Starting phenix.real_space_refine on Fri Jun 27 14:18:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8pdr_17619/06_2025/8pdr_17619.cif Found real_map, /net/cci-nas-00/data/ceres_data/8pdr_17619/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8pdr_17619/06_2025/8pdr_17619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8pdr_17619/06_2025/8pdr_17619.map" model { file = "/net/cci-nas-00/data/ceres_data/8pdr_17619/06_2025/8pdr_17619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8pdr_17619/06_2025/8pdr_17619.cif" } resolution = 4.0 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 18.20, per 1000 atoms: 0.57 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: 7.76 Conformation dependent library (CDL) restraints added in 3.7 seconds 7788 Ramachandran restraints generated. 3894 Oldfield, 0 Emsley, 3894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7304 Finding SS restraints... Secondary structure from input PDB file: 220 helices and 22 sheets defined 68.2% alpha, 5.3% beta 0 base pairs and 55 stacking pairs defined. Time for finding SS restraints: 10.26 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: 11.24 Time building geometry restraints manager: 9.16 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: 0.29 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' } ncs_group { reference = chain 'a' selection = chain 'c' selection = chain 'b' selection = chain 'e' selection = chain 'd' selection = chain 'g' selection = chain 'f' selection = chain 'i' selection = chain 'h' selection = chain 'k' selection = chain 'j' } ncs_group { reference = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 6.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.180 Check model and map are aligned: 0.240 Set scattering table: 0.280 Process input model: 74.700 Find NCS groups from input model: 0.720 Set up NCS constraints: 0.250 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: 0.020 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 86.440 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.002 TRP H 123 HIS 0.004 0.001 HIS K 56 PHE 0.016 0.002 PHE J 169 TYR 0.026 0.003 TYR F 53 ARG 0.003 0.000 ARG I 293 Details of bonding type rmsd hydrogen bonds : bond 0.12779 ( 1849) hydrogen bonds : angle 6.41933 ( 5382) covalent geometry : bond 0.00471 (32758) covalent geometry : angle 0.60726 (44517) 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 : 3.420 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: 0.7386 (mmm) REVERT: F 250 GLN cc_start: 0.8263 (mt0) cc_final: 0.8000 (mt0) REVERT: F 342 VAL cc_start: 0.7452 (t) cc_final: 0.7162 (m) REVERT: J 82 ILE cc_start: 0.5833 (mt) cc_final: 0.5513 (mm) REVERT: K 110 ASP cc_start: 0.5879 (m-30) cc_final: 0.5522 (m-30) REVERT: K 172 LEU cc_start: 0.4657 (mt) cc_final: 0.4432 (mt) REVERT: K 272 MET cc_start: -0.1358 (mmm) cc_final: -0.1680 (ttm) outliers start: 0 outliers final: 0 residues processed: 878 average time/residue: 0.5294 time to fit residues: 715.9165 Evaluate side-chains 408 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 408 time to evaluate : 3.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 325 optimal weight: 8.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 301 optimal weight: 4.9990 chunk 116 optimal weight: 6.9990 chunk 183 optimal weight: 4.9990 chunk 224 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN B 220 HIS B 246 ASN B 303 HIS ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 317 ASN D 81 GLN ** D 112 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN F 112 GLN F 275 HIS F 279 GLN F 306 GLN G 112 GLN G 150 GLN ** H 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 112 GLN ** I 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 GLN J 112 GLN ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4246 r_free = 0.4246 target = 0.115205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.089292 restraints weight = 125808.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.088957 restraints weight = 76537.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.089608 restraints weight = 59142.243| |-----------------------------------------------------------------------------| r_work (final): 0.3727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 32767 Z= 0.192 Angle : 0.704 11.318 44517 Z= 0.367 Chirality : 0.044 0.209 5236 Planarity : 0.005 0.079 5401 Dihedral : 12.146 74.340 5500 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 1.94 % Allowed : 10.89 % Favored : 87.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.73 (0.13), residues: 3894 helix: 0.92 (0.10), residues: 2585 sheet: -0.83 (0.28), residues: 231 loop : -0.02 (0.18), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP J 123 HIS 0.007 0.002 HIS F 56 PHE 0.027 0.003 PHE G 169 TYR 0.027 0.002 TYR B 69 ARG 0.010 0.001 ARG G 339 Details of bonding type rmsd hydrogen bonds : bond 0.04436 ( 1849) hydrogen bonds : angle 4.86812 ( 5382) covalent geometry : bond 0.00427 (32758) covalent geometry : angle 0.70450 (44517) Misc. bond : bond 0.00249 ( 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 486 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 421 time to evaluate : 3.638 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 22 GLN cc_start: 0.7103 (mp10) cc_final: 0.6794 (pp30) REVERT: A 231 LEU cc_start: 0.7749 (tp) cc_final: 0.7054 (mm) REVERT: C 167 LEU cc_start: 0.8749 (tp) cc_final: 0.8441 (tp) REVERT: D 53 TYR cc_start: 0.4183 (p90) cc_final: 0.3252 (p90) REVERT: E 287 GLU cc_start: 0.8314 (tp30) cc_final: 0.8043 (tp30) REVERT: H 156 ASP cc_start: 0.7805 (m-30) cc_final: 0.7598 (m-30) REVERT: H 172 LEU cc_start: 0.8617 (mt) cc_final: 0.8284 (tt) REVERT: I 96 ARG cc_start: 0.7516 (mtm110) cc_final: 0.7192 (ptt-90) REVERT: K 81 GLN cc_start: 0.6656 (tm-30) cc_final: 0.6230 (pp30) REVERT: K 146 ILE cc_start: 0.5641 (mm) cc_final: 0.4957 (pt) REVERT: K 211 TYR cc_start: 0.5405 (t80) cc_final: 0.5142 (m-80) REVERT: O 456 MET cc_start: 0.3343 (mmt) cc_final: 0.0253 (mmt) outliers start: 65 outliers final: 35 residues processed: 472 average time/residue: 0.4755 time to fit residues: 368.3303 Evaluate side-chains 340 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 305 time to evaluate : 3.