Starting phenix.real_space_refine on Thu Feb 5 12:09:02 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lip_63119/02_2026/9lip_63119.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lip_63119/02_2026/9lip_63119.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.48 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9lip_63119/02_2026/9lip_63119.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lip_63119/02_2026/9lip_63119.map" model { file = "/net/cci-nas-00/data/ceres_data/9lip_63119/02_2026/9lip_63119.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lip_63119/02_2026/9lip_63119.cif" } resolution = 3.48 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.031 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: 4 Type Number sf(0) Gaussians S 36 5.16 5 C 10944 2.51 5 N 2832 2.21 5 O 3156 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 149 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16968 Number of models: 1 Model: "" Number of chains: 48 Chain: "Q" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "R" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "S" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "T" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "U" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "V" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "W" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "X" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "A" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "B" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "C" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "D" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "E" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "F" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "G" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "H" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "I" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "J" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "K" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "L" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "M" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "N" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "O" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "P" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "g" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "h" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "i" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "j" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "k" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "l" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "m" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "n" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "Y" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "Z" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "a" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "b" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "c" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "d" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "e" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "f" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "o" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "p" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "q" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "r" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Chain: "s" Number of atoms: 167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 24, 167 Classifications: {'peptide': 24} Link IDs: {'PTRANS': 1, 'TRANS': 22} Chain: "t" Number of atoms: 584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 584 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 3, 'TRANS': 71} Chain: "u" Number of atoms: 526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 68, 526 Classifications: {'peptide': 68} Link IDs: {'PTRANS': 5, 'TRANS': 62} Chain: "v" Number of atoms: 137 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 137 Classifications: {'peptide': 17} Link IDs: {'TRANS': 16} Time building chain proxies: 4.14, per 1000 atoms: 0.24 Number of scatterers: 16968 At special positions: 0 Unit cell: (344.45, 161.85, 84.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 36 16.00 O 3156 8.00 N 2832 7.00 C 10944 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.42 Conformation dependent library (CDL) restraints added in 775.5 milliseconds 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4056 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 45 sheets defined 2.8% alpha, 47.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'R' and resid 175 through 177 No H-bonds generated for 'chain 'R' and resid 175 through 177' Processing helix chain 'S' and resid 249 through 253 removed outlier: 3.955A pdb=" N ALA S 252 " --> pdb=" O GLY S 249 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU S 253 " --> pdb=" O TYR S 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 249 through 253' Processing helix chain 'V' and resid 175 through 177 No H-bonds generated for 'chain 'V' and resid 175 through 177' Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.982A pdb=" N ALA C 252 " --> pdb=" O GLY C 249 " (cutoff:3.500A) removed outlier: 4.467A pdb=" N GLU C 253 " --> pdb=" O TYR C 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 249 through 253' Processing helix chain 'G' and resid 249 through 253 removed outlier: 3.886A pdb=" N ALA G 252 " --> pdb=" O GLY G 249 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLU G 253 " --> pdb=" O TYR G 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 249 through 253' Processing helix chain 'K' and resid 249 through 253 removed outlier: 4.020A pdb=" N ALA K 252 " --> pdb=" O GLY K 249 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N GLU K 253 " --> pdb=" O TYR K 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 249 through 253' Processing helix chain 'O' and resid 249 through 253 removed outlier: 3.947A pdb=" N ALA O 252 " --> pdb=" O GLY O 249 " (cutoff:3.500A) removed outlier: 4.103A pdb=" N GLU O 253 " --> pdb=" O TYR O 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 249 through 253' Processing helix chain 'h' and resid 175 through 177 No H-bonds generated for 'chain 'h' and resid 175 through 177' Processing helix chain 'i' and resid 249 through 253 removed outlier: 3.955A pdb=" N ALA i 252 " --> pdb=" O GLY i 249 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU i 253 " --> pdb=" O TYR i 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'i' and resid 249 through 253' Processing helix chain 'l' and resid 175 through 177 No H-bonds generated for 'chain 'l' and resid 175 through 177' Processing helix chain 'Z' and resid 175 through 177 No H-bonds generated for 'chain 'Z' and resid 175 through 177' Processing helix chain 'e' and resid 249 through 253 removed outlier: 3.960A pdb=" N ALA e 252 " --> pdb=" O GLY e 249 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N GLU e 253 " --> pdb=" O TYR e 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'e' and resid 249 through 253' Processing helix chain 'p' and resid 175 through 177 No H-bonds generated for 'chain 'p' and resid 175 through 177' Processing helix chain 'q' and resid 249 through 253 removed outlier: 3.955A pdb=" N ALA q 252 " --> pdb=" O GLY q 249 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N GLU q 253 " --> pdb=" O TYR q 250 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 249 through 