Starting phenix.real_space_refine on Tue Aug 26 00:18:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdr_17619/08_2025/8pdr_17619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdr_17619/08_2025/8pdr_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_2025/8pdr_17619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2025/8pdr_17619.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2025/8pdr_17619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdr_17619/08_2025/8pdr_17619.map" } 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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 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: {'RNA': 7} Modifications used: {'rna2p_pyr': 1, 'rna3p_pyr': 6} Link IDs: {'rna2p': 1, 'rna3p': 5} Time building chain proxies: 7.02, per 1000 atoms: 0.22 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: 3.10 Conformation dependent library (CDL) restraints added in 1.5 seconds Enol-peptide restraints added in 953.7 nanoseconds 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: 3.68 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: 6.18 Time building geometry restraints manager: 4.08 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: 41940 1.17 - 2.34: 2139 2.34 - 3.52: 306 3.52 - 4.69: 110 4.69 - 5.86: 22 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: 18188 17.20 - 34.40: 1567 34.40 - 51.59: 221 51.59 - 68.79: 88 68.79 - 85.99: 132 Dihedral angle restraints: 20196 sinusoidal: 8800 harmonic: 11396 Sorted by residual: dihedral pdb=" CA GLY I 311 " pdb=" C GLY I 311 " pdb=" N LEU I 312 " pdb=" CA LEU I 312 " ideal model delta harmonic sigma weight residual 180.00 161.57 18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA GLY G 311 " pdb=" C GLY G 311 " pdb=" N LEU G 312 " pdb=" CA LEU G 312 " ideal model delta harmonic sigma weight residual 180.00 161.61 18.39 0 5.00e+00 4.00e-02 1.35e+01 dihedral pdb=" CA GLY F 311 " pdb=" C GLY F 311 " pdb=" N LEU F 312 " pdb=" CA LEU F 312 " ideal model delta harmonic sigma weight residual 180.00 161.63 18.37 0 5.00e+00 4.00e-02 1.35e+01 ... (remaining 20193 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 2828 0.028 - 0.057: 1505 0.057 - 0.085: 630 0.085 - 0.114: 198 0.114 - 0.142: 75 Chirality restraints: 5236 Sorted by residual: chirality pdb=" CA VAL D 119 " pdb=" N VAL D 119 " pdb=" C VAL D 119 " pdb=" CB VAL D 119 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA VAL C 119 " pdb=" N VAL C 119 " pdb=" C VAL C 119 " pdb=" CB VAL C 119 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.99e-01 chirality pdb=" CA VAL H 119 " pdb=" N VAL H 119 " pdb=" C VAL H 119 " pdb=" CB VAL H 119 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.89e-01 ... (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: 0.12 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: 6.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 0.540 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 31.370 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.130 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:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5386 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 : 0.607 5.861 44517 Z= 0.345 Chirality : 0.043 0.142 5236 Planarity : 0.004 0.027 5401 Dihedral : 14.927 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 aren 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 covalent geometry : bond 0.00471 (32758) covalent geometry : angle 0.60726 (44517) hydrogen bonds : bond 0.12779 ( 1849) hydrogen bonds : angle 6.41933 ( 5382) Misc. bond : bond 0.24934 ( 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 : 1.859 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: 0.2301 time to fit residues: 310.5363 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 : 1.026 ------------------------------------------------------------------------------- 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: 5.9990 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... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 68 GLN B 220 HIS ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 303 HIS B 306 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN 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 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 279 GLN F 306 GLN ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN G 306 GLN ** H 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.111013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.085943 restraints weight = 127681.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.085174 restraints weight = 86940.801| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3663 r_free = 0.3663 target = 0.085676 restraints weight = 70500.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.085866 restraints weight = 54600.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.085941 restraints weight = 52383.465| |-----------------------------------------------------------------------------| r_work (final): 0.3653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.096 32767 Z= 0.295 Angle : 0.847 11.900 44517 Z= 0.441 Chirality : 0.049 0.233 5236 Planarity : 0.006 0.083 5401 Dihedral : 12.474 82.226 5500 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 2.60 % Allowed : 11.54 % Favored : 85.86 % 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 aren not related in a simple way. whole: 0.37 (0.13), residues: 3894 helix: 0.60 (0.10), residues: 2552 sheet: -0.95 (0.28), residues: 231 loop : -0.01 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG G 339 TYR 0.029 0.003 TYR B 69 PHE 0.034 0.003 PHE G 169 TRP 0.022 0.002 TRP J 123 HIS 0.009 0.002 HIS D 56 Details of bonding type rmsd covalent geometry : bond 0.00636 (32758) covalent geometry : angle 0.84668 (44517) hydrogen bonds : bond 0.05082 ( 1849) hydrogen bonds : angle 5.28393 ( 5382) Misc. bond : bond 0.00246 ( 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 493 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 406 time to evaluate : 1.291 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: A 22 GLN cc_start: 0.7161 (mp10) cc_final: 0.6786 (pp30) REVERT: B 145 ASN cc_start: 0.8055 (m110) cc_final: 0.7432 (p0) REVERT: B 249 MET cc_start: 0.7267 (mmm) cc_final: 0.7049 (mmm) REVERT: C 116 ILE cc_start: 0.8699 (mp) cc_final: 0.8445 (mm) REVERT: C 135 MET cc_start: 0.7211 (tpp) cc_final: 0.7006 (tpt) REVERT: C 167 