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain D residue 23 TYR Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain G residue 224 PHE 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 342 VAL Chi-restraints excluded: chain H residue 24 THR Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 272 MET Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 213 LEU 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 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 234 optimal weight: 3.9990 chunk 193 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 380 optimal weight: 20.0000 chunk 357 optimal weight: 8.9990 chunk 218 optimal weight: 9.9990 chunk 376 optimal weight: 9.9990 chunk 272 optimal weight: 6.9990 chunk 173 optimal weight: 5.9990 chunk 320 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN B 68 GLN ** B 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 150 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 250 GLN F 275 HIS ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** H 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN H 150 GLN H 246 ASN H 275 HIS H 320 ASN I 150 GLN I 306 GLN I 320 ASN I 328 ASN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 117 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 148 GLN ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 303 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 ASN K 15 HIS K 85 ASN K 279 GLN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.108959 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.084875 restraints weight = 129201.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.083422 restraints weight = 95033.853| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.084215 restraints weight = 86268.414| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.075 32767 Z= 0.285 Angle : 0.791 12.206 44517 Z= 0.413 Chirality : 0.047 0.260 5236 Planarity : 0.006 0.130 5401 Dihedral : 12.355 75.559 5500 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.03 % Favored : 97.97 % Rotamer: Outliers : 3.32 % Allowed : 13.49 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.13), residues: 3894 helix: 0.72 (0.10), residues: 2552 sheet: -0.79 (0.28), residues: 231 loop : -0.12 (0.18), residues: 1111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 261 HIS 0.010 0.002 HIS G 56 PHE 0.036 0.004 PHE C 348 TYR 0.027 0.003 TYR F 23 ARG 0.028 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04889 ( 1849) hydrogen bonds : angle 5.19110 ( 5382) covalent geometry : bond 0.00623 (32758) covalent geometry : angle 0.79098 (44517) Misc. bond : bond 0.00163 ( 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 457 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 346 time to evaluate : 3.594 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: A 91 GLN cc_start: 0.8018 (mm110) cc_final: 0.7713 (mp10) REVERT: A 258 MET cc_start: 0.3558 (tpt) cc_final: 0.3332 (tpt) REVERT: B 69 TYR cc_start: 0.8171 (t80) cc_final: 0.7919 (t80) REVERT: B 216 GLN cc_start: 0.8181 (OUTLIER) cc_final: 0.7826 (pm20) REVERT: D 53 TYR cc_start: 0.5183 (p90) cc_final: 0.4556 (p90) REVERT: D 272 MET cc_start: 0.5683 (mmt) cc_final: 0.5343 (mmt) REVERT: E 76 SER cc_start: 0.8021 (OUTLIER) cc_final: 0.7807 (p) REVERT: E 341 ARG cc_start: 0.7373 (ptt180) cc_final: 0.7166 (ptt-90) REVERT: F 90 VAL cc_start: 0.8708 (m) cc_final: 0.8460 (p) REVERT: F 129 LYS cc_start: 0.9601 (ttpt) cc_final: 0.9237 (tppt) REVERT: F 258 MET cc_start: 0.8524 (mmm) cc_final: 0.7975 (tpp) REVERT: I 135 MET cc_start: 0.1681 (tpt) cc_final: 0.1227 (tpp) REVERT: I 169 PHE cc_start: 0.8502 (t80) cc_final: 0.8139 (t80) REVERT: I 216 GLN cc_start: 0.8510 (OUTLIER) cc_final: 0.8298 (pm20) REVERT: J 22 GLN cc_start: 0.7769 (mp10) cc_final: 0.6600 (tt0) REVERT: J 123 TRP cc_start: 0.5466 (t60) cc_final: 0.4772 (t60) REVERT: K 146 ILE cc_start: 0.5357 (mm) cc_final: 0.4685 (pt) REVERT: O 456 MET cc_start: 0.3469 (mmt) cc_final: 0.0267 (mmt) REVERT: V 456 MET cc_start: 0.3706 (mmp) cc_final: 0.2759 (mmm) outliers start: 111 outliers final: 69 residues processed: 437 average time/residue: 0.4180 time to fit residues: 298.8157 Evaluate side-chains 340 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 268 time to evaluate : 3.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain A residue 161 LEU Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 269 ASN 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 264 ILE Chi-restraints excluded: chain C residue 352 GLU 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 79 VAL 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 307 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 76 SER Chi-restraints excluded: chain E residue 113 MET Chi-restraints excluded: chain E residue 250 GLN Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 35 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 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 276 VAL Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 76 SER Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 174 SER 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 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 191 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 35 VAL Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 216 GLN Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain 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 224 PHE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 122 optimal weight: 0.8980 chunk 77 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 243 optimal weight: 8.9990 chunk 266 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 216 optimal weight: 4.9990 chunk 323 optimal weight: 9.9990 chunk 20 optimal weight: 6.9990 chunk 204 optimal weight: 0.7980 chunk 126 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 GLN B 150 GLN B 256 GLN C 220 HIS D 112 GLN D 216 GLN D 270 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN E 15 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 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 270 ASN G 320 ASN G 328 ASN H 246 ASN H 275 HIS ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 GLN J 150 GLN K 15 HIS K 150 GLN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.112354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3736 r_free = 0.3736 target = 0.087607 restraints weight = 127891.