Starting phenix.real_space_refine on Tue Aug 26 10:23:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8rmk_19362/08_2025/8rmk_19362.cif Found real_map, /net/cci-nas-00/data/ceres_data/8rmk_19362/08_2025/8rmk_19362.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.07 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8rmk_19362/08_2025/8rmk_19362.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8rmk_19362/08_2025/8rmk_19362.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8rmk_19362/08_2025/8rmk_19362.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8rmk_19362/08_2025/8rmk_19362.map" } resolution = 3.07 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= 0.008 sd= 0.057 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 132 5.16 5 C 23122 2.51 5 N 6259 2.21 5 O 6589 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 22 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 36113 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2281 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2281 Classifications: {'peptide': 286} Link IDs: {'PTRANS': 15, 'TRANS': 270} Chain breaks: 1 Chain: "L" Number of atoms: 960 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 960 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'PLC': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, M, N, O, P, Q, R, S, T, U, V Time building chain proxies: 3.96, per 1000 atoms: 0.11 Number of scatterers: 36113 At special positions: 0 Unit cell: (200.43, 200.43, 134.93, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 132 16.00 P 11 15.00 O 6589 8.00 N 6259 7.00 C 23122 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=33, symmetry=0 Simple disulfide: pdb=" SG CYS A 46 " - pdb=" SG CYS A 130 " distance=2.03 Simple disulfide: pdb=" SG CYS A 48 " - pdb=" SG CYS A 162 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 96 " distance=2.04 Simple disulfide: pdb=" SG CYS B 46 " - pdb=" SG CYS B 130 " distance=2.03 Simple disulfide: pdb=" SG CYS C 46 " - pdb=" SG CYS C 130 " distance=2.03 Simple disulfide: pdb=" SG CYS D 46 " - pdb=" SG CYS D 130 " distance=2.03 Simple disulfide: pdb=" SG CYS E 46 " - pdb=" SG CYS E 130 " distance=2.03 Simple disulfide: pdb=" SG CYS F 46 " - pdb=" SG CYS F 130 " distance=2.03 Simple disulfide: pdb=" SG CYS G 46 " - pdb=" SG CYS G 130 " distance=2.03 Simple disulfide: pdb=" SG CYS H 46 " - pdb=" SG CYS H 130 " distance=2.03 Simple disulfide: pdb=" SG CYS I 46 " - pdb=" SG CYS I 130 " distance=2.03 Simple disulfide: pdb=" SG CYS J 46 " - pdb=" SG CYS J 130 " distance=2.03 Simple disulfide: pdb=" SG CYS K 46 " - pdb=" SG CYS K 130 " distance=2.03 Simple disulfide: pdb=" SG CYS B 48 " - pdb=" SG CYS B 162 " distance=2.03 Simple disulfide: pdb=" SG CYS C 48 " - pdb=" SG CYS C 162 " distance=2.03 Simple disulfide: pdb=" SG CYS D 48 " - pdb=" SG CYS D 162 " distance=2.03 Simple disulfide: pdb=" SG CYS E 48 " - pdb=" SG CYS E 162 " distance=2.03 Simple disulfide: pdb=" SG CYS F 48 " - pdb=" SG CYS F 162 " distance=2.03 Simple disulfide: pdb=" SG CYS G 48 " - pdb=" SG CYS G 162 " distance=2.03 Simple disulfide: pdb=" SG CYS H 48 " - pdb=" SG CYS H 162 " distance=2.03 Simple disulfide: pdb=" SG CYS I 48 " - pdb=" SG CYS I 162 " distance=2.03 Simple disulfide: pdb=" SG CYS J 48 " - pdb=" SG CYS J 162 " distance=2.03 Simple disulfide: pdb=" SG CYS K 48 " - pdb=" SG CYS K 162 " distance=2.03 Simple disulfide: pdb=" SG CYS M 22 " - pdb=" SG CYS M 96 " distance=2.04 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.04 Simple disulfide: pdb=" SG CYS O 22 " - pdb=" SG CYS O 96 " distance=2.04 Simple disulfide: pdb=" SG CYS P 22 " - pdb=" SG CYS P 96 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 22 " - pdb=" SG CYS Q 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 22 " - pdb=" SG CYS R 96 " distance=2.04 Simple disulfide: pdb=" SG CYS S 22 " - pdb=" SG CYS S 96 " distance=2.04 Simple disulfide: pdb=" SG CYS T 22 " - pdb=" SG CYS T 96 " distance=2.04 Simple disulfide: pdb=" SG CYS U 22 " - pdb=" SG CYS U 96 " distance=2.04 Simple disulfide: pdb=" SG CYS V 22 " - pdb=" SG CYS V 96 " distance=2.04 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: 4.16 Conformation dependent library (CDL) restraints added in 2.1 seconds Enol-peptide restraints added in 1.2 microseconds 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8426 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 44 sheets defined 53.0% alpha, 17.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 52 through 76 Proline residue: A 64 - end of helix Processing helix chain 'A' and resid 77 through 90 Processing helix chain 'A' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR A 99 " --> pdb=" O SER A 95 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 125 Processing helix chain 'A' and resid 125 through 133 Processing helix chain 'A' and resid 134 through 136 No H-bonds generated for 'chain 'A' and resid 134 through 136' Processing helix chain 'A' and resid 152 through 160 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU A 174 " --> pdb=" O SER A 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR A 182 " --> pdb=" O ARG A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 252 Processing helix chain 'A' and resid 257 through 267 Processing helix chain 'A' and resid 274 through 280 Processing helix chain 'A' and resid 297 through 304 Processing helix chain 'A' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'L' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR L 91 " --> pdb=" O PRO L 88 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 76 Proline residue: B 64 - end of helix Processing helix chain 'B' and resid 77 through 90 Processing helix chain 'B' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR B 99 " --> pdb=" O SER B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 125 Processing helix chain 'B' and resid 125 through 133 Processing helix chain 'B' and resid 134 through 136 No H-bonds generated for 'chain 'B' and resid 134 through 136' Processing helix chain 'B' and resid 152 through 160 Processing helix chain 'B' and resid 161 through 163 No H-bonds generated for 'chain 'B' and resid 161 through 163' Processing helix chain 'B' and resid 166 through 168 No H-bonds generated for 'chain 'B' and resid 166 through 168' Processing helix chain 'B' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU B 174 " --> pdb=" O SER B 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR B 182 " --> pdb=" O ARG B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 213 through 252 Processing helix chain 'B' and resid 257 through 267 Processing helix chain 'B' and resid 274 through 280 Processing helix chain 'B' and resid 297 through 304 Processing helix chain 'B' and resid 323 through 329 removed outlier: 3.725A pdb=" N PHE B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) Processing helix chain 'C' and resid 52 through 76 Proline residue: C 64 - end of helix Processing helix chain 'C' and resid 77 through 90 Processing helix chain 'C' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR C 99 " --> pdb=" O SER C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 111 through 125 Processing helix chain 'C' and resid 125 through 133 Processing helix chain 'C' and resid 134 through 136 No H-bonds generated for 'chain 'C' and resid 134 through 136' Processing helix chain 'C' and resid 152 through 160 Processing helix chain 'C' and resid 161 through 163 No H-bonds generated for 'chain 'C' and resid 161 through 163' Processing helix chain 'C' and resid 166 through 168 No H-bonds generated for 'chain 'C' and resid 166 through 168' Processing helix chain 'C' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU C 174 " --> pdb=" O SER C 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR C 182 " --> pdb=" O ARG C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 213 through 252 Processing helix chain 'C' and resid 257 through 267 Processing helix chain 'C' and resid 274 through 280 Processing helix chain 'C' and resid 297 through 304 Processing helix chain 'C' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 76 Proline residue: D 64 - end of helix Processing helix chain 'D' and resid 77 through 90 Processing helix chain 'D' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR D 99 " --> pdb=" O SER D 95 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 125 Processing helix chain 'D' and resid 125 through 133 Processing helix chain 'D' and resid 134 through 136 No H-bonds generated for 'chain 'D' and resid 134 through 136' Processing helix chain 'D' and resid 152 through 160 Processing helix chain 'D' and resid 161 through 163 No H-bonds generated for 'chain 'D' and resid 161 through 163' Processing helix chain 'D' and resid 166 through 168 No H-bonds generated for 'chain 'D' and resid 166 through 168' Processing helix chain 'D' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU D 174 " --> pdb=" O SER D 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR D 182 " --> pdb=" O ARG D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 252 Processing helix chain 'D' and resid 257 through 267 Processing helix chain 'D' and resid 274 through 280 Processing helix chain 'D' and resid 297 through 304 Processing helix chain 'D' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 76 Proline residue: E 64 - end of helix Processing helix chain 'E' and resid 77 through 90 Processing helix chain 'E' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR E 99 " --> pdb=" O SER E 95 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 125 Processing helix chain 'E' and resid 125 through 133 Processing helix chain 'E' and resid 134 through 136 No H-bonds generated for 'chain 'E' and resid 134 through 136' Processing helix chain 'E' and resid 152 through 160 Processing helix chain 'E' and resid 161 through 163 No H-bonds generated for 'chain 'E' and resid 161 through 163' Processing helix chain 'E' and resid 166 through 168 No H-bonds generated for 'chain 'E' and resid 166 through 168' Processing helix chain 'E' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU E 174 " --> pdb=" O SER E 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR E 182 " --> pdb=" O ARG E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 213 through 252 Processing helix chain 'E' and resid 257 through 267 Processing helix chain 'E' and resid 274 through 280 Processing helix chain 'E' and resid 297 through 304 Processing helix chain 'E' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE E 329 " --> pdb=" O LEU E 325 " (cutoff:3.500A) Processing helix chain 'F' and resid 52 through 76 Proline residue: F 64 - end of helix Processing helix chain 'F' and resid 77 through 90 Processing helix chain 'F' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR F 99 " --> pdb=" O SER F 95 " (cutoff:3.500A) Processing helix chain 'F' and resid 111 through 125 Processing helix chain 'F' and resid 125 through 133 Processing helix chain 'F' and resid 134 through 136 No H-bonds generated for 'chain 'F' and resid 134 through 136' Processing helix chain 'F' and resid 152 through 160 Processing helix chain 'F' and resid 161 through 163 No H-bonds generated for 'chain 'F' and resid 