LEU cc_start: 0.8881 (tp) cc_final: 0.8611 (tp) REVERT: E 135 MET cc_start: 0.8884 (ttt) cc_final: 0.8644 (ttt) REVERT: E 341 ARG cc_start: 0.7590 (ptt180) cc_final: 0.7289 (ptt-90) REVERT: F 90 VAL cc_start: 0.8308 (m) cc_final: 0.8083 (p) REVERT: F 258 MET cc_start: 0.8339 (mmm) cc_final: 0.8027 (tpp) REVERT: H 156 ASP cc_start: 0.7761 (m-30) cc_final: 0.7548 (m-30) REVERT: H 183 THR cc_start: 0.8373 (m) cc_final: 0.8130 (p) REVERT: H 249 MET cc_start: 0.8617 (mmt) cc_final: 0.8380 (mmt) REVERT: J 22 GLN cc_start: 0.7835 (mp10) cc_final: 0.6439 (tt0) REVERT: J 214 PHE cc_start: 0.7082 (m-10) cc_final: 0.6601 (m-10) REVERT: K 81 GLN cc_start: 0.6681 (tm-30) cc_final: 0.6253 (pp30) REVERT: K 146 ILE cc_start: 0.5553 (mm) cc_final: 0.4893 (pt) REVERT: K 177 GLU cc_start: 0.8175 (tp30) cc_final: 0.7886 (pm20) REVERT: V 456 MET cc_start: 0.3104 (mmt) cc_final: 0.0412 (mtp) outliers start: 87 outliers final: 48 residues processed: 478 average time/residue: 0.2092 time to fit residues: 161.3907 Evaluate side-chains 342 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 294 time to evaluate : 1.250 ------------------------------------------------------------------------------- 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 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 38 SER 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 229 LYS 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 335 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 17 ILE 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 I residue 18 LEU 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 J residue 313 LEU 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: 0.7980 chunk 134 optimal weight: 0.6980 chunk 219 optimal weight: 7.9990 chunk 182 optimal weight: 0.8980 chunk 249 optimal weight: 10.0000 chunk 86 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 177 optimal weight: 7.9990 chunk 94 optimal weight: 0.9980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 150 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN C 150 GLN C 220 HIS C 270 ASN 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 303 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 ** H 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS J 112 GLN J 150 GLN K 85 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.113328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3746 r_free = 0.3746 target = 0.087936 restraints weight = 129491.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.086967 restraints weight = 82686.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.087759 restraints weight = 63762.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.087852 restraints weight = 50960.432| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.087893 restraints weight = 49395.355| |-----------------------------------------------------------------------------| r_work (final): 0.3691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.5006 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= 0.129 Angle : 0.591 9.763 44517 Z= 0.308 Chirality : 0.041 0.196 5236 Planarity : 0.004 0.037 5401 Dihedral : 11.981 77.104 5500 Min Nonbonded Distance : 2.267 Molprobity Statistics. All-atom Clashscore : 11.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 2.12 % Allowed : 13.40 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.13), residues: 3894 helix: 1.26 (0.10), residues: 2563 sheet: -0.68 (0.28), residues: 231 loop : -0.06 (0.18), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 339 TYR 0.025 0.001 TYR B 69 PHE 0.030 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 covalent geometry : bond 0.00282 (32758) covalent geometry : angle 0.59070 (44517) hydrogen bonds : bond 0.03851 ( 1849) hydrogen bonds : angle 4.48950 ( 5382) Misc. bond : bond 0.00115 ( 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 433 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 362 time to evaluate : 1.302 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 91 GLN cc_start: 0.8022 (mm110) cc_final: 0.7772 (mp10) REVERT: C 167 LEU cc_start: 0.8765 (tp) cc_final: 0.8476 (tp) REVERT: D 45 THR cc_start: 0.7592 (m) cc_final: 0.7283 (m) REVERT: E 48 CYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8884 (t) REVERT: E 287 GLU cc_start: 0.8285 (tp30) cc_final: 0.8011 (tp30) REVERT: F 90 VAL cc_start: 0.8319 (m) cc_final: 0.7999 (p) REVERT: F 129 LYS cc_start: 0.9605 (ttpt) cc_final: 0.9238 (tppt) REVERT: I 65 ILE cc_start: 0.9465 (mm) cc_final: 0.8899 (tt) REVERT: I 216 GLN cc_start: 0.8533 (OUTLIER) cc_final: 0.8286 (pm20) REVERT: J 123 TRP cc_start: 0.5507 (t60) cc_final: 0.4796 (t60) REVERT: J 226 GLU cc_start: 0.7233 (tt0) cc_final: 0.6961 (tt0) REVERT: K 146 ILE cc_start: 0.5591 (mm) cc_final: 0.5008 (pt) REVERT: K 177 GLU cc_start: 0.8313 (tp30) cc_final: 0.8024 (pm20) REVERT: K 211 TYR cc_start: 0.5428 (OUTLIER) cc_final: 0.5018 (m-10) REVERT: K 220 HIS cc_start: 0.7929 (OUTLIER) cc_final: 0.7715 (m-70) outliers start: 71 outliers final: 40 residues processed: 412 average time/residue: 0.1838 time to fit residues: 126.2870 Evaluate side-chains 333 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 289 time to evaluate : 1.036 ------------------------------------------------------------------------------- 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 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 D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL 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 18 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 72 THR 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 342 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 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 I residue 18 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 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 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 211 TYR 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: 1.9990 chunk 328 optimal weight: 5.9990 chunk 110 optimal weight: 6.9990 chunk 216 optimal weight: 0.6980 chunk 242 optimal weight: 7.9990 chunk 214 optimal weight: 0.8980 chunk 184 optimal weight: 10.0000 chunk 91 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 203 optimal weight: 1.9990 chunk 351 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 246 ASN I 150 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4172 r_free = 0.4172 target = 0.111249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086273 restraints weight = 127773.437| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.085026 restraints weight = 85667.