 0.7980 chunk 84 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 272 optimal weight: 0.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 267 ASN E 62 ASN F 62 ASN G 36 ASN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 242 GLN I 267 ASN I 272 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.108409 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.061448 restraints weight = 58902.442| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 2.99 r_work: 0.2598 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2598 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2597 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2597 r_free = 0.2597 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2597 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.2737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 24785 Z= 0.118 Angle : 0.475 9.843 33980 Z= 0.266 Chirality : 0.037 0.127 3861 Planarity : 0.003 0.028 3992 Dihedral : 18.227 103.410 4581 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.00 % Favored : 99.00 % Rotamer: Outliers : 0.62 % Allowed : 13.54 % Favored : 85.84 % 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 aren not related in a simple way. whole: 1.35 (0.17), residues: 2803 helix: 1.59 (0.15), residues: 1323 sheet: 0.09 (0.24), residues: 517 loop : 0.58 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 306 TYR 0.037 0.001 TYR I 191 PHE 0.013 0.001 PHE A 126 HIS 0.004 0.000 HIS I 199 Details of bonding type rmsd covalent geometry : bond 0.00254 (24785) covalent geometry : angle 0.47510 (33980) hydrogen bonds : bond 0.02702 ( 1295) hydrogen bonds : angle 4.08585 ( 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 243 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 229 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8500 (mp0) cc_final: 0.8217 (mp0) REVERT: A 178 TYR cc_start: 0.8338 (m-80) cc_final: 0.7877 (m-80) REVERT: A 188 ASN cc_start: 0.8491 (m-40) cc_final: 0.8187 (m110) REVERT: A 199 HIS cc_start: 0.8572 (t-90) cc_final: 0.8148 (t-90) REVERT: A 210 MET cc_start: 0.8775 (ptt) cc_final: 0.8130 (ppp) REVERT: A 290 ASN cc_start: 0.8178 (m-40) cc_final: 0.7909 (m110) REVERT: B 43 GLU cc_start: 0.9056 (pt0) cc_final: 0.8770 (pp20) REVERT: B 62 ASN cc_start: 0.9043 (m-40) cc_final: 0.8653 (t0) REVERT: B 68 GLU cc_start: 0.8921 (mt-10) cc_final: 0.8627 (tm-30) REVERT: B 202 GLN cc_start: 0.9122 (tt0) cc_final: 0.8801 (tp-100) REVERT: B 235 ARG cc_start: 0.8366 (ttp-170) cc_final: 0.7872 (ttm170) REVERT: C 57 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8557 (tttt) REVERT: C 59 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8133 (mt-10) REVERT: C 68 GLU cc_start: 0.7594 (tm-30) cc_final: 0.7251 (tm-30) REVERT: C 213 GLU cc_start: 0.8395 (OUTLIER) cc_final: 0.8035 (tm-30) REVERT: D 67 SER cc_start: 0.8199 (t) cc_final: 0.7830 (p) REVERT: D 68 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8291 (tm-30) REVERT: D 72 ASP cc_start: 0.8845 (m-30) cc_final: 0.8526 (m-30) REVERT: D 176 GLU cc_start: 0.8504 (mm-30) cc_final: 0.8069 (mm-30) REVERT: D 202 GLN cc_start: 0.9081 (tt0) cc_final: 0.8601 (tm-30) REVERT: D 306 ARG cc_start: 0.8413 (ttm110) cc_final: 0.8176 (tpt-90) REVERT: E 30 GLN cc_start: 0.8609 (mt0) cc_final: 0.8324 (tm130) REVERT: E 43 GLU cc_start: 0.8654 (OUTLIER) cc_final: 0.8395 (pp20) REVERT: F 27 ARG cc_start: 0.8820 (mtp180) cc_final: 0.8059 (tpp-160) REVERT: F 30 GLN cc_start: 0.8859 (tm-30) cc_final: 0.8584 (mp10) REVERT: F 43 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8717 (mm-30) REVERT: F 202 GLN cc_start: 0.8740 (tt0) cc_final: 0.8468 (tm-30) REVERT: F 247 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8275 (ttp80) REVERT: F 306 ARG cc_start: 0.8520 (ttt180) cc_final: 0.8129 (ttp-110) REVERT: G 202 GLN cc_start: 0.8833 (tt0) cc_final: 0.8278 (tm-30) REVERT: G 306 ARG cc_start: 0.7800 (tpp-160) cc_final: 0.7534 (tpp-160) REVERT: H 23 GLN cc_start: 0.9173 (mt0) cc_final: 0.8967 (mt0) REVERT: H 29 GLU cc_start: 0.8774 (tp30) cc_final: 0.8553 (mm-30) REVERT: H 88 THR cc_start: 0.8810 (m) cc_final: 0.8468 (t) REVERT: H 274 ASP cc_start: 0.8900 (m-30) cc_final: 0.8172 (p0) REVERT: I 96 ARG cc_start: 0.6843 (mtp85) cc_final: 0.5306 (mtm180) REVERT: I 163 GLU cc_start: 0.8743 (mt-10) cc_final: 0.8449 (mt-10) REVERT: I 216 TYR cc_start: 0.8693 (m-80) cc_final: 0.8078 (m-80) outliers start: 14 outliers final: 10 residues processed: 241 average time/residue: 0.7931 time to fit residues: 215.3271 Evaluate side-chains 233 residues out of total 2253 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 221 time to evaluate : 0.916 ------------------------------------------------------------------------------- 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 213 GLU 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 H residue 103 THR Chi-restraints excluded: chain I residue 284 LYS Chi-restraints excluded: chain I residue 326 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 35 optimal weight: 2.9990 chunk 228 optimal weight: 6.9990 chunk 204 optimal weight: 4.9990 chunk 188 optimal weight: 1.9990 chunk 130 optimal weight: 4.9990 chunk 193 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 121 optimal weight: 2.9990 chunk 278 optimal weight: 10.0000 chunk 104 optimal weight: 0.8980 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 94 GLN A 267 ASN E 62 ASN F 62 ASN H 62 ASN ** I 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 272 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.107156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.059718 restraints weight = 66620.190| |-----------------------------------------------------------------------------| r_work (start): 0.2736 rms_B_bonded: 3.13 r_work: 0.2555 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2555 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2598 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2598 r_free = 0.2598 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2598 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8511 moved from start: 0.2652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 24785 Z= 0.187 Angle : 0.506 9.514 33980 Z= 0.280 Chirality : 0.038 0.138 3861 Planarity : 0.003 0.028 3992 Dihedral : 18.295 104.282 4581 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Rotamer: Outliers : 0.80 % Allowed : 13.67 % Favored : 85.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.33 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.17), residues: 2803 helix: 1.58 (0.15), residues: 1323 sheet: 0.07 (0.24), residues: 517 loop : 0.58 (0.21), residues: 963 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 306 TYR 0.030 0.001 TYR I 191 PHE 0.012 0.001 PHE A 126 HIS 0.009 0.001 HIS I 199 Details of bonding type rmsd covalent geometry : bond 0.00424 (24785) covalent geometry : angle 0.50562 (33980) hydrogen bonds : bond 0.03084 ( 1295) hydrogen bonds : angle 4.18032 ( 3480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10839.27 seconds wall clock time: 184 minutes 40.54 seconds (11080.54 seconds total)