Starting phenix.real_space_refine on Fri Mar 22 03:26:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdr_17619/03_2024/8pdr_17619.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdr_17619/03_2024/8pdr_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdr_17619/03_2024/8pdr_17619.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdr_17619/03_2024/8pdr_17619.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdr_17619/03_2024/8pdr_17619.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8pdr_17619/03_2024/8pdr_17619.pdb" } 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 Residue "A GLU 43": "OE1" <-> "OE2" Residue "A GLU 109": "OE1" <-> "OE2" Residue "A GLU 126": "OE1" <-> "OE2" Residue "A ARG 132": "NH1" <-> "NH2" Residue "A GLU 181": "OE1" <-> "OE2" Residue "A GLU 215": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "B GLU 43": "OE1" <-> "OE2" Residue "B GLU 109": "OE1" <-> "OE2" Residue "B GLU 126": "OE1" <-> "OE2" Residue "B ARG 132": "NH1" <-> "NH2" Residue "B GLU 181": "OE1" <-> "OE2" Residue "B GLU 215": "OE1" <-> "OE2" Residue "B GLU 352": "OE1" <-> "OE2" Residue "C GLU 43": "OE1" <-> "OE2" Residue "C GLU 109": "OE1" <-> "OE2" Residue "C GLU 126": "OE1" <-> "OE2" Residue "C ARG 132": "NH1" <-> "NH2" Residue "C GLU 181": "OE1" <-> "OE2" Residue "C GLU 215": "OE1" <-> "OE2" Residue "C GLU 352": "OE1" <-> "OE2" Residue "D GLU 43": "OE1" <-> "OE2" Residue "D GLU 109": "OE1" <-> "OE2" Residue "D GLU 126": "OE1" <-> "OE2" Residue "D ARG 132": "NH1" <-> "NH2" Residue "D GLU 181": "OE1" <-> "OE2" Residue "D GLU 215": "OE1" <-> "OE2" Residue "D GLU 352": "OE1" <-> "OE2" Residue "E GLU 43": "OE1" <-> "OE2" Residue "E GLU 109": "OE1" <-> "OE2" Residue "E GLU 126": "OE1" <-> "OE2" Residue "E ARG 132": "NH1" <-> "NH2" Residue "E GLU 181": "OE1" <-> "OE2" Residue "E GLU 215": "OE1" <-> "OE2" Residue "E GLU 352": "OE1" <-> "OE2" Residue "F GLU 43": "OE1" <-> "OE2" Residue "F GLU 109": "OE1" <-> "OE2" Residue "F GLU 126": "OE1" <-> "OE2" Residue "F ARG 132": "NH1" <-> "NH2" Residue "F GLU 181": "OE1" <-> "OE2" Residue "F GLU 215": "OE1" <-> "OE2" Residue "F GLU 352": "OE1" <-> "OE2" Residue "G GLU 43": "OE1" <-> "OE2" Residue "G GLU 109": "OE1" <-> "OE2" Residue "G GLU 126": "OE1" <-> "OE2" Residue "G ARG 132": "NH1" <-> "NH2" Residue "G GLU 181": "OE1" <-> "OE2" Residue "G GLU 215": "OE1" <-> "OE2" Residue "G GLU 352": "OE1" <-> "OE2" Residue "H GLU 43": "OE1" <-> "OE2" Residue "H GLU 109": "OE1" <-> "OE2" Residue "H GLU 126": "OE1" <-> "OE2" Residue "H ARG 132": "NH1" <-> "NH2" Residue "H GLU 181": "OE1" <-> "OE2" Residue "H GLU 215": "OE1" <-> "OE2" Residue "H GLU 352": "OE1" <-> "OE2" Residue "I GLU 43": "OE1" <-> "OE2" Residue "I GLU 109": "OE1" <-> "OE2" Residue "I GLU 126": "OE1" <-> "OE2" Residue "I ARG 132": "NH1" <-> "NH2" Residue "I GLU 181": "OE1" <-> "OE2" Residue "I GLU 215": "OE1" <-> "OE2" Residue "I GLU 352": "OE1" <-> "OE2" Residue "J GLU 43": "OE1" <-> "OE2" Residue "J GLU 109": "OE1" <-> "OE2" Residue "J GLU 126": "OE1" <-> "OE2" Residue "J ARG 132": "NH1" <-> "NH2" Residue "J GLU 181": "OE1" <-> "OE2" Residue "J GLU 215": "OE1" <-> "OE2" Residue "J GLU 352": "OE1" <-> "OE2" Residue "K GLU 43": "OE1" <-> "OE2" Residue "K GLU 109": "OE1" <-> "OE2" Residue "K GLU 126": "OE1" <-> "OE2" Residue "K ARG 132": "NH1" <-> "NH2" Residue "K GLU 181": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K GLU 352": "OE1" <-> "OE2" Time to flip residues: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 15.84, per 1000 atoms: 0.49 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 - 3.50 Amino acid : False - 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=0, symmetry=0 Time building additional restraints: 12.55 Conformation dependent library (CDL) restraints added in 5.9 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: 9.97 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: 10.26 Time building geometry restraints manager: 13.62 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: 99.50 - 106.41: 973 106.41 - 113.31: 18259 113.31 - 120.22: 12455 120.22 - 127.13: 12610 127.13 - 134.04: 220 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: 20 1.46 - 2.32: 108 2.32 - 3.18: 28996 3.18 - 4.04: 85862 4.04 - 4.90: 159149 Warning: very small nonbonded interaction distances. Nonbonded interactions: 274135 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 274130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' } ncs_group { reference = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' selection = chain 'e' selection = chain 'f' selection = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 15.000 Check model and map are aligned: 0.430 Set scattering table: 0.300 Process input model: 86.120 Find NCS groups from input model: 2.170 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 109.980 ------------------------------------------------------------------------------- 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 : 0.005 0.056 32758 Z= 0.308 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 878 time to evaluate : 3.981 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: 0.4729 time to fit residues: 636.5492 Evaluate side-chains 408 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 408 time to evaluate : 3.633 ------------------------------------------------------------------------------- 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: 7.9990 chunk 291 optimal weight: 3.9990 chunk 161 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 196 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 301 optimal weight: 6.9990 chunk 116 optimal weight: 5.9990 chunk 183 optimal weight: 6.9990 chunk 224 optimal weight: 6.9990 chunk 349 optimal weight: 10.0000 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 246 ASN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN D 328 ASN E 15 HIS ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 112 GLN E 150 GLN E 270 ASN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 328 ASN F 112 GLN ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 279 GLN F 303 HIS F 306 GLN G 112 GLN G 150 GLN ** H 150 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN L 453 GLN Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6013 moved from start: 0.3954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.078 32758 Z= 0.313 Angle : 0.704 11.294 44517 Z= 0.368 Chirality : 0.044 0.197 5236 Planarity : 0.005 0.043 5401 Dihedral : 12.082 74.054 5500 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Rotamer: Outliers : 2.12 % Allowed : 11.27 % Favored : 86.60 % 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: 0.84 (0.13), residues: 3894 helix: 1.02 (0.10), residues: 2574 sheet: -0.97 (0.27), residues: 231 loop : 0.06 (0.18), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 123 HIS 0.009 0.002 HIS I 15 PHE 0.028 0.003 PHE G 169 TYR 0.024 0.002 TYR B 69 ARG 0.010 0.001 ARG G 339 *********************** 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 482 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 411 time to evaluate : 3.459 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: B 249 MET cc_start: 0.7372 (mmm) cc_final: 0.7169 (mmm) REVERT: B 258 MET cc_start: 0.6483 (mtm) cc_final: 0.6277 (mtm) REVERT: B 358 LEU cc_start: 0.6700 (mt) cc_final: 0.6198 (mt) REVERT: C 159 ILE cc_start: 0.7457 (mm) cc_final: 0.7204 (mm) REVERT: D 53 TYR cc_start: 0.3332 (p90) cc_final: 0.2757 (p90) REVERT: D 250 GLN cc_start: 0.7631 (mt0) cc_final: 0.7413 (mm-40) REVERT: F 241 GLU cc_start: 0.7896 (OUTLIER) cc_final: 0.7692 (tt0) REVERT: F 342 VAL cc_start: 0.7697 (t) cc_final: 0.7381 (m) REVERT: I 224 PHE cc_start: 0.6752 (t80) cc_final: 0.6469 (t80) REVERT: K 146 ILE cc_start: 0.5041 (mm) cc_final: 0.4529 (pt) REVERT: O 456 MET cc_start: 0.0539 (mmt) cc_final: -0.1314 (mmt) outliers start: 71 outliers final: 46 residues processed: 470 average time/residue: 0.4213 time to fit residues: 320.7668 Evaluate side-chains 339 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 292 time to evaluate : 3.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LYS Chi-restraints excluded: chain B residue 269 ASN Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain D residue 47 LEU 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 11 LEU Chi-restraints excluded: chain E residue 48 CYS 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 233 SER Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 241 GLU Chi-restraints excluded: chain F residue 282 LEU Chi-restraints excluded: chain F residue 286 THR Chi-restraints excluded: chain G residue 17 ILE Chi-restraints excluded: chain G residue 28 ASP Chi-restraints excluded: chain G residue 76 SER 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 307 SER 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 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 47 LEU Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 235 SER Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain L residue 455 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 194 optimal weight: 4.9990 chunk 108 optimal weight: 1.9990 chunk 290 optimal weight: 30.0000 chunk 238 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 chunk 350 optimal weight: 9.9990 chunk 378 optimal weight: 4.9990 chunk 311 optimal weight: 0.9980 chunk 347 optimal weight: 2.9990 chunk 119 optimal weight: 0.9990 chunk 280 optimal weight: 3.