161 through 163' Processing helix chain 'F' and resid 166 through 168 No H-bonds generated for 'chain 'F' and resid 166 through 168' Processing helix chain 'F' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU F 174 " --> pdb=" O SER F 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR F 182 " --> pdb=" O ARG F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 213 through 252 Processing helix chain 'F' and resid 257 through 267 Processing helix chain 'F' and resid 274 through 280 Processing helix chain 'F' and resid 297 through 304 Processing helix chain 'F' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE F 329 " --> pdb=" O LEU F 325 " (cutoff:3.500A) Processing helix chain 'G' and resid 52 through 76 Proline residue: G 64 - end of helix Processing helix chain 'G' and resid 77 through 90 Processing helix chain 'G' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR G 99 " --> pdb=" O SER G 95 " (cutoff:3.500A) Processing helix chain 'G' and resid 111 through 125 Processing helix chain 'G' and resid 125 through 133 Processing helix chain 'G' and resid 134 through 136 No H-bonds generated for 'chain 'G' and resid 134 through 136' Processing helix chain 'G' and resid 152 through 160 Processing helix chain 'G' and resid 161 through 163 No H-bonds generated for 'chain 'G' and resid 161 through 163' Processing helix chain 'G' and resid 166 through 168 No H-bonds generated for 'chain 'G' and resid 166 through 168' Processing helix chain 'G' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU G 174 " --> pdb=" O SER G 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR G 182 " --> pdb=" O ARG G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 213 through 252 Processing helix chain 'G' and resid 257 through 267 Processing helix chain 'G' and resid 274 through 280 Processing helix chain 'G' and resid 297 through 304 Processing helix chain 'G' and resid 323 through 329 removed outlier: 3.725A pdb=" N PHE G 329 " --> pdb=" O LEU G 325 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 76 Proline residue: H 64 - end of helix Processing helix chain 'H' and resid 77 through 90 Processing helix chain 'H' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR H 99 " --> pdb=" O SER H 95 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 125 Processing helix chain 'H' and resid 125 through 133 Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 152 through 160 Processing helix chain 'H' and resid 161 through 163 No H-bonds generated for 'chain 'H' and resid 161 through 163' Processing helix chain 'H' and resid 166 through 168 No H-bonds generated for 'chain 'H' and resid 166 through 168' Processing helix chain 'H' and resid 169 through 210 removed outlier: 3.596A pdb=" N GLU H 174 " --> pdb=" O SER H 170 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N TYR H 182 " --> pdb=" O ARG H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 213 through 252 Processing helix chain 'H' and resid 257 through 267 Processing helix chain 'H' and resid 274 through 280 Processing helix chain 'H' and resid 297 through 304 Processing helix chain 'H' and resid 323 through 329 removed outlier: 3.725A pdb=" N PHE H 329 " --> pdb=" O LEU H 325 " (cutoff:3.500A) Processing helix chain 'I' and resid 52 through 76 Proline residue: I 64 - end of helix Processing helix chain 'I' and resid 77 through 90 Processing helix chain 'I' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR I 99 " --> pdb=" O SER I 95 " (cutoff:3.500A) Processing helix chain 'I' and resid 111 through 125 Processing helix chain 'I' and resid 125 through 133 Processing helix chain 'I' and resid 134 through 136 No H-bonds generated for 'chain 'I' and resid 134 through 136' Processing helix chain 'I' and resid 152 through 160 Processing helix chain 'I' and resid 161 through 163 No H-bonds generated for 'chain 'I' and resid 161 through 163' Processing helix chain 'I' and resid 166 through 168 No H-bonds generated for 'chain 'I' and resid 166 through 168' Processing helix chain 'I' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU I 174 " --> pdb=" O SER I 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR I 182 " --> pdb=" O ARG I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 213 through 252 Processing helix chain 'I' and resid 257 through 267 Processing helix chain 'I' and resid 274 through 280 Processing helix chain 'I' and resid 297 through 304 Processing helix chain 'I' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE I 329 " --> pdb=" O LEU I 325 " (cutoff:3.500A) Processing helix chain 'J' and resid 52 through 76 Proline residue: J 64 - end of helix Processing helix chain 'J' and resid 77 through 90 Processing helix chain 'J' and resid 95 through 111 removed outlier: 3.651A pdb=" N THR J 99 " --> pdb=" O SER J 95 " (cutoff:3.500A) Processing helix chain 'J' and resid 111 through 125 Processing helix chain 'J' and resid 125 through 133 Processing helix chain 'J' and resid 134 through 136 No H-bonds generated for 'chain 'J' and resid 134 through 136' Processing helix chain 'J' and resid 152 through 160 Processing helix chain 'J' and resid 161 through 163 No H-bonds generated for 'chain 'J' and resid 161 through 163' Processing helix chain 'J' and resid 166 through 168 No H-bonds generated for 'chain 'J' and resid 166 through 168' Processing helix chain 'J' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU J 174 " --> pdb=" O SER J 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR J 182 " --> pdb=" O ARG J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 213 through 252 Processing helix chain 'J' and resid 257 through 267 Processing helix chain 'J' and resid 274 through 280 Processing helix chain 'J' and resid 297 through 304 Processing helix chain 'J' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE J 329 " --> pdb=" O LEU J 325 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 76 Proline residue: K 64 - end of helix Processing helix chain 'K' and resid 77 through 90 Processing helix chain 'K' and resid 95 through 111 removed outlier: 3.650A pdb=" N THR K 99 " --> pdb=" O SER K 95 " (cutoff:3.500A) Processing helix chain 'K' and resid 111 through 125 Processing helix chain 'K' and resid 125 through 133 Processing helix chain 'K' and resid 134 through 136 No H-bonds generated for 'chain 'K' and resid 134 through 136' Processing helix chain 'K' and resid 152 through 160 Processing helix chain 'K' and resid 161 through 163 No H-bonds generated for 'chain 'K' and resid 161 through 163' Processing helix chain 'K' and resid 166 through 168 No H-bonds generated for 'chain 'K' and resid 166 through 168' Processing helix chain 'K' and resid 169 through 210 removed outlier: 3.595A pdb=" N GLU K 174 " --> pdb=" O SER K 170 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR K 182 " --> pdb=" O ARG K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 213 through 252 Processing helix chain 'K' and resid 257 through 267 Processing helix chain 'K' and resid 274 through 280 Processing helix chain 'K' and resid 297 through 304 Processing helix chain 'K' and resid 323 through 329 removed outlier: 3.726A pdb=" N PHE K 329 " --> pdb=" O LEU K 325 " (cutoff:3.500A) Processing helix chain 'M' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR M 91 " --> pdb=" O PRO M 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR N 91 " --> pdb=" O PRO N 88 " (cutoff:3.500A) Processing helix chain 'O' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR O 91 " --> pdb=" O PRO O 88 " (cutoff:3.500A) Processing helix chain 'P' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR P 91 " --> pdb=" O PRO P 88 " (cutoff:3.500A) Processing helix chain 'Q' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR Q 91 " --> pdb=" O PRO Q 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR R 91 " --> pdb=" O PRO R 88 " (cutoff:3.500A) Processing helix chain 'S' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR S 91 " --> pdb=" O PRO S 88 " (cutoff:3.500A) Processing helix chain 'T' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR T 91 " --> pdb=" O PRO T 88 " (cutoff:3.500A) Processing helix chain 'U' and resid 87 through 91 removed outlier: 3.512A pdb=" N THR U 91 " --> pdb=" O PRO U 88 " (cutoff:3.500A) Processing helix chain 'V' and resid 87 through 91 removed outlier: 3.511A pdb=" N THR V 91 " --> pdb=" O PRO V 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 289 through 290 Processing sheet with id=AA2, first strand: chain 'A' and resid 315 through 319 removed outlier: 5.117A pdb=" N ASN A 315 " --> pdb=" O GLU V 114 " (cutoff:3.500A) removed outlier: 6.698A pdb=" N GLU V 114 " --> pdb=" O ASN A 315 " (cutoff:3.500A) removed outlier: 5.323A pdb=" N GLU A 317 " --> pdb=" O TYR V 112 " (cutoff:3.500A) removed outlier: 7.348A pdb=" N TYR V 112 " --> pdb=" O GLU A 317 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'V' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP V 36 " --> pdb=" O VAL V 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA V 50 " --> pdb=" O LEU V 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU V 34 " --> pdb=" O ALA V 50 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 3 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP L 36 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA L 50 " --> pdb=" O LEU L 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU L 34 " --> pdb=" O ALA L 50 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 103 through 105 Processing sheet with id=AA7, first strand: chain 'B' and resid 289 through 290 Processing sheet with id=AA8, first strand: chain 'C' and resid 289 through 290 Processing sheet with id=AA9, first strand: chain 'C' and resid 315 through 319 removed outlier: 5.344A pdb=" N ASN C 315 " --> pdb=" O GLU M 114 " (cutoff:3.500A) removed outlier: 6.962A pdb=" N GLU M 114 " --> pdb=" O ASN C 315 " (cutoff:3.500A) removed outlier: 5.559A pdb=" N GLU C 317 " --> pdb=" O TYR M 112 " (cutoff:3.500A) removed outlier: 7.559A pdb=" N TYR M 112 " --> pdb=" O GLU C 317 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N TYR M 110 " --> pdb=" O ALA C 319 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'M' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP M 36 " --> pdb=" O VAL M 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA M 50 " --> pdb=" O LEU M 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU M 34 " --> pdb=" O ALA M 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 289 through 290 Processing sheet with id=AB3, first strand: chain 'D' and resid 315 through 319 removed outlier: 5.109A pdb=" N ASN D 315 " --> pdb=" O GLU N 114 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N GLU N 114 " --> pdb=" O ASN D 315 " (cutoff:3.500A) removed outlier: 5.151A pdb=" N GLU D 317 " --> pdb=" O TYR N 112 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N TYR N 112 " --> pdb=" O GLU D 317 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'N' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP N 36 " --> pdb=" O VAL N 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA N 50 " --> pdb=" O LEU N 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU N 34 " --> pdb=" O ALA N 50 