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.086098 restraints weight = 72427.384| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.085874 restraints weight = 57308.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.086206 restraints weight = 53793.129| |-----------------------------------------------------------------------------| r_work (final): 0.3655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7362 moved from start: 0.5577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 32767 Z= 0.165 Angle : 0.613 10.367 44517 Z= 0.318 Chirality : 0.041 0.213 5236 Planarity : 0.004 0.091 5401 Dihedral : 11.898 73.805 5500 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.51 % Allowed : 14.53 % Favored : 82.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.13), residues: 3894 helix: 1.35 (0.10), residues: 2563 sheet: -0.63 (0.29), residues: 231 loop : -0.10 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 339 TYR 0.026 0.002 TYR B 69 PHE 0.028 0.002 PHE G 169 TRP 0.012 0.001 TRP J 123 HIS 0.005 0.001 HIS F 117 Details of bonding type rmsd covalent geometry : bond 0.00363 (32758) covalent geometry : angle 0.61321 (44517) hydrogen bonds : bond 0.03849 ( 1849) hydrogen bonds : angle 4.50009 ( 5382) Misc. bond : bond 0.00156 ( 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 399 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 315 time to evaluate : 1.186 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: A 91 GLN cc_start: 0.7957 (mm110) cc_final: 0.7684 (mp10) REVERT: A 201 MET cc_start: 0.7172 (ptt) cc_final: 0.6692 (ppp) REVERT: B 216 GLN cc_start: 0.8210 (OUTLIER) cc_final: 0.7737 (pm20) REVERT: E 48 CYS cc_start: 0.9281 (OUTLIER) cc_final: 0.8779 (t) REVERT: F 21 SER cc_start: 0.8349 (t) cc_final: 0.8132 (p) REVERT: F 90 VAL cc_start: 0.8485 (m) cc_final: 0.8205 (p) REVERT: F 129 LYS cc_start: 0.9600 (ttpt) cc_final: 0.9235 (tppt) REVERT: F 215 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8106 (tm-30) REVERT: F 258 MET cc_start: 0.8389 (mmm) cc_final: 0.8045 (tpp) REVERT: H 17 ILE cc_start: 0.8877 (OUTLIER) cc_final: 0.8591 (mt) REVERT: H 111 LEU cc_start: 0.7851 (mt) cc_final: 0.7438 (mt) REVERT: H 113 MET cc_start: 0.7566 (ptp) cc_final: 0.7298 (ptp) REVERT: H 183 THR cc_start: 0.8159 (m) cc_final: 0.7925 (p) REVERT: H 248 PHE cc_start: 0.7935 (t80) cc_final: 0.7651 (t80) REVERT: I 47 LEU cc_start: 0.9033 (OUTLIER) cc_final: 0.8792 (mm) REVERT: I 65 ILE cc_start: 0.9455 (mm) cc_final: 0.8908 (tt) REVERT: J 22 GLN cc_start: 0.7707 (mp10) cc_final: 0.6244 (tt0) REVERT: J 123 TRP cc_start: 0.5606 (t60) cc_final: 0.4885 (t60) REVERT: K 146 ILE cc_start: 0.5280 (mm) cc_final: 0.4696 (pt) REVERT: K 177 GLU cc_start: 0.8228 (tp30) cc_final: 0.8012 (pm20) REVERT: K 211 TYR cc_start: 0.5208 (OUTLIER) cc_final: 0.4662 (m-10) REVERT: V 456 MET cc_start: 0.3472 (mmp) cc_final: 0.2996 (mmm) outliers start: 84 outliers final: 53 residues processed: 383 average time/residue: 0.1590 time to fit residues: 102.4720 Evaluate side-chains 331 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 273 time to evaluate : 1.240 ------------------------------------------------------------------------------- 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 276 VAL Chi-restraints excluded: chain C residue 52 LEU 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 18 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 48 CYS Chi-restraints excluded: chain E residue 263 VAL 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 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE 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 35 VAL 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 18 LEU Chi-restraints excluded: chain H residue 32 THR 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 H residue 349 SER 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 124 VAL 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 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 203 optimal weight: 0.4980 chunk 236 optimal weight: 5.9990 chunk 376 optimal weight: 4.9990 chunk 58 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 320 optimal weight: 10.0000 chunk 148 optimal weight: 4.9990 chunk 209 optimal weight: 4.9990 chunk 157 optimal weight: 0.6980 chunk 262 optimal weight: 7.9990 chunk 293 optimal weight: 0.3980 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 270 ASN G 328 ASN H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 150 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.110886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086684 restraints weight = 128697.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.085380 restraints weight = 89715.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.086379 restraints weight = 77306.464| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.086264 restraints weight = 58140.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086481 restraints weight = 54758.710| |-----------------------------------------------------------------------------| r_work (final): 0.3664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.6023 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= 0.157 Angle : 0.600 10.805 44517 Z= 0.310 Chirality : 0.041 0.271 5236 Planarity : 0.004 0.059 5401 Dihedral : 11.848 73.752 5500 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 12.