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 GLN B 150 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 256 GLN C 150 GLN ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 GLN D 112 GLN ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 270 ASN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 328 ASN ** E 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 275 HIS ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 306 GLN ** E 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 81 GLN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** H 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 HIS I 150 GLN I 306 GLN ** I 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 150 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 81 GLN K 150 GLN ** R 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6146 moved from start: 0.5034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 32758 Z= 0.271 Angle : 0.632 10.466 44517 Z= 0.330 Chirality : 0.042 0.210 5236 Planarity : 0.004 0.037 5401 Dihedral : 11.964 73.699 5500 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 16.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 2.93 % Allowed : 13.22 % Favored : 83.85 % 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: 1.16 (0.13), residues: 3894 helix: 1.33 (0.10), residues: 2486 sheet: -0.61 (0.29), residues: 231 loop : 0.03 (0.18), residues: 1177 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP J 123 HIS 0.008 0.002 HIS I 15 PHE 0.031 0.003 PHE C 348 TYR 0.029 0.002 TYR B 69 ARG 0.006 0.001 ARG A 221 *********************** 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 448 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 98 poor density : 350 time to evaluate : 3.580 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: C 273 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6738 (tp) REVERT: D 45 THR cc_start: 0.6753 (m) cc_final: 0.6523 (m) REVERT: D 250 GLN cc_start: 0.7669 (mt0) cc_final: 0.7282 (mm-40) REVERT: D 258 MET cc_start: 0.8861 (mmm) cc_final: 0.8503 (tpp) REVERT: E 161 LEU cc_start: 0.8572 (tp) cc_final: 0.8122 (tp) REVERT: E 314 SER cc_start: 0.8507 (t) cc_final: 0.8247 (t) REVERT: J 22 GLN cc_start: 0.5335 (mp10) cc_final: 0.4546 (tt0) REVERT: K 146 ILE cc_start: 0.4937 (mm) cc_final: 0.4391 (pt) REVERT: O 456 MET cc_start: 0.0559 (mmt) cc_final: -0.1404 (mmt) outliers start: 98 outliers final: 50 residues processed: 427 average time/residue: 0.4068 time to fit residues: 286.1381 Evaluate side-chains 332 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 281 time to evaluate : 4.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 117 HIS Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 10 ASP Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 35 VAL 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 276 VAL Chi-restraints excluded: chain G residue 17 ILE 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 342 VAL 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 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L 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 346 optimal weight: 10.0000 chunk 263 optimal weight: 2.9990 chunk 181 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 235 optimal weight: 0.7980 chunk 351 optimal weight: 0.6980 chunk 372 optimal weight: 0.7980 chunk 183 optimal weight: 6.9990 chunk 333 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS D 81 GLN D 216 GLN ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 150 GLN F 275 HIS ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 320 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS H 320 ASN I 15 HIS I 306 GLN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 112 GLN J 150 GLN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 220 HIS K 275 HIS ** R 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6093 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32758 Z= 0.180 Angle : 0.574 11.177 44517 Z= 0.296 Chirality : 0.040 0.251 5236 Planarity : 0.003 0.044 5401 Dihedral : 11.858 73.750 5500 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 2.63 % Allowed : 14.65 % Favored : 82.72 % 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 (0.13), residues: 3894 helix: 1.58 (0.10), residues: 2497 sheet: -0.52 (0.29), residues: 231 loop : 0.01 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 123 HIS 0.004 0.001 HIS G 220 PHE 0.034 0.002 PHE J 214 TYR 0.028 0.001 TYR B 69 ARG 0.009 0.000 ARG F 339 *********************** 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 412 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 324 time to evaluate : 3.378 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: B 258 MET cc_start: 0.6780 (mtm) cc_final: 0.6468 (mtm) REVERT: C 273 LEU cc_start: 0.6964 (OUTLIER) cc_final: 0.6711 (tp) REVERT: D 216 GLN cc_start: 0.7524 (OUTLIER) cc_final: 0.7240 (mt0) REVERT: D 250 GLN cc_start: 0.7325 (mt0) cc_final: 0.6901 (mm110) REVERT: F 271 ILE cc_start: 0.8088 (pt) cc_final: 0.7690 (mm) REVERT: F 290 ASP cc_start: 0.7297 (m-30) cc_final: 0.6753 (m-30) REVERT: J 22 GLN cc_start: 0.5185 (mp10) cc_final: 0.4572 (tt0) REVERT: K 146 ILE cc_start: 0.4967 (mm) cc_final: 0.4451 (pt) REVERT: O 456 MET cc_start: 0.0368 (mmt) cc_final: -0.1202 (mmt) outliers start: 88 outliers final: 54 residues processed: 396 average time/residue: 0.4081 time to fit residues: 265.3251 Evaluate side-chains 333 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 277 time to evaluate : 3.