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 289 through 290 Processing sheet with id=AB6, first strand: chain 'E' and resid 315 through 319 removed outlier: 5.671A pdb=" N TYR O 110 " --> pdb=" O MET E 318 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'O' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP O 36 " --> pdb=" O VAL O 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA O 50 " --> pdb=" O LEU O 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU O 34 " --> pdb=" O ALA O 50 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'F' and resid 289 through 290 Processing sheet with id=AB9, first strand: chain 'F' and resid 315 through 319 removed outlier: 5.675A pdb=" N TYR P 110 " --> pdb=" O MET F 318 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'P' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP P 36 " --> pdb=" O VAL P 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA P 50 " --> pdb=" O LEU P 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU P 34 " --> pdb=" O ALA P 50 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 289 through 290 Processing sheet with id=AC3, first strand: chain 'G' and resid 315 through 319 removed outlier: 5.718A pdb=" N TYR Q 110 " --> pdb=" O MET G 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'Q' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP Q 36 " --> pdb=" O VAL Q 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA Q 50 " --> pdb=" O LEU Q 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU Q 34 " --> pdb=" O ALA Q 50 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 289 through 290 Processing sheet with id=AC6, first strand: chain 'H' and resid 315 through 319 removed outlier: 5.760A pdb=" N TYR R 110 " --> pdb=" O MET H 318 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'R' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP R 36 " --> pdb=" O VAL R 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA R 50 " --> pdb=" O LEU R 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU R 34 " --> pdb=" O ALA R 50 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 289 through 290 Processing sheet with id=AC9, first strand: chain 'I' and resid 315 through 319 removed outlier: 5.780A pdb=" N TYR S 110 " --> pdb=" O MET I 318 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'S' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP S 36 " --> pdb=" O VAL S 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA S 50 " --> pdb=" O LEU S 34 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N LEU S 34 " --> pdb=" O ALA S 50 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 289 through 290 Processing sheet with id=AD3, first strand: chain 'J' and resid 315 through 319 removed outlier: 4.938A pdb=" N ASN J 315 " --> pdb=" O GLU T 114 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLU T 114 " --> pdb=" O ASN J 315 " (cutoff:3.500A) removed outlier: 5.330A pdb=" N GLU J 317 " --> pdb=" O TYR T 112 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N TYR T 112 " --> pdb=" O GLU J 317 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR T 110 " --> pdb=" O ALA J 319 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'T' and resid 58 through 60 removed outlier: 6.947A pdb=" N TRP T 36 " --> pdb=" O VAL T 48 " (cutoff:3.500A) removed outlier: 4.486A pdb=" N ALA T 50 " --> pdb=" O LEU T 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU T 34 " --> pdb=" O ALA T 50 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 289 through 290 Processing sheet with id=AD6, first strand: chain 'K' and resid 315 through 319 removed outlier: 4.865A pdb=" N ASN K 315 " --> pdb=" O GLU U 114 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N GLU U 114 " --> pdb=" O ASN K 315 " (cutoff:3.500A) removed outlier: 5.351A pdb=" N GLU K 317 " --> pdb=" O TYR U 112 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N TYR U 112 " --> pdb=" O GLU K 317 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N TYR U 110 " --> pdb=" O ALA K 319 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'U' and resid 58 through 60 removed outlier: 6.948A pdb=" N TRP U 36 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N ALA U 50 " --> pdb=" O LEU U 34 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N LEU U 34 " --> pdb=" O ALA U 50 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'M' and resid 3 through 7 Processing sheet with id=AD9, first strand: chain 'N' and resid 3 through 7 Processing sheet with id=AE1, first strand: chain 'O' and resid 3 through 7 Processing sheet with id=AE2, first strand: chain 'P' and resid 3 through 7 Processing sheet with id=AE3, first strand: chain 'Q' and resid 3 through 7 Processing sheet with id=AE4, first strand: chain 'R' and resid 3 through 7 Processing sheet with id=AE5, first strand: chain 'S' and resid 3 through 7 Processing sheet with id=AE6, first strand: chain 'T' and resid 3 through 7 Processing sheet with id=AE7, first strand: chain 'U' and resid 3 through 7 Processing sheet with id=AE8, first strand: chain 'V' and resid 3 through 7 2083 hydrogen bonds defined for protein. 6078 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.79 Time building geometry restraints manager: 5.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 6463 1.33 - 1.45: 10139 1.45 - 1.57: 20215 1.57 - 1.69: 22 1.69 - 1.81: 154 Bond restraints: 36993 Sorted by residual: bond pdb=" CB TYR R 33 " pdb=" CG TYR R 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 3.01e+00 bond pdb=" CB TYR M 33 " pdb=" CG TYR M 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.98e+00 bond pdb=" CB TYR N 33 " pdb=" CG TYR N 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.92e+00 bond pdb=" CB TYR O 33 " pdb=" CG TYR O 33 " ideal model delta sigma weight residual 1.512 1.474 0.038 2.20e-02 2.07e+03 2.91e+00 bond pdb=" CB TYR Q 33 " pdb=" CG TYR Q 33 " ideal model delta sigma weight residual 1.512 1.475 0.037 2.20e-02 2.07e+03 2.90e+00 ... (remaining 36988 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 49404 2.08 - 4.17: 723 4.17 - 6.25: 110 6.25 - 8.33: 22 8.33 - 10.42: 11 Bond angle restraints: 50270 Sorted by residual: angle pdb=" C SER N 101 " pdb=" CA SER N 101 " pdb=" CB SER N 101 " ideal model delta sigma weight residual 117.23 109.10 8.13 1.36e+00 5.41e-01 3.57e+01 angle pdb=" C SER M 101 " pdb=" CA SER M 101 " pdb=" CB SER M 101 " ideal model delta sigma weight residual 117.23 109.12 8.11 1.36e+00 5.41e-01 3.56e+01 angle pdb=" C SER U 101 " pdb=" CA SER U 101 " pdb=" CB SER U 101 " ideal model delta sigma weight residual 117.23 109.12 8.11 1.36e+00 5.41e-01 3.56e+01 angle pdb=" C SER T 101 " pdb=" CA SER T 101 " pdb=" CB SER T 101 " ideal model delta sigma weight residual 117.23 109.13 8.10 1.36e+00 5.41e-01 3.55e+01 angle pdb=" C SER V 101 " pdb=" CA SER V 101 " pdb=" CB SER V 101 " ideal model delta sigma weight residual 117.23 109.14 8.09 1.36e+00 5.41e-01 3.54e+01 ... (remaining 50265 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.20: 21406 34.20 - 68.40: 462 68.40 - 102.59: 11 102.59 - 136.79: 0 136.79 - 170.99: 44 Dihedral angle restraints: 21923 sinusoidal: 8778 harmonic: 13145 Sorted by residual: dihedral pdb=" C2' PLC I 401 " pdb=" C' PLC I 401 " pdb=" C1' PLC I 401 " pdb=" O' PLC I 401 " ideal model delta sinusoidal sigma weight residual -11.03 159.96 -170.99 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C2' PLC H 401 " pdb=" C' PLC H 401 " pdb=" C1' PLC H 401 " pdb=" O' PLC H 401 " ideal model delta sinusoidal sigma weight residual -11.03 159.95 -170.98 1 3.00e+01 1.11e-03 2.12e+01 dihedral pdb=" C2' PLC J 401 " pdb=" C' PLC J 401 " pdb=" C1' PLC J 401 " pdb=" O' PLC J 401 " ideal model delta sinusoidal sigma weight residual -11.03 159.94 -170.97 1 3.00e+01 1.11e-03 2.12e+01 ... (remaining 21920 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 3550 0.034 - 0.068: 1379 0.068 - 0.102: 348 0.102 - 0.136: 146 0.136 - 0.170: 22 Chirality restraints: 5445 Sorted by residual: chirality pdb=" CA TYR H 287 " pdb=" N TYR H 287 " pdb=" C TYR H 287 " pdb=" CB TYR H 287 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR G 287 " pdb=" N TYR G 287 " pdb=" C TYR G 287 " pdb=" CB TYR G 287 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.20e-01 chirality pdb=" CA TYR B 287 " pdb=" N TYR B 287 " pdb=" C TYR B 287 " pdb=" CB TYR B 287 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.17e-01 ... (remaining 5442 not shown) Planarity restraints: 6457 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP S 52 " -0.024 2.00e-02 2.50e+03 1.99e-02 9.86e+00 pdb=" CG TRP S 52 " 0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP S 52 " -0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP S 52 " -0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP S 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP S 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP S 52 " 0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP S 52 " -0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP S 52 " -0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP S 52 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP V 52 " 0.024 2.00e-02 2.50e+03 1.99e-02 9.86e+00 pdb=" CG TRP V 52 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP V 52 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP V 52 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP V 52 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP V 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP V 52 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP V 52 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP V 52 " 0.012 2.00e-02 2.50e+03 pdb=" CH2 TRP V 52 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP N 52 " 0.024 2.00e-02 2.50e+03 1.98e-02 9.81e+00 pdb=" CG TRP N 52 " -0.052 2.00e-02 2.50e+03 pdb=" CD1 TRP N 52 " 0.021 2.00e-02 2.50e+03 pdb=" CD2 TRP N 52 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP N 52 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP N 52 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP N 52 " -0.006 2.00e-02 2.50e+03 pdb=" CZ2 TRP N 52 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP N 52 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP N 52 " -0.002 2.00e-02 2.50e+03 ... (remaining 6454 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7903 2.79 - 3.31: 34684 3.31 - 3.84: 58911 3.84 - 4.37: 69654 4.37 - 4.90: 119145 Nonbonded interactions: 290297 Sorted by model distance: nonbonded pdb=" O LEU C 122 " pdb=" OG SER C 184 " model vdw 2.257 3.040 nonbonded pdb=" O LEU B 122 " pdb=" OG SER B 184 " model vdw 2.257 3.040 nonbonded pdb=" O LEU D 122 " pdb=" OG SER D 184 " model vdw 2.257 3.040 nonbonded pdb=" O LEU G 122 " pdb=" OG SER G 184 " model vdw 2.257 3.040 nonbonded pdb=" O LEU E 122 " pdb=" OG SER E 184 " model vdw 2.257 3.040 ... (remaining 290292 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: 0.13 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.530 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 28.770 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.090 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:1.