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 2.75 % Allowed : 14.71 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.28 (0.13), residues: 3894 helix: 1.44 (0.10), residues: 2563 sheet: -0.57 (0.29), residues: 231 loop : -0.07 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 78 TYR 0.029 0.002 TYR B 69 PHE 0.028 0.002 PHE J 210 TRP 0.009 0.001 TRP J 123 HIS 0.004 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00346 (32758) covalent geometry : angle 0.60009 (44517) hydrogen bonds : bond 0.03720 ( 1849) hydrogen bonds : angle 4.42856 ( 5382) Misc. bond : bond 0.00144 ( 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 407 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 315 time to evaluate : 1.405 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: A 91 GLN cc_start: 0.8019 (mm110) cc_final: 0.7713 (mp10) REVERT: A 201 MET cc_start: 0.7098 (ptt) cc_final: 0.6613 (ppp) REVERT: B 216 GLN cc_start: 0.8177 (OUTLIER) cc_final: 0.7694 (pm20) REVERT: C 135 MET cc_start: 0.7251 (tpt) cc_final: 0.7048 (tpp) REVERT: C 272 MET cc_start: 0.7552 (mtm) cc_final: 0.6694 (mtm) REVERT: E 287 GLU cc_start: 0.8083 (tp30) cc_final: 0.7779 (tp30) REVERT: F 90 VAL cc_start: 0.8575 (m) cc_final: 0.8304 (p) REVERT: F 129 LYS cc_start: 0.9610 (ttpt) cc_final: 0.9238 (tppt) REVERT: F 135 MET cc_start: 0.8375 (ttm) cc_final: 0.7515 (tmm) REVERT: F 258 MET cc_start: 0.8396 (mmm) cc_final: 0.8037 (tpp) REVERT: F 271 ILE cc_start: 0.8508 (pt) cc_final: 0.8284 (mm) REVERT: F 347 LEU cc_start: 0.8603 (OUTLIER) cc_final: 0.8385 (mm) REVERT: G 231 LEU cc_start: 0.7690 (OUTLIER) cc_final: 0.7206 (mm) REVERT: H 17 ILE cc_start: 0.8819 (OUTLIER) cc_final: 0.8549 (mt) REVERT: H 111 LEU cc_start: 0.7819 (mt) cc_final: 0.7571 (mt) REVERT: H 113 MET cc_start: 0.7568 (ptp) cc_final: 0.7250 (ptp) REVERT: H 183 THR cc_start: 0.8220 (m) cc_final: 0.7972 (p) REVERT: H 248 PHE cc_start: 0.8067 (t80) cc_final: 0.7817 (t80) REVERT: I 47 LEU cc_start: 0.9064 (OUTLIER) cc_final: 0.8861 (mm) REVERT: I 65 ILE cc_start: 0.9499 (mm) cc_final: 0.9014 (tt) REVERT: I 77 GLU cc_start: 0.8248 (tm-30) cc_final: 0.8038 (tp30) REVERT: J 22 GLN cc_start: 0.7452 (mp10) cc_final: 0.6049 (tt0) REVERT: J 123 TRP cc_start: 0.5311 (t60) cc_final: 0.4595 (t60) REVERT: K 146 ILE cc_start: 0.5380 (mm) cc_final: 0.4713 (pt) REVERT: K 211 TYR cc_start: 0.5015 (OUTLIER) cc_final: 0.4656 (m-10) REVERT: Q 456 MET cc_start: 0.7670 (mtm) cc_final: 0.6859 (mmm) REVERT: S 452 TYR cc_start: 0.8275 (m-80) cc_final: 0.7638 (m-80) REVERT: V 456 MET cc_start: 0.3197 (mmp) cc_final: 0.2529 (mmm) outliers start: 92 outliers final: 60 residues processed: 388 average time/residue: 0.1890 time to fit residues: 123.8141 Evaluate side-chains 336 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 270 time to evaluate : 1.269 ------------------------------------------------------------------------------- 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 289 TYR Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 216 GLN 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 D residue 23 TYR Chi-restraints excluded: chain D residue 35 VAL 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 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 17 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 THR 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 263 VAL 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 35 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 LEU 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 17 ILE 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 H residue 243 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 346 optimal weight: 3.9990 chunk 291 optimal weight: 8.9990 chunk 175 optimal weight: 0.7980 chunk 160 optimal weight: 2.9990 chunk 241 optimal weight: 0.9990 chunk 270 optimal weight: 7.9990 chunk 336 optimal weight: 10.0000 chunk 223 optimal weight: 9.9990 chunk 267 optimal weight: 3.9990 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... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 91 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** 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 279 GLN K 68 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4134 r_free = 0.4134 target = 0.109086 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.085775 restraints weight = 128680.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.083631 restraints weight = 98884.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.084872 restraints weight = 90592.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084632 restraints weight = 65771.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.084743 restraints weight = 62301.153| |-----------------------------------------------------------------------------| r_work (final): 0.3626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 moved from start: 0.6575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 32767 Z= 0.201 Angle : 0.663 10.775 44517 Z= 0.343 Chirality : 0.043 0.330 5236 Planarity : 0.004 0.062 5401 Dihedral : 11.937 74.534 5500 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 14.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 3.23 % Allowed : 15.49 % Favored : 81.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.26 (0.13), residues: 3894 helix: 1.48 (0.10), residues: 2508 sheet: -0.55 (0.29), residues: 231 loop : -0.14 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG I 78 TYR 0.093 0.002 TYR B 23 PHE 0.033 0.003 PHE G 210 TRP 0.010 0.001 TRP D 123 HIS 0.006 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00445 (32758) covalent geometry : angle 0.66325 (44517) hydrogen bonds : bond 0.03987 ( 1849) hydrogen bonds : angle 4.62846 ( 5382) Misc. bond : bond 0.00143 ( 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 401 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 293 time to evaluate : 0.864 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 201 MET cc_start: 0.7108 (ptt) cc_final: 0.6606 (ppp) REVERT: B 17 ILE cc_start: 0.7783 (OUTLIER) cc_final: 0.7467 (mm) REVERT: B 216 GLN cc_start: 0.8188 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: C 135 MET cc_start: 0.7473 (tpt) cc_final: 0.7196 (tpp) REVERT: C 249 MET cc_start: 0.6466 (tpp) cc_final: 0.5886 (tpp) REVERT: D 113 MET cc_start: 0.6993 (ppp) cc_final: 0.6713 (tmm) REVERT: E 53 TYR cc_start: 0.6867 (p90) cc_final: 0.6272 (p90) REVERT: E 135 MET cc_start: 0.8790 (ppp) cc_final: 0.8394 (ppp) REVERT: E 216 GLN cc_start: 0.7865 (OUTLIER) cc_final: 0.7662 (mp10) REVERT: F 90 VAL cc_start: 0.8667 (m) cc_final: 0.8428 (p) REVERT: F 129 LYS cc_start: 0.9619 (ttpt) cc_final: 0.9219 (tppt) REVERT: F 258 MET cc_start: 0.8357 (mmm) cc_final: 0.7899 (tpp) REVERT: F 271 ILE cc_start: 0.8397 (pt) cc_final: 0.8193 (mm) REVERT: F 347 LEU cc_start: 0.8684 (OUTLIER) cc_final: 0.8376 (mm) REVERT: G 139 LEU cc_start: 0.8607 (mt) cc_final: 0.8339 (pp) REVERT: G 231 LEU cc_start: 0.7947 (OUTLIER) cc_final: 0.7324 (mm) REVERT: H 17 ILE cc_start: 0.8851 (OUTLIER) cc_final: 0.8616 (mt) REVERT: H 51 ILE cc_start: 0.8402 (mt) cc_final: 0.8185 (mm) REVERT: H 94 LEU cc_start: 0.8660 (OUTLIER) cc_final: 0.8402 (tp) REVERT: H 111 LEU cc_start: 0.7831 (mt) cc_final: 0.7602 (mt) REVERT: H 183 THR cc_start: 0.8269 (m) cc_final: 