Starting phenix.real_space_refine on Sun Aug 9 01:51:38 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2026/8pdr_17619.cif" } resolution = 4.0 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= 0.001 sd= 0.019 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 77 5.49 5 S 132 5.16 5 C 20053 2.51 5 N 5522 2.21 5 O 6358 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 77 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 32142 Number of models: 1 Model: "" Number of chains: 33 Chain: "A" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "B" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "C" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "D" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "E" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "F" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "G" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "H" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "I" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "K" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 351, 2721 Classifications: {'peptide': 351} Link IDs: {'PTRANS': 11, 'TRANS': 339} Chain: "L" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "M" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "N" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "O" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "P" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "Q" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "R" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "S" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "T" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "U" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "V" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 61 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "a" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "b" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "c" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "d" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "e" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "f" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "g" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "h" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "i" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "j" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Chain: "k" Number of atoms: 140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 140 Classifications: {'RNAv2': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 6.40, per 1000 atoms: 0.20 Number of scatterers: 32142 At special positions: 0 Unit cell: (119.7, 200.55, 195.3, 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 77 15.00 O 6358 8.00 N 5522 7.00 C 20053 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 31726 O5' C i 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 31026 O5' C d 400 .*. O " rejected from bonding due to valence issues. Atom "ATOM 30886 O5' C c 400 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=9, symmetry=0 Number of additional bonds: simple=9, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.40 Conformation dependent library (CDL) restraints added in 1.2 seconds 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7304 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 22 sheets defined 68.2% alpha, 5.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 3.67 Creating SS restraints... Processing helix chain 'A' and resid 10 through 20 Processing helix chain 'A' and resid 37 through 39 No H-bonds generated for 'chain 'A' and resid 37 through 39' Processing helix chain 'A' and resid 40 through 51 removed outlier: 3.614A pdb=" N LEU A 47 " --> pdb=" O GLU A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 75 through 86 Processing helix chain 'A' and resid 120 through 142 removed outlier: 3.570A pdb=" N VAL A 124 " --> pdb=" O GLU A 120 " (cutoff:3.500A) Processing helix chain 'A' and resid 147 through 151 Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.909A pdb=" N LYS A 171 " --> pdb=" O LEU A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG A 189 " --> pdb=" O ARG A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 198 Processing helix chain 'A' and resid 202 through 217 Processing helix chain 'A' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG A 221 " --> pdb=" O LYS A 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER A 222 " --> pdb=" O VAL A 218 " (cutoff:3.500A) Processing helix chain 'A' and resid 238 through 251 Processing helix chain 'A' and resid 256 through 268 removed outlier: 3.650A pdb=" N ARG A 260 " --> pdb=" O GLN A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 275 through 280 Processing helix chain 'A' and resid 281 through 296 Processing helix chain 'A' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY A 300 " --> pdb=" O PRO A 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 297 through 300' Processing helix chain 'A' and resid 318 through 332 Processing helix chain 'A' and resid 344 through 360 Processing helix chain 'B' and resid 11 through 20 Processing helix chain 'B' and resid 37 through 39 No H-bonds generated for 'chain 'B' and resid 37 through 39' Processing helix chain 'B' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU B 47 " --> pdb=" O GLU B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 61 through 75 Processing helix chain 'B' and resid 75 through 86 Processing helix chain 'B' and resid 120 through 142 removed outlier: 3.569A pdb=" N VAL B 124 " --> pdb=" O GLU B 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 147 through 151 Processing helix chain 'B' and resid 156 through 171 removed outlier: 3.910A pdb=" N LYS B 171 " --> pdb=" O LEU B 167 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 191 removed outlier: 3.884A pdb=" N ARG B 189 " --> pdb=" O ARG B 185 " (cutoff:3.500A) Processing helix chain 'B' and resid 191 through 198 Processing helix chain 'B' and resid 202 through 217 Processing helix chain 'B' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG B 221 " --> pdb=" O LYS B 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER B 222 " --> pdb=" O VAL B 218 " (cutoff:3.500A) Processing helix chain 'B' and resid 238 through 251 Processing helix chain 'B' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG B 260 " --> pdb=" O GLN B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 270 through 274 Processing helix chain 'B' and resid 275 through 280 Processing helix chain 'B' and resid 281 through 296 Processing helix chain 'B' and resid 297 through 300 removed outlier: 3.763A pdb=" N GLY B 300 " --> pdb=" O PRO B 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 297 through 300' Processing helix chain 'B' and resid 318 through 332 Processing helix chain 'B' and resid 344 through 360 Processing helix chain 'C' and resid 11 through 20 Processing helix chain 'C' and resid 37 through 39 No H-bonds generated for 'chain 'C' and resid 37 through 39' Processing helix chain 'C' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU C 47 " --> pdb=" O GLU C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 61 through 75 Processing helix chain 'C' and resid 75 through 86 Processing helix chain 'C' and resid 120 through 142 removed outlier: 3.569A pdb=" N VAL C 124 " --> pdb=" O GLU C 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 156 through 171 removed outlier: 3.909A pdb=" N LYS C 171 " --> pdb=" O LEU C 167 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG C 189 " --> pdb=" O ARG C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 191 through 198 Processing helix chain 'C' and resid 202 through 217 Processing helix chain 'C' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG C 221 " --> pdb=" O LYS C 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER C 222 " --> pdb=" O VAL C 218 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 251 Processing helix chain 'C' and resid 256 through 268 removed outlier: 3.650A pdb=" N ARG C 260 " --> pdb=" O GLN C 256 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 274 Processing helix chain 'C' and resid 275 through 280 Processing helix chain 'C' and resid 281 through 296 Processing helix chain 'C' and resid 297 through 300 removed outlier: 3.763A pdb=" N GLY C 300 " --> pdb=" O PRO C 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 297 through 300' Processing helix chain 'C' and resid 318 through 332 Processing helix chain 'C' and resid 344 through 360 Processing helix chain 'D' and resid 11 through 20 Processing helix chain 'D' and resid 37 through 39 No H-bonds generated for 'chain 'D' and resid 37 through 39' Processing helix chain 'D' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU D 47 " --> pdb=" O GLU D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 61 through 75 Processing helix chain 'D' and resid 75 through 86 Processing helix chain 'D' and resid 120 through 142 removed outlier: 3.569A pdb=" N VAL D 124 " --> pdb=" O GLU D 120 " (cutoff:3.500A) Processing helix chain 'D' and resid 147 through 151 Processing helix chain 'D' and resid 156 through 171 removed outlier: 3.909A pdb=" N LYS D 171 " --> pdb=" O LEU D 167 " (cutoff:3.500A) Processing helix chain 'D' and resid 175 through 191 removed outlier: 3.882A pdb=" N ARG D 189 " --> pdb=" O ARG D 185 " (cutoff:3.500A) Processing helix chain 'D' and resid 191 through 198 Processing helix chain 'D' and resid 202 through 217 