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.086377 restraints weight = 86767.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.087108 restraints weight = 71402.605| |-----------------------------------------------------------------------------| r_work (final): 0.3675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.5737 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= 0.131 Angle : 0.603 13.531 44517 Z= 0.312 Chirality : 0.041 0.220 5236 Planarity : 0.005 0.214 5401 Dihedral : 11.989 73.884 5500 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.45 % Allowed : 15.52 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.13), residues: 3894 helix: 1.29 (0.10), residues: 2563 sheet: -0.65 (0.29), residues: 231 loop : -0.10 (0.19), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP J 123 HIS 0.005 0.001 HIS G 220 PHE 0.035 0.002 PHE J 214 TYR 0.032 0.002 TYR F 23 ARG 0.045 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03806 ( 1849) hydrogen bonds : angle 4.47476 ( 5382) covalent geometry : bond 0.00282 (32758) covalent geometry : angle 0.60337 (44517) Misc. bond : bond 0.00436 ( 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 409 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 327 time to evaluate : 3.332 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: A 69 TYR cc_start: 0.7053 (t80) cc_final: 0.6681 (t80) REVERT: A 91 GLN cc_start: 0.7929 (mm110) cc_final: 0.7678 (mp10) REVERT: B 69 TYR cc_start: 0.8112 (t80) cc_final: 0.7782 (t80) REVERT: B 216 GLN cc_start: 0.8171 (OUTLIER) cc_final: 0.7759 (pm20) REVERT: C 272 MET cc_start: 0.7461 (mtm) cc_final: 0.6450 (ttp) REVERT: D 11 LEU cc_start: 0.8694 (tp) cc_final: 0.8472 (tp) REVERT: D 13 TYR cc_start: 0.7992 (m-80) cc_final: 0.7626 (m-80) REVERT: D 53 TYR cc_start: 0.4918 (p90) cc_final: 0.4636 (p90) REVERT: D 272 MET cc_start: 0.5338 (mmt) cc_final: 0.4977 (mmt) REVERT: D 295 MET cc_start: 0.8466 (tpp) cc_final: 0.8227 (mmt) REVERT: E 287 GLU cc_start: 0.8205 (tp30) cc_final: 0.7846 (tp30) REVERT: F 90 VAL cc_start: 0.8653 (m) cc_final: 0.8371 (p) REVERT: F 129 LYS cc_start: 0.9568 (ttpt) cc_final: 0.9250 (tppt) REVERT: F 135 MET cc_start: 0.8233 (ttm) cc_final: 0.7451 (tmm) REVERT: F 258 MET cc_start: 0.8269 (mmm) cc_final: 0.7933 (tpp) REVERT: F 339 ARG cc_start: 0.7594 (mtm-85) cc_final: 0.7263 (mtm-85) REVERT: H 111 LEU cc_start: 0.7927 (mt) cc_final: 0.7563 (mt) REVERT: H 113 MET cc_start: 0.7539 (ptp) cc_final: 0.7267 (ptp) REVERT: H 183 THR cc_start: 0.8272 (m) cc_final: 0.8040 (p) REVERT: I 135 MET cc_start: 0.1804 (tpt) cc_final: 0.1479 (tpp) REVERT: I 272 MET cc_start: 0.5261 (ttm) cc_final: 0.4923 (ttm) REVERT: J 22 GLN cc_start: 0.7636 (mp10) cc_final: 0.6230 (tm-30) REVERT: J 123 TRP cc_start: 0.5521 (t60) cc_final: 0.4803 (t60) REVERT: J 287 GLU cc_start: 0.8236 (tp30) cc_final: 0.8023 (tp30) REVERT: K 146 ILE cc_start: 0.5302 (mm) cc_final: 0.4701 (pt) REVERT: K 177 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7073 (pm20) REVERT: K 211 TYR cc_start: 0.4998 (OUTLIER) cc_final: 0.4629 (m-10) REVERT: O 456 MET cc_start: 0.3654 (mmt) cc_final: 0.0158 (mmt) REVERT: Q 456 MET cc_start: 0.7647 (mtm) cc_final: 0.6767 (mmm) REVERT: V 456 MET cc_start: 0.3803 (mmp) cc_final: 0.3030 (mmm) outliers start: 82 outliers final: 43 residues processed: 389 average time/residue: 0.4079 time to fit residues: 263.1816 Evaluate side-chains 324 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 279 time to evaluate : 3.568 ------------------------------------------------------------------------------- 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 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 216 GLN Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain F residue 21 SER 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 342 VAL Chi-restraints excluded: chain G residue 174 SER 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 94 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 243 LEU 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 224 PHE Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 14 optimal weight: 1.9990 chunk 285 optimal weight: 3.9990 chunk 65 optimal weight: 9.9990 chunk 169 optimal weight: 0.0970 chunk 109 optimal weight: 10.0000 chunk 286 optimal weight: 1.9990 chunk 261 optimal weight: 3.9990 chunk 320 optimal weight: 8.9990 chunk 101 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 322 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 306 GLN D 91 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS H 275 HIS I 306 GLN ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 22 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4144 r_free = 0.4144 target = 0.109551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.085856 restraints weight = 128307.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.083842 restraints weight = 98874.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.084555 restraints weight = 89863.309| |-----------------------------------------------------------------------------| r_work (final): 0.3624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32767 Z= 0.196 Angle : 0.658 9.759 44517 Z= 0.343 Chirality : 0.042 0.242 5236 Planarity : 0.005 0.159 5401 Dihedral : 12.036 73.784 5500 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 14.