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37026 Z= 0.148 Angle : 0.611 10.416 50336 Z= 0.337 Chirality : 0.041 0.170 5445 Planarity : 0.004 0.025 6457 Dihedral : 15.808 170.988 13398 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.45 % Allowed : 9.55 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.73 (0.13), residues: 4455 helix: 2.23 (0.11), residues: 2123 sheet: 1.03 (0.18), residues: 814 loop : -0.32 (0.17), residues: 1518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 45 TYR 0.031 0.002 TYR Q 33 PHE 0.022 0.002 PHE F 329 TRP 0.052 0.003 TRP S 52 HIS 0.005 0.001 HIS B 88 Details of bonding type rmsd covalent geometry : bond 0.00302 (36993) covalent geometry : angle 0.61119 (50270) SS BOND : bond 0.00376 ( 33) SS BOND : angle 0.37900 ( 66) hydrogen bonds : bond 0.15810 ( 2061) hydrogen bonds : angle 6.16995 ( 6078) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 384 time to evaluate : 1.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7685 (m-70) cc_final: 0.7355 (m-70) REVERT: A 172 PHE cc_start: 0.7842 (m-80) cc_final: 0.7585 (m-80) REVERT: B 155 GLU cc_start: 0.7343 (mm-30) cc_final: 0.7078 (mp0) REVERT: B 173 ARG cc_start: 0.6833 (ttt90) cc_final: 0.6449 (ttp80) REVERT: C 172 PHE cc_start: 0.7299 (m-80) cc_final: 0.7089 (m-80) REVERT: C 203 LYS cc_start: 0.8133 (tttp) cc_final: 0.7888 (tttp) REVERT: C 317 GLU cc_start: 0.8083 (mt-10) cc_final: 0.7823 (mm-30) REVERT: D 102 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7671 (mm) REVERT: D 137 ASP cc_start: 0.8007 (t0) cc_final: 0.7236 (t0) REVERT: E 152 HIS cc_start: 0.7144 (m-70) cc_final: 0.6882 (m-70) REVERT: F 100 PHE cc_start: 0.7081 (t80) cc_final: 0.6716 (t80) REVERT: H 171 ASP cc_start: 0.8359 (m-30) cc_final: 0.7890 (m-30) REVERT: H 203 LYS cc_start: 0.8249 (tttp) cc_final: 0.7937 (tttt) REVERT: H 206 LYS cc_start: 0.8413 (ttpp) cc_final: 0.8207 (tttp) REVERT: H 291 GLN cc_start: 0.8119 (mt0) cc_final: 0.7905 (mm-40) REVERT: H 318 MET cc_start: 0.8681 (ptm) cc_final: 0.8457 (mtm) REVERT: I 206 LYS cc_start: 0.8389 (ttpp) cc_final: 0.8154 (tttm) REVERT: I 260 ASP cc_start: 0.8243 (m-30) cc_final: 0.7939 (m-30) REVERT: I 317 GLU cc_start: 0.8067 (mt-10) cc_final: 0.7819 (mt-10) REVERT: J 100 PHE cc_start: 0.6897 (t80) cc_final: 0.6392 (t80) REVERT: J 102 LEU cc_start: 0.7992 (OUTLIER) cc_final: 0.7792 (mm) REVERT: J 321 LEU cc_start: 0.8597 (pp) cc_final: 0.8376 (pp) REVERT: K 102 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7463 (mm) REVERT: K 318 MET cc_start: 0.8710 (ptm) cc_final: 0.8395 (mtm) REVERT: M 95 TYR cc_start: 0.7404 (m-80) cc_final: 0.7042 (m-80) REVERT: N 32 SER cc_start: 0.6436 (m) cc_final: 0.6004 (p) REVERT: N 34 LEU cc_start: 0.7692 (mt) cc_final: 0.7490 (mm) REVERT: O 32 SER cc_start: 0.6481 (m) cc_final: 0.6162 (p) REVERT: P 32 SER cc_start: 0.6574 (m) cc_final: 0.6353 (p) REVERT: P 83 MET cc_start: 0.4448 (mmm) cc_final: 0.3010 (tmm) REVERT: Q 95 TYR cc_start: 0.7043 (m-80) cc_final: 0.6579 (m-80) REVERT: R 34 LEU cc_start: 0.8408 (mt) cc_final: 0.8143 (mm) REVERT: R 95 TYR cc_start: 0.6499 (m-80) cc_final: 0.6228 (m-80) REVERT: S 34 LEU cc_start: 0.7763 (mt) cc_final: 0.7511 (mm) REVERT: S 95 TYR cc_start: 0.7013 (m-80) cc_final: 0.6661 (m-80) REVERT: T 34 LEU cc_start: 0.8162 (mt) cc_final: 0.7945 (mm) REVERT: T 83 MET cc_start: 0.4270 (mmm) cc_final: 0.3687 (ppp) REVERT: T 95 TYR cc_start: 0.7072 (m-80) cc_final: 0.6849 (m-80) REVERT: U 34 LEU cc_start: 0.8215 (mt) cc_final: 0.7930 (mm) REVERT: U 83 MET cc_start: 0.4627 (mmm) cc_final: 0.3982 (ppp) REVERT: V 95 TYR cc_start: 0.6730 (m-80) cc_final: 0.6462 (m-80) REVERT: V 103 GLN cc_start: 0.6346 (mp10) cc_final: 0.6122 (mp10) outliers start: 17 outliers final: 2 residues processed: 394 average time/residue: 0.2220 time to fit residues: 141.5312 Evaluate side-chains 269 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 264 time to evaluate : 1.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain C residue 261 GLU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain K residue 102 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 432 optimal weight: 0.5980 chunk 197 optimal weight: 0.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 0.9990 chunk 20 optimal weight: 4.9990 chunk 132 optimal weight: 5.9990 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 40.0000 chunk 424 optimal weight: 0.0010 overall best weight: 0.7190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN A 246 ASN L 39 GLN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 246 ASN C 152 HIS C 246 ASN D 229 GLN D 246 ASN E 246 ASN F 229 GLN F 246 ASN G 246 ASN H 229 GLN H 246 ASN I 246 ASN J 246 ASN K 246 ASN M 39 GLN M 103 GLN M 113 ASN N 39 GLN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 GLN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 39 GLN P 103 GLN Q 39 GLN Q 103 GLN R 39 GLN ** R 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 39 GLN S 103 GLN T 39 GLN T 103 GLN U 39 GLN ** U 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 113 ASN V 39 GLN ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.199640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.144496 restraints weight = 46254.285| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 1.70 r_work: 0.3441 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 37026 Z= 0.124 Angle : 0.553 11.784 50336 Z= 0.279 Chirality : 0.039 0.152 5445 Planarity : 0.004 0.043 6457 Dihedral : 15.882 162.297 5424 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.26 % Allowed : 10.53 % Favored : 88.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.07 (0.13), residues: 4455 helix: 2.50 (0.11), residues: 2178 sheet: 1.14 (0.18), residues: 814 loop : -0.24 (0.17), residues: 1463 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 173 TYR 0.018 0.002 TYR S 110 PHE 0.016 0.001 PHE J 329 TRP 0.011 0.001 TRP P 116 HIS 0.005 0.001 HIS H 88 Details of bonding type rmsd covalent geometry : bond 0.00260 (36993) covalent geometry : angle 0.55268 (50270) SS BOND : bond 0.00320 ( 33) SS BOND : angle 0.43908 ( 66) hydrogen bonds : bond 0.04110 ( 2061) hydrogen bonds : angle 4.24171 ( 6078) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 312 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 265 time to evaluate : 1.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 152 HIS cc_start: 0.7397 (m-70) cc_final: 0.7136 (m-70) REVERT: A 175 GLU cc_start: 0.7917 (tp30) cc_final: 0.7593 (tt0) REVERT: A 329 PHE cc_start: 0.6079 (m-80) cc_final: 0.5632 (m-10) REVERT: B 228 ASP cc_start: 0.8008 (m-30) cc_final: 0.7728 (m-30) REVERT: B 317 GLU cc_start: 0.8457 (mt-10) cc_final: 0.8108 (mm-30) REVERT: C 317 GLU cc_start: 0.8272 (mt-10) cc_final: 0.7921 (mm-30) REVERT: C 318 MET cc_start: 0.8565 (ptp) cc_final: 0.8237 (ptp) REVERT: D 102 LEU cc_start: 0.7816 (OUTLIER) cc_final: 0.7399 (mm) REVERT: D 137 ASP cc_start: 0.8152 (t0) cc_final: 0.7393 (t0) REVERT: E 102 LEU cc_start: 0.7527 (OUTLIER) cc_final: 0.7153 (mm) REVERT: F 100 PHE cc_start: 0.7179 (t80) cc_final: 0.6879 (t80) REVERT: G 102 LEU cc_start: 0.8092 (OUTLIER) cc_final: 0.7738 (mm) REVERT: H 203 LYS cc_start: 0.8274 (tttp) cc_final: 0.7796 (mtpt) REVERT: H 291 GLN cc_start: 0.8467 (mt0) cc_final: 0.8192 (mm-40) REVERT: I 206 LYS cc_start: 0.8325 (ttpp) cc_final: 0.8064 (tttm) REVERT: I 317 GLU cc_start: 0.8362 (mt-10) cc_final: 0.8102 (mt-10) REVERT: I 321 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8558 (pp) REVERT: J 100 PHE cc_start: 0.7048 (t80) cc_final: 0.6571 (t80) REVERT: J 102 LEU cc_start: 0.7685 (OUTLIER) cc_final: 0.7367 (mm) REVERT: J 318 MET cc_start: 0.8617 (ptp) cc_final: 0.8338 (mtm) REVERT: J 321 LEU cc_start: 0.8690 (OUTLIER) cc_final: 0.8288 (pp) REVERT: K 102 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7340 (mm) REVERT: K 228 ASP cc_start: 0.8272 (m-30) cc_final: 0.8070 (m-30) REVERT: K 291 GLN cc_start: 0.8185 (mt0) cc_final: 0.7976 (mt0) REVERT: K 318 MET cc_start: 0.8459 (ptm) cc_final: 0.8136 (mtm) REVERT: K 321 LEU cc_start: 0.8804 (OUTLIER) cc_final: 0.8460 (pp) REVERT: M 46 GLU cc_start: 0.6788 (pm20) cc_final: 0.6556 (pm20) REVERT: M 95 TYR cc_start: 0.7285 (m-80) cc_final: 0.6845 (m-80) REVERT: N 83 MET cc_start: 0.4792 (mmm) cc_final: 0.2959 (tmm) REVERT: P 83 MET cc_start: 0.4903 (mmm) cc_final: 0.3415 (tmm) REVERT: Q 95 TYR cc_start: 0.7144 (m-80) cc_final: 0.6731 (m-80) REVERT: R 32 SER cc_start: 0.6993 (m) cc_final: 0.6719 (p) REVERT: R 95 TYR cc_start: 0.6525 (m-80) cc_final: 0.6290 (m-80) REVERT: S 34 LEU cc_start: 0.7597 (mt) cc_final: 0.7336 (mm) REVERT: S 83 MET cc_start: 0.4121 (OUTLIER) cc_final: 0.3915 (tmm) REVERT: S 95 TYR cc_start: 0.7208 (m-80) cc_final: 0.6384 (m-80) REVERT: T 83 MET cc_start: 0.4777 (mmm) cc_final: 0.3910 (ppp) REVERT: U 83 MET cc_start: 0.4959 (mmm) cc_final: 0.4235 (ppp) REVERT: U 101 SER cc_start: 0.7191 (t) cc_final: 0.6850 (t) REVERT: V 46 GLU cc_start: 0.8026 (tp30) cc_final: 0.7055 (pm20) REVERT: V 95 TYR cc_start: 0.6549 (m-80) cc_final: 0.6342 (m-80) outliers start: 47 outliers final: 21 residues processed: 296 average time/residue: 0.2184 time to fit residues: 106.4843 Evaluate side-chains 268 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 238 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 288 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain S residue 83 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 27 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 386 optimal weight: 5.9990 chunk 406 optimal weight: 40.0000 chunk 195 optimal weight: 2.9990 chunk 326 optimal weight: 0.9980 chunk 95 optimal weight: 4.9990 chunk 107 optimal weight: 9.9990 chunk 285 optimal weight: 0.7980 chunk 257 optimal weight: 3.9990 chunk 247 optimal weight: 9.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 290 ASN H 229 GLN M 103 GLN N 103 GLN ** O 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 103 GLN R 103 GLN T 103 GLN U 103 GLN V 103 GLN V 113 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4317 r_free = 0.4317 target = 0.194320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.137463 restraints weight = 45816.109| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 1.75 r_work: 0.3330 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.3204 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.1777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 37026 Z= 0.222 Angle : 0.636 16.691 50336 Z= 0.315 Chirality : 0.044 0.193 5445 Planarity : 0.005 0.052 6457 Dihedral : 15.774 169.030 5418 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 7.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 2.30 % Allowed : 10.91 % Favored : 86.