Processing helix chain 'D' and resid 217 through 233 removed outlier: 3.901A pdb=" N ARG D 221 " --> pdb=" O LYS D 217 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER D 222 " --> pdb=" O VAL D 218 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 251 Processing helix chain 'D' and resid 256 through 268 removed outlier: 3.650A pdb=" N ARG D 260 " --> pdb=" O GLN D 256 " (cutoff:3.500A) Processing helix chain 'D' and resid 270 through 274 Processing helix chain 'D' and resid 275 through 280 Processing helix chain 'D' and resid 281 through 296 Processing helix chain 'D' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY D 300 " --> pdb=" O PRO D 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 297 through 300' Processing helix chain 'D' and resid 318 through 332 Processing helix chain 'D' and resid 344 through 360 Processing helix chain 'E' and resid 11 through 20 Processing helix chain 'E' and resid 37 through 39 No H-bonds generated for 'chain 'E' and resid 37 through 39' Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU E 47 " --> pdb=" O GLU E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 61 through 75 Processing helix chain 'E' and resid 75 through 86 Processing helix chain 'E' and resid 120 through 142 removed outlier: 3.568A pdb=" N VAL E 124 " --> pdb=" O GLU E 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 151 Processing helix chain 'E' and resid 156 through 171 removed outlier: 3.910A pdb=" N LYS E 171 " --> pdb=" O LEU E 167 " (cutoff:3.500A) Processing helix chain 'E' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG E 189 " --> pdb=" O ARG E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 191 through 198 Processing helix chain 'E' and resid 202 through 217 Processing helix chain 'E' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG E 221 " --> pdb=" O LYS E 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER E 222 " --> pdb=" O VAL E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 238 through 251 Processing helix chain 'E' and resid 256 through 268 removed outlier: 3.650A pdb=" N ARG E 260 " --> pdb=" O GLN E 256 " (cutoff:3.500A) Processing helix chain 'E' and resid 270 through 274 Processing helix chain 'E' and resid 275 through 280 Processing helix chain 'E' and resid 281 through 296 Processing helix chain 'E' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY E 300 " --> pdb=" O PRO E 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 297 through 300' Processing helix chain 'E' and resid 318 through 332 Processing helix chain 'E' and resid 344 through 360 Processing helix chain 'F' and resid 11 through 20 Processing helix chain 'F' and resid 37 through 39 No H-bonds generated for 'chain 'F' and resid 37 through 39' Processing helix chain 'F' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU F 47 " --> pdb=" O GLU F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 61 through 75 Processing helix chain 'F' and resid 75 through 86 Processing helix chain 'F' and resid 120 through 142 removed outlier: 3.569A pdb=" N VAL F 124 " --> pdb=" O GLU F 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 147 through 151 Processing helix chain 'F' and resid 156 through 171 removed outlier: 3.908A pdb=" N LYS F 171 " --> pdb=" O LEU F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG F 189 " --> pdb=" O ARG F 185 " (cutoff:3.500A) Processing helix chain 'F' and resid 191 through 198 Processing helix chain 'F' and resid 202 through 217 Processing helix chain 'F' and resid 217 through 233 removed outlier: 3.901A pdb=" N ARG F 221 " --> pdb=" O LYS F 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER F 222 " --> pdb=" O VAL F 218 " (cutoff:3.500A) Processing helix chain 'F' and resid 238 through 251 Processing helix chain 'F' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG F 260 " --> pdb=" O GLN F 256 " (cutoff:3.500A) Processing helix chain 'F' and resid 270 through 274 Processing helix chain 'F' and resid 275 through 280 Processing helix chain 'F' and resid 281 through 296 Processing helix chain 'F' and resid 297 through 300 removed outlier: 3.761A pdb=" N GLY F 300 " --> pdb=" O PRO F 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 297 through 300' Processing helix chain 'F' and resid 318 through 332 Processing helix chain 'F' and resid 344 through 360 Processing helix chain 'G' and resid 11 through 20 Processing helix chain 'G' and resid 37 through 39 No H-bonds generated for 'chain 'G' and resid 37 through 39' Processing helix chain 'G' and resid 40 through 51 removed outlier: 3.612A pdb=" N LEU G 47 " --> pdb=" O GLU G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 61 through 75 Processing helix chain 'G' and resid 75 through 86 Processing helix chain 'G' and resid 120 through 142 removed outlier: 3.570A pdb=" N VAL G 124 " --> pdb=" O GLU G 120 " (cutoff:3.500A) Processing helix chain 'G' and resid 147 through 151 Processing helix chain 'G' and resid 156 through 171 removed outlier: 3.908A pdb=" N LYS G 171 " --> pdb=" O LEU G 167 " (cutoff:3.500A) Processing helix chain 'G' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG G 189 " --> pdb=" O ARG G 185 " (cutoff:3.500A) Processing helix chain 'G' and resid 191 through 198 Processing helix chain 'G' and resid 202 through 217 Processing helix chain 'G' and resid 217 through 233 removed outlier: 3.901A pdb=" N ARG G 221 " --> pdb=" O LYS G 217 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N SER G 222 " --> pdb=" O VAL G 218 " (cutoff:3.500A) Processing helix chain 'G' and resid 238 through 251 Processing helix chain 'G' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG G 260 " --> pdb=" O GLN G 256 " (cutoff:3.500A) Processing helix chain 'G' and resid 270 through 274 Processing helix chain 'G' and resid 275 through 280 Processing helix chain 'G' and resid 281 through 296 Processing helix chain 'G' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY G 300 " --> pdb=" O PRO G 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 297 through 300' Processing helix chain 'G' and resid 318 through 332 Processing helix chain 'G' and resid 344 through 360 Processing helix chain 'H' and resid 11 through 20 Processing helix chain 'H' and resid 37 through 39 No H-bonds generated for 'chain 'H' and resid 37 through 39' Processing helix chain 'H' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU H 47 " --> pdb=" O GLU H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 75 Processing helix chain 'H' and resid 75 through 86 Processing helix chain 'H' and resid 120 through 142 removed outlier: 3.570A pdb=" N VAL H 124 " --> pdb=" O GLU H 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 151 Processing helix chain 'H' and resid 156 through 171 removed outlier: 3.909A pdb=" N LYS H 171 " --> pdb=" O LEU H 167 " (cutoff:3.500A) Processing helix chain 'H' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG H 189 " --> pdb=" O ARG H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 198 Processing helix chain 'H' and resid 202 through 217 Processing helix chain 'H' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG H 221 " --> pdb=" O LYS H 217 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N SER H 222 " --> pdb=" O VAL H 218 " (cutoff:3.500A) Processing helix chain 'H' and resid 238 through 251 Processing helix chain 'H' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG H 260 " --> pdb=" O GLN H 256 " (cutoff:3.500A) Processing helix chain 'H' and resid 270 through 274 Processing helix chain 'H' and resid 275 through 280 Processing helix chain 'H' and resid 281 through 296 Processing helix chain 'H' and resid 297 through 300 removed outlier: 3.763A pdb=" N GLY H 300 " --> pdb=" O PRO H 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 297 through 300' Processing helix chain 'H' and resid 318 through 332 Processing helix chain 'H' and resid 344 through 360 Processing helix chain 'I' and resid 11 through 20 Processing helix chain 'I' and resid 37 through 39 No H-bonds generated for 'chain 'I' and resid 37 through 39' Processing helix chain 'I' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU I 47 " --> pdb=" O GLU I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 61 through 75 Processing helix chain 'I' and resid 75 through 86 Processing helix chain 'I' and resid 120 through 142 removed outlier: 3.570A pdb=" N VAL I 124 " --> pdb=" O GLU I 120 " (cutoff:3.500A) Processing helix chain 'I' and resid 147 through 151 Processing helix chain 'I' and resid 156 through 171 removed outlier: 3.910A pdb=" N LYS I 171 " --> pdb=" O LEU I 167 " (cutoff:3.500A) Processing helix chain 'I' and resid 175 through 191 removed outlier: 3.883A pdb=" N ARG I 189 " --> pdb=" O ARG I 185 " (cutoff:3.500A) Processing helix chain 'I' and resid 191 through 198 Processing helix chain 'I' and resid 202 through 217 Processing helix chain 'I' and resid 217 through 233 removed outlier: 3.902A pdb=" N ARG I 221 " --> pdb=" O LYS I 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER I 222 " --> pdb=" O VAL I 218 " (cutoff:3.500A) Processing helix chain 'I' and resid 238 through 251 Processing helix chain 'I' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG I 260 " --> pdb=" O GLN I 256 " (cutoff:3.500A) Processing helix chain 'I' and resid 270 through 274 Processing helix chain 'I' and resid 275 through 280 Processing helix chain 'I' and resid 281 through 296 Processing helix chain 'I' and resid 297 through 300 