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.69 % Allowed : 15.61 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.13), residues: 3894 helix: 1.25 (0.10), residues: 2574 sheet: -0.58 (0.29), residues: 231 loop : -0.17 (0.19), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 123 HIS 0.006 0.001 HIS F 117 PHE 0.036 0.003 PHE K 224 TYR 0.023 0.002 TYR F 23 ARG 0.021 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.04111 ( 1849) hydrogen bonds : angle 4.69062 ( 5382) covalent geometry : bond 0.00432 (32758) covalent geometry : angle 0.65817 (44517) Misc. bond : bond 0.00219 ( 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 398 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 308 time to evaluate : 5.198 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: A 91 GLN cc_start: 0.8031 (mm110) cc_final: 0.7760 (mp10) REVERT: B 69 TYR cc_start: 0.8087 (t80) cc_final: 0.7683 (t80) REVERT: B 201 MET cc_start: 0.5571 (OUTLIER) cc_final: 0.5128 (mtm) REVERT: B 216 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7728 (pm20) REVERT: C 272 MET cc_start: 0.7425 (mtm) cc_final: 0.6902 (mtm) REVERT: D 53 TYR cc_start: 0.5411 (p90) cc_final: 0.5136 (p90) REVERT: D 135 MET cc_start: 0.8698 (ttt) cc_final: 0.8244 (ttt) REVERT: E 287 GLU cc_start: 0.8246 (tp30) cc_final: 0.8041 (tp30) REVERT: F 90 VAL cc_start: 0.8738 (m) cc_final: 0.8513 (p) REVERT: F 129 LYS cc_start: 0.9593 (ttpt) cc_final: 0.9250 (tppt) REVERT: F 135 MET cc_start: 0.8218 (ttm) cc_final: 0.7414 (tmm) REVERT: F 258 MET cc_start: 0.8499 (mmm) cc_final: 0.8057 (tpp) REVERT: G 231 LEU cc_start: 0.7977 (OUTLIER) cc_final: 0.7312 (mm) REVERT: H 111 LEU cc_start: 0.7886 (mt) cc_final: 0.7517 (mt) REVERT: H 183 THR cc_start: 0.8188 (m) cc_final: 0.7930 (p) REVERT: H 248 PHE cc_start: 0.8018 (t80) cc_final: 0.7621 (t80) REVERT: I 169 PHE cc_start: 0.8517 (t80) cc_final: 0.8209 (t80) REVERT: I 191 LEU cc_start: 0.7868 (pp) cc_final: 0.7482 (tp) REVERT: J 22 GLN cc_start: 0.7815 (mp10) cc_final: 0.6599 (tt0) REVERT: J 123 TRP cc_start: 0.5493 (t60) cc_final: 0.4769 (t60) REVERT: J 287 GLU cc_start: 0.8320 (tp30) cc_final: 0.8106 (tp30) REVERT: J 295 MET cc_start: 0.8535 (mmm) cc_final: 0.8330 (mpp) REVERT: K 104 LYS cc_start: 0.6579 (mmtt) cc_final: 0.5912 (tppt) REVERT: K 146 ILE cc_start: 0.4901 (mm) cc_final: 0.4502 (pt) REVERT: K 211 TYR cc_start: 0.5329 (OUTLIER) cc_final: 0.4859 (m-10) REVERT: K 224 PHE cc_start: 0.8417 (t80) cc_final: 0.7890 (t80) REVERT: O 456 MET cc_start: 0.3868 (mmt) cc_final: 0.0519 (mmt) REVERT: Q 452 TYR cc_start: 0.7623 (m-80) cc_final: 0.7326 (m-80) REVERT: Q 456 MET cc_start: 0.7926 (mtm) cc_final: 0.7263 (mmm) REVERT: V 456 MET cc_start: 0.2979 (mmp) cc_final: 0.2221 (mmm) outliers start: 90 outliers final: 62 residues processed: 373 average time/residue: 0.5641 time to fit residues: 357.4168 Evaluate side-chains 327 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 261 time to evaluate : 4.429 ------------------------------------------------------------------------------- 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 201 MET 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 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 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 35 VAL Chi-restraints excluded: chain E residue 263 VAL 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 264 ILE Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 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 307 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 335 ILE Chi-restraints excluded: chain 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 94 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 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 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 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 211 TYR Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain M residue 456 MET 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 182 optimal weight: 2.9990 chunk 74 optimal weight: 1.9990 chunk 192 optimal weight: 0.6980 chunk 367 optimal weight: 5.9990 chunk 360 optimal weight: 20.0000 chunk 136 optimal weight: 4.9990 chunk 133 optimal weight: 1.9990 chunk 152 optimal weight: 7.9990 chunk 39 optimal weight: 8.9990 chunk 266 optimal weight: 0.7980 chunk 224 optimal weight: 0.4980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 68 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 85 ASN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS H 275 HIS ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4171 r_free = 0.4171 target = 0.111063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.086419 restraints weight = 128921.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.085076 restraints weight = 87937.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.085780 restraints weight = 73945.685| |-----------------------------------------------------------------------------| r_work (final): 0.3650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.6488 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 32767 Z= 0.133 Angle : 0.602 12.686 44517 Z= 0.307 Chirality : 0.041 0.238 5236 Planarity : 0.004 0.178 5401 Dihedral : 11.942 73.843 5500 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 2.48 % Allowed : 16.21 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.14), residues: 3894 helix: 1.46 (0.10), residues: 2574 sheet: -0.51 (0.30), residues: 231 loop : -0.13 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 123 HIS 0.004 0.001 HIS F 117 PHE 0.029 0.002 PHE K 224 TYR 0.032 0.001 TYR I 227 ARG 0.007 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03644 ( 1849) hydrogen bonds : angle 4.41414 ( 5382) covalent geometry : bond 0.00295 (32758) covalent geometry : angle 0.60213 (44517) Misc. bond : bond 0.00232 ( 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 392 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 309 time to evaluate : 4.311 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: A 91 GLN cc_start: 0.8021 (mm110) cc_final: 0.7772 (mp10) REVERT: A 287 GLU cc_start: 0.4832 (mm-30) cc_final: 0.4345 (pt0) REVERT: B 69 TYR cc_start: 0.8060 (t80) cc_final: 0.7628 (t80) REVERT: B 210 PHE cc_start: 