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 283 LYS Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 23 TYR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 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 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L 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 309 optimal weight: 7.9990 chunk 211 optimal weight: 0.6980 chunk 5 optimal weight: 10.0000 chunk 277 optimal weight: 1.9990 chunk 153 optimal weight: 10.0000 chunk 317 optimal weight: 20.0000 chunk 257 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 190 optimal weight: 0.7980 chunk 334 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 41 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS I 15 HIS I 320 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 328 ASN ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6132 moved from start: 0.5804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 32758 Z= 0.193 Angle : 0.569 11.122 44517 Z= 0.293 Chirality : 0.040 0.222 5236 Planarity : 0.004 0.048 5401 Dihedral : 11.794 73.693 5500 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 2.60 % Allowed : 15.43 % Favored : 81.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.53 (0.13), residues: 3894 helix: 1.68 (0.10), residues: 2497 sheet: -0.44 (0.30), residues: 231 loop : -0.01 (0.18), residues: 1166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 123 HIS 0.005 0.001 HIS C 220 PHE 0.031 0.002 PHE G 210 TYR 0.037 0.002 TYR D 69 ARG 0.007 0.000 ARG F 339 *********************** 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 402 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 87 poor density : 315 time to evaluate : 3.597 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: B 249 MET cc_start: 0.7080 (mmm) cc_final: 0.6879 (mmt) REVERT: B 258 MET cc_start: 0.6649 (mtm) cc_final: 0.6401 (mtm) REVERT: C 273 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6906 (tp) REVERT: F 290 ASP cc_start: 0.7171 (m-30) cc_final: 0.6718 (m-30) REVERT: J 22 GLN cc_start: 0.5061 (mp10) cc_final: 0.4820 (tt0) REVERT: K 146 ILE cc_start: 0.4859 (mm) cc_final: 0.4328 (pt) REVERT: O 450 ASP cc_start: 0.3970 (p0) cc_final: 0.3693 (p0) REVERT: O 456 MET cc_start: 0.0681 (mmt) cc_final: -0.1080 (mmt) REVERT: S 452 TYR cc_start: 0.5719 (m-80) cc_final: 0.5371 (m-80) outliers start: 87 outliers final: 66 residues processed: 382 average time/residue: 0.4130 time to fit residues: 259.5057 Evaluate side-chains 345 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 278 time to evaluate : 3.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 267 SER Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 161 LEU Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 324 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain 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 273 LEU Chi-restraints excluded: chain G residue 282 LEU Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 28 ASP 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 234 SER Chi-restraints excluded: chain I residue 243 LEU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain L 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 125 optimal weight: 3.9990 chunk 335 optimal weight: 20.0000 chunk 73 optimal weight: 0.3980 chunk 218 optimal weight: 2.9990 chunk 91 optimal weight: 4.9990 chunk 372 optimal weight: 8.9990 chunk 309 optimal weight: 0.9980 chunk 172 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 chunk 123 optimal weight: 5.9990 chunk 195 optimal weight: 2.9990 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 220 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 306 GLN ** E 148 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS ** G 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS H 279 GLN ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 15 HIS ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6161 moved from start: 0.6194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 32758 Z= 0.199 Angle : 0.576 11.846 44517 Z= 0.296 Chirality : 0.040 0.254 5236 Planarity : 0.004 0.038 5401 Dihedral : 11.809 73.754 5500 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 2.75 % Allowed : 16.06 % Favored : 81.19 % 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: 1.55 (0.14), residues: 3894 helix: 1.71 (0.10), residues: 2508 sheet: -0.44 (0.30), residues: 231 loop : -0.04 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 123 HIS 0.003 0.001 HIS D 303 PHE 0.035 0.002 PHE H 169 TYR 0.032 0.001 TYR B 69 ARG 0.008 0.000 ARG E 132 *********************** 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 407 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 92 poor density : 315 time to evaluate : 3.702 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: C 258 MET cc_start: 0.7557 (mmt) cc_final: 0.7350 (mmt) REVERT: C 273 LEU cc_start: 0.7118 (OUTLIER) cc_final: 0.6895 (tp) REVERT: D 216 GLN cc_start: 0.7522 (OUTLIER) cc_final: 0.7305 (mt0) REVERT: D 295 MET cc_start: 0.7830 (tpt) cc_final: 0.7543 (mmm) REVERT: G 226 GLU cc_start: 0.6854 (tp30) cc_final: 0.6650 (tp30) REVERT: J 22 GLN cc_start: 0.5083 (mp10) cc_final: 0.4793 (tm-30) REVERT: K 146 ILE cc_start: 0.4890 (mm) cc_final: 0.4436 (pt) REVERT: O 456 MET cc_start: 0.0692 (mmt) cc_final: -0.0890 (mmt) REVERT: S 452 TYR cc_start: 0.5942 (m-80) cc_final: 0.5513 (m-80) outliers start: 92 outliers final: 66 residues processed: 383 average time/residue: 0.4156 time to fit residues: 261.6394 Evaluate side-chains 340 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 272 time to evaluate : 3.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain C residue 273 LEU Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 216 GLN Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 113 MET Chi-restraints excluded: chain G residue 174 SER 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 307 SER 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 88 SER Chi-restraints excluded: chain H residue 126 GLU Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain L 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 359 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 212 optimal weight: 4.9990 chunk 272 optimal weight: 7.9990 chunk 210 optimal weight: 0.9980 chunk 313 optimal weight: 4.9990 chunk 208 optimal weight: 1.9990 chunk 371 optimal weight: 20.0000 chunk 232 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 171 optimal weight: 3.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 216 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 148 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 328 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS I 15 HIS ** I 306 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 279 GLN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 81 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 112 GLN ** P 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6219 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 32758 Z= 0.229 Angle : 0.609 11.153 44517 Z= 0.312 Chirality : 0.040 0.255 5236 Planarity : 0.004 0.042 5401 Dihedral : 11.849 73.735 5500 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.59 % Rotamer: Outliers : 2.78 % Allowed : 16.75 % Favored : 80.47 % 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: 1.51 (0.14), residues: 3894 helix: 1.67 (0.10), residues: 2508 sheet: -0.49 (0.30), residues: 231 loop : -0.05 (0.19), residues: 1155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP J 123 HIS 0.007 0.001 HIS C 275 PHE 0.029 0.002 PHE K 224 TYR 0.055 0.002 TYR D 69 ARG 0.005 0.000 ARG F 339 *********************** 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 385 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 292 time to evaluate : 3.609 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: B 216 GLN cc_start: 0.6985 (OUTLIER) cc_final: 0.6661 (pm20) REVERT: D 238 SER cc_start: 0.7589 (OUTLIER) cc_final: 0.7387 (p) REVERT: E 241 GLU cc_start: 0.7777 (pp20) cc_final: 0.7074 (pp20) REVERT: G 231 LEU cc_start: 0.7949 (OUTLIER) cc_final: 0.7659 (mm) REVERT: J 22 GLN cc_start: 0.5148 (mp10) cc_final: 0.4876 (tm-30) REVERT: M 456 MET cc_start: 0.3460 (mtm) cc_final: 0.3181 (mtm) REVERT: O 456 MET cc_start: 0.0913 (mmt) cc_final: -0.0830 (mmt) REVERT: S 452 TYR cc_start: 0.5816 (m-80) cc_final: 0.5404 (m-80) outliers start: 93 outliers final: 73 residues processed: 365 average time/residue: 0.4045 time to fit residues: 243.0519 Evaluate side-chains 340 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 264 time to evaluate : 3.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 114 LEU Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 113 MET 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 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 334 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 234 SER Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain S residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 229 optimal weight: 0.0370 chunk 148 optimal weight: 0.8980 chunk 221 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 72 optimal weight: 0.9980 chunk 71 optimal weight: 8.9990 chunk 235 optimal weight: 1.9990 chunk 252 optimal weight: 5.9990 chunk 183 optimal weight: 4.9990 chunk 34 optimal weight: 9.9990 chunk 291 optimal weight: 7.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 220 HIS D 216 GLN ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 306 GLN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 270 ASN ** J 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6180 moved from start: 0.6840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 32758 Z= 0.189 Angle : 0.603 12.924 44517 Z= 0.305 Chirality : 0.040 0.361 5236 Planarity : 0.004 0.046 5401 Dihedral : 11.824 73.777 5500 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 15.