removed outlier: 3.762A pdb=" N GLY I 300 " --> pdb=" O PRO I 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 297 through 300' Processing helix chain 'I' and resid 318 through 332 Processing helix chain 'I' and resid 344 through 360 Processing helix chain 'J' and resid 11 through 20 Processing helix chain 'J' and resid 37 through 39 No H-bonds generated for 'chain 'J' and resid 37 through 39' Processing helix chain 'J' and resid 40 through 51 removed outlier: 3.613A pdb=" N LEU J 47 " --> pdb=" O GLU J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 61 through 75 Processing helix chain 'J' and resid 75 through 86 Processing helix chain 'J' and resid 120 through 142 removed outlier: 3.569A pdb=" N VAL J 124 " --> pdb=" O GLU J 120 " (cutoff:3.500A) Processing helix chain 'J' and resid 147 through 151 Processing helix chain 'J' and resid 156 through 171 removed outlier: 3.909A pdb=" N LYS J 171 " --> pdb=" O LEU J 167 " (cutoff:3.500A) Processing helix chain 'J' and resid 175 through 191 removed outlier: 3.884A pdb=" N ARG J 189 " --> pdb=" O ARG J 185 " (cutoff:3.500A) Processing helix chain 'J' and resid 191 through 198 Processing helix chain 'J' and resid 202 through 217 Processing helix chain 'J' and resid 217 through 233 removed outlier: 3.903A pdb=" N ARG J 221 " --> pdb=" O LYS J 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER J 222 " --> pdb=" O VAL J 218 " (cutoff:3.500A) Processing helix chain 'J' and resid 238 through 251 Processing helix chain 'J' and resid 256 through 268 removed outlier: 3.651A pdb=" N ARG J 260 " --> pdb=" O GLN J 256 " (cutoff:3.500A) Processing helix chain 'J' and resid 270 through 274 Processing helix chain 'J' and resid 275 through 280 Processing helix chain 'J' and resid 281 through 296 Processing helix chain 'J' and resid 297 through 300 removed outlier: 3.763A pdb=" N GLY J 300 " --> pdb=" O PRO J 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 297 through 300' Processing helix chain 'J' and resid 318 through 332 Processing helix chain 'J' and resid 344 through 360 Processing helix chain 'K' and resid 11 through 20 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 40 through 51 removed outlier: 3.612A pdb=" N LEU K 47 " --> pdb=" O GLU K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 61 through 75 Processing helix chain 'K' and resid 75 through 86 Processing helix chain 'K' and resid 120 through 142 removed outlier: 3.569A pdb=" N VAL K 124 " --> pdb=" O GLU K 120 " (cutoff:3.500A) Processing helix chain 'K' and resid 147 through 151 Processing helix chain 'K' and resid 156 through 171 removed outlier: 3.909A pdb=" N LYS K 171 " --> pdb=" O LEU K 167 " (cutoff:3.500A) Processing helix chain 'K' and resid 175 through 191 removed outlier: 3.884A pdb=" N ARG K 189 " --> pdb=" O ARG K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 191 through 198 Processing helix chain 'K' and resid 202 through 217 Processing helix chain 'K' and resid 217 through 233 removed outlier: 3.901A pdb=" N ARG K 221 " --> pdb=" O LYS K 217 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N SER K 222 " --> pdb=" O VAL K 218 " (cutoff:3.500A) Processing helix chain 'K' and resid 238 through 251 Processing helix chain 'K' and resid 256 through 268 removed outlier: 3.650A pdb=" N ARG K 260 " --> pdb=" O GLN K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 270 through 274 Processing helix chain 'K' and resid 275 through 280 Processing helix chain 'K' and resid 281 through 296 Processing helix chain 'K' and resid 297 through 300 removed outlier: 3.761A pdb=" N GLY K 300 " --> pdb=" O PRO K 297 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 297 through 300' Processing helix chain 'K' and resid 318 through 332 Processing helix chain 'K' and resid 344 through 360 Processing sheet with id=AA1, first strand: chain 'A' and resid 32 through 35 Processing sheet with id=AA2, first strand: chain 'A' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU A 111 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 32 through 35 Processing sheet with id=AA4, first strand: chain 'B' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU B 111 " --> pdb=" O LEU B 100 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 32 through 35 Processing sheet with id=AA6, first strand: chain 'C' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU C 111 " --> pdb=" O LEU C 100 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 32 through 35 Processing sheet with id=AA8, first strand: chain 'D' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU D 111 " --> pdb=" O LEU D 100 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 32 through 35 Processing sheet with id=AB1, first strand: chain 'E' and resid 96 through 104 removed outlier: 7.875A pdb=" N LEU E 111 " --> pdb=" O LEU E 100 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 32 through 35 Processing sheet with id=AB3, first strand: chain 'F' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU F 111 " --> pdb=" O LEU F 100 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 32 through 35 Processing sheet with id=AB5, first strand: chain 'G' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU G 111 " --> pdb=" O LEU G 100 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 32 through 35 Processing sheet with id=AB7, first strand: chain 'H' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU H 111 " --> pdb=" O LEU H 100 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 32 through 35 Processing sheet with id=AB9, first strand: chain 'I' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU I 111 " --> pdb=" O LEU I 100 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'J' and resid 32 through 35 Processing sheet with id=AC2, first strand: chain 'J' and resid 96 through 104 removed outlier: 7.876A pdb=" N LEU J 111 " --> pdb=" O LEU J 100 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'K' and resid 32 through 35 Processing sheet with id=AC4, first strand: chain 'K' and resid 96 through 104 removed outlier: 7.875A pdb=" N LEU K 111 " --> pdb=" O LEU K 100 " (cutoff:3.500A) 1849 hydrogen bonds defined for protein. 5382 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 55 stacking parallelities Total time for adding SS restraints: 5.93 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10113 1.34 - 1.45: 4147 1.45 - 1.57: 18124 1.57 - 1.69: 143 1.69 - 1.80: 231 Bond restraints: 32758 Sorted by residual: bond pdb=" CB VAL F 92 " pdb=" CG1 VAL F 92 " ideal model delta sigma weight residual 1.521 1.465 0.056 3.30e-02 9.18e+02 2.90e+00 bond pdb=" CB VAL D 92 " pdb=" CG1 VAL D 92 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.76e+00 bond pdb=" CB VAL I 92 " pdb=" CG1 VAL I 92 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.75e+00 bond pdb=" CB VAL B 92 " pdb=" CG1 VAL B 92 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.74e+00 bond pdb=" CB VAL A 92 " pdb=" CG1 VAL A 92 " ideal model delta sigma weight residual 1.521 1.467 0.054 3.30e-02 9.18e+02 2.72e+00 ... (remaining 32753 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.17: 41703 1.17 - 2.34: 2225 2.34 - 3.52: 418 3.52 - 4.69: 138 4.69 - 5.86: 33 Bond angle restraints: 44517 Sorted by residual: angle pdb=" C LEU E 52 " pdb=" N TYR E 53 " pdb=" CA TYR E 53 " ideal model delta sigma weight residual 122.60 118.71 3.89 1.56e+00 4.11e-01 6.21e+00 angle pdb=" C LEU B 52 " pdb=" N TYR B 53 " pdb=" CA TYR B 53 " ideal model delta sigma weight residual 122.60 118.75 3.85 1.56e+00 4.11e-01 6.08e+00 angle pdb=" C LEU G 52 " pdb=" N TYR G 53 " pdb=" CA TYR G 53 " ideal model delta sigma weight residual 122.60 118.77 3.83 1.56e+00 4.11e-01 6.02e+00 angle pdb=" C LEU I 52 " pdb=" N TYR I 53 " pdb=" CA TYR I 53 " ideal model delta sigma weight residual 122.60 118.80 3.80 1.56e+00 4.11e-01 5.94e+00 angle pdb=" C LEU A 52 " pdb=" N TYR A 53 " pdb=" CA TYR A 53 " ideal model delta sigma weight residual 122.60 118.80 3.80 1.56e+00 4.11e-01 5.93e+00 ... (remaining 44512 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 18045 17.20 - 34.40: 1633 34.40 - 51.59: 254 51.59 - 68.79: 121 68.79 - 85.99: 143 Dihedral angle restraints: 20196 sinusoidal: 8800 harmonic: 11396 Sorted by residual: dihedral pdb=" C4' C b 403 " pdb=" C3' C b 403 " pdb=" C2' C b 403 " pdb=" C1' C b 403 " ideal model delta sinusoidal sigma weight residual 36.34 -33.85 70.19 1 3.10e+00 1.04e-01 6.60e+02 dihedral pdb=" C4' C e 403 " pdb=" C3' C e 403 " pdb=" C2' C e 403 " pdb=" C1' C e 403 " ideal model delta sinusoidal sigma weight residual 36.34 -33.84 70.18 1 3.10e+00 1.04e-01 6.60e+02 dihedral pdb=" C4' C k 403 " pdb=" C3' C k 403 " pdb=" C2' C k 403 " pdb=" C1' C k 403 " ideal model delta sinusoidal sigma weight residual 36.34 -33.82 70.17 1 3.10e+00 1.04e-01 6.60e+02 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.060: 4334 0.060 - 0.120: 763 0.120 - 0.179: 51 0.179 - 0.239: 66 0.239 - 0.299: 22 Chirality restraints: 5236 Sorted by residual: chirality pdb=" C2' C g 403 " pdb=" C3' C g 403 " pdb=" O2' C g 403 " pdb=" C1' C g 403 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' C i 403 " pdb=" C3' C i 403 " pdb=" O2' C i 403 " pdb=" C1' C i 403 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.23e+00 chirality pdb=" C2' C c 403 " pdb=" C3' C c 403 " pdb=" O2' C c 403 " pdb=" C1' C c 403 " both_signs ideal model delta sigma weight residual False -2.79 -2.49 -0.30 2.00e-01 2.50e+01 2.22e+00 ... (remaining 5233 not