0.8017 (p) REVERT: H 248 PHE cc_start: 0.8053 (t80) cc_final: 0.7780 (t80) REVERT: H 266 ARG cc_start: 0.7532 (ttt180) cc_final: 0.6688 (ttt180) REVERT: I 47 LEU cc_start: 0.9066 (OUTLIER) cc_final: 0.8852 (mm) REVERT: I 65 ILE cc_start: 0.9520 (mm) cc_final: 0.9070 (tt) REVERT: I 77 GLU cc_start: 0.8167 (tm-30) cc_final: 0.7913 (mm-30) REVERT: I 83 LEU cc_start: 0.8272 (OUTLIER) cc_final: 0.8053 (mp) REVERT: J 22 GLN cc_start: 0.7672 (mp10) cc_final: 0.6534 (tt0) REVERT: J 123 TRP cc_start: 0.5392 (t60) cc_final: 0.4574 (t60) REVERT: J 214 PHE cc_start: 0.6650 (m-10) cc_final: 0.6177 (m-10) REVERT: K 146 ILE cc_start: 0.4738 (mm) cc_final: 0.4367 (pt) REVERT: K 172 LEU cc_start: 0.5577 (OUTLIER) cc_final: 0.4040 (tt) REVERT: P 456 MET cc_start: 0.7027 (mpp) cc_final: 0.6464 (mpp) REVERT: Q 456 MET cc_start: 0.7802 (mtm) cc_final: 0.7115 (mmm) REVERT: S 452 TYR cc_start: 0.8285 (m-80) cc_final: 0.7682 (m-80) outliers start: 108 outliers final: 71 residues processed: 376 average time/residue: 0.1753 time to fit residues: 110.7123 Evaluate side-chains 345 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 264 time to evaluate : 1.277 ------------------------------------------------------------------------------- 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 A residue 352 GLU 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 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 161 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 277 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 201 MET Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 215 GLU Chi-restraints excluded: chain F residue 231 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 263 VAL 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 35 VAL Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 231 LEU 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 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 17 ILE Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 83 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 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 172 LEU Chi-restraints excluded: chain K residue 211 TYR Chi-restraints excluded: chain K residue 321 PHE 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: 7.9990 chunk 54 optimal weight: 10.0000 chunk 236 optimal weight: 6.9990 chunk 304 optimal weight: 7.9990 chunk 293 optimal weight: 6.9990 chunk 352 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 229 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 139 optimal weight: 10.0000 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 68 GLN B 81 GLN B 91 GLN ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN B 328 ASN C 81 GLN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 306 GLN D 306 GLN ** E 284 GLN ** 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 328 ASN K 279 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4189 r_free = 0.4189 target = 0.110524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.089668 restraints weight = 135095.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3773 r_free = 0.3773 target = 0.089401 restraints weight = 125747.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.090017 restraints weight = 104984.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3786 r_free = 0.3786 target = 0.089907 restraints weight = 75296.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.090200 restraints weight = 70704.913| |-----------------------------------------------------------------------------| r_work (final): 0.3784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7379 moved from start: 0.7294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 32767 Z= 0.249 Angle : 0.730 11.292 44517 Z= 0.378 Chirality : 0.045 0.344 5236 Planarity : 0.005 0.074 5401 Dihedral : 12.066 74.028 5500 Min Nonbonded Distance : 2.311 Molprobity Statistics. All-atom Clashscore : 16.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.38 % Allowed : 16.00 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.77 (0.13), residues: 3894 helix: 1.04 (0.10), residues: 2574 sheet: -0.65 (0.29), residues: 231 loop : -0.28 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG I 78 TYR 0.038 0.002 TYR B 69 PHE 0.035 0.003 PHE G 210 TRP 0.016 0.002 TRP H 123 HIS 0.007 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00548 (32758) covalent geometry : angle 0.73003 (44517) hydrogen bonds : bond 0.04359 ( 1849) hydrogen bonds : angle 4.92494 ( 5382) Misc. bond : bond 0.00243 ( 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 399 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 286 time to evaluate : 1.527 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: A 201 MET cc_start: 0.6855 (ptt) cc_final: 0.6405 (ppp) REVERT: B 17 ILE cc_start: 0.7710 (OUTLIER) cc_final: 0.7431 (mm) REVERT: B 216 GLN cc_start: 0.8179 (OUTLIER) cc_final: 0.7769 (pm20) REVERT: C 135 MET cc_start: 0.7121 (tpt) cc_final: 0.6905 (tpp) REVERT: C 249 MET cc_start: 0.6408 (tpp) cc_final: 0.5871 (tpp) REVERT: D 113 MET cc_start: 0.7143 (ppp) cc_final: 0.6730 (tmm) REVERT: E 287 GLU cc_start: 0.8069 (tp30) cc_final: 0.7792 (tp30) REVERT: F 129 LYS cc_start: 0.9434 (ttpt) cc_final: 0.9075 (tppt) REVERT: F 135 MET cc_start: 0.7960 (ttm) cc_final: 0.7140 (tmm) REVERT: F 210 PHE cc_start: 0.8860 (OUTLIER) cc_final: 0.8380 (m-80) REVERT: F 258 MET cc_start: 0.8315 (mmm) cc_final: 0.7840 (tpp) REVERT: G 231 LEU cc_start: 0.8026 (OUTLIER) cc_final: 0.7537 (mm) REVERT: H 51 ILE cc_start: 0.8474 (mt) cc_final: 0.8236 (mm) REVERT: H 111 LEU cc_start: 0.7419 (mt) cc_final: 0.7104 (mt) REVERT: H 248 PHE cc_start: 0.7898 (t80) cc_final: 0.7548 (t80) REVERT: I 65 ILE cc_start: 0.9366 (mm) cc_final: 0.9000 (tt) REVERT: I 83 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7954 (mp) REVERT: I 169 PHE cc_start: 0.8239 (t80) cc_final: 0.8006 (t80) REVERT: J 22 GLN cc_start: 0.7792 (mp10) cc_final: 0.6619 (tm-30) REVERT: J 123 TRP cc_start: 0.4971 (t60) cc_final: 0.4272 (t60) REVERT: K 104 LYS cc_start: 0.6961 (mmtt) cc_final: 0.6058 (mmtt) REVERT: K 110 ASP cc_start: 0.6810 (m-30) cc_final: 0.6578 (t0) REVERT: K 211 TYR cc_start: 0.4709 (OUTLIER) cc_final: 0.4397 (m-80) REVERT: O 456 MET cc_start: 0.3621 (mmt) cc_final: 0.2915 (mmm) REVERT: Q 456 MET cc_start: 0.7796 (mtm) cc_final: 0.7287 (mmm) REVERT: S 452 TYR cc_start: 0.8059 (m-80) cc_final: 0.7849 (m-80) REVERT: V 456 MET cc_start: 0.1826 (mmp) cc_final: 0.1218 (mmm) outliers start: 113 outliers final: 82 residues processed: 374 average time/residue: 0.1815 time to fit residues: 113.6780 Evaluate side-chains 346 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 258 time to evaluate : 1.324 ------------------------------------------------------------------------------- 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 A residue 352 GLU 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 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 23 TYR Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 47 LEU 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 238 SER Chi-restraints excluded: chain D residue 277 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 183 THR Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 17 ILE Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 231 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 263 VAL 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 46 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 231 LEU 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 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 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 243 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 83 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 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 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 35 VAL 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 K residue 321 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 172 optimal weight: 2.9990 chunk 376 optimal weight: 0.6980 chunk 79 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 173 optimal weight: 0.5980 chunk 221 optimal weight: 0.9980 chunk 271 optimal weight: 9.9990 chunk 325 optimal weight: 40.0000 chunk 28 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 chunk 323 optimal weight: 1.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS C 275 HIS E 148 GLN E 284 GLN H 250 GLN H 275 HIS H 279 GLN ** H 306 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 = 0.4236 r_free = 0.4236 target = 0.113359 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.092270 restraints weight = 134507.554| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.092340 restraints weight = 109109.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.092826 restraints weight = 86744.114| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.092826 restraints weight = 65567.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.093031 restraints weight = 61224.379| |-----------------------------------------------------------------------------| r_work (final): 0.3840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.7346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32767 Z= 0.135 Angle : 0.628 12.339 44517 Z= 0.319 Chirality : 0.041 0.346 5236 Planarity : 0.004 0.050 5401 Dihedral : 11.899 73.982 5500 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 12.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 2.42 % Allowed : 17.14 % Favored : 80.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.17 (0.14), residues: 3894 helix: 1.39 (0.10), residues: 2574 sheet: -0.59 (0.29), residues: 231 loop : -0.24 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 78 TYR 0.032 0.002 TYR D 69 PHE 0.028 0.002 PHE J 214 TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS F 220 Details of bonding type rmsd covalent geometry : bond 0.00303 (32758) covalent geometry : angle 0.62791 (44517) hydrogen bonds : bond 0.03693 ( 1849) hydrogen bonds : angle 4.44847 ( 5382) Misc. bond : bond 0.00202 ( 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 381 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 300 time to evaluate : 0.934 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 201 MET cc_start: 0.6880 (ptt) cc_final: 0.6106 (ppp) REVERT: B 17 ILE cc_start: 0.7365 (OUTLIER) cc_final: 0.7062 (mm) REVERT: B 210 PHE cc_start: 0.7704 (OUTLIER) cc_final: 0.7503 (t80) REVERT: B 216 GLN cc_start: 0.8185 (OUTLIER) cc_final: 0.7767 (pm20) REVERT: C 135 MET cc_start: 0.7162 (tpt) cc_final: 0.6937 (tpp) REVERT: C 163 CYS cc_start: 0.7675 (m) cc_final: 0.6461 (t) REVERT: C 272 MET cc_start: 0.7727 (mtm) cc_final: 0.7316 (ttp) REVERT: C 295 MET cc_start: 0.8012 (mpp) cc_final: 0.7785 (mmt) REVERT: D 113 MET cc_start: 0.7145 (ppp) cc_final: 0.6796 (tmm) REVERT: D 135 MET cc_start: 0.8619 (ppp) cc_final: 0.8115 (ppp) REVERT: D 238 SER cc_start: 0.8193 (OUTLIER) cc_final: 0.6737 (p) REVERT: D 295 MET cc_start: 0.8407 (mmt) cc_final: 0.7967 (mmt) REVERT: E 287 GLU cc_start: 0.7796 (tp30) cc_final: 0.7553 (tp30) REVERT: F 129 LYS cc_start: 0.9427 (ttpt) cc_final: 0.9146 (tppt) REVERT: F 135 MET cc_start: 0.7952 (ttm) cc_final: 0.7385 (tmm) REVERT: F 210 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.8193 (m-80) REVERT: F 258 MET cc_start: 0.8295 (mmm) cc_final: 0.7887 (tpp) REVERT: G 135 MET cc_start: 0.8714 (tpp) cc_final: 0.8345 (tpt) REVERT: H 51 ILE cc_start: 0.8322 (mt) cc_final: 0.8087 (mm) REVERT: H 111 LEU cc_start: 0.7623 (mt) cc_final: 0.7356 (mt) REVERT: H 183 THR cc_start: 0.8196 (m) cc_final: 0.7958 (p) REVERT: H 248 PHE cc_start: 0.7953 (t80) cc_final: 0.7673 (t80) REVERT: I 42 GLN cc_start: 0.7397 (OUTLIER) cc_final: 0.7167 (pm20) REVERT: I 65 ILE cc_start: 0.9349 (mm) cc_final: 0.8970 (tt) REVERT: I 249 MET cc_start: 0.6983 (tpt) cc_final: 0.6743 (tpt) REVERT: J 22 GLN cc_start: 0.7453 (mp10) cc_final: 0.6805 (tt0) REVERT: K 211 TYR cc_start: 0.4872 (OUTLIER) cc_final: 0.4422 (m-80) REVERT: P 456 MET cc_start: 0.6650 (mpp) cc_final: 0.6088 (mpp) REVERT: S 452 TYR cc_start: 0.8111 (m-80) cc_final: 0.7893 (m-80) REVERT: V 456 MET cc_start: 0.1746 (mmp) cc_final: 0.1181 (mmm) outliers start: 81 outliers final: 61 residues processed: 359 average time/residue: 0.1620 time to fit residues: 98.8207 Evaluate side-chains 337 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 269 time to evaluate : 1.249 ------------------------------------------------------------------------------- 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 A residue 352 GLU 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 276 VAL Chi-restraints excluded: chain B residue 313 LEU 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 292 VAL 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 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 307 SER Chi-restraints excluded: chain F residue 95 THR 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 263 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 46 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 191 LEU 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 299 SER Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 334 ILE 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 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 42 GLN 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 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 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 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: 8.9990 chunk 371 optimal weight: 9.9990 chunk 383 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 313 optimal weight: 6.9990 chunk 323 optimal weight: 7.9990 chunk 369 optimal weight: 0.9990 chunk 181 optimal weight: 5.9990 chunk 243 optimal weight: 10.0000 chunk 191 optimal weight: 2.