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.54 % Allowed : 17.19 % Favored : 80.26 % 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: 1.59 (0.14), residues: 3894 helix: 1.73 (0.10), residues: 2519 sheet: -0.48 (0.30), residues: 231 loop : 0.00 (0.19), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 123 HIS 0.012 0.001 HIS C 220 PHE 0.040 0.002 PHE J 214 TYR 0.042 0.001 TYR D 69 ARG 0.006 0.000 ARG E 84 *********************** 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 376 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 291 time to evaluate : 3.653 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: B 216 GLN cc_start: 0.7014 (OUTLIER) cc_final: 0.6599 (pm20) REVERT: C 163 CYS cc_start: 0.6660 (m) cc_final: 0.6193 (t) REVERT: D 238 SER cc_start: 0.7468 (OUTLIER) cc_final: 0.7254 (p) REVERT: E 241 GLU cc_start: 0.7741 (pp20) cc_final: 0.7066 (pp20) REVERT: F 210 PHE cc_start: 0.8230 (OUTLIER) cc_final: 0.7774 (m-80) REVERT: F 216 GLN cc_start: 0.7956 (OUTLIER) cc_final: 0.7568 (mt0) REVERT: G 86 SER cc_start: 0.8094 (OUTLIER) cc_final: 0.7718 (t) REVERT: G 282 LEU cc_start: 0.7560 (OUTLIER) cc_final: 0.7237 (tt) REVERT: J 22 GLN cc_start: 0.5168 (mp10) cc_final: 0.4964 (tm-30) REVERT: J 167 LEU cc_start: 0.5681 (mt) cc_final: 0.5458 (mt) REVERT: M 456 MET cc_start: 0.3322 (mtm) cc_final: 0.3117 (mtm) REVERT: O 456 MET cc_start: 0.0995 (mmt) cc_final: -0.0767 (mmt) REVERT: S 452 TYR cc_start: 0.5735 (m-80) cc_final: 0.5328 (m-80) outliers start: 85 outliers final: 68 residues processed: 354 average time/residue: 0.4250 time to fit residues: 250.4693 Evaluate side-chains 335 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 261 time to evaluate : 4.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 216 GLN Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain B residue 338 TYR Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 180 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 238 SER Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 314 SER Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 180 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 216 GLN Chi-restraints excluded: chain F residue 231 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 35 VAL Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 129 LYS 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 282 LEU Chi-restraints excluded: chain G residue 307 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain G residue 342 VAL Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain I residue 18 LEU Chi-restraints excluded: chain I residue 28 ASP Chi-restraints excluded: chain I residue 117 HIS Chi-restraints excluded: chain I residue 210 PHE Chi-restraints excluded: chain I residue 212 ASP Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain I residue 307 SER Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 258 MET 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 337 optimal weight: 4.9990 chunk 355 optimal weight: 10.0000 chunk 324 optimal weight: 9.9990 chunk 345 optimal weight: 9.9990 chunk 208 optimal weight: 4.9990 chunk 150 optimal weight: 8.9990 chunk 271 optimal weight: 0.9990 chunk 106 optimal weight: 10.0000 chunk 312 optimal weight: 8.9990 chunk 327 optimal weight: 7.9990 chunk 344 optimal weight: 0.9980 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 GLN ** A 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 81 GLN ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 270 ASN B 328 ASN C 306 GLN D 91 GLN ** D 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 22 GLN ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 303 HIS ** G 56 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 306 GLN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS ** I 15 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 328 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 279 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6434 moved from start: 0.7667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 32758 Z= 0.418 Angle : 0.788 12.453 44517 Z= 0.407 Chirality : 0.045 0.376 5236 Planarity : 0.005 0.058 5401 Dihedral : 12.211 79.308 5500 Min Nonbonded Distance : 2.021 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 3.11 % Allowed : 17.22 % Favored : 79.67 % 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: 0.65 (0.13), residues: 3894 helix: 0.93 (0.10), residues: 2585 sheet: -0.76 (0.30), residues: 231 loop : -0.27 (0.19), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP J 123 HIS 0.008 0.002 HIS D 303 PHE 0.049 0.003 PHE B 210 TYR 0.052 0.003 TYR D 69 ARG 0.007 0.001 ARG E 27 *********************** 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 371 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 267 time to evaluate : 3.870 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: E 22 GLN cc_start: 0.5071 (OUTLIER) cc_final: 0.4522 (tm-30) REVERT: F 210 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.8048 (m-80) REVERT: F 216 GLN cc_start: 0.8073 (OUTLIER) cc_final: 0.7870 (mt0) REVERT: F 290 ASP cc_start: 0.6954 (m-30) cc_final: 0.6638 (m-30) REVERT: G 35 VAL cc_start: 0.6594 (m) cc_final: 0.6394 (m) REVERT: I 169 PHE cc_start: 0.7209 (OUTLIER) cc_final: 0.6975 (t80) REVERT: J 22 GLN cc_start: 0.5723 (mp10) cc_final: 0.5121 (tm-30) outliers start: 104 outliers final: 82 residues processed: 351 average time/residue: 0.4036 time to fit residues: 235.4751 Evaluate side-chains 325 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 239 time to evaluate : 3.