shown) Planarity restraints: 5401 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' C c 402 " 0.021 2.00e-02 2.50e+03 1.13e-02 2.87e+00 pdb=" N1 C c 402 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C c 402 " -0.000 2.00e-02 2.50e+03 pdb=" O2 C c 402 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C c 402 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C c 402 " 0.000 2.00e-02 2.50e+03 pdb=" N4 C c 402 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C c 402 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C c 402 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C i 402 " 0.021 2.00e-02 2.50e+03 1.12e-02 2.83e+00 pdb=" N1 C i 402 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C i 402 " 0.000 2.00e-02 2.50e+03 pdb=" O2 C i 402 " -0.003 2.00e-02 2.50e+03 pdb=" N3 C i 402 " 0.002 2.00e-02 2.50e+03 pdb=" C4 C i 402 " 0.000 2.00e-02 2.50e+03 pdb=" N4 C i 402 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C i 402 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C i 402 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' C h 402 " 0.021 2.00e-02 2.50e+03 1.12e-02 2.80e+00 pdb=" N1 C h 402 " -0.025 2.00e-02 2.50e+03 pdb=" C2 C h 402 " -0.000 2.00e-02 2.50e+03 pdb=" O2 C h 402 " -0.002 2.00e-02 2.50e+03 pdb=" N3 C h 402 " 0.001 2.00e-02 2.50e+03 pdb=" C4 C h 402 " 0.000 2.00e-02 2.50e+03 pdb=" N4 C h 402 " 0.007 2.00e-02 2.50e+03 pdb=" C5 C h 402 " -0.001 2.00e-02 2.50e+03 pdb=" C6 C h 402 " -0.002 2.00e-02 2.50e+03 ... (remaining 5398 not shown) Histogram of nonbonded interaction distances: 0.60 - 1.46: 17 1.46 - 2.32: 98 2.32 - 3.18: 28973 3.18 - 4.04: 85862 4.04 - 4.90: 159149 Warning: very small nonbonded interaction distances. Nonbonded interactions: 274099 Sorted by model distance: nonbonded pdb=" O3' C j 406 " pdb=" OP1 C k 400 " model vdw 0.603 3.040 nonbonded pdb=" OG SER D 267 " pdb=" CE LYS E 283 " model vdw 0.691 3.440 nonbonded pdb=" OG SER E 267 " pdb=" CE LYS F 283 " model vdw 0.767 3.440 nonbonded pdb=" CG2 VAL A 190 " pdb=" OP2 C b 400 " model vdw 0.961 3.460 nonbonded pdb=" OG SER C 267 " pdb=" CE LYS D 283 " model vdw 1.023 3.440 ... (remaining 274094 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' } 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' } 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 group one per residue 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: 4.060 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: 0.040 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 29.810 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5297 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.465 32767 Z= 0.461 Angle : 0.642 5.861 44517 Z= 0.347 Chirality : 0.052 0.299 5236 Planarity : 0.004 0.027 5401 Dihedral : 15.609 85.991 12892 Min Nonbonded Distance : 0.603 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % 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 are not related in a simple way. whole: 0.34 (0.13), residues: 3894 helix: 0.52 (0.11), residues: 2486 sheet: -1.48 (0.27), residues: 231 loop : 0.28 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 293 TYR 0.026 0.003 TYR F 53 PHE 0.016 0.002 PHE J 169 TRP 0.007 0.002 TRP H 123 HIS 0.004 0.001 HIS K 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00473 / 0.21 (32758) covalent geometry : angle 0.64238 / 0.35 (44517) hydrogen bonds : bond 0.12779 / 8.50 ( 1849) hydrogen bonds : angle 6.41933 / 4.60 ( 5382) Misc. bond : bond 0.24934 / 14.92 ( 9) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 878 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 878 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 258 MET cc_start: 0.7599 (mmm) cc_final: 0.7385 (mmm) REVERT: F 250 GLN cc_start: 0.8263 (mt0) cc_final: 0.8002 (mt0) REVERT: F 342 VAL cc_start: 0.7452 (t) cc_final: 0.7164 (m) REVERT: J 82 ILE cc_start: 0.5833 (mt) cc_final: 0.5503 (mm) REVERT: K 110 ASP cc_start: 0.5879 (m-30) cc_final: 0.5505 (m-30) REVERT: K 272 MET cc_start: -0.1358 (mmm) cc_final: -0.1679 (ttm) REVERT: L 452 TYR cc_start: 0.2137 (m-80) cc_final: 0.1923 (m-80) outliers start: 0 outliers final: 0 residues processed: 878 average time/residue: 0.2221 time to fit residues: 303.2919 Evaluate side-chains 416 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 416 time to evaluate : 1.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 248 optimal weight: 4.9990 chunk 207 optimal weight: 4.9990 chunk 155 optimal weight: 0.7980 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 4.9990 chunk 298 optimal weight: 5.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 246 ASN B 68 GLN B 220 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 148 GLN D 150 GLN D 216 GLN D 270 ASN D 317 ASN D 328 ASN E 15 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 148 GLN E 150 GLN E 270 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN ** F 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 279 GLN F 303 HIS F 306 GLN G 112 GLN G 306 GLN H 320 ASN I 112 GLN I 320 ASN ** J 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS Total number of N/Q/H flips: 28 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.111648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3616 r_free = 0.3616 target = 0.083348 restraints weight = 127724.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083424 restraints weight = 88336.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083865 restraints weight = 61980.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.084105 restraints weight = 55797.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.084246 restraints weight = 52020.435| |-----------------------------------------------------------------------------| r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7437 moved from start: 0.4473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.099 32767 Z= 0.285 Angle : 0.934 15.117 44517 Z= 0.440 Chirality : 0.061 0.646 5236 Planarity : 0.006 0.094 5401 Dihedral : 13.036 125.928 5500 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 15.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.28 % Favored : 98.72 % Rotamer: Outliers : 2.48 % Allowed : 11.18 % Favored : 86.33 % 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 are not related in a simple way. whole: 0.54 (0.13), residues: 3894 helix: 0.73 (0.10), residues: 2552 sheet: -0.90 (0.28), residues: 231 loop : 0.08 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 78 TYR 0.027 0.003 TYR B 69 PHE 0.033 0.003 PHE G 169 TRP 0.021 0.002 TRP J 123 HIS 0.009 0.002 HIS D 56 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.28 (32758) covalent geometry : angle 0.93395 / 0.44 (44517) hydrogen bonds : bond 0.04938 / 3.28 ( 1849) hydrogen bonds : angle 5.18551 / 3.72 ( 5382) Misc. bond : bond 0.00219 / 0.12 ( 9) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 398 time to evaluate : 1.242 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7221 (mp10) cc_final: 0.6834 (pp30) REVERT: A 91 GLN cc_start: 0.8059 (mm110) cc_final: 0.7706 (mp10) REVERT: B 145 ASN cc_start: 0.8102 (m110) cc_final: 0.7419 (p0) REVERT: B 216 GLN cc_start: 0.8241 (OUTLIER) cc_final: 0.7725 (pm20) REVERT: B 249 MET cc_start: 0.7375 (mmm) cc_final: 0.7172 (mmm) REVERT: C 116 ILE cc_start: 0.8745 (mp) cc_final: 0.8493 (mm) REVERT: C 167 LEU cc_start: 0.8858 (tp) cc_final: 0.8556 (tp) REVERT: D 53 TYR cc_start: 0.4688 (p90) cc_final: 0.3858 (p90) REVERT: E 341 ARG cc_start: 0.7463 (ptt180) cc_final: 0.6956 (ptt-90) REVERT: F 90 VAL cc_start: 0.8162 (m) cc_final: 0.7891 (p) REVERT: F 258 MET cc_start: 0.8224 (mmm) cc_final: 0.7961 (tpp) REVERT: H 156 ASP cc_start: 0.7934 (m-30) cc_final: 0.7712 (m-30) REVERT: H 183 THR cc_start: 0.8343 (m) cc_final: 0.8103 (p) REVERT: I 60 LYS cc_start: 0.7314 (OUTLIER) cc_final: 0.6759 (ptmt) REVERT: I 61 TYR cc_start: 0.8571 (m-80) cc_final: 0.7618 (m-10) REVERT: I 96 ARG cc_start: 0.7491 (mtm110) cc_final: 0.7164 (ptt-90) REVERT: J 22 GLN cc_start: 0.7713 (mp10) cc_final: 0.6239 (tt0) REVERT: J 214 PHE cc_start: 0.7175 (m-10) cc_final: 0.6642 (m-10) REVERT: K 81 GLN cc_start: 0.6667 (tm-30) cc_final: 0.6281 (pp30) REVERT: K 82 ILE cc_start: 0.7722 (mt) cc_final: 0.7500 (mt) REVERT: K 146 ILE cc_start: 0.5656 (mm) cc_final: 0.5001 (pt) REVERT: K 177 GLU cc_start: 0.8365 (tp30) cc_final: 0.7968 (pm20) REVERT: K 211 TYR cc_start: 0.5407 (t80) cc_final: 0.5148 (m-80) REVERT: M 456 MET cc_start: 0.2741 (mtp) cc_final: 0.2502 (mtp) REVERT: O 456 MET cc_start: 0.3949 (mmt) cc_final: 0.1278 (mmt) REVERT: V 456 MET cc_start: 0.3966 (mmt) cc_final: 0.0230 (mtp) outliers start: 83 outliers final: 50 residues processed: 463 average time/residue: 0.1995 time to fit residues: 150.6597 Evaluate side-chains 346 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 294 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 277 SER Chi-restraints excluded: chain D residue 282 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 190 VAL Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 190 VAL Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 17 ILE Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 272 MET Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 60 LYS Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 235 SER Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain L residue 455 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 184 optimal weight: 6.9990 chunk 134 optimal weight: 0.8980 chunk 219 optimal weight: 8.9990 chunk 182 optimal weight: 3.9990 chunk 249 optimal weight: 8.9990 chunk 86 optimal weight: 0.6980 chunk 66 optimal weight: 5.9990 chunk 14 optimal weight: 0.0470 chunk 74 optimal weight: 0.9990 chunk 177 optimal weight: 4.9990 chunk 94 optimal weight: 0.6980 overall best weight: 0.6680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 150 GLN B 150 GLN B 246 ASN B 256 GLN C 150 GLN C 220 HIS D 112 GLN D 148 GLN D 270 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 112 GLN F 150 GLN F 250 GLN F 275 HIS ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 150 GLN G 320 ASN H 150 GLN H 246 ASN J 112 GLN J 150 GLN J 303 HIS ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4227 r_free = 0.4227 target = 0.114202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3748 r_free = 0.3748 target = 0.088161 restraints weight = 126768.