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.67 (0.13), residues: 4455 helix: 2.13 (0.11), residues: 2167 sheet: 0.96 (0.18), residues: 836 loop : -0.36 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 288 TYR 0.033 0.002 TYR F 54 PHE 0.023 0.002 PHE K 329 TRP 0.025 0.002 TRP Q 52 HIS 0.008 0.002 HIS D 88 Details of bonding type rmsd covalent geometry : bond 0.00533 (36993) covalent geometry : angle 0.63556 (50270) SS BOND : bond 0.00428 ( 33) SS BOND : angle 0.61745 ( 66) hydrogen bonds : bond 0.04997 ( 2061) hydrogen bonds : angle 4.19955 ( 6078) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 237 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 175 GLU cc_start: 0.7890 (tp30) cc_final: 0.7589 (tm-30) REVERT: L 81 LEU cc_start: 0.5377 (OUTLIER) cc_final: 0.4732 (tp) REVERT: B 228 ASP cc_start: 0.8025 (m-30) cc_final: 0.7823 (m-30) REVERT: C 286 LEU cc_start: 0.8409 (OUTLIER) cc_final: 0.7928 (mt) REVERT: D 100 PHE cc_start: 0.7362 (t80) cc_final: 0.6992 (t80) REVERT: D 102 LEU cc_start: 0.7874 (OUTLIER) cc_final: 0.7368 (mm) REVERT: D 109 ARG cc_start: 0.7761 (ttt-90) cc_final: 0.7060 (ttt-90) REVERT: E 102 LEU cc_start: 0.7578 (OUTLIER) cc_final: 0.7133 (mm) REVERT: F 100 PHE cc_start: 0.7237 (t80) cc_final: 0.6940 (t80) REVERT: F 286 LEU cc_start: 0.8492 (OUTLIER) cc_final: 0.8141 (mt) REVERT: G 102 LEU cc_start: 0.8102 (OUTLIER) cc_final: 0.7665 (mm) REVERT: G 318 MET cc_start: 0.8736 (OUTLIER) cc_final: 0.8497 (mtm) REVERT: H 228 ASP cc_start: 0.8301 (m-30) cc_final: 0.8046 (m-30) REVERT: H 291 GLN cc_start: 0.8554 (mt0) cc_final: 0.8281 (mm-40) REVERT: I 102 LEU cc_start: 0.7736 (mm) cc_final: 0.7533 (mm) REVERT: I 206 LYS cc_start: 0.8476 (ttpp) cc_final: 0.8136 (tttm) REVERT: I 321 LEU cc_start: 0.8830 (OUTLIER) cc_final: 0.8131 (pp) REVERT: J 100 PHE cc_start: 0.7118 (t80) cc_final: 0.6620 (t80) REVERT: J 102 LEU cc_start: 0.7734 (OUTLIER) cc_final: 0.7331 (mm) REVERT: J 321 LEU cc_start: 0.8805 (OUTLIER) cc_final: 0.8347 (pp) REVERT: K 102 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7334 (mm) REVERT: K 291 GLN cc_start: 0.8275 (mt0) cc_final: 0.7986 (mt0) REVERT: K 321 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8504 (pp) REVERT: K 329 PHE cc_start: 0.5993 (m-80) cc_final: 0.5738 (m-80) REVERT: M 46 GLU cc_start: 0.6862 (pm20) cc_final: 0.6541 (pm20) REVERT: M 95 TYR cc_start: 0.7345 (m-80) cc_final: 0.6792 (m-80) REVERT: O 108 ARG cc_start: 0.8533 (mmt180) cc_final: 0.8282 (mpt180) REVERT: Q 95 TYR cc_start: 0.7454 (m-80) cc_final: 0.7151 (m-80) REVERT: R 32 SER cc_start: 0.7122 (m) cc_final: 0.6907 (p) REVERT: R 46 GLU cc_start: 0.8299 (tp30) cc_final: 0.7069 (pm20) REVERT: R 95 TYR cc_start: 0.6695 (m-80) cc_final: 0.6488 (m-80) REVERT: S 34 LEU cc_start: 0.7904 (mt) cc_final: 0.7600 (mm) REVERT: S 83 MET cc_start: 0.4660 (mtp) cc_final: 0.4127 (tmm) REVERT: T 83 MET cc_start: 0.4508 (mmm) cc_final: 0.3538 (ppp) REVERT: U 83 MET cc_start: 0.5081 (mmm) cc_final: 0.4287 (ppp) REVERT: V 46 GLU cc_start: 0.8055 (tp30) cc_final: 0.7115 (pm20) outliers start: 86 outliers final: 51 residues processed: 316 average time/residue: 0.2079 time to fit residues: 107.7397 Evaluate side-chains 272 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 209 time to evaluate : 1.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 112 VAL Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 318 MET Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 102 LEU Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 79 THR Chi-restraints excluded: chain K residue 102 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain V residue 32 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 4 optimal weight: 1.9990 chunk 439 optimal weight: 6.9990 chunk 97 optimal weight: 2.9990 chunk 288 optimal weight: 0.9980 chunk 299 optimal weight: 0.7980 chunk 263 optimal weight: 2.9990 chunk 59 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 218 optimal weight: 9.9990 chunk 37 optimal weight: 30.0000 chunk 267 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN ** L 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 229 GLN F 229 GLN M 103 GLN ** N 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 103 GLN ** P 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 103 GLN T 103 GLN U 113 ASN ** V 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.194254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.121398 restraints weight = 45652.876| |-----------------------------------------------------------------------------| r_work (start): 0.3419 rms_B_bonded: 2.42 r_work: 0.3270 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3131 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 37026 Z= 0.120 Angle : 0.545 15.199 50336 Z= 0.270 Chirality : 0.039 0.150 5445 Planarity : 0.004 0.046 6457 Dihedral : 15.333 171.022 5418 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 1.90 % Allowed : 11.68 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.00 (0.13), residues: 4455 helix: 2.45 (0.11), residues: 2200 sheet: 1.03 (0.18), residues: 836 loop : -0.30 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 173 TYR 0.022 0.002 TYR L 110 PHE 0.018 0.001 PHE J 329 TRP 0.016 0.001 TRP P 52 HIS 0.004 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00267 (36993) covalent geometry : angle 0.54493 (50270) SS BOND : bond 0.00263 ( 33) SS BOND : angle 0.37539 ( 66) hydrogen bonds : bond 0.03897 ( 2061) hydrogen bonds : angle 3.96426 ( 6078) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 223 time to evaluate : 1.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 228 ASP cc_start: 0.8186 (m-30) cc_final: 0.7971 (m-30) REVERT: D 100 PHE cc_start: 0.7258 (t80) cc_final: 0.6879 (t80) REVERT: D 109 ARG cc_start: 0.7917 (ttt-90) cc_final: 0.7154 (ttt-90) REVERT: D 206 LYS cc_start: 0.8403 (ttpp) cc_final: 0.8170 (tttm) REVERT: E 49 SER cc_start: 0.9172 (m) cc_final: 0.8815 (t) REVERT: E 102 LEU cc_start: 0.7350 (OUTLIER) cc_final: 0.6973 (mm) REVERT: E 124 ARG cc_start: 0.8331 (mtt90) cc_final: 0.8065 (mtt-85) REVERT: E 160 PHE cc_start: 0.8139 (OUTLIER) cc_final: 0.7864 (m-10) REVERT: E 175 GLU cc_start: 0.7678 (tp30) cc_final: 0.7388 (tt0) REVERT: E 286 LEU cc_start: 0.8363 (OUTLIER) cc_final: 0.8091 (mp) REVERT: F 100 PHE cc_start: 0.7099 (t80) cc_final: 0.6829 (t80) REVERT: G 102 LEU cc_start: 0.8000 (OUTLIER) cc_final: 0.7649 (mm) REVERT: G 160 PHE cc_start: 0.8199 (OUTLIER) cc_final: 0.7704 (m-80) REVERT: G 233 ARG cc_start: 0.8831 (tpt170) cc_final: 0.8623 (tpt170) REVERT: H 228 ASP cc_start: 0.8355 (m-30) cc_final: 0.8123 (m-30) REVERT: H 291 GLN cc_start: 0.8603 (mt0) cc_final: 0.8277 (mm-40) REVERT: I 175 GLU cc_start: 0.7753 (tp30) cc_final: 0.7391 (tt0) REVERT: I 206 LYS cc_start: 0.8543 (ttpp) cc_final: 0.8313 (ttpt) REVERT: I 321 LEU cc_start: 0.8767 (OUTLIER) cc_final: 0.7942 (pp) REVERT: J 100 PHE cc_start: 0.7016 (t80) cc_final: 0.6548 (t80) REVERT: J 321 LEU cc_start: 0.8626 (OUTLIER) cc_final: 0.8221 (pp) REVERT: K 291 GLN cc_start: 0.8472 (mt0) cc_final: 0.8224 (mt0) REVERT: K 321 LEU cc_start: 0.8736 (OUTLIER) cc_final: 0.8412 (pp) REVERT: M 46 GLU cc_start: 0.6848 (pm20) cc_final: 0.6532 (pm20) REVERT: M 95 TYR cc_start: 0.7198 (m-80) cc_final: 0.6701 (m-80) REVERT: N 105 ASN cc_start: 0.7824 (p0) cc_final: 0.7525 (p0) REVERT: P 83 MET cc_start: 0.4722 (mmm) cc_final: 0.3323 (tmm) REVERT: Q 81 LEU cc_start: 0.6515 (OUTLIER) cc_final: 0.6277 (tp) REVERT: Q 95 TYR cc_start: 0.7359 (m-80) cc_final: 0.7092 (m-80) REVERT: R 95 TYR cc_start: 0.6616 (m-80) cc_final: 0.6380 (m-80) REVERT: S 34 LEU cc_start: 0.7924 (mt) cc_final: 0.7587 (mm) REVERT: S 83 MET cc_start: 0.4798 (mtp) cc_final: 0.4014 (tmm) REVERT: T 83 MET cc_start: 0.4720 (mmm) cc_final: 0.3661 (ppp) REVERT: U 83 MET cc_start: 0.5210 (mmm) cc_final: 0.4323 (ppp) REVERT: V 46 GLU cc_start: 0.8185 (tp30) cc_final: 0.7074 (pm20) REVERT: V 81 LEU cc_start: 0.6437 (OUTLIER) cc_final: 0.5975 (tp) outliers start: 71 outliers final: 48 residues processed: 281 average time/residue: 0.2318 time to fit residues: 105.0033 Evaluate side-chains 265 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 207 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 262 GLU Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 229 GLN Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 111 optimal weight: 1.9990 chunk 198 optimal weight: 3.9990 chunk 301 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 310 optimal weight: 1.9990 chunk 102 optimal weight: 0.7980 chunk 339 optimal weight: 20.0000 chunk 132 optimal weight: 4.9990 chunk 297 optimal weight: 6.9990 chunk 151 optimal weight: 2.9990 chunk 175 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 229 GLN ** M 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 103 GLN P 103 GLN Q 103 GLN ** T 103 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.193555 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.125719 restraints weight = 45249.165| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 2.25 r_work: 0.3246 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 37026 Z= 0.180 Angle : 0.588 16.662 50336 Z= 0.290 Chirality : 0.041 0.178 5445 Planarity : 0.004 0.053 6457 Dihedral : 14.952 173.862 5412 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 7.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.05 % Allowed : 10.94 % Favored : 86.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 1.87 (0.13), residues: 4455 helix: 2.32 (0.11), residues: 2189 sheet: 1.10 (0.19), residues: 836 loop : -0.38 (0.17), residues: 1430 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 288 TYR 0.026 0.002 TYR F 54 PHE 0.019 0.001 PHE J 329 TRP 0.020 0.002 TRP S 52 HIS 0.006 0.001 HIS C 88 Details of bonding type rmsd covalent geometry : bond 0.00432 (36993) covalent geometry : angle 0.58810 (50270) SS BOND : bond 0.00351 ( 33) SS BOND : angle 0.53503 ( 66) hydrogen bonds : bond 0.04436 ( 2061) hydrogen bonds : angle 3.99919 ( 6078) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 215 time to evaluate : 1.165 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: L 81 LEU cc_start: 0.5413 (OUTLIER) cc_final: 0.4765 (tp) REVERT: B 228 ASP cc_start: 0.8193 (m-30) cc_final: 0.7989 (m-30) REVERT: C 286 LEU cc_start: 0.8367 (OUTLIER) cc_final: 0.7814 (mt) REVERT: D 100 PHE cc_start: 0.7303 (t80) cc_final: 0.6927 (t80) REVERT: D 109 ARG cc_start: 0.7840 (ttt-90) cc_final: 0.7210 (ttt-90) REVERT: E 102 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7109 (mm) REVERT: E 160 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7986 (m-10) REVERT: E 175 GLU cc_start: 0.7702 (tp30) cc_final: 0.7424 (tt0) REVERT: E 286 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.8129 (mp) REVERT: F 100 PHE cc_start: 0.7201 (t80) cc_final: 0.6925 (t80) REVERT: F 286 LEU cc_start: 0.8387 (OUTLIER) cc_final: 0.8065 (mt) REVERT: G 102 LEU cc_start: 0.8063 (OUTLIER) cc_final: 0.7680 (mm) REVERT: G 160 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7803 (m-80) REVERT: G 229 GLN cc_start: 0.8903 (tt0) cc_final: 0.8702 (tt0) REVERT: H 228 ASP cc_start: 0.8383 (m-30) cc_final: 0.8158 (m-30) REVERT: H 291 GLN cc_start: 0.8418 (mt0) cc_final: 0.8128 (mm-40) REVERT: I 175 GLU cc_start: 0.7762 (tp30) cc_final: 0.7446 (tt0) REVERT: I 206 LYS cc_start: 0.8604 (ttpp) cc_final: 0.8328 (ttpt) REVERT: I 321 LEU cc_start: 0.8781 (OUTLIER) cc_final: 0.8087 (pp) REVERT: J 100 PHE cc_start: 0.7081 (t80) cc_final: 0.6576 (t80) REVERT: J 129 VAL cc_start: 0.8770 (m) cc_final: 0.8554 (t) REVERT: J 321 LEU cc_start: 0.8715 (OUTLIER) cc_final: 0.8303 (pp) REVERT: K 291 GLN cc_start: 0.8437 (mt0) cc_final: 0.8082 (mm-40) REVERT: K 321 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8456 (pp) REVERT: M 34 LEU cc_start: 0.7950 (mt) cc_final: 0.7732 (mm) REVERT: M 46 GLU cc_start: 0.6990 (pm20) cc_final: 0.6662 (pm20) REVERT: M 95 TYR cc_start: 0.7274 (m-80) cc_final: 0.6406 (m-80) REVERT: N 105 ASN cc_start: 0.7955 (p0) cc_final: 0.7659 (p0) REVERT: P 83 MET cc_start: 0.4850 (mmm) cc_final: 0.3301 (tmm) REVERT: Q 81 LEU cc_start: 0.6511 (OUTLIER) cc_final: 0.6258 (tp) REVERT: Q 95 TYR cc_start: 0.7502 (m-80) cc_final: 0.7272 (m-80) REVERT: R 46 GLU cc_start: 0.8381 (tp30) cc_final: 0.7090 (pm20) REVERT: S 34 LEU cc_start: 0.8222 (mt) cc_final: 0.7893 (mm) REVERT: S 83 MET cc_start: 0.4579 (mtp) cc_final: 0.3879 (tmm) REVERT: T 83 MET cc_start: 0.4707 (mmm) cc_final: 0.3760 (ppp) REVERT: U 81 LEU cc_start: 0.6914 (OUTLIER) cc_final: 0.5904 (mt) REVERT: V 46 GLU cc_start: 0.8291 (tp30) cc_final: 0.7083 (pm20) REVERT: V 81 LEU cc_start: 0.6257 (OUTLIER) cc_final: 0.5773 (tp) outliers start: 114 outliers final: 65 residues processed: 318 average time/residue: 0.2272 time to fit residues: 117.5281 Evaluate side-chains 282 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 203 time to evaluate : 1.