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU 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 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain C residue 263 VAL Chi-restraints excluded: chain C residue 264 ILE Chi-restraints excluded: chain C residue 268 SER Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 189 ARG Chi-restraints excluded: chain D residue 263 VAL Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain D residue 347 LEU Chi-restraints excluded: chain E residue 22 GLN Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 201 MET Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain E residue 263 VAL Chi-restraints excluded: chain E residue 264 ILE Chi-restraints excluded: chain E residue 324 VAL Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 161 LEU Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 216 GLN Chi-restraints excluded: chain F residue 231 LEU Chi-restraints excluded: chain F residue 236 THR Chi-restraints excluded: chain F residue 238 SER Chi-restraints excluded: chain F residue 264 ILE Chi-restraints excluded: chain F residue 276 VAL Chi-restraints excluded: chain F residue 342 VAL Chi-restraints excluded: chain G residue 23 TYR Chi-restraints excluded: chain G residue 24 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 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 335 ILE Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 223 LEU Chi-restraints excluded: chain H residue 292 VAL Chi-restraints excluded: chain H residue 307 SER Chi-restraints excluded: chain 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 169 PHE 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 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 160 ILE Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain L residue 455 ILE Chi-restraints excluded: chain T residue 452 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 385 random chunks: chunk 227 optimal weight: 0.9980 chunk 365 optimal weight: 0.9980 chunk 223 optimal weight: 7.9990 chunk 173 optimal weight: 2.9990 chunk 254 optimal weight: 8.9990 chunk 383 optimal weight: 6.9990 chunk 353 optimal weight: 5.9990 chunk 305 optimal weight: 2.9990 chunk 31 optimal weight: 5.9990 chunk 235 optimal weight: 0.0980 chunk 187 optimal weight: 0.9980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 15 HIS ** E 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 275 HIS F 303 HIS F 320 ASN F 344 ASN ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 275 HIS I 15 HIS I 328 ASN ** J 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 320 ASN ** K 80 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6249 moved from start: 0.7663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 32758 Z= 0.205 Angle : 0.652 13.840 44517 Z= 0.331 Chirality : 0.042 0.369 5236 Planarity : 0.004 0.089 5401 Dihedral : 12.017 90.915 5500 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer: Outliers : 2.33 % Allowed : 18.27 % Favored : 79.40 % 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: 1.10 (0.14), residues: 3894 helix: 1.31 (0.10), residues: 2585 sheet: -0.67 (0.30), residues: 231 loop : -0.17 (0.20), residues: 1078 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP J 123 HIS 0.010 0.001 HIS C 220 PHE 0.045 0.003 PHE J 214 TYR 0.037 0.002 TYR D 69 ARG 0.004 0.000 ARG F 339 ********************** 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 361 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 283 time to evaluate : 3.628 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: E 241 GLU cc_start: 0.7771 (pp20) cc_final: 0.7116 (pp20) REVERT: F 86 SER cc_start: 0.7821 (p) cc_final: 0.7371 (t) REVERT: F 172 LEU cc_start: 0.9199 (OUTLIER) cc_final: 0.8601 (tp) REVERT: F 210 PHE cc_start: 0.8240 (OUTLIER) cc_final: 0.7861 (m-80) REVERT: G 35 VAL cc_start: 0.6457 (m) cc_final: 0.6216 (m) REVERT: G 282 LEU cc_start: 0.7517 (OUTLIER) cc_final: 0.7245 (tt) REVERT: I 245 VAL cc_start: 0.8591 (m) cc_final: 0.8097 (t) REVERT: J 22 GLN cc_start: 0.5687 (mp10) cc_final: 0.5241 (tm-30) REVERT: J 135 MET cc_start: -0.1541 (OUTLIER) cc_final: -0.2973 (mtt) REVERT: J 258 MET cc_start: 0.7312 (pmm) cc_final: 0.6993 (mpp) REVERT: K 104 LYS cc_start: 0.6672 (mmtt) cc_final: 0.5680 (mttp) REVERT: P 456 MET cc_start: 0.2290 (mmt) cc_final: 0.1738 (mmt) outliers start: 78 outliers final: 63 residues processed: 346 average time/residue: 0.3952 time to fit residues: 227.4723 Evaluate side-chains 318 residues out of total 3344 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 251 time to evaluate : 4.