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087717 restraints weight = 78119.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.088427 restraints weight = 57403.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.088447 restraints weight = 48243.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.088544 restraints weight = 46995.575| |-----------------------------------------------------------------------------| r_work (final): 0.3704 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7266 moved from start: 0.4796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32767 Z= 0.126 Angle : 0.680 14.632 44517 Z= 0.315 Chirality : 0.051 0.520 5236 Planarity : 0.004 0.132 5401 Dihedral : 12.667 134.465 5500 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.85 % Favored : 99.15 % Rotamer: Outliers : 2.03 % Allowed : 12.92 % Favored : 85.05 % 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 are not related in a simple way. whole: 1.14 (0.13), residues: 3894 helix: 1.29 (0.10), residues: 2563 sheet: -0.56 (0.29), residues: 231 loop : -0.02 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 260 TYR 0.025 0.001 TYR B 69 PHE 0.028 0.002 PHE G 169 TRP 0.019 0.001 TRP J 123 HIS 0.007 0.001 HIS G 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.13 (32758) covalent geometry : angle 0.68045 / 0.32 (44517) hydrogen bonds : bond 0.03821 / 2.53 ( 1849) hydrogen bonds : angle 4.46982 / 3.20 ( 5382) Misc. bond : bond 0.00153 / 0.10 ( 9) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 367 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 69 TYR cc_start: 0.9026 (t80) cc_final: 0.8597 (t80) REVERT: C 167 LEU cc_start: 0.8772 (tp) cc_final: 0.8450 (tp) REVERT: D 53 TYR cc_start: 0.4620 (p90) cc_final: 0.3551 (p90) REVERT: E 48 CYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8811 (t) REVERT: E 287 GLU cc_start: 0.8229 (tp30) cc_final: 0.7922 (tp30) REVERT: F 111 LEU cc_start: 0.8625 (tt) cc_final: 0.8028 (mp) REVERT: F 129 LYS cc_start: 0.9606 (ttpt) cc_final: 0.9249 (tppt) REVERT: F 358 LEU cc_start: 0.9135 (OUTLIER) cc_final: 0.8924 (mm) REVERT: H 88 SER cc_start: 0.7823 (OUTLIER) cc_final: 0.7494 (p) REVERT: H 248 PHE cc_start: 0.7749 (t80) cc_final: 0.7424 (t80) REVERT: I 61 TYR cc_start: 0.8353 (m-80) cc_final: 0.7821 (m-10) REVERT: I 96 ARG cc_start: 0.7651 (mtm110) cc_final: 0.7197 (ptt-90) REVERT: I 191 LEU cc_start: 0.8232 (tp) cc_final: 0.7968 (tt) REVERT: I 216 GLN cc_start: 0.8501 (OUTLIER) cc_final: 0.8206 (pm20) REVERT: J 123 TRP cc_start: 0.5740 (t60) cc_final: 0.4964 (t60) REVERT: K 51 ILE cc_start: 0.3667 (tp) cc_final: 0.3441 (mm) REVERT: K 81 GLN cc_start: 0.6773 (tm-30) cc_final: 0.6420 (pp30) REVERT: K 146 ILE cc_start: 0.5611 (mm) cc_final: 0.5012 (pt) REVERT: K 177 GLU cc_start: 0.8291 (tp30) cc_final: 0.8036 (pm20) REVERT: K 220 HIS cc_start: 0.7832 (OUTLIER) cc_final: 0.7603 (m-70) REVERT: O 456 MET cc_start: 0.3182 (mmt) cc_final: 0.0075 (mmt) REVERT: Q 455 ILE cc_start: 0.8639 (mm) cc_final: 0.8414 (mm) REVERT: Q 456 MET cc_start: 0.7720 (mtm) cc_final: 0.6932 (mpp) REVERT: R 456 MET cc_start: -0.0328 (mtt) cc_final: -0.0796 (mtt) outliers start: 68 outliers final: 33 residues processed: 419 average time/residue: 0.1903 time to fit residues: 132.3981 Evaluate side-chains 330 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 292 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 358 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 349 SER Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain K residue 220 HIS Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 68 optimal weight: 10.0000 chunk 328 optimal weight: 8.9990 chunk 110 optimal weight: 7.9990 chunk 216 optimal weight: 0.9990 chunk 242 optimal weight: 8.9990 chunk 214 optimal weight: 0.7980 chunk 184 optimal weight: 0.9980 chunk 91 optimal weight: 0.6980 chunk 100 optimal weight: 7.9990 chunk 203 optimal weight: 0.2980 chunk 351 optimal weight: 20.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN H 246 ASN I 150 GLN K 85 ASN K 150 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.113766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.087772 restraints weight = 129123.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.087257 restraints weight = 79694.229| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3718 r_free = 0.3718 target = 0.088070 restraints weight = 58449.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3719 r_free = 0.3719 target = 0.088099 restraints weight = 48470.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3720 r_free = 0.3720 target = 0.088147 restraints weight = 47336.141| |-----------------------------------------------------------------------------| r_work (final): 0.3692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 32767 Z= 0.123 Angle : 0.677 14.395 44517 Z= 0.309 Chirality : 0.050 0.490 5236 Planarity : 0.004 0.082 5401 Dihedral : 12.531 132.368 5500 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.08 % Favored : 98.92 % Rotamer: Outliers : 1.85 % Allowed : 14.17 % Favored : 83.97 % 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 are not related in a simple way. whole: 1.31 (0.14), residues: 3894 helix: 1.45 (0.10), residues: 2563 sheet: -0.52 (0.29), residues: 231 loop : -0.03 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 78 TYR 0.025 0.001 TYR B 69 PHE 0.036 0.002 PHE J 210 TRP 0.012 0.001 TRP J 123 HIS 0.004 0.001 HIS C 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 (32758) covalent geometry : angle 0.67726 / 0.31 (44517) hydrogen bonds : bond 0.03585 / 2.38 ( 1849) hydrogen bonds : angle 4.34427 / 3.10 ( 5382) Misc. bond : bond 0.00276 / 0.20 ( 9) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 405 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 343 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 69 TYR cc_start: 0.7038 (t80) cc_final: 0.6630 (t80) REVERT: A 201 MET cc_start: 0.7223 (ptt) cc_final: 0.6634 (ppp) REVERT: B 216 GLN cc_start: 0.8124 (OUTLIER) cc_final: 0.7667 (pm20) REVERT: C 69 TYR cc_start: 0.9108 (t80) cc_final: 0.8835 (t80) REVERT: C 135 MET cc_start: 0.7325 (tpp) cc_final: 0.7063 (tpp) REVERT: C 167 LEU cc_start: 0.8777 (tp) cc_final: 0.8549 (tp) REVERT: C 272 MET cc_start: 0.7604 (mtm) cc_final: 0.6804 (ttp) REVERT: D 13 TYR cc_start: 0.7803 (m-80) cc_final: 0.7300 (m-80) REVERT: D 45 THR cc_start: 0.7705 (m) cc_final: 0.7453 (m) REVERT: D 53 TYR cc_start: 0.4876 (p90) cc_final: 0.4200 (p90) REVERT: D 258 MET cc_start: 0.9042 (mmm) cc_final: 0.8653 (tpp) REVERT: E 48 CYS cc_start: 0.9350 (OUTLIER) cc_final: 0.8921 (t) REVERT: E 287 GLU cc_start: 0.8312 (tp30) cc_final: 0.8040 (tp30) REVERT: F 129 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9241 (tppt) REVERT: F 347 LEU cc_start: 0.8570 (OUTLIER) cc_final: 0.8316 (mm) REVERT: H 88 SER cc_start: 0.7966 (OUTLIER) cc_final: 0.7643 (p) REVERT: H 183 THR cc_start: 0.8140 (m) cc_final: 0.7892 (p) REVERT: I 96 ARG cc_start: 0.7588 (mtm110) cc_final: 0.7168 (ptt-90) REVERT: I 191 LEU cc_start: 0.8229 (tp) cc_final: 0.7915 (tt) REVERT: I 216 GLN cc_start: 0.8531 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: J 123 TRP cc_start: 0.5561 (t60) cc_final: 0.4832 (t60) REVERT: J 226 GLU cc_start: 0.7316 (tt0) cc_final: 0.6620 (pp20) REVERT: K 81 GLN cc_start: 0.6534 (tm-30) cc_final: 0.6139 (pp30) REVERT: K 146 ILE cc_start: 0.5629 (mm) cc_final: 0.5034 (pt) REVERT: K 172 LEU cc_start: 0.5941 (mt) cc_final: 0.4119 (tt) REVERT: K 177 GLU cc_start: 0.8277 (tp30) cc_final: 0.8046 (pm20) REVERT: K 201 MET cc_start: 0.2210 (pmm) cc_final: 0.1930 (pmm) REVERT: K 211 TYR cc_start: 0.5473 (t80) cc_final: 0.5128 (m-80) REVERT: O 456 MET cc_start: 0.3322 (mmt) cc_final: 0.0080 (mmt) REVERT: V 456 MET cc_start: 0.3746 (mmp) cc_final: 0.2997 (mmm) outliers start: 62 outliers final: 39 residues processed: 388 average time/residue: 0.1809 time to fit residues: 118.4097 Evaluate side-chains 322 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 278 time to evaluate : 1.079 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 212 ASP Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 258 MET Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 203 optimal weight: 0.5980 chunk 236 optimal weight: 2.9990 chunk 376 optimal weight: 9.9990 chunk 58 optimal weight: 0.7980 chunk 70 optimal weight: 10.0000 chunk 320 optimal weight: 5.9990 chunk 148 optimal weight: 3.9990 chunk 209 optimal weight: 6.9990 chunk 157 optimal weight: 1.9990 chunk 262 optimal weight: 0.9980 chunk 293 optimal weight: 4.