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 81 LEU Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 264 ILE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 112 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 229 GLN Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 301 LYS Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain Q residue 71 SER Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain U residue 81 LEU Chi-restraints excluded: chain V residue 81 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 6 optimal weight: 4.9990 chunk 150 optimal weight: 0.9980 chunk 206 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 309 optimal weight: 0.8980 chunk 182 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 79 optimal weight: 0.0970 chunk 142 optimal weight: 2.9990 chunk 277 optimal weight: 10.0000 chunk 98 optimal weight: 0.6980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN E 229 GLN ** T 103 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 = 0.4334 r_free = 0.4334 target = 0.196087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.141717 restraints weight = 45937.221| |-----------------------------------------------------------------------------| r_work (start): 0.3707 rms_B_bonded: 1.79 r_work: 0.3378 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3244 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3244 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 37026 Z= 0.115 Angle : 0.538 14.607 50336 Z= 0.266 Chirality : 0.038 0.147 5445 Planarity : 0.003 0.049 6457 Dihedral : 14.363 170.083 5412 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.49 % Allowed : 11.28 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.15 (0.13), residues: 4455 helix: 2.60 (0.11), residues: 2200 sheet: 1.16 (0.19), residues: 836 loop : -0.32 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 240 TYR 0.017 0.001 TYR C 54 PHE 0.017 0.001 PHE A 329 TRP 0.019 0.001 TRP V 52 HIS 0.003 0.001 HIS J 238 Details of bonding type rmsd covalent geometry : bond 0.00255 (36993) covalent geometry : angle 0.53840 (50270) SS BOND : bond 0.00241 ( 33) SS BOND : angle 0.39427 ( 66) hydrogen bonds : bond 0.03787 ( 2061) hydrogen bonds : angle 3.87531 ( 6078) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 299 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 206 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.8649 (mt) cc_final: 0.8371 (mt) REVERT: L 95 TYR cc_start: 0.6912 (m-80) cc_final: 0.6297 (m-80) REVERT: B 175 GLU cc_start: 0.8056 (OUTLIER) cc_final: 0.7744 (tt0) REVERT: B 228 ASP cc_start: 0.8074 (m-30) cc_final: 0.7857 (m-30) REVERT: C 291 GLN cc_start: 0.8585 (mt0) cc_final: 0.8320 (mm-40) REVERT: D 100 PHE cc_start: 0.7404 (t80) cc_final: 0.7063 (t80) REVERT: D 109 ARG cc_start: 0.7746 (ttt-90) cc_final: 0.7071 (ttt-90) REVERT: D 263 LEU cc_start: 0.8284 (OUTLIER) cc_final: 0.7576 (mt) REVERT: E 102 LEU cc_start: 0.7460 (OUTLIER) cc_final: 0.7118 (mm) REVERT: E 160 PHE cc_start: 0.8167 (OUTLIER) cc_final: 0.7879 (m-10) REVERT: E 286 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.8083 (mp) REVERT: F 100 PHE cc_start: 0.7225 (t80) cc_final: 0.6956 (t80) REVERT: F 175 GLU cc_start: 0.7858 (tp30) cc_final: 0.7597 (tt0) REVERT: F 286 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7911 (mt) REVERT: G 102 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7761 (mm) REVERT: G 160 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7757 (m-80) REVERT: G 229 GLN cc_start: 0.8780 (tt0) cc_final: 0.8579 (tt0) REVERT: H 291 GLN cc_start: 0.8575 (mt0) cc_final: 0.8331 (mm-40) REVERT: I 175 GLU cc_start: 0.7748 (tp30) cc_final: 0.7462 (tt0) REVERT: I 206 LYS cc_start: 0.8644 (ttpp) cc_final: 0.8361 (ttpt) REVERT: I 321 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.7949 (pp) REVERT: J 100 PHE cc_start: 0.7161 (t80) cc_final: 0.6676 (t80) REVERT: J 129 VAL cc_start: 0.8741 (m) cc_final: 0.8527 (t) REVERT: J 175 GLU cc_start: 0.7607 (tp30) cc_final: 0.7369 (tt0) REVERT: J 321 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8274 (pp) REVERT: K 321 LEU cc_start: 0.8790 (OUTLIER) cc_final: 0.8464 (pp) REVERT: M 34 LEU cc_start: 0.7774 (mt) cc_final: 0.7562 (mm) REVERT: M 46 GLU cc_start: 0.7099 (pm20) cc_final: 0.6772 (pm20) REVERT: M 95 TYR cc_start: 0.7272 (m-80) cc_final: 0.7005 (m-80) REVERT: N 100 THR cc_start: 0.7673 (OUTLIER) cc_final: 0.7205 (t) REVERT: P 83 MET cc_start: 0.4777 (mmm) cc_final: 0.3275 (tmm) REVERT: P 100 THR cc_start: 0.7287 (OUTLIER) cc_final: 0.6927 (t) REVERT: Q 81 LEU cc_start: 0.6565 (OUTLIER) cc_final: 0.6256 (tp) REVERT: Q 95 TYR cc_start: 0.7498 (m-80) cc_final: 0.7260 (m-80) REVERT: R 83 MET cc_start: 0.5636 (mpp) cc_final: 0.4074 (tmm) REVERT: S 34 LEU cc_start: 0.8240 (mt) cc_final: 0.7945 (mm) REVERT: S 83 MET cc_start: 0.4747 (mtp) cc_final: 0.4196 (tmm) REVERT: T 46 GLU cc_start: 0.8485 (tp30) cc_final: 0.8147 (tp30) REVERT: T 83 MET cc_start: 0.4474 (mmm) cc_final: 0.3673 (ppp) REVERT: U 83 MET cc_start: 0.4963 (mmm) cc_final: 0.3838 (ppp) REVERT: V 46 GLU cc_start: 0.8255 (tp30) cc_final: 0.7138 (pm20) REVERT: V 81 LEU cc_start: 0.6463 (OUTLIER) cc_final: 0.5915 (tp) outliers start: 93 outliers final: 66 residues processed: 284 average time/residue: 0.2492 time to fit residues: 113.5274 Evaluate side-chains 279 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 198 time to evaluate : 1.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 68 PHE Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 261 GLU Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 317 GLU Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 81 LEU Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 81 LEU Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 421 optimal weight: 10.0000 chunk 342 optimal weight: 7.9990 chunk 156 optimal weight: 3.9990 chunk 168 optimal weight: 6.9990 chunk 65 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 414 optimal weight: 0.0050 chunk 125 optimal weight: 3.9990 chunk 312 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 417 optimal weight: 2.9990 overall best weight: 1.7800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 229 GLN J 315 ASN T 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.194848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.140026 restraints weight = 46068.538| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.80 r_work: 0.3352 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 37026 Z= 0.155 Angle : 0.565 15.906 50336 Z= 0.279 Chirality : 0.040 0.167 5445 Planarity : 0.004 0.045 6457 Dihedral : 13.851 175.888 5412 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 2.81 % Allowed : 11.31 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.07 (0.13), residues: 4455 helix: 2.52 (0.11), residues: 2200 sheet: 1.18 (0.19), residues: 836 loop : -0.35 (0.17), residues: 1419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 298 TYR 0.022 0.002 TYR F 54 PHE 0.019 0.001 PHE J 329 TRP 0.020 0.002 TRP V 52 HIS 0.004 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00367 (36993) covalent geometry : angle 0.56548 (50270) SS BOND : bond 0.00320 ( 33) SS BOND : angle 0.48462 ( 66) hydrogen bonds : bond 0.04122 ( 2061) hydrogen bonds : angle 3.90050 ( 6078) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 209 time to evaluate : 1.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 201 LEU cc_start: 0.8659 (mt) cc_final: 0.8369 (mt) REVERT: L 95 TYR cc_start: 0.7096 (m-80) cc_final: 0.6523 (m-80) REVERT: B 175 GLU cc_start: 0.8066 (OUTLIER) cc_final: 0.7720 (tt0) REVERT: B 228 ASP cc_start: 0.8093 (m-30) cc_final: 0.7874 (m-30) REVERT: C 286 LEU cc_start: 0.8299 (OUTLIER) cc_final: 0.7724 (mp) REVERT: C 291 GLN cc_start: 0.8625 (mt0) cc_final: 0.8322 (mm-40) REVERT: D 100 PHE cc_start: 0.7492 (t80) cc_final: 0.7127 (t80) REVERT: D 109 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7119 (ttt-90) REVERT: D 263 LEU cc_start: 0.8394 (OUTLIER) cc_final: 0.7685 (mt) REVERT: E 102 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.7138 (mm) REVERT: E 160 PHE cc_start: 0.8232 (OUTLIER) cc_final: 0.8009 (m-10) REVERT: E 286 LEU cc_start: 0.8434 (OUTLIER) cc_final: 0.8160 (mp) REVERT: F 100 PHE cc_start: 0.7253 (t80) cc_final: 0.6997 (t80) REVERT: F 175 GLU cc_start: 0.7879 (tp30) cc_final: 0.7625 (tt0) REVERT: F 286 LEU cc_start: 0.8354 (OUTLIER) cc_final: 0.8015 (mt) REVERT: G 102 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7764 (mm) REVERT: G 160 PHE cc_start: 0.8341 (OUTLIER) cc_final: 0.7874 (m-80) REVERT: G 298 ARG cc_start: 0.8903 (OUTLIER) cc_final: 0.8517 (ptp-170) REVERT: H 291 GLN cc_start: 0.8405 (mt0) cc_final: 0.8171 (mm-40) REVERT: I 102 LEU cc_start: 0.7861 (OUTLIER) cc_final: 0.7474 (mm) REVERT: I 175 GLU cc_start: 0.7775 (tp30) cc_final: 0.7491 (tt0) REVERT: I 206 LYS cc_start: 0.8653 (ttpp) cc_final: 0.8371 (ttpt) REVERT: I 321 LEU cc_start: 0.8803 (OUTLIER) cc_final: 0.7985 (pp) REVERT: J 100 PHE cc_start: 0.7188 (t80) cc_final: 0.6682 (t80) REVERT: J 129 VAL cc_start: 0.8772 (m) cc_final: 0.8551 (t) REVERT: J 291 GLN cc_start: 0.8759 (mt0) cc_final: 0.8513 (mm-40) REVERT: J 321 LEU cc_start: 0.8706 (OUTLIER) cc_final: 0.8309 (pp) REVERT: K 291 GLN cc_start: 0.8455 (mt0) cc_final: 0.8225 (mm-40) REVERT: K 321 LEU cc_start: 0.8838 (OUTLIER) cc_final: 0.8504 (pp) REVERT: M 46 GLU cc_start: 0.7021 (pm20) cc_final: 0.6680 (pm20) REVERT: M 95 TYR cc_start: 0.7373 (m-80) cc_final: 0.7013 (m-80) REVERT: N 83 MET cc_start: 0.4552 (mmm) cc_final: 0.2826 (tmm) REVERT: P 83 MET cc_start: 0.4946 (mmm) cc_final: 0.3390 (tmm) REVERT: P 100 THR cc_start: 0.7604 (OUTLIER) cc_final: 0.7209 (t) REVERT: Q 95 TYR cc_start: 0.7491 (m-80) cc_final: 0.7252 (m-80) REVERT: R 46 GLU cc_start: 0.8300 (tp30) cc_final: 0.7152 (pm20) REVERT: R 83 MET cc_start: 0.5658 (mpp) cc_final: 0.4088 (tmm) REVERT: S 34 LEU cc_start: 0.8267 (mt) cc_final: 0.7960 (mm) REVERT: S 83 MET cc_start: 0.4590 (mtp) cc_final: 0.4096 (tmm) REVERT: T 83 MET cc_start: 0.4478 (mmm) cc_final: 0.3688 (ppp) REVERT: V 46 GLU cc_start: 0.8254 (tp30) cc_final: 0.7148 (pm20) REVERT: V 81 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.5923 (tp) outliers start: 105 outliers final: 74 residues processed: 299 average time/residue: 0.2481 time to fit residues: 119.5517 Evaluate side-chains 295 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 205 time to evaluate : 1.