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 24 THR Chi-restraints excluded: chain A residue 31 THR Chi-restraints excluded: chain A residue 96 ARG Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 263 VAL Chi-restraints excluded: chain A residue 352 GLU Chi-restraints excluded: chain B residue 231 LEU Chi-restraints excluded: chain B residue 276 VAL Chi-restraints excluded: chain C residue 35 VAL Chi-restraints excluded: chain C residue 52 LEU Chi-restraints excluded: chain C residue 126 GLU Chi-restraints excluded: chain C residue 193 ASP Chi-restraints excluded: chain D residue 28 ASP Chi-restraints excluded: chain D residue 35 VAL Chi-restraints excluded: chain D residue 48 CYS Chi-restraints excluded: chain D residue 157 THR Chi-restraints excluded: chain D residue 167 LEU Chi-restraints excluded: chain D residue 307 SER Chi-restraints excluded: chain E residue 35 VAL Chi-restraints excluded: chain E residue 216 GLN Chi-restraints excluded: chain E residue 238 SER Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 95 THR Chi-restraints excluded: chain F residue 172 LEU Chi-restraints excluded: chain F residue 210 PHE Chi-restraints excluded: chain F residue 231 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 23 TYR Chi-restraints excluded: chain G residue 24 THR Chi-restraints excluded: chain G residue 33 THR Chi-restraints excluded: chain G residue 46 LEU Chi-restraints excluded: chain G residue 86 SER Chi-restraints excluded: chain G residue 174 SER 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 307 SER Chi-restraints excluded: chain G residue 334 ILE Chi-restraints excluded: chain H residue 47 LEU Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 191 LEU Chi-restraints excluded: chain H residue 302 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 307 SER Chi-restraints excluded: chain J residue 23 TYR Chi-restraints excluded: chain J residue 28 ASP Chi-restraints excluded: chain J residue 35 VAL Chi-restraints excluded: chain J residue 117 HIS Chi-restraints excluded: chain J residue 135 MET Chi-restraints excluded: chain J residue 157 THR Chi-restraints excluded: chain J residue 235 SER Chi-restraints excluded: chain J residue 307 SER Chi-restraints excluded: chain J residue 312 LEU Chi-restraints excluded: chain K residue 35 VAL Chi-restraints excluded: chain K residue 39 SER Chi-restraints excluded: chain K residue 200 ARG Chi-restraints excluded: chain K residue 211 TYR Chi-restraints excluded: chain L 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 242 optimal weight: 0.8980 chunk 325 optimal weight: 0.7980 chunk 93 optimal weight: 0.7980 chunk 281 optimal weight: 8.9990 chunk 45 optimal weight: 8.9990 chunk 84 optimal weight: 0.4980 chunk 305 optimal weight: 0.8980 chunk 128 optimal weight: 0.6980 chunk 314 optimal weight: 6.9990 chunk 38 optimal weight: 0.0000 chunk 56 optimal weight: 5.9990 overall best weight: 0.5584 ------------------------------------------------------------------------------- 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** ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 269 ASN ** C 275 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 284 GLN ** G 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 246 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 91 GLN ** J 317 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.111745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.088511 restraints weight = 132849.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.087846 restraints weight = 95761.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.088705 restraints weight = 79230.689| |-----------------------------------------------------------------------------| r_work (final): 0.3699 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7297 moved from start: 0.7765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 32758 Z= 0.176 Angle : 0.620 14.021 44517 Z= 0.315 Chirality : 0.041 0.382 5236 Planarity : 0.004 0.087 5401 Dihedral : 11.913 89.416 5500 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 15.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.73 % Allowed : 19.23 % Favored : 79.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.51 (0.10), residues: 2574 sheet: -0.57 (0.30), residues: 231 loop : -0.03 (0.20), residues: 1089 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP J 123 HIS 0.008 0.001 HIS C 220 PHE 0.030 0.002 PHE C 210 TYR 0.034 0.001 TYR D 69 ARG 0.005 0.000 ARG F 339 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6361.69 seconds wall clock time: 117 minutes 3.44 seconds (7023.44 seconds total)