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 91 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 15 HIS D 216 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN E 317 ASN ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN K 275 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.112259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.087437 restraints weight = 128526.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.086472 restraints weight = 85559.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.087173 restraints weight = 67877.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087362 restraints weight = 52901.724| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.087460 restraints weight = 50792.239| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.5777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 32767 Z= 0.147 Angle : 0.707 15.336 44517 Z= 0.321 Chirality : 0.052 0.552 5236 Planarity : 0.004 0.060 5401 Dihedral : 12.507 133.328 5500 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.27 % Allowed : 14.86 % Favored : 82.86 % 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 are not related in a simple way. whole: 1.39 (0.14), residues: 3894 helix: 1.52 (0.10), residues: 2563 sheet: -0.50 (0.29), residues: 231 loop : -0.02 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG I 78 TYR 0.035 0.002 TYR D 69 PHE 0.036 0.002 PHE K 224 TRP 0.009 0.001 TRP G 123 HIS 0.007 0.001 HIS F 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.15 (32758) covalent geometry : angle 0.70680 / 0.32 (44517) hydrogen bonds : bond 0.03609 / 2.38 ( 1849) hydrogen bonds : angle 4.36716 / 3.10 ( 5382) Misc. bond : bond 0.00120 / 0.08 ( 9) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 312 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7877 (mp10) cc_final: 0.7090 (tp40) REVERT: A 201 MET cc_start: 0.7012 (ptt) cc_final: 0.6427 (tmm) REVERT: B 216 GLN cc_start: 0.8114 (OUTLIER) cc_final: 0.7649 (pm20) REVERT: D 13 TYR cc_start: 0.8047 (m-80) cc_final: 0.7562 (m-80) REVERT: E 48 CYS cc_start: 0.9366 (OUTLIER) cc_final: 0.8619 (t) REVERT: E 287 GLU cc_start: 0.8263 (tp30) cc_final: 0.8005 (tp30) REVERT: F 21 SER cc_start: 0.8304 (t) cc_final: 0.8042 (p) REVERT: F 129 LYS cc_start: 0.9602 (ttpt) cc_final: 0.9233 (tppt) REVERT: F 258 MET cc_start: 0.8401 (mmm) cc_final: 0.8117 (tpp) REVERT: F 347 LEU cc_start: 0.8510 (OUTLIER) cc_final: 0.8261 (mm) REVERT: H 183 THR cc_start: 0.8109 (m) cc_final: 0.7888 (p) REVERT: H 266 ARG cc_start: 0.7679 (ttt180) cc_final: 0.6806 (ttt180) REVERT: I 96 ARG cc_start: 0.7639 (mtm110) cc_final: 0.7255 (mtm-85) REVERT: J 123 TRP cc_start: 0.5360 (t60) cc_final: 0.4618 (t60) REVERT: J 226 GLU cc_start: 0.7259 (tt0) cc_final: 0.6330 (pp20) REVERT: J 285 VAL cc_start: 0.8643 (t) cc_final: 0.8223 (p) REVERT: K 104 LYS cc_start: 0.6798 (mmtt) cc_final: 0.5890 (tppt) REVERT: K 146 ILE cc_start: 0.5489 (mm) cc_final: 0.4825 (pt) REVERT: K 172 LEU cc_start: 0.6140 (mt) cc_final: 0.4311 (tt) REVERT: K 177 GLU cc_start: 0.8335 (tp30) cc_final: 0.8091 (pm20) REVERT: K 201 MET cc_start: 0.2288 (pmm) cc_final: 0.1889 (pmm) REVERT: K 211 TYR cc_start: 0.5113 (t80) cc_final: 0.4897 (m-80) REVERT: K 216 GLN cc_start: 0.3950 (OUTLIER) cc_final: 0.3720 (mp10) REVERT: O 456 MET cc_start: 0.3416 (mmt) cc_final: 0.0435 (mmt) REVERT: S 452 TYR cc_start: 0.8236 (m-80) cc_final: 0.7652 (m-80) REVERT: V 456 MET cc_start: 0.3320 (mmp) cc_final: 0.2545 (mmm) outliers start: 76 outliers final: 57 residues processed: 371 average time/residue: 0.1861 time to fit residues: 116.5861 Evaluate side-chains 337 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 276 time to evaluate : 1.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 216 GLN Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 0.7980 chunk 291 optimal weight: 5.9990 chunk 175 optimal weight: 2.9990 chunk 160 optimal weight: 4.9990 chunk 241 optimal weight: 3.9990 chunk 270 optimal weight: 2.9990 chunk 336 optimal weight: 8.9990 chunk 223 optimal weight: 6.9990 chunk 267 optimal weight: 1.9990 chunk 312 optimal weight: 10.0000 chunk 179 optimal weight: 7.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN B 42 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN F 320 ASN F 344 ASN G 112 GLN G 270 ASN G 328 ASN H 81 GLN H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.109559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.086224 restraints weight = 129506.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.084537 restraints weight = 100373.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085195 restraints weight = 85665.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.085508 restraints weight = 63202.957| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085555 restraints weight = 60355.905| |-----------------------------------------------------------------------------| r_work (final): 0.3647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.6531 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 32767 Z= 0.207 Angle : 0.798 15.434 44517 Z= 0.366 Chirality : 0.056 0.730 5236 Planarity : 0.005 0.070 5401 Dihedral : 12.649 136.239 5500 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.99 % Allowed : 15.31 % Favored : 81.70 % 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 are not related in a simple way. whole: 1.18 (0.13), residues: 3894 helix: 1.33 (0.10), residues: 2574 sheet: -0.56 (0.29), residues: 231 loop : -0.07 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG A 78 TYR 0.078 0.002 TYR B 23 PHE 0.031 0.003 PHE B 248 TRP 0.015 0.002 TRP I 261 HIS 0.007 0.001 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00460 / 0.21 (32758) covalent geometry : angle 0.79845 / 0.37 (44517) hydrogen bonds : bond 0.04036 / 2.64 ( 1849) hydrogen bonds : angle 4.63984 / 3.30 ( 5382) Misc. bond : bond 0.00227 / 0.13 ( 9) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 399 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 299 time to evaluate : 1.163 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7747 (mp10) cc_final: 0.7284 (mp10) REVERT: A 201 MET cc_start: 0.6992 (ptt) cc_final: 0.6392 (tmm) REVERT: A 287 GLU cc_start: 0.5162 (mm-30) cc_final: 0.4572 (pt0) REVERT: B 17 ILE cc_start: 0.7587 (OUTLIER) cc_final: 0.7261 (mm) REVERT: B 216 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: C 272 MET cc_start: 0.7527 (mtm) cc_final: 0.6230 (ttp) REVERT: D 113 MET cc_start: 0.7651 (ppp) cc_final: 0.7081 (tmm) REVERT: E 287 GLU cc_start: 0.8096 (tp30) cc_final: 0.7885 (tp30) REVERT: F 129 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9223 (tppt) REVERT: F 258 MET cc_start: 0.8236 (mmm) cc_final: 0.7885 (tpp) REVERT: F 347 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8291 (mm) REVERT: G 231 LEU cc_start: 0.7951 (OUTLIER) cc_final: 0.7298 (mm) REVERT: H 183 THR cc_start: 0.8187 (m) cc_final: 0.7948 (p) REVERT: I 96 ARG cc_start: 0.7725 (mtm110) cc_final: 0.7327 (mpp-170) REVERT: I 295 MET cc_start: 0.8596 (mmm) cc_final: 0.8343 (mmm) REVERT: J 94 LEU cc_start: 0.7163 (tp) cc_final: 0.6914 (mm) REVERT: J 123 TRP cc_start: 0.5396 (t60) cc_final: 0.4555 (t60) REVERT: J 226 GLU cc_start: 0.7143 (tt0) cc_final: 0.6190 (pp20) REVERT: J 295 MET cc_start: 0.8606 (mmm) cc_final: 0.8249 (mpp) REVERT: K 104 LYS cc_start: 0.6635 (mmtt) cc_final: 0.6113 (tppt) REVERT: K 146 ILE cc_start: 0.4713 (mm) cc_final: 0.4395 (pt) REVERT: K 177 GLU cc_start: 0.8286 (tp30) cc_final: 0.8037 (pm20) REVERT: K 201 MET cc_start: 0.2053 (pmm) cc_final: 0.1836 (pmm) REVERT: O 456 MET cc_start: 0.3891 (mmt) cc_final: 0.0767 (mmt) REVERT: S 452 TYR cc_start: 0.8197 (m-80) cc_final: 0.7621 (m-80) REVERT: V 456 MET cc_start: 0.2813 (mmp) cc_final: 0.2101 (mmm) outliers start: 100 outliers final: 64 residues processed: 374 average time/residue: 0.1913 time to fit residues: 120.0267 Evaluate side-chains 332 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 264 time to evaluate : 1.045 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain F residue 347 LEU Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 258 MET Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 5 optimal weight: 5.9990 chunk 54 optimal weight: 10.0000 chunk 236 optimal weight: 1.9990 chunk 304 optimal weight: 8.9990 chunk 293 optimal weight: 0.8980 chunk 352 optimal weight: 30.0000 chunk 31 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 229 optimal weight: 0.0770 chunk 70 optimal weight: 0.0970 chunk 139 optimal weight: 9.9990 overall best weight: 1.8140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 317 ASN G 112 GLN H 275 HIS H 279 GLN ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 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 = 0.4154 r_free = 0.4154 target = 0.110215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.086959 restraints weight = 128737.334| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.085169 restraints weight = 96558.749| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.085908 restraints weight = 83799.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.086274 restraints weight = 61314.