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 270 ASN C 328 ASN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 15 HIS ** K 56 HIS ** 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 = 0.4173 r_free = 0.4173 target = 0.109901 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3794 r_free = 0.3794 target = 0.088926 restraints weight = 133484.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.088710 restraints weight = 121547.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.089159 restraints weight = 105361.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.089106 restraints weight = 72732.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.089295 restraints weight = 67738.521| |-----------------------------------------------------------------------------| r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.7807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 32767 Z= 0.273 Angle : 0.754 12.716 44517 Z= 0.390 Chirality : 0.045 0.382 5236 Planarity : 0.005 0.079 5401 Dihedral : 12.124 73.675 5500 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 17.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 2.87 % Allowed : 17.34 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.69 (0.13), residues: 3894 helix: 1.00 (0.10), residues: 2574 sheet: -0.76 (0.29), residues: 231 loop : -0.35 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG C 78 TYR 0.037 0.003 TYR B 69 PHE 0.033 0.003 PHE B 248 TRP 0.011 0.002 TRP A 261 HIS 0.008 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00602 (32758) covalent geometry : angle 0.75408 (44517) hydrogen bonds : bond 0.04413 ( 1849) hydrogen bonds : angle 4.96586 ( 5382) Misc. bond : bond 0.00349 ( 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 364 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 268 time to evaluate : 1.351 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: A 201 MET cc_start: 0.7012 (ptt) cc_final: 0.6699 (tmm) REVERT: B 17 ILE cc_start: 0.7462 (OUTLIER) cc_final: 0.7165 (mm) REVERT: B 210 PHE cc_start: 0.8176 (OUTLIER) cc_final: 0.7806 (t80) REVERT: B 216 GLN cc_start: 0.8230 (OUTLIER) cc_final: 0.7806 (pm20) REVERT: C 135 MET cc_start: 0.7213 (tpt) cc_final: 0.6960 (tpp) REVERT: C 249 MET cc_start: 0.6622 (tpp) cc_final: 0.5757 (tpp) REVERT: D 113 MET cc_start: 0.7160 (ppp) cc_final: 0.6801 (tmm) REVERT: F 129 LYS cc_start: 0.9385 (ttpt) cc_final: 0.9092 (tppt) REVERT: F 210 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8374 (m-80) REVERT: F 258 MET cc_start: 0.8319 (mmm) cc_final: 0.8046 (tpp) REVERT: H 111 LEU cc_start: 0.7357 (mt) cc_final: 0.7114 (mt) REVERT: H 248 PHE cc_start: 0.7908 (t80) cc_final: 0.7571 (t80) REVERT: I 65 ILE cc_start: 0.9381 (mm) cc_final: 0.9037 (tt) REVERT: J 22 GLN cc_start: 0.7702 (mp10) cc_final: 0.6998 (tt0) REVERT: J 249 MET cc_start: 0.7346 (OUTLIER) cc_final: 0.6762 (tpt) REVERT: J 295 MET cc_start: 0.8554 (mmm) cc_final: 0.7981 (mpp) REVERT: K 104 LYS cc_start: 0.6964 (mmtt) cc_final: 0.6236 (mmtm) REVERT: K 224 PHE cc_start: 0.7877 (t80) cc_final: 0.7643 (t80) REVERT: K 337 MET cc_start: 0.8325 (ppp) cc_final: 0.8116 (ppp) REVERT: P 456 MET cc_start: 0.6630 (mpp) cc_final: 0.5903 (mpp) REVERT: S 452 TYR cc_start: 0.8243 (m-80) cc_final: 0.8032 (m-80) REVERT: V 456 MET cc_start: 0.1900 (mmp) cc_final: 0.1275 (mmm) outliers start: 96 outliers final: 72 residues processed: 339 average time/residue: 0.1777 time to fit residues: 103.0380 Evaluate side-chains 325 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 248 time to evaluate : 1.100 ------------------------------------------------------------------------------- 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 248 PHE 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 116 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 B residue 313 LEU Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 302 LEU Chi-restraints excluded: chain C residue 312 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 277 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 183 THR Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 231 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 342 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 191 LEU 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 299 SER Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 334 ILE 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 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 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 176 ILE 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 35 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 39 optimal weight: 5.9990 chunk 47 optimal weight: 7.9990 chunk 359 optimal weight: 6.9990 chunk 171 optimal weight: 2.9990 chunk 124 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 200 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 chunk 88 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 273 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS G 81 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 256 GLN H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 56 HIS ** 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 = 0.4231 r_free = 0.4231 target = 0.113313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.091715 restraints weight = 133976.701| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.090904 restraints weight = 106037.