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 264 ILE Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 68 PHE Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 263 LEU Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 139 SER Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 318 MET Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 71 SER Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 81 LEU Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 25 SER Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 80 optimal weight: 0.0470 chunk 302 optimal weight: 0.8980 chunk 239 optimal weight: 1.9990 chunk 187 optimal weight: 0.9990 chunk 143 optimal weight: 0.5980 chunk 155 optimal weight: 3.9990 chunk 411 optimal weight: 5.9990 chunk 194 optimal weight: 0.8980 chunk 37 optimal weight: 10.0000 chunk 301 optimal weight: 0.9980 chunk 74 optimal weight: 2.9990 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN ** E 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 76 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.197234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.143955 restraints weight = 46204.708| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 1.80 r_work: 0.3403 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3270 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 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 : 0.002 0.027 37026 Z= 0.103 Angle : 0.517 13.634 50336 Z= 0.256 Chirality : 0.038 0.135 5445 Planarity : 0.003 0.039 6457 Dihedral : 12.876 164.568 5412 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 2.49 % Allowed : 11.74 % Favored : 85.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.41 (0.13), residues: 4455 helix: 2.85 (0.11), residues: 2200 sheet: 1.49 (0.19), residues: 814 loop : -0.37 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 240 TYR 0.015 0.001 TYR G 287 PHE 0.015 0.001 PHE J 329 TRP 0.019 0.001 TRP L 52 HIS 0.003 0.001 HIS E 238 Details of bonding type rmsd covalent geometry : bond 0.00221 (36993) covalent geometry : angle 0.51692 (50270) SS BOND : bond 0.00237 ( 33) SS BOND : angle 0.42963 ( 66) hydrogen bonds : bond 0.03463 ( 2061) hydrogen bonds : angle 3.77624 ( 6078) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 223 time to evaluate : 1.419 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7141 (t80) cc_final: 0.6613 (m-80) REVERT: A 201 LEU cc_start: 0.8654 (mt) cc_final: 0.8374 (mt) REVERT: L 37 PHE cc_start: 0.7670 (m-80) cc_final: 0.7146 (m-80) REVERT: L 95 TYR cc_start: 0.7028 (m-80) cc_final: 0.6412 (m-80) REVERT: L 100 THR cc_start: 0.7393 (OUTLIER) cc_final: 0.7093 (t) REVERT: B 175 GLU cc_start: 0.7974 (tp30) cc_final: 0.7606 (tt0) REVERT: B 228 ASP cc_start: 0.8039 (m-30) cc_final: 0.7818 (m-30) REVERT: C 291 GLN cc_start: 0.8586 (mt0) cc_final: 0.8338 (mm-40) REVERT: D 81 ASN cc_start: 0.8024 (p0) cc_final: 0.7766 (p0) REVERT: D 100 PHE cc_start: 0.7281 (t80) cc_final: 0.6926 (t80) REVERT: D 109 ARG cc_start: 0.7712 (ttt-90) cc_final: 0.7029 (ttt-90) REVERT: D 263 LEU cc_start: 0.8202 (OUTLIER) cc_final: 0.7520 (mt) REVERT: E 102 LEU cc_start: 0.7428 (OUTLIER) cc_final: 0.7102 (mm) REVERT: E 160 PHE cc_start: 0.8037 (OUTLIER) cc_final: 0.7824 (m-10) REVERT: E 286 LEU cc_start: 0.8320 (OUTLIER) cc_final: 0.8056 (mp) REVERT: F 100 PHE cc_start: 0.7182 (t80) cc_final: 0.6950 (t80) REVERT: F 175 GLU cc_start: 0.7892 (tp30) cc_final: 0.7615 (tt0) REVERT: G 102 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7748 (mm) REVERT: G 160 PHE cc_start: 0.8201 (OUTLIER) cc_final: 0.7660 (m-80) REVERT: G 298 ARG cc_start: 0.8871 (OUTLIER) cc_final: 0.8299 (ptp-170) REVERT: H 291 GLN cc_start: 0.8580 (mt0) cc_final: 0.8349 (mm-40) REVERT: I 102 LEU cc_start: 0.7762 (OUTLIER) cc_final: 0.7397 (mm) REVERT: I 206 LYS cc_start: 0.8741 (ttpp) cc_final: 0.8486 (ttpt) REVERT: I 321 LEU cc_start: 0.8737 (OUTLIER) cc_final: 0.8008 (pp) REVERT: J 100 PHE cc_start: 0.7097 (t80) cc_final: 0.6638 (t80) REVERT: J 291 GLN cc_start: 0.8738 (mt0) cc_final: 0.8521 (mm-40) REVERT: J 321 LEU cc_start: 0.8563 (OUTLIER) cc_final: 0.8187 (pp) REVERT: K 152 HIS cc_start: 0.7583 (m-70) cc_final: 0.7380 (m-70) REVERT: K 321 LEU cc_start: 0.8743 (OUTLIER) cc_final: 0.8441 (pp) REVERT: M 46 GLU cc_start: 0.7077 (pm20) cc_final: 0.6749 (pm20) REVERT: M 95 TYR cc_start: 0.7327 (m-80) cc_final: 0.7056 (m-80) REVERT: N 83 MET cc_start: 0.4485 (mmm) cc_final: 0.2832 (tmm) REVERT: N 100 THR cc_start: 0.7691 (OUTLIER) cc_final: 0.7212 (t) REVERT: P 83 MET cc_start: 0.5070 (mmm) cc_final: 0.3492 (tmm) REVERT: P 100 THR cc_start: 0.7560 (OUTLIER) cc_final: 0.7143 (t) REVERT: Q 95 TYR cc_start: 0.7517 (m-80) cc_final: 0.7290 (m-80) REVERT: R 46 GLU cc_start: 0.8285 (tp30) cc_final: 0.7099 (pm20) REVERT: S 34 LEU cc_start: 0.8240 (mt) cc_final: 0.7938 (mm) REVERT: S 83 MET cc_start: 0.4507 (mtp) cc_final: 0.4094 (tmm) REVERT: T 46 GLU cc_start: 0.8444 (tp30) cc_final: 0.8096 (tp30) REVERT: T 83 MET cc_start: 0.4425 (mmm) cc_final: 0.3607 (ppp) REVERT: U 100 THR cc_start: 0.7922 (OUTLIER) cc_final: 0.7638 (t) REVERT: V 46 GLU cc_start: 0.8228 (tp30) cc_final: 0.7156 (pm20) REVERT: V 81 LEU cc_start: 0.6453 (OUTLIER) cc_final: 0.5759 (tp) outliers start: 93 outliers final: 64 residues processed: 295 average time/residue: 0.2477 time to fit residues: 117.3010 Evaluate side-chains 298 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 218 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 68 PHE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain H residue 321 LEU Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 160 PHE Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 298 ARG Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 160 PHE Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 15 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 290 optimal weight: 1.9990 chunk 381 optimal weight: 7.9990 chunk 433 optimal weight: 5.9990 chunk 356 optimal weight: 20.0000 chunk 189 optimal weight: 6.9990 chunk 4 optimal weight: 0.8980 chunk 184 optimal weight: 0.9980 chunk 347 optimal weight: 10.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN T 103 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4312 r_free = 0.4312 target = 0.193903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3750 r_free = 0.3750 target = 0.138048 restraints weight = 46067.882| |-----------------------------------------------------------------------------| r_work (start): 0.3661 rms_B_bonded: 1.76 r_work: 0.3338 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3206 rms_B_bonded: 3.66 restraints_weight: 0.2500 r_work (final): 0.3206 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.2643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 37026 Z= 0.180 Angle : 0.597 16.770 50336 Z= 0.294 Chirality : 0.042 0.181 5445 Planarity : 0.004 0.048 6457 Dihedral : 12.406 134.946 5412 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.51 % Favored : 97.49 % Rotamer: Outliers : 2.51 % Allowed : 12.06 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.13 (0.13), residues: 4455 helix: 2.55 (0.11), residues: 2189 sheet: 1.49 (0.19), residues: 814 loop : -0.46 (0.17), residues: 1452 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 288 TYR 0.027 0.002 TYR F 54 PHE 0.014 0.001 PHE A 329 TRP 0.027 0.002 TRP L 52 HIS 0.006 0.001 HIS A 238 Details of bonding type rmsd covalent geometry : bond 0.00431 (36993) covalent geometry : angle 0.59700 (50270) SS BOND : bond 0.00364 ( 33) SS BOND : angle 0.58705 ( 66) hydrogen bonds : bond 0.04379 ( 2061) hydrogen bonds : angle 3.91216 ( 6078) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 215 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7099 (t80) cc_final: 0.6601 (m-80) REVERT: A 201 LEU cc_start: 0.8642 (mt) cc_final: 0.8317 (mt) REVERT: L 95 TYR cc_start: 0.7084 (m-80) cc_final: 0.6506 (m-80) REVERT: B 175 GLU cc_start: 0.8020 (tp30) cc_final: 0.7670 (tt0) REVERT: B 228 ASP cc_start: 0.8080 (m-30) cc_final: 0.7861 (m-30) REVERT: C 229 GLN cc_start: 0.8653 (tt0) cc_final: 0.8441 (tt0) REVERT: C 286 LEU cc_start: 0.8342 (OUTLIER) cc_final: 0.7797 (mp) REVERT: C 291 GLN cc_start: 0.8593 (mt0) cc_final: 0.8288 (mm-40) REVERT: D 100 PHE cc_start: 0.7437 (t80) cc_final: 0.7065 (t80) REVERT: D 109 ARG cc_start: 0.7744 (ttt-90) cc_final: 0.7033 (ttt-90) REVERT: D 263 LEU cc_start: 0.8304 (OUTLIER) cc_final: 0.7652 (mt) REVERT: E 102 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7095 (mm) REVERT: E 160 PHE cc_start: 0.8211 (OUTLIER) cc_final: 0.7993 (m-10) REVERT: E 286 LEU cc_start: 0.8443 (OUTLIER) cc_final: 0.8147 (mp) REVERT: F 100 PHE cc_start: 0.7331 (t80) cc_final: 0.7085 (t80) REVERT: F 175 GLU cc_start: 0.7847 (tp30) cc_final: 0.7547 (tt0) REVERT: F 286 LEU cc_start: 0.8350 (OUTLIER) cc_final: 0.8004 (mt) REVERT: G 102 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7717 (mm) REVERT: G 160 PHE cc_start: 0.8326 (OUTLIER) cc_final: 0.7772 (m-10) REVERT: G 298 ARG cc_start: 0.8947 (OUTLIER) cc_final: 0.8493 (ptp-170) REVERT: H 291 GLN cc_start: 0.8373 (mt0) cc_final: 0.8128 (mm-40) REVERT: I 102 LEU cc_start: 0.7838 (OUTLIER) cc_final: 0.7443 (mm) REVERT: I 206 LYS cc_start: 0.8597 (ttpp) cc_final: 0.8325 (ttpt) REVERT: I 321 LEU cc_start: 0.8705 (OUTLIER) cc_final: 0.8099 (pp) REVERT: J 100 PHE cc_start: 0.7115 (t80) cc_final: 0.6611 (t80) REVERT: J 291 GLN cc_start: 0.8791 (mt0) cc_final: 0.8497 (mm-40) REVERT: J 321 LEU cc_start: 0.8665 (OUTLIER) cc_final: 0.8279 (pp) REVERT: K 291 GLN cc_start: 0.8506 (mt0) cc_final: 0.8261 (mm-40) REVERT: K 321 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8470 (pp) REVERT: M 46 GLU cc_start: 0.7079 (pm20) cc_final: 0.6749 (pm20) REVERT: M 95 TYR cc_start: 0.7135 (m-80) cc_final: 0.6755 (m-80) REVERT: N 83 MET cc_start: 0.4586 (mmm) cc_final: 0.2838 (tmm) REVERT: N 103 GLN cc_start: 0.7579 (mp-120) cc_final: 0.7329 (mp10) REVERT: P 83 MET cc_start: 0.5196 (mmm) cc_final: 0.3511 (tmm) REVERT: P 100 THR cc_start: 0.7851 (OUTLIER) cc_final: 0.7388 (t) REVERT: Q 95 TYR cc_start: 0.7512 (m-80) cc_final: 0.7249 (m-80) REVERT: R 46 GLU cc_start: 0.8340 (tp30) cc_final: 0.7154 (pm20) REVERT: S 34 LEU cc_start: 0.8268 (mt) cc_final: 0.7952 (mm) REVERT: S 68 PHE cc_start: 0.3296 (OUTLIER) cc_final: 0.1526 (m-80) REVERT: S 83 MET cc_start: 0.4595 (mtp) cc_final: 0.3743 (tmm) REVERT: T 46 GLU cc_start: 0.8517 (tp30) cc_final: 0.8160 (tp30) REVERT: T 83 MET cc_start: 0.4530 (mmm) cc_final: 0.3628 (ppp) REVERT: V 46 GLU cc_start: 0.8375 (tp30) cc_final: 0.7240 (pm20) REVERT: V 81 LEU cc_start: 0.6455 (OUTLIER) cc_final: 0.5798 (tp) outliers start: 94 outliers final: 69 residues processed: 293 average time/residue: 0.2460 time to fit residues: 116.3779 Evaluate side-chains 297 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 212 time to evaluate : 1.