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.086357 restraints weight = 58305.462| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.6797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32767 Z= 0.164 Angle : 0.762 15.970 44517 Z= 0.345 Chirality : 0.055 0.815 5236 Planarity : 0.004 0.110 5401 Dihedral : 12.856 178.339 5500 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.51 % Allowed : 16.36 % Favored : 81.13 % 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 are not related in a simple way. whole: 1.36 (0.13), residues: 3894 helix: 1.54 (0.10), residues: 2508 sheet: -0.53 (0.29), residues: 231 loop : -0.08 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.024 0.001 ARG E 78 TYR 0.033 0.002 TYR B 69 PHE 0.028 0.002 PHE G 210 TRP 0.012 0.002 TRP I 261 HIS 0.005 0.001 HIS C 275 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (32758) covalent geometry : angle 0.76177 / 0.35 (44517) hydrogen bonds : bond 0.03734 / 2.45 ( 1849) hydrogen bonds : angle 4.46937 / 3.18 ( 5382) Misc. bond : bond 0.00272 / 0.18 ( 9) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 295 time to evaluate : 1.232 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7849 (mp10) cc_final: 0.7352 (mp10) REVERT: A 201 MET cc_start: 0.6863 (ptt) cc_final: 0.6354 (tmm) REVERT: B 17 ILE cc_start: 0.7510 (OUTLIER) cc_final: 0.7178 (mm) REVERT: B 216 GLN cc_start: 0.8174 (OUTLIER) cc_final: 0.7702 (pm20) REVERT: C 163 CYS cc_start: 0.7884 (m) cc_final: 0.6764 (t) REVERT: D 113 MET cc_start: 0.7680 (ppp) cc_final: 0.7066 (tmm) REVERT: D 238 SER cc_start: 0.8478 (OUTLIER) cc_final: 0.8231 (p) REVERT: E 241 GLU cc_start: 0.7774 (pp20) cc_final: 0.7212 (pp20) REVERT: E 287 GLU cc_start: 0.8111 (tp30) cc_final: 0.7772 (tp30) REVERT: F 129 LYS cc_start: 0.9589 (ttpt) cc_final: 0.9224 (tppt) REVERT: F 135 MET cc_start: 0.7914 (ttm) cc_final: 0.7599 (tmm) REVERT: F 258 MET cc_start: 0.8303 (mmm) cc_final: 0.7969 (tpp) REVERT: H 183 THR cc_start: 0.8120 (m) cc_final: 0.7879 (p) REVERT: H 224 PHE cc_start: 0.7193 (t80) cc_final: 0.6901 (t80) REVERT: I 96 ARG cc_start: 0.7696 (mtm110) cc_final: 0.7323 (mpp-170) REVERT: J 94 LEU cc_start: 0.7289 (tp) cc_final: 0.7058 (mm) REVERT: J 123 TRP cc_start: 0.5278 (t60) cc_final: 0.4436 (t60) REVERT: J 285 VAL cc_start: 0.8679 (t) cc_final: 0.8229 (p) REVERT: J 295 MET cc_start: 0.8583 (mmm) cc_final: 0.8230 (mpp) REVERT: K 104 LYS cc_start: 0.6692 (mmtt) cc_final: 0.6088 (tppt) REVERT: K 146 ILE cc_start: 0.4521 (mm) cc_final: 0.4282 (pt) REVERT: K 172 LEU cc_start: 0.5942 (mt) cc_final: 0.4288 (tt) REVERT: K 177 GLU cc_start: 0.8222 (tp30) cc_final: 0.8007 (pm20) REVERT: K 201 MET cc_start: 0.2258 (OUTLIER) cc_final: 0.1990 (pmm) REVERT: K 224 PHE cc_start: 0.8306 (t80) cc_final: 0.7977 (t80) REVERT: O 456 MET cc_start: 0.3950 (mmt) cc_final: 0.0744 (mmt) REVERT: Q 456 MET cc_start: 0.7217 (mpp) cc_final: 0.7014 (mpp) REVERT: V 456 MET cc_start: 0.2697 (mmp) cc_final: 0.2029 (mmm) outliers start: 84 outliers final: 64 residues processed: 355 average time/residue: 0.1820 time to fit residues: 108.6229 Evaluate side-chains 332 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 264 time to evaluate : 1.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 24 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 201 MET Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 172 optimal weight: 3.9990 chunk 376 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 173 optimal weight: 3.9990 chunk 221 optimal weight: 2.9990 chunk 271 optimal weight: 10.0000 chunk 325 optimal weight: 4.9990 chunk 28 optimal weight: 20.0000 chunk 265 optimal weight: 4.9990 chunk 323 optimal weight: 8.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN B 68 GLN B 270 ASN B 275 HIS B 328 ASN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4212 r_free = 0.4212 target = 0.111932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.091188 restraints weight = 134649.800| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.090536 restraints weight = 118231.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091457 restraints weight = 92178.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091272 restraints weight = 66475.629| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091579 restraints weight = 64212.868| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7302 moved from start: 0.7178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 32767 Z= 0.208 Angle : 0.817 16.452 44517 Z= 0.373 Chirality : 0.056 0.896 5236 Planarity : 0.005 0.102 5401 Dihedral : 12.731 133.597 5500 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.75 % Allowed : 16.21 % Favored : 81.04 % 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 are not related in a simple way. whole: 1.06 (0.13), residues: 3894 helix: 1.25 (0.10), residues: 2574 sheet: -0.61 (0.29), residues: 231 loop : -0.11 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.047 0.001 ARG E 78 TYR 0.036 0.002 TYR B 69 PHE 0.047 0.003 PHE J 214 TRP 0.014 0.002 TRP A 261 HIS 0.006 0.001 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00464 / 0.21 (32758) covalent geometry : angle 0.81720 / 0.37 (44517) hydrogen bonds : bond 0.04014 / 2.63 ( 1849) hydrogen bonds : angle 4.66783 / 3.33 ( 5382) Misc. bond : bond 0.00347 / 0.24 ( 9) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 278 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 GLN cc_start: 0.7534 (mp10) cc_final: 0.7012 (mp10) REVERT: A 201 MET cc_start: 0.6611 (ptt) cc_final: 0.6350 (tmm) REVERT: B 17 ILE cc_start: 0.7445 (OUTLIER) cc_final: 0.7163 (mm) REVERT: B 210 PHE cc_start: 0.7861 (OUTLIER) cc_final: 0.7640 (t80) REVERT: B 216 GLN cc_start: 0.8135 (OUTLIER) cc_final: 0.7710 (pm20) REVERT: C 295 MET cc_start: 0.7726 (mpp) cc_final: 0.7340 (mmt) REVERT: D 113 MET cc_start: 0.7576 (OUTLIER) cc_final: 0.6984 (tmm) REVERT: D 238 SER cc_start: 0.8358 (OUTLIER) cc_final: 0.8080 (p) REVERT: E 135 MET cc_start: 0.8582 (ptm) cc_final: 0.8332 (tmm) REVERT: E 287 GLU cc_start: 0.7903 (tp30) cc_final: 0.7672 (tp30) REVERT: F 129 LYS cc_start: 0.9465 (ttpt) cc_final: 0.9148 (tppt) REVERT: F 135 MET cc_start: 0.7790 (ttm) cc_final: 0.7551 (tmm) REVERT: F 271 ILE cc_start: 0.8398 (pt) cc_final: 0.8129 (mm) REVERT: H 183 THR cc_start: 0.8183 (m) cc_final: 0.7934 (p) REVERT: I 96 ARG cc_start: 0.7759 (mtm110) cc_final: 0.7404 (mpp-170) REVERT: J 94 LEU cc_start: 0.7088 (tp) cc_final: 0.6857 (mm) REVERT: J 226 GLU cc_start: 0.6826 (tt0) cc_final: 0.5986 (pp20) REVERT: J 285 VAL cc_start: 0.8453 (t) cc_final: 0.7965 (p) REVERT: K 102 LYS cc_start: 0.6210 (ttmm) cc_final: 0.5781 (mmtt) REVERT: K 104 LYS cc_start: 0.6835 (mmtt) cc_final: 0.6166 (tppt) REVERT: K 224 PHE cc_start: 0.7887 (t80) cc_final: 0.7670 (t80) REVERT: O 456 MET cc_start: 0.3173 (mmt) cc_final: 0.0147 (mmt) REVERT: V 456 MET cc_start: 0.1871 (mmp) cc_final: 0.1296 (mmm) outliers start: 92 outliers final: 73 residues processed: 344 average time/residue: 0.1893 time to fit residues: 109.4224 Evaluate side-chains 335 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 257 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 17 ILE Chi-restraints excluded: chain B residue 210 PHE Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 18 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 36 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain H residue 342 VAL Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 381 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 371 optimal weight: 20.0000 chunk 383 optimal weight: 9.9990 chunk 20 optimal weight: 8.9990 chunk 313 optimal weight: 0.4980 chunk 323 optimal weight: 10.0000 chunk 369 optimal weight: 5.9990 chunk 181 optimal weight: 0.7980 chunk 243 optimal weight: 5.9990 chunk 191 optimal weight: 0.7980 overall best weight: 1.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 HIS ** 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 = 0.4132 r_free = 0.4132 target = 0.109894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.087027 restraints weight = 133080.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085283 restraints weight = 105561.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085941 restraints weight = 91614.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.086150 restraints weight = 67049.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.086249 restraints weight = 64008.967| |-----------------------------------------------------------------------------| r_work (final): 0.3644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7381 moved from start: 0.7388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 32767 Z= 0.165 Angle : 0.792 16.615 44517 Z= 0.357 Chirality : 0.056 0.934 5236 Planarity : 0.006 0.362 5401 Dihedral : 12.968 170.299 5500 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.81 % Allowed : 16.42 % Favored : 80.77 % 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 are not related in a simple way. whole: 1.16 (0.14), residues: 3894 helix: 1.34 (0.10), residues: 2574 sheet: -0.63 (0.29), residues: 231 loop : -0.12 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG E 78 TYR 0.047 0.002 TYR F 23 PHE 0.030 0.002 PHE I 169 TRP 0.014 0.002 TRP A 261 HIS 0.005 0.001 HIS F 117 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.16 (32758) covalent geometry : angle 0.79221 / 0.36 (44517) hydrogen bonds : bond 0.03820 / 2.49 ( 1849) hydrogen bonds : angle 4.55458 / 3.25 ( 5382) Misc. bond : bond 0.00357 / 0.26 ( 9) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 380 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 286 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 GLN cc_start: 0.7586 (OUTLIER) cc_final: 0.7287 (mm110) REVERT: A 91 GLN cc_start: 0.7881 (mp10) cc_final: 0.7344 (mp10) REVERT: A 201 MET cc_start: 0.6888 (ptt) cc_final: 