0.7449 (OUTLIER) cc_final: 0.7229 (t80) REVERT: D 53 TYR cc_start: 0.5759 (p90) cc_final: 0.5495 (p90) REVERT: D 135 MET cc_start: 0.8551 (ttt) cc_final: 0.8189 (ttm) REVERT: E 135 MET cc_start: 0.9185 (ttt) cc_final: 0.8928 (tmm) REVERT: E 241 GLU cc_start: 0.7866 (pp20) cc_final: 0.7274 (pp20) REVERT: E 287 GLU cc_start: 0.8160 (tp30) cc_final: 0.7788 (tp30) REVERT: F 90 VAL cc_start: 0.8627 (m) cc_final: 0.8413 (p) REVERT: F 129 LYS cc_start: 0.9601 (ttpt) cc_final: 0.9235 (tppt) REVERT: F 139 LEU cc_start: 0.8416 (mt) cc_final: 0.8114 (pp) REVERT: F 215 GLU cc_start: 0.8424 (mm-30) cc_final: 0.8154 (tm-30) REVERT: F 258 MET cc_start: 0.8363 (mmm) cc_final: 0.8020 (tpp) REVERT: F 271 ILE cc_start: 0.8226 (pt) cc_final: 0.7965 (mm) REVERT: F 339 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7630 (mtm-85) REVERT: G 231 LEU cc_start: 0.7696 (OUTLIER) cc_final: 0.7242 (mm) REVERT: H 111 LEU cc_start: 0.7848 (mt) cc_final: 0.7572 (mt) REVERT: H 113 MET cc_start: 0.7644 (ptp) cc_final: 0.7401 (ptp) REVERT: H 183 THR cc_start: 0.8090 (m) cc_final: 0.7853 (p) REVERT: J 22 GLN cc_start: 0.7739 (mp10) cc_final: 0.6351 (tt0) REVERT: J 123 TRP cc_start: 0.5394 (t60) cc_final: 0.4664 (t60) REVERT: J 295 MET cc_start: 0.8541 (mmm) cc_final: 0.8292 (mpp) REVERT: K 104 LYS cc_start: 0.6641 (mmtt) cc_final: 0.5962 (mmtt) REVERT: K 211 TYR cc_start: 0.5053 (OUTLIER) cc_final: 0.4580 (m-10) REVERT: K 221 ARG cc_start: 0.6513 (mtp180) cc_final: 0.6162 (ptp-170) REVERT: O 456 MET cc_start: 0.3878 (mmt) cc_final: 0.0793 (mmt) REVERT: Q 452 TYR cc_start: 0.7595 (m-80) cc_final: 0.7390 (m-80) REVERT: Q 456 MET cc_start: 0.7878 (mtm) cc_final: 0.6908 (mmm) REVERT: S 452 TYR cc_start: 0.8282 (m-80) cc_final: 0.7732 (m-80) REVERT: V 456 MET cc_start: 0.2985 (mmp) cc_final: 0.2243 (mmm) outliers start: 83 outliers final: 64 residues processed: 368 average time/residue: 0.4084 time to fit residues: 252.8432 Evaluate side-chains 348 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 281 time to evaluate : 3.438 ------------------------------------------------------------------------------- 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 145 ASN 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 313 LEU Chi-restraints excluded: chain D residue 23 TYR 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 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 272 MET Chi-restraints excluded: chain E residue 307 SER Chi-restraints excluded: chain F residue 21 SER Chi-restraints excluded: chain F residue 23 TYR 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 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 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 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 126 GLU 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 64 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 230 optimal weight: 2.9990 chunk 156 optimal weight: 0.7980 chunk 372 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 358 optimal weight: 20.0000 chunk 240 optimal weight: 4.9990 chunk 296 optimal weight: 5.9990 chunk 332 optimal weight: 1.9990 chunk 78 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 270 ASN B 328 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** J 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 68 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.109456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.085853 restraints weight = 129489.209| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.083508 restraints weight = 102484.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.084547 restraints weight = 94513.296| |-----------------------------------------------------------------------------| r_work (final): 0.3625 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.6924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 32767 Z= 0.179 Angle : 0.648 13.037 44517 Z= 0.332 Chirality : 0.042 0.259 5236 Planarity : 0.005 0.161 5401 Dihedral : 11.987 73.772 5500 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 14.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.81 % Allowed : 16.57 % Favored : 80.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.14), residues: 3894 helix: 1.37 (0.10), residues: 2574 sheet: -0.59 (0.30), residues: 231 loop : -0.14 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 123 HIS 0.006 0.001 HIS F 117 PHE 0.027 0.003 PHE B 248 TYR 0.028 0.002 TYR I 227 ARG 0.023 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03883 ( 1849) hydrogen bonds : angle 4.57276 ( 5382) covalent geometry : bond 0.00397 (32758) covalent geometry : angle 0.64833 (44517) Misc. bond : bond 0.00279 ( 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 382 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 288 time to evaluate : 3.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9127 (tt) cc_final: 0.8835 (mt) REVERT: B 69 TYR cc_start: 0.8029 (t80) cc_final: 0.7501 (t80) REVERT: B 210 PHE cc_start: 0.7582 (OUTLIER) cc_final: 0.7334 (t80) REVERT: C 163 CYS cc_start: 0.7726 (m) cc_final: 0.6258 (t) REVERT: D 53 TYR cc_start: 0.6109 (p90) cc_final: 0.5738 (p90) REVERT: D 135 MET cc_start: 0.8642 (ttt) cc_final: 0.8333 (ttm) REVERT: E 287 GLU cc_start: 0.8166 (tp30) cc_final: 0.7861 (tp30) REVERT: F 90 VAL cc_start: 0.8750 (m) cc_final: 0.8545 (p) REVERT: F 129 LYS cc_start: 0.9610 (ttpt) cc_final: 0.9233 (tppt) REVERT: F 135 MET cc_start: 0.8119 (ttm) cc_final: 0.7384 (tmm) REVERT: F 210 PHE cc_start: 0.8876 (OUTLIER) cc_final: 0.8428 (m-80) REVERT: F 271 ILE cc_start: 0.8051 (pt) cc_final: 0.7765 (mm) REVERT: G 231 LEU cc_start: 0.7956 (OUTLIER) cc_final: 0.7353 (mm) REVERT: H 111 LEU cc_start: 0.7865 (mt) cc_final: 0.7384 (mt) REVERT: H 113 MET cc_start: 0.7730 (ptp) cc_final: 0.7489 (ptp) REVERT: H 248 PHE cc_start: 0.7975 (t80) cc_final: 0.7540 (t80) REVERT: I 135 MET cc_start: 0.2596 (tpt) cc_final: 0.2374 (mmt) REVERT: J 22 GLN cc_start: 0.7853 (mp10) cc_final: 0.6448 (tt0) REVERT: J 123 TRP cc_start: 0.5440 (t60) cc_final: 0.4623 (t60) REVERT: K 104 LYS cc_start: 0.6609 (mmtt) cc_final: 0.6074 (tppt) REVERT: K 211 TYR cc_start: 0.4896 (OUTLIER) cc_final: 0.4511 (m-10) REVERT: O 456 MET cc_start: 0.4225 (mmt) cc_final: 0.3393 (mmm) REVERT: Q 452 TYR cc_start: 0.7698 (m-80) cc_final: 0.7488 (m-80) REVERT: Q 456 MET cc_start: 0.8128 (mtm) cc_final: 0.7330 (mmm) REVERT: V 456 MET cc_start: 0.3069 (mmp) cc_final: 0.2343 (mmm) outliers start: 94 outliers final: 74 residues processed: 357 average time/residue: 0.4023 time to fit residues: 239.7011 Evaluate side-chains 348 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 270 time to evaluate : 3.679 ------------------------------------------------------------------------------- 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 116 ILE Chi-restraints excluded: chain B residue 145 ASN 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 313 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 167 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 272 MET 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 21 SER Chi-restraints excluded: chain F residue 23 TYR 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 210 PHE Chi-restraints excluded: chain F residue 233 SER Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 24 THR 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 86 SER Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 231 LEU Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 324 VAL Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 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 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 24 optimal weight: 9.9990 chunk 84 optimal weight: 0.0670 chunk 124 optimal weight: 2.9990 chunk 247 optimal weight: 9.9990 chunk 254 optimal weight: 0.7980 chunk 189 optimal weight: 2.9990 chunk 315 optimal weight: 7.9990 chunk 123 optimal weight: 2.9990 chunk 305 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 185 optimal weight: 9.9990 overall best weight: 1.7724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 306 GLN E 148 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS J 270 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.109848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.086094 restraints weight = 128093.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.084097 restraints weight = 99473.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.084987 restraints weight = 88225.386| |-----------------------------------------------------------------------------| r_work (final): 0.3634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.7116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 32767 Z= 0.159 Angle : 0.641 11.097 44517 Z= 0.328 Chirality : 0.041 0.272 5236 Planarity : 0.005 0.157 5401 Dihedral : 11.934 73.768 5500 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 13.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.66 % Allowed : 17.14 % Favored : 80.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.25 (0.14), residues: 3894 helix: 1.43 (0.10), residues: 2574 sheet: -0.63 (0.29), residues: 231 loop : -0.12 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 123 HIS 0.005 0.001 HIS F 117 PHE 0.032 0.002 PHE H 169 TYR 0.060 0.002 TYR B 23 ARG 0.039 0.001 ARG A 78 Details of bonding type rmsd hydrogen bonds : bond 0.03786 ( 1849) hydrogen bonds : angle 4.50403 ( 5382) covalent geometry : bond 0.00358 (32758) covalent geometry : angle 0.64120 (44517) Misc. bond : bond 0.00351 ( 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 380 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 291 time to evaluate : 3.965 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: A 161 LEU cc_start: 0.9153 (tt) cc_final: 0.8882 (mt) REVERT: B 69 TYR cc_start: 0.8042 (t80) cc_final: 0.7528 (t80) REVERT: B 210 PHE cc_start: 0.7537 (OUTLIER) cc_final: 0.7287 (t80) REVERT: C 163 CYS cc_start: 0.7870 (m) cc_final: 0.6588 (t) REVERT: D 53 TYR cc_start: 0.6175 (p90) cc_final: 0.5856 (p90) REVERT: D 272 MET cc_start: 0.5562 (mmt) cc_final: 0.5258 (mmt) REVERT: E 241 GLU cc_start: 0.7792 (pp20) cc_final: 0.7212 (pp20) REVERT: E 287 GLU cc_start: 0.8140 (tp30) cc_final: 0.7789 (tp30) REVERT: F 90 VAL cc_start: 0.8671 (m) cc_final: 0.8443 (p) REVERT: F 129 LYS cc_start: 0.9611 (ttpt) cc_final: 0.9224 (tppt) REVERT: F 135 MET cc_start: 0.8107 (ttm) cc_final: 0.7387 (tmm) REVERT: F 210 PHE cc_start: 0.8851 (OUTLIER) cc_final: 0.8375 (m-80) REVERT: F 339 ARG cc_start: 0.8047 (mtm-85) cc_final: 0.7690 (mtm-85) REVERT: G 125 GLU cc_start: 0.8664 (mm-30) cc_final: 0.8351 (mm-30) REVERT: G 231 LEU cc_start: 0.7826 (OUTLIER) cc_final: 0.7302 (mm) REVERT: H 113 MET cc_start: 0.7733 (ptp) cc_final: 0.7481 (ptp) REVERT: H 248 PHE cc_start: 0.7930 (t80) cc_final: 0.7594 (t80) REVERT: I 249 MET cc_start: 0.7158 (tpt) cc_final: 0.6909 (tpt) REVERT: J 22 GLN cc_start: 0.7835 (mp10) cc_final: 0.6423 (tt0) REVERT: J 123 TRP cc_start: 0.5319 (t60) cc_final: 0.4503 (t60) REVERT: K 104 LYS cc_start: 0.6570 (mmtt) cc_final: 0.6068 (tppt) REVERT: K 211 TYR cc_start: 0.4920 (OUTLIER) cc_final: 0.4651 (m-80) REVERT: O 456 MET cc_start: 0.4328 (mmt) cc_final: 0.1171 (mmt) REVERT: Q 452 TYR cc_start: 0.7762 (m-80) cc_final: 0.7553 (m-80) REVERT: Q 456 MET cc_start: 0.8078 (mtm) cc_final: 0.7344 (mmm) REVERT: V 456 MET cc_start: 0.2771 (mmp) cc_final: 0.2012 (mmm) outliers start: 89 outliers final: 67 residues processed: 354 average time/residue: 0.4263 time to fit residues: 256.7692 Evaluate side-chains 341 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 270 time to evaluate : 3.