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.091514 restraints weight = 87448.888| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091752 restraints weight = 65763.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.091836 restraints weight = 63590.945| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.7804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 32767 Z= 0.133 Angle : 0.654 13.012 44517 Z= 0.331 Chirality : 0.042 0.379 5236 Planarity : 0.004 0.044 5401 Dihedral : 12.010 73.917 5500 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.88 % Allowed : 18.60 % Favored : 79.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.07 (0.14), residues: 3894 helix: 1.33 (0.10), residues: 2563 sheet: -0.69 (0.29), residues: 231 loop : -0.27 (0.20), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 78 TYR 0.041 0.002 TYR D 69 PHE 0.029 0.002 PHE K 224 TRP 0.012 0.001 TRP A 261 HIS 0.004 0.001 HIS I 220 Details of bonding type rmsd covalent geometry : bond 0.00299 (32758) covalent geometry : angle 0.65364 (44517) hydrogen bonds : bond 0.03760 ( 1849) hydrogen bonds : angle 4.51961 ( 5382) Misc. bond : bond 0.00253 ( 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 342 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 279 time to evaluate : 1.018 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 201 MET cc_start: 0.6748 (ptt) cc_final: 0.6546 (tmm) REVERT: B 17 ILE cc_start: 0.7376 (OUTLIER) cc_final: 0.7069 (mm) REVERT: B 216 GLN cc_start: 0.8186 (OUTLIER) cc_final: 0.7756 (pm20) REVERT: B 269 ASN cc_start: 0.4671 (m-40) cc_final: 0.4216 (t0) REVERT: C 135 MET cc_start: 0.7111 (tpt) cc_final: 0.6887 (tpp) REVERT: C 272 MET cc_start: 0.7688 (mtm) cc_final: 0.7262 (ttp) REVERT: C 295 MET cc_start: 0.7813 (mpp) cc_final: 0.7585 (mmt) REVERT: D 53 TYR cc_start: 0.6667 (p90) cc_final: 0.6437 (p90) REVERT: D 238 SER cc_start: 0.8252 (OUTLIER) cc_final: 0.6829 (p) REVERT: D 241 GLU cc_start: 0.7341 (pp20) cc_final: 0.7062 (pp20) REVERT: D 258 MET cc_start: 0.8725 (mmm) cc_final: 0.8299 (tpp) REVERT: E 241 GLU cc_start: 0.7879 (pp20) cc_final: 0.7150 (pp20) REVERT: F 129 LYS cc_start: 0.9458 (ttpt) cc_final: 0.9152 (tppt) REVERT: F 210 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.8261 (m-80) REVERT: H 183 THR cc_start: 0.8132 (m) cc_final: 0.7881 (p) REVERT: H 248 PHE cc_start: 0.8024 (t80) cc_final: 0.7739 (t80) REVERT: I 65 ILE cc_start: 0.9377 (mm) cc_final: 0.8945 (tt) REVERT: J 94 LEU cc_start: 0.7265 (tp) cc_final: 0.7028 (mm) REVERT: J 249 MET cc_start: 0.7397 (OUTLIER) cc_final: 0.6859 (tpt) REVERT: J 295 MET cc_start: 0.8451 (mmm) cc_final: 0.7897 (mpp) REVERT: K 110 ASP cc_start: 0.6832 (m-30) cc_final: 0.6470 (t0) REVERT: O 456 MET cc_start: 0.4966 (mmm) cc_final: 0.3281 (mmp) REVERT: P 456 MET cc_start: 0.6770 (mpp) cc_final: 0.6164 (mpp) REVERT: Q 456 MET cc_start: 0.7676 (mmm) cc_final: 0.7346 (mmm) REVERT: T 456 MET cc_start: 0.1408 (mmt) cc_final: 0.0477 (mmt) REVERT: V 456 MET cc_start: 0.1990 (mmp) cc_final: 0.1507 (mmm) outliers start: 63 outliers final: 52 residues processed: 325 average time/residue: 0.1814 time to fit residues: 99.5798 Evaluate side-chains 321 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 264 time to evaluate : 1.160 ------------------------------------------------------------------------------- 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 248 PHE 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 B residue 313 LEU 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 238 SER 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 307 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 113 MET Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 231 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 342 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 191 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 334 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 191 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 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 257 THR Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 176 ILE Chi-restraints excluded: chain J residue 249 MET Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 156 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 376 optimal weight: 5.9990 chunk 188 optimal weight: 1.9990 chunk 290 optimal weight: 7.9990 chunk 278 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 139 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 54 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 87 optimal weight: 1.9990 chunk 294 optimal weight: 0.9980 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 22 GLN H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN I 256 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4215 r_free = 0.4215 target = 0.112273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.091311 restraints weight = 133533.010| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.090778 restraints weight = 108696.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3819 r_free = 0.3819 target = 0.091593 restraints weight = 100987.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.091338 restraints weight = 72676.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.091722 restraints weight = 68648.692| |-----------------------------------------------------------------------------| r_work (final): 0.3815 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7318 moved from start: 0.7975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 32767 Z= 0.162 Angle : 0.662 13.485 44517 Z= 0.339 Chirality : 0.042 0.380 5236 Planarity : 0.004 0.051 5401 Dihedral : 12.065 73.714 5500 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 14.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 2.00 % Allowed : 18.75 % Favored : 79.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.14), residues: 3894 helix: 1.33 (0.10), residues: 2574 sheet: -0.69 (0.29), residues: 231 loop : -0.28 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG A 78 TYR 0.033 0.002 TYR D 69 PHE 0.028 0.002 PHE B 248 TRP 0.012 0.001 TRP A 261 HIS 0.005 0.001 HIS D 303 Details of bonding type rmsd covalent geometry : bond 0.00365 (32758) covalent geometry : angle 0.66213 (44517) hydrogen bonds : bond 0.03802 ( 1849) hydrogen bonds : angle 4.58015 ( 5382) Misc. bond : bond 0.00216 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5104.01 seconds wall clock time: 89 minutes 57.29 seconds (5397.29 seconds total)