0.6296 (tmm) REVERT: B 216 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7758 (pm20) REVERT: B 309 LYS cc_start: 0.8384 (ttpt) cc_final: 0.7877 (ttmt) REVERT: C 295 MET cc_start: 0.7937 (mpp) cc_final: 0.7572 (mmt) REVERT: D 53 TYR cc_start: 0.5510 (p90) cc_final: 0.5002 (p90) REVERT: D 113 MET cc_start: 0.7411 (OUTLIER) cc_final: 0.6974 (tmm) REVERT: D 238 SER cc_start: 0.8364 (OUTLIER) cc_final: 0.7166 (p) REVERT: E 135 MET cc_start: 0.8695 (ptm) cc_final: 0.8485 (tmm) REVERT: E 287 GLU cc_start: 0.8029 (tp30) cc_final: 0.7684 (tp30) REVERT: F 129 LYS cc_start: 0.9581 (ttpt) cc_final: 0.9230 (tppt) REVERT: F 135 MET cc_start: 0.7860 (ttm) cc_final: 0.7562 (tmm) REVERT: F 210 PHE cc_start: 0.8809 (OUTLIER) cc_final: 0.8237 (m-80) REVERT: G 135 MET cc_start: 0.9022 (tpt) cc_final: 0.8807 (tpt) REVERT: H 183 THR cc_start: 0.8106 (m) cc_final: 0.7855 (p) REVERT: I 96 ARG cc_start: 0.7704 (mtm110) cc_final: 0.7324 (mpp-170) REVERT: I 287 GLU cc_start: 0.8695 (mm-30) cc_final: 0.8476 (mm-30) REVERT: J 94 LEU cc_start: 0.7198 (tp) cc_final: 0.6930 (mm) REVERT: J 135 MET cc_start: -0.3384 (OUTLIER) cc_final: -0.3611 (mtt) REVERT: J 226 GLU cc_start: 0.7075 (tt0) cc_final: 0.6053 (pp20) REVERT: J 249 MET cc_start: 0.7358 (OUTLIER) cc_final: 0.6967 (tpt) REVERT: J 285 VAL cc_start: 0.8662 (t) cc_final: 0.8199 (p) REVERT: J 295 MET cc_start: 0.8566 (mmm) cc_final: 0.7902 (mpp) REVERT: K 102 LYS cc_start: 0.6161 (ttmm) cc_final: 0.5767 (mmtt) REVERT: K 104 LYS cc_start: 0.6680 (mmtt) cc_final: 0.6089 (tppt) REVERT: K 211 TYR cc_start: 0.5281 (OUTLIER) cc_final: 0.4499 (m-10) REVERT: K 224 PHE cc_start: 0.8242 (t80) cc_final: 0.8007 (t80) REVERT: K 287 GLU cc_start: 0.8232 (tp30) cc_final: 0.7921 (mp0) REVERT: K 337 MET cc_start: 0.8419 (ppp) cc_final: 0.8188 (ppp) REVERT: O 456 MET cc_start: 0.3982 (mmt) cc_final: 0.0656 (mmt) REVERT: Q 456 MET cc_start: 0.7404 (mpp) cc_final: 0.7075 (mpp) REVERT: V 456 MET cc_start: 0.2663 (mmp) cc_final: 0.1955 (mmm) outliers start: 94 outliers final: 70 residues processed: 350 average time/residue: 0.1910 time to fit residues: 112.3404 Evaluate side-chains 347 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 269 time to evaluate : 1.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 41 GLN Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 211 TYR Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 39 optimal weight: 8.9990 chunk 47 optimal weight: 5.9990 chunk 359 optimal weight: 0.0470 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 200 optimal weight: 0.5980 chunk 11 optimal weight: 1.9990 chunk 88 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 273 optimal weight: 1.9990 overall best weight: 0.9080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 220 HIS ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS H 256 GLN ** H 306 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 = 0.4162 r_free = 0.4162 target = 0.111505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.088755 restraints weight = 131932.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.087063 restraints weight = 102635.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.087900 restraints weight = 88151.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.088164 restraints weight = 64449.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.088375 restraints weight = 62272.991| |-----------------------------------------------------------------------------| r_work (final): 0.3682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.7473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 32767 Z= 0.133 Angle : 0.791 16.408 44517 Z= 0.357 Chirality : 0.055 0.956 5236 Planarity : 0.004 0.062 5401 Dihedral : 12.945 177.103 5500 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.33 % Allowed : 17.25 % Favored : 80.41 % 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 are not related in a simple way. whole: 1.26 (0.14), residues: 3894 helix: 1.47 (0.10), residues: 2563 sheet: -0.62 (0.29), residues: 231 loop : -0.18 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG E 132 TYR 0.102 0.002 TYR F 23 PHE 0.030 0.002 PHE I 169 TRP 0.023 0.002 TRP A 261 HIS 0.004 0.001 HIS I 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.13 (32758) covalent geometry : angle 0.79120 / 0.36 (44517) hydrogen bonds : bond 0.03692 / 2.42 ( 1849) hydrogen bonds : angle 4.44965 / 3.19 ( 5382) Misc. bond : bond 0.00524 / 0.37 ( 9) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 372 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 294 time to evaluate : 1.260 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.8737 (tt0) cc_final: 0.8536 (pp30) REVERT: A 91 GLN cc_start: 0.7871 (mp10) cc_final: 0.7347 (mp10) REVERT: A 201 MET cc_start: 0.6846 (ptt) cc_final: 0.6231 (tmm) REVERT: B 216 GLN cc_start: 0.8199 (OUTLIER) cc_final: 0.7755 (pm20) REVERT: C 135 MET cc_start: 0.7007 (mmm) cc_final: 0.6708 (mmm) REVERT: C 295 MET cc_start: 0.7981 (mpp) cc_final: 0.7620 (mmt) REVERT: D 113 MET cc_start: 0.7372 (OUTLIER) cc_final: 0.6918 (tmm) REVERT: E 135 MET cc_start: 0.8569 (ptm) cc_final: 0.8364 (tmm) REVERT: E 287 GLU cc_start: 0.7947 (tp30) cc_final: 0.7542 (tp30) REVERT: F 129 LYS cc_start: 0.9562 (ttpt) cc_final: 0.9232 (tppt) REVERT: F 135 MET cc_start: 0.7889 (ttm) cc_final: 0.7622 (tmm) REVERT: F 210 PHE cc_start: 0.8801 (OUTLIER) cc_final: 0.8323 (m-80) REVERT: H 183 THR cc_start: 0.8032 (m) cc_final: 0.7816 (p) REVERT: I 96 ARG cc_start: 0.7713 (mtm110) cc_final: 0.7322 (mpp-170) REVERT: I 249 MET cc_start: 0.6951 (tpt) cc_final: 0.6736 (tpt) REVERT: J 94 LEU cc_start: 0.7228 (tp) cc_final: 0.7001 (mm) REVERT: J 167 LEU cc_start: 0.7480 (mt) cc_final: 0.7251 (mt) REVERT: J 226 GLU cc_start: 0.7230 (tt0) cc_final: 0.6188 (pp20) REVERT: J 249 MET cc_start: 0.7364 (OUTLIER) cc_final: 0.6936 (tpt) REVERT: J 295 MET cc_start: 0.8545 (mmm) cc_final: 0.7916 (mpp) REVERT: K 102 LYS cc_start: 0.6173 (ttmm) cc_final: 0.5724 (mmtt) REVERT: K 211 TYR cc_start: 0.5256 (OUTLIER) cc_final: 0.4400 (m-10) REVERT: K 287 GLU cc_start: 0.8188 (tp30) cc_final: 0.7869 (mp0) REVERT: K 337 MET cc_start: 0.8354 (ppp) cc_final: 0.8101 (ppp) REVERT: O 456 MET cc_start: 0.4116 (mmt) cc_final: 0.3034 (mmm) REVERT: Q 452 TYR cc_start: 0.7450 (m-80) cc_final: 0.7247 (m-80) REVERT: Q 456 MET cc_start: 0.7302 (mpp) cc_final: 0.6941 (mpp) REVERT: V 456 MET cc_start: 0.2582 (mmp) cc_final: 0.1963 (mmm) outliers start: 78 outliers final: 62 residues processed: 348 average time/residue: 0.1897 time to fit residues: 111.5988 Evaluate side-chains 342 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 275 time to evaluate : 1.536 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 248 PHE Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 289 TYR Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 113 MET Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 222 SER Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 299 SER Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 211 TYR Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 376 optimal weight: 20.0000 chunk 188 optimal weight: 0.0010 chunk 290 optimal weight: 5.9990 chunk 278 optimal weight: 10.0000 chunk 17 optimal weight: 7.9990 chunk 139 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 54 optimal weight: 6.9990 chunk 371 optimal weight: 20.0000 chunk 87 optimal weight: 8.9990 chunk 294 optimal weight: 0.0770 overall best weight: 3.2150 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 41 GLN B 81 GLN B 269 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 256 GLN ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.110765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3837 r_free = 0.3837 target = 0.090420 restraints weight = 134373.404| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3778 r_free = 0.3778 target = 0.089797 restraints weight = 125452.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.089965 restraints weight = 103016.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.090244 restraints weight = 74893.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3795 r_free = 0.3795 target = 0.090483 restraints weight = 68717.670| |-----------------------------------------------------------------------------| r_work (final): 0.3790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.7955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 32767 Z= 0.250 Angle : 0.900 16.680 44517 Z= 0.416 Chirality : 0.059 0.962 5236 Planarity : 0.005 0.080 5401 Dihedral : 13.101 175.429 5500 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 17.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 2.45 % Allowed : 17.52 % Favored : 80.02 % 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 are not related in a simple way. whole: 0.82 (0.13), residues: 3894 helix: 1.09 (0.10), residues: 2574 sheet: -0.82 (0.29), residues: 231 loop : -0.25 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG E 78 TYR 0.079 0.003 TYR F 23 PHE 0.046 0.003 PHE B 210 TRP 0.018 0.002 TRP A 261 HIS 0.008 0.002 HIS D 303 Details of bonding type rmsd/Z covalent geometry : bond 0.00554 / 0.25 (32758) covalent geometry : angle 0.89980 / 0.42 (44517) hydrogen bonds : bond 0.04345 / 2.85 ( 1849) hydrogen bonds : angle 4.90699 / 3.51 ( 5382) Misc. bond : bond 0.00541 / 0.37 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5406.89 seconds wall clock time: 95 minutes 12.43 seconds (5712.43 seconds total)