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 LEU 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 145 ASN 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 313 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 263 VAL 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 23 TYR 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 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 307 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 86 SER 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 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 47 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 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 176 ILE 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 2 optimal weight: 20.0000 chunk 210 optimal weight: 1.9990 chunk 270 optimal weight: 8.9990 chunk 279 optimal weight: 8.9990 chunk 140 optimal weight: 2.9990 chunk 384 optimal weight: 7.9990 chunk 240 optimal weight: 3.9990 chunk 165 optimal weight: 0.5980 chunk 353 optimal weight: 20.0000 chunk 237 optimal weight: 5.9990 chunk 195 optimal weight: 0.6980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 81 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 81 GLN H 275 HIS I 256 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4224 r_free = 0.4224 target = 0.112475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3864 r_free = 0.3864 target = 0.091613 restraints weight = 134654.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.090740 restraints weight = 121996.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.091406 restraints weight = 98130.825| |-----------------------------------------------------------------------------| r_work (final): 0.3809 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7329 moved from start: 0.7389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 32767 Z= 0.175 Angle : 0.658 13.217 44517 Z= 0.338 Chirality : 0.042 0.308 5236 Planarity : 0.005 0.177 5401 Dihedral : 11.950 73.738 5500 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.69 % Allowed : 17.25 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.20 (0.14), residues: 3894 helix: 1.39 (0.10), residues: 2574 sheet: -0.65 (0.29), residues: 231 loop : -0.14 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 261 HIS 0.005 0.001 HIS D 303 PHE 0.033 0.003 PHE H 169 TYR 0.034 0.002 TYR D 23 ARG 0.018 0.001 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 1849) hydrogen bonds : angle 4.55545 ( 5382) covalent geometry : bond 0.00391 (32758) covalent geometry : angle 0.65823 (44517) Misc. bond : bond 0.00447 ( 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 366 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 276 time to evaluate : 3.468 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.8958 (tt) cc_final: 0.8752 (mt) REVERT: B 69 TYR cc_start: 0.7995 (t80) cc_final: 0.7502 (t80) REVERT: C 163 CYS cc_start: 0.7709 (m) cc_final: 0.6465 (t) REVERT: D 24 THR cc_start: 0.6876 (p) cc_final: 0.6648 (t) REVERT: D 272 MET cc_start: 0.5292 (mmt) cc_final: 0.4990 (mmt) REVERT: E 241 GLU cc_start: 0.7843 (pp20) cc_final: 0.7180 (pp20) REVERT: E 287 GLU cc_start: 0.7865 (tp30) cc_final: 0.7566 (tp30) REVERT: F 90 VAL cc_start: 0.8721 (m) cc_final: 0.8503 (p) REVERT: F 129 LYS cc_start: 0.9443 (ttpt) cc_final: 0.9154 (tppt) REVERT: F 135 MET cc_start: 0.7952 (ttm) cc_final: 0.7319 (tmm) REVERT: F 210 PHE cc_start: 0.8785 (OUTLIER) cc_final: 0.8281 (m-80) REVERT: G 125 GLU cc_start: 0.8310 (mm-30) cc_final: 0.8077 (mm-30) REVERT: G 231 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7470 (mm) REVERT: H 113 MET cc_start: 0.7251 (ptp) cc_final: 0.7021 (ptp) REVERT: H 248 PHE cc_start: 0.7800 (t80) cc_final: 0.7521 (t80) REVERT: I 135 MET cc_start: 0.2641 (tpt) cc_final: 0.2215 (mmt) REVERT: I 289 TYR cc_start: 0.6864 (m-80) cc_final: 0.6608 (m-10) REVERT: J 22 GLN cc_start: 0.7653 (mp10) cc_final: 0.6332 (tt0) REVERT: K 104 LYS cc_start: 0.6699 (mmtt) cc_final: 0.6199 (tppt) REVERT: K 110 ASP cc_start: 0.6705 (m-30) cc_final: 0.6233 (t70) REVERT: O 456 MET cc_start: 0.3688 (mmt) cc_final: -0.0351 (ttt) REVERT: Q 456 MET cc_start: 0.7870 (mtm) cc_final: 0.7356 (mmm) REVERT: V 456 MET cc_start: 0.1819 (mmp) cc_final: 0.1242 (mmm) outliers start: 90 outliers final: 74 residues processed: 339 average time/residue: 0.3828 time to fit residues: 219.5273 Evaluate side-chains 341 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 265 time to evaluate : 3.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 LEU 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 116 ILE Chi-restraints excluded: chain B residue 145 ASN 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 313 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 45 THR Chi-restraints excluded: chain D residue 47 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 236 THR Chi-restraints excluded: chain E residue 263 VAL 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 21 SER Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 95 THR 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 307 SER Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 86 SER 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 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 47 LEU Chi-restraints excluded: chain H residue 94 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 243 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 124 VAL Chi-restraints excluded: chain I residue 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 176 ILE 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 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 172 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 261 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 84 optimal weight: 0.5980 chunk 188 optimal weight: 0.8980 chunk 195 optimal weight: 1.9990 chunk 239 optimal weight: 0.0270 chunk 83 optimal weight: 7.9990 chunk 306 optimal weight: 10.0000 chunk 325 optimal weight: 20.0000 overall best weight: 0.9042 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS E 284 GLN H 250 GLN H 275 HIS ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.111269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.088606 restraints weight = 134170.567| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.087757 restraints weight = 100250.