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 THR Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 68 PHE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 160 PHE Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 139 SER Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 102 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 254 VAL Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 68 PHE Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 118 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 197 optimal weight: 0.9980 chunk 395 optimal weight: 9.9990 chunk 164 optimal weight: 3.9990 chunk 70 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 chunk 93 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN E 229 GLN M 105 ASN V 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4300 r_free = 0.4300 target = 0.193296 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.127379 restraints weight = 45886.567| |-----------------------------------------------------------------------------| r_work (start): 0.3520 rms_B_bonded: 2.29 r_work: 0.3278 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.3140 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8279 moved from start: 0.2683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37026 Z= 0.115 Angle : 0.538 14.771 50336 Z= 0.266 Chirality : 0.039 0.142 5445 Planarity : 0.003 0.042 6457 Dihedral : 11.903 132.284 5412 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.33 % Allowed : 12.35 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.34 (0.13), residues: 4455 helix: 2.74 (0.11), residues: 2200 sheet: 1.56 (0.19), residues: 814 loop : -0.39 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 233 TYR 0.018 0.001 TYR C 54 PHE 0.016 0.001 PHE J 329 TRP 0.023 0.001 TRP L 52 HIS 0.003 0.001 HIS J 238 Details of bonding type rmsd covalent geometry : bond 0.00253 (36993) covalent geometry : angle 0.53795 (50270) SS BOND : bond 0.00249 ( 33) SS BOND : angle 0.44110 ( 66) hydrogen bonds : bond 0.03719 ( 2061) hydrogen bonds : angle 3.81354 ( 6078) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8910 Ramachandran restraints generated. 4455 Oldfield, 0 Emsley, 4455 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 215 time to evaluate : 1.387 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 100 PHE cc_start: 0.7115 (t80) cc_final: 0.6534 (m-80) REVERT: A 201 LEU cc_start: 0.8657 (mt) cc_final: 0.8366 (mt) REVERT: L 37 PHE cc_start: 0.7605 (m-80) cc_final: 0.7044 (m-80) REVERT: L 95 TYR cc_start: 0.6972 (m-80) cc_final: 0.6318 (m-80) REVERT: L 100 THR cc_start: 0.7690 (OUTLIER) cc_final: 0.7416 (t) REVERT: B 175 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7715 (tt0) REVERT: B 228 ASP cc_start: 0.8228 (m-30) cc_final: 0.8015 (m-30) REVERT: C 286 LEU cc_start: 0.8217 (OUTLIER) cc_final: 0.7629 (mp) REVERT: C 291 GLN cc_start: 0.8666 (mt0) cc_final: 0.8328 (mm-40) REVERT: D 81 ASN cc_start: 0.8155 (p0) cc_final: 0.7844 (p0) REVERT: D 100 PHE cc_start: 0.7393 (t80) cc_final: 0.7012 (t80) REVERT: D 109 ARG cc_start: 0.7812 (ttt-90) cc_final: 0.7067 (ttt-90) REVERT: D 168 ASN cc_start: 0.7100 (OUTLIER) cc_final: 0.6732 (t0) REVERT: D 263 LEU cc_start: 0.8269 (OUTLIER) cc_final: 0.7562 (mt) REVERT: E 102 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7069 (mm) REVERT: E 286 LEU cc_start: 0.8356 (OUTLIER) cc_final: 0.8062 (mp) REVERT: F 100 PHE cc_start: 0.7233 (t80) cc_final: 0.7024 (t80) REVERT: F 175 GLU cc_start: 0.7969 (tp30) cc_final: 0.7633 (tt0) REVERT: G 102 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7709 (mm) REVERT: G 160 PHE cc_start: 0.8261 (OUTLIER) cc_final: 0.7712 (m-80) REVERT: G 298 ARG cc_start: 0.8933 (OUTLIER) cc_final: 0.8574 (ptp-170) REVERT: H 291 GLN cc_start: 0.8462 (mt0) cc_final: 0.8179 (mm-40) REVERT: I 102 LEU cc_start: 0.7733 (OUTLIER) cc_final: 0.7359 (mm) REVERT: I 206 LYS cc_start: 0.8736 (ttpp) cc_final: 0.8509 (ttpt) REVERT: I 321 LEU cc_start: 0.8754 (OUTLIER) cc_final: 0.8059 (pp) REVERT: J 100 PHE cc_start: 0.7049 (t80) cc_final: 0.6600 (t80) REVERT: J 291 GLN cc_start: 0.8907 (mt0) cc_final: 0.8575 (mm110) REVERT: J 321 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8270 (pp) REVERT: K 291 GLN cc_start: 0.8661 (mt0) cc_final: 0.8340 (mm-40) REVERT: K 321 LEU cc_start: 0.8746 (OUTLIER) cc_final: 0.8451 (pp) REVERT: M 46 GLU cc_start: 0.7002 (pm20) cc_final: 0.6690 (pm20) REVERT: M 95 TYR cc_start: 0.7022 (m-80) cc_final: 0.6743 (m-80) REVERT: N 83 MET cc_start: 0.4505 (mmm) cc_final: 0.2772 (tmm) REVERT: P 83 MET cc_start: 0.5131 (mmm) cc_final: 0.3464 (tmm) REVERT: P 100 THR cc_start: 0.7930 (OUTLIER) cc_final: 0.7496 (t) REVERT: Q 95 TYR cc_start: 0.7462 (m-80) cc_final: 0.7219 (m-80) REVERT: R 46 GLU cc_start: 0.8396 (tp30) cc_final: 0.7034 (pm20) REVERT: R 100 THR cc_start: 0.7995 (OUTLIER) cc_final: 0.7650 (t) REVERT: S 34 LEU cc_start: 0.8273 (mt) cc_final: 0.7972 (mm) REVERT: S 83 MET cc_start: 0.4733 (mtp) cc_final: 0.4165 (tmm) REVERT: T 34 LEU cc_start: 0.8227 (mm) cc_final: 0.7852 (mm) REVERT: T 46 GLU cc_start: 0.8615 (tp30) cc_final: 0.8313 (tp30) REVERT: T 83 MET cc_start: 0.4627 (mmm) cc_final: 0.3645 (ppp) REVERT: U 100 THR cc_start: 0.8156 (OUTLIER) cc_final: 0.7849 (t) REVERT: V 46 GLU cc_start: 0.8392 (tp30) cc_final: 0.7180 (pm20) REVERT: V 81 LEU cc_start: 0.6433 (OUTLIER) cc_final: 0.5892 (tp) outliers start: 87 outliers final: 65 residues processed: 286 average time/residue: 0.2433 time to fit residues: 112.7355 Evaluate side-chains 295 residues out of total 3740 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 212 time to evaluate : 1.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 229 GLN Chi-restraints excluded: chain A residue 254 VAL Chi-restraints excluded: chain A residue 257 ASN Chi-restraints excluded: chain A residue 261 GLU Chi-restraints excluded: chain A residue 298 ARG Chi-restraints excluded: chain L residue 28 ILE Chi-restraints excluded: chain L residue 100 THR Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 175 GLU Chi-restraints excluded: chain B residue 257 ASN Chi-restraints excluded: chain B residue 298 ARG Chi-restraints excluded: chain B residue 321 LEU Chi-restraints excluded: chain C residue 79 THR Chi-restraints excluded: chain C residue 86 CYS Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 119 VAL Chi-restraints excluded: chain C residue 286 LEU Chi-restraints excluded: chain C residue 298 ARG Chi-restraints excluded: chain C residue 321 LEU Chi-restraints excluded: chain D residue 79 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 160 PHE Chi-restraints excluded: chain D residue 168 ASN Chi-restraints excluded: chain D residue 229 GLN Chi-restraints excluded: chain D residue 257 ASN Chi-restraints excluded: chain D residue 263 LEU Chi-restraints excluded: chain D residue 321 LEU Chi-restraints excluded: chain E residue 79 THR Chi-restraints excluded: chain E residue 102 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 254 VAL Chi-restraints excluded: chain E residue 257 ASN Chi-restraints excluded: chain E residue 286 LEU Chi-restraints excluded: chain E residue 298 ARG Chi-restraints excluded: chain E residue 321 LEU Chi-restraints excluded: chain F residue 86 CYS Chi-restraints excluded: chain F residue 119 VAL Chi-restraints excluded: chain F residue 254 VAL Chi-restraints excluded: chain F residue 257 ASN Chi-restraints excluded: chain F residue 286 LEU Chi-restraints excluded: chain F residue 298 ARG Chi-restraints excluded: chain F residue 321 LEU Chi-restraints excluded: chain G residue 86 CYS Chi-restraints excluded: chain G residue 102 LEU Chi-restraints excluded: chain G residue 160 PHE Chi-restraints excluded: chain G residue 298 ARG Chi-restraints excluded: chain G residue 321 LEU Chi-restraints excluded: chain H residue 119 VAL Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 261 GLU Chi-restraints excluded: chain H residue 286 LEU Chi-restraints excluded: chain H residue 298 ARG Chi-restraints excluded: chain I residue 79 THR Chi-restraints excluded: chain I residue 102 LEU Chi-restraints excluded: chain I residue 254 VAL Chi-restraints excluded: chain I residue 257 ASN Chi-restraints excluded: chain I residue 261 GLU Chi-restraints excluded: chain I residue 321 LEU Chi-restraints excluded: chain J residue 119 VAL Chi-restraints excluded: chain J residue 254 VAL Chi-restraints excluded: chain J residue 257 ASN Chi-restraints excluded: chain J residue 261 GLU Chi-restraints excluded: chain J residue 298 ARG Chi-restraints excluded: chain J residue 321 LEU Chi-restraints excluded: chain K residue 119 VAL Chi-restraints excluded: chain K residue 254 VAL Chi-restraints excluded: chain K residue 257 ASN Chi-restraints excluded: chain K residue 261 GLU Chi-restraints excluded: chain K residue 298 ARG Chi-restraints excluded: chain K residue 321 LEU Chi-restraints excluded: chain N residue 81 LEU Chi-restraints excluded: chain N residue 100 THR Chi-restraints excluded: chain O residue 100 THR Chi-restraints excluded: chain P residue 100 THR Chi-restraints excluded: chain Q residue 100 THR Chi-restraints excluded: chain R residue 100 THR Chi-restraints excluded: chain S residue 100 THR Chi-restraints excluded: chain T residue 100 THR Chi-restraints excluded: chain U residue 100 THR Chi-restraints excluded: chain V residue 81 LEU Chi-restraints excluded: chain V residue 100 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 440 random chunks: chunk 149 optimal weight: 0.0980 chunk 202 optimal weight: 0.7980 chunk 87 optimal weight: 1.9990 chunk 310 optimal weight: 0.6980 chunk 299 optimal weight: 0.9990 chunk 112 optimal weight: 2.9990 chunk 201 optimal weight: 1.9990 chunk 437 optimal weight: 6.9990 chunk 142 optimal weight: 0.9980 chunk 146 optimal weight: 7.9990 chunk 344 optimal weight: 20.0000 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 229 GLN D 229 GLN ** M 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.193825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.125772 restraints weight = 45533.098| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 2.17 r_work: 0.3318 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3185 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3185 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 37026 Z= 0.105 Angle : 0.527 14.554 50336 Z= 0.260 Chirality : 0.038 0.143 5445 Planarity : 0.003 0.039 6457 Dihedral : 11.444 131.030 5412 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.27 % Allowed : 12.41 % Favored : 85.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % 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: 2.43 (0.13), residues: 4455 helix: 2.84 (0.11), residues: 2200 sheet: 1.58 (0.19), residues: 814 loop : -0.37 (0.17), residues: 1441 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 240 TYR 0.016 0.001 TYR G 287 PHE 0.015 0.001 PHE J 329 TRP 0.020 0.001 TRP L 52 HIS 0.003 0.001 HIS L 111 Details of bonding type rmsd covalent geometry : bond 0.00228 (36993) covalent geometry : angle 0.52709 (50270) SS BOND : bond 0.00231 ( 33) SS BOND : angle 0.45737 ( 66) hydrogen bonds : bond 0.03571 ( 2061) hydrogen bonds : angle 3.78166 ( 6078) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11657.67 seconds wall clock time: 199 minutes 38.09 seconds (11978.09 seconds total)