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3717 r_free = 0.3717 target = 0.088655 restraints weight = 89675.958| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7485 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= 0.125 Angle : 0.627 12.685 44517 Z= 0.319 Chirality : 0.041 0.303 5236 Planarity : 0.005 0.203 5401 Dihedral : 11.912 73.743 5500 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.06 % Allowed : 17.97 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.14), residues: 3894 helix: 1.53 (0.10), residues: 2574 sheet: -0.58 (0.30), residues: 231 loop : -0.10 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 261 HIS 0.003 0.001 HIS F 220 PHE 0.034 0.002 PHE J 244 TYR 0.049 0.002 TYR F 23 ARG 0.014 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03591 ( 1849) hydrogen bonds : angle 4.35630 ( 5382) covalent geometry : bond 0.00278 (32758) covalent geometry : angle 0.62719 (44517) Misc. bond : bond 0.00372 ( 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 367 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 298 time to evaluate : 3.434 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 LEU cc_start: 0.9159 (tt) cc_final: 0.8957 (mt) REVERT: B 69 TYR cc_start: 0.8015 (t80) cc_final: 0.7455 (t80) REVERT: C 163 CYS cc_start: 0.7726 (m) cc_final: 0.6830 (t) REVERT: C 210 PHE cc_start: 0.8232 (m-80) cc_final: 0.7907 (m-80) REVERT: D 258 MET cc_start: 0.8861 (mmm) cc_final: 0.8266 (tpp) REVERT: D 272 MET cc_start: 0.5298 (mmt) cc_final: 0.4985 (mmt) REVERT: E 241 GLU cc_start: 0.7747 (pp20) cc_final: 0.7154 (pp20) REVERT: E 287 GLU cc_start: 0.8010 (tp30) cc_final: 0.7601 (tp30) REVERT: F 129 LYS cc_start: 0.9544 (ttpt) cc_final: 0.9160 (tppt) REVERT: F 139 LEU cc_start: 0.8601 (mt) cc_final: 0.8298 (pp) REVERT: F 210 PHE cc_start: 0.8786 (OUTLIER) cc_final: 0.8243 (m-80) REVERT: G 125 GLU cc_start: 0.8481 (mm-30) cc_final: 0.8218 (mm-30) REVERT: H 113 MET cc_start: 0.7526 (ptp) cc_final: 0.7284 (ptp) REVERT: H 248 PHE cc_start: 0.7876 (t80) cc_final: 0.7616 (t80) REVERT: I 135 MET cc_start: 0.3063 (tpt) cc_final: 0.2683 (mmt) REVERT: I 289 TYR cc_start: 0.7084 (m-80) cc_final: 0.6719 (m-10) REVERT: J 22 GLN cc_start: 0.7611 (mp10) cc_final: 0.6263 (tt0) REVERT: J 258 MET cc_start: 0.8774 (pmm) cc_final: 0.8059 (mpp) REVERT: K 104 LYS cc_start: 0.6662 (mmtt) cc_final: 0.6120 (tppt) REVERT: K 110 ASP cc_start: 0.6799 (m-30) cc_final: 0.6291 (t70) REVERT: O 456 MET cc_start: 0.3701 (mmt) cc_final: 0.0454 (mmt) REVERT: Q 452 TYR cc_start: 0.7505 (m-80) cc_final: 0.7301 (m-80) REVERT: Q 456 MET cc_start: 0.7845 (mtm) cc_final: 0.6956 (mmm) REVERT: V 456 MET cc_start: 0.2100 (mmp) cc_final: 0.1560 (mmm) outliers start: 69 outliers final: 64 residues processed: 342 average time/residue: 0.3789 time to fit residues: 220.0177 Evaluate side-chains 333 residues out of total 3344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 268 time to evaluate : 3.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 52 LEU 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 A residue 352 GLU Chi-restraints excluded: chain B residue 116 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 313 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 183 THR Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 263 VAL 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 21 SER Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 29 VAL Chi-restraints excluded: chain F residue 95 THR 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 272 MET Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 174 SER Chi-restraints excluded: chain G residue 191 LEU Chi-restraints excluded: chain G residue 224 PHE Chi-restraints excluded: chain G residue 273 LEU Chi-restraints excluded: chain G residue 292 VAL Chi-restraints excluded: chain G residue 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 47 LEU Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 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 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 176 ILE Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER 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 181 optimal weight: 0.9980 chunk 223 optimal weight: 20.0000 chunk 42 optimal weight: 0.0970 chunk 308 optimal weight: 1.9990 chunk 252 optimal weight: 0.9980 chunk 232 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 256 optimal weight: 9.9990 chunk 16 optimal weight: 1.9990 chunk 281 optimal weight: 0.9980 chunk 190 optimal weight: 0.2980 overall best weight: 0.6778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 275 HIS ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 279 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 GLN I 328 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.115017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3914 r_free = 0.3914 target = 0.094176 restraints weight = 134176.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.092529 restraints weight = 107878.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.093469 restraints weight = 83647.851| |-----------------------------------------------------------------------------| r_work (final): 0.3847 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.7603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32767 Z= 0.120 Angle : 0.622 12.782 44517 Z= 0.315 Chirality : 0.040 0.279 5236 Planarity : 0.004 0.074 5401 Dihedral : 12.141 172.767 5500 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 2.00 % Allowed : 18.72 % Favored : 79.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.14), residues: 3894 helix: 1.57 (0.10), residues: 2574 sheet: -0.53 (0.30), residues: 231 loop : -0.10 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP J 123 HIS 0.005 0.001 HIS E 220 PHE 0.036 0.002 PHE K 224 TYR 0.066 0.002 TYR F 23 ARG 0.022 0.000 ARG E 78 Details of bonding type rmsd hydrogen bonds : bond 0.03516 ( 1849) hydrogen bonds : angle 4.30791 ( 5382) covalent geometry : bond 0.00265 (32758) covalent geometry : angle 0.62207 (44517) Misc. bond : bond 0.00400 ( 9) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10848.91 seconds wall clock time: 195 minutes 2.89 seconds (11702.89 seconds total)