253' Processing helix chain 't' and resid 175 through 177 No H-bonds generated for 'chain 't' and resid 175 through 177' Processing sheet with id=AA1, first strand: chain 'Q' and resid 68 through 72 Processing sheet with id=AA2, first strand: chain 'Q' and resid 76 through 77 removed outlier: 6.101A pdb=" N THR Q 76 " --> pdb=" O THR R 210 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA R 201 " --> pdb=" O VAL R 188 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'R' and resid 215 through 221 removed outlier: 3.508A pdb=" N HIS S 278 " --> pdb=" O LEU S 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'T' and resid 477 through 486 Processing sheet with id=AA5, first strand: chain 'U' and resid 69 through 72 Processing sheet with id=AA6, first strand: chain 'U' and resid 69 through 72 Processing sheet with id=AA7, first strand: chain 'U' and resid 76 through 77 removed outlier: 6.031A pdb=" N THR U 76 " --> pdb=" O THR V 210 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA V 201 " --> pdb=" O VAL V 188 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'V' and resid 215 through 221 Processing sheet with id=AA9, first strand: chain 'X' and resid 476 through 486 Processing sheet with id=AB1, first strand: chain 'A' and resid 68 through 72 removed outlier: 3.514A pdb=" N SER B 168 " --> pdb=" O ILE A 86 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 159 through 162 removed outlier: 3.756A pdb=" N ALA B 201 " --> pdb=" O VAL B 188 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N HIS B 190 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 215 through 221 Processing sheet with id=AB4, first strand: chain 'D' and resid 476 through 486 Processing sheet with id=AB5, first strand: chain 'E' and resid 68 through 72 Processing sheet with id=AB6, first strand: chain 'E' and resid 76 through 77 removed outlier: 6.898A pdb=" N VAL F 188 " --> pdb=" O LEU F 200 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N HIS F 202 " --> pdb=" O VAL F 186 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N VAL F 186 " --> pdb=" O HIS F 202 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N SER F 204 " --> pdb=" O MET F 184 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N MET F 184 " --> pdb=" O SER F 204 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ALA F 206 " --> pdb=" O HIS F 182 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N HIS F 182 " --> pdb=" O ALA F 206 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 215 through 221 Processing sheet with id=AB8, first strand: chain 'H' and resid 476 through 486 Processing sheet with id=AB9, first strand: chain 'I' and resid 68 through 72 removed outlier: 3.514A pdb=" N ALA I 82 " --> pdb=" O ILE J 172 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N ILE J 172 " --> pdb=" O ALA I 82 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N SER J 168 " --> pdb=" O ILE I 86 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'I' and resid 76 through 77 removed outlier: 6.160A pdb=" N THR I 76 " --> pdb=" O THR J 210 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL J 188 " --> pdb=" O LEU J 200 " (cutoff:3.500A) removed outlier: 4.425A pdb=" N HIS J 202 " --> pdb=" O VAL J 186 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N VAL J 186 " --> pdb=" O HIS J 202 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N SER J 204 " --> pdb=" O MET J 184 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N MET J 184 " --> pdb=" O SER J 204 " (cutoff:3.500A) removed outlier: 4.404A pdb=" N ALA J 206 " --> pdb=" O HIS J 182 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N HIS J 182 " --> pdb=" O ALA J 206 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'J' and resid 215 through 221 Processing sheet with id=AC3, first strand: chain 'M' and resid 68 through 72 Processing sheet with id=AC4, first strand: chain 'M' and resid 76 through 77 removed outlier: 6.830A pdb=" N VAL N 188 " --> pdb=" O LEU N 200 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N HIS N 202 " --> pdb=" O VAL N 186 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL N 186 " --> pdb=" O HIS N 202 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N SER N 204 " --> pdb=" O MET N 184 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N MET N 184 " --> pdb=" O SER N 204 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N ALA N 206 " --> pdb=" O HIS N 182 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N HIS N 182 " --> pdb=" O ALA N 206 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 215 through 221 Processing sheet with id=AC6, first strand: chain 'g' and resid 68 through 72 Processing sheet with id=AC7, first strand: chain 'g' and resid 76 through 77 removed outlier: 6.101A pdb=" N THR g 76 " --> pdb=" O THR h 210 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA h 201 " --> pdb=" O VAL h 188 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'h' and resid 215 through 221 removed outlier: 3.500A pdb=" N LEU i 238 " --> pdb=" O HIS i 278 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS i 278 " --> pdb=" O LEU i 238 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'k' and resid 69 through 72 Processing sheet with id=AD1, first strand: chain 'k' and resid 69 through 72 Processing sheet with id=AD2, first strand: chain 'k' and resid 76 through 77 removed outlier: 6.032A pdb=" N THR k 76 " --> pdb=" O THR l 210 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA l 201 " --> pdb=" O VAL l 188 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'l' and resid 215 through 221 Processing sheet with id=AD4, first strand: chain 'Y' and resid 68 through 72 removed outlier: 3.634A pdb=" N LYS Y 69 " --> pdb=" O ALA Y 87 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA Y 87 " --> pdb=" O LYS Y 69 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 159 through 162 removed outlier: 3.628A pdb=" N TYR Z 151 " --> pdb=" O VAL Z 162 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ALA Z 201 " --> pdb=" O VAL Z 188 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'Z' and resid 215 through 221 Processing sheet with id=AD7, first strand: chain 'b' and resid 476 through 486 Processing sheet with id=AD8, first strand: chain 'c' and resid 68 through 72 Processing sheet with id=AD9, first strand: chain 'c' and resid 76 through 77 removed outlier: 6.888A pdb=" N VAL d 188 " --> pdb=" O LEU d 200 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N HIS d 202 " --> pdb=" O VAL d 186 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL d 186 " --> pdb=" O HIS d 202 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N SER d 204 " --> pdb=" O MET d 184 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N MET d 184 " --> pdb=" O SER d 204 " (cutoff:3.500A) removed outlier: 4.371A pdb=" N ALA d 206 " --> pdb=" O HIS d 182 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N HIS d 182 " --> pdb=" O ALA d 206 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'd' and resid 215 through 221 removed outlier: 3.560A pdb=" N LEU e 238 " --> pdb=" O HIS e 278 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS e 278 " --> pdb=" O LEU e 238 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'f' and resid 477 through 486 Processing sheet with id=AE3, first strand: chain 'o' and resid 68 through 72 Processing sheet with id=AE4, first strand: chain 'o' and resid 76 through 77 removed outlier: 6.101A pdb=" N THR o 76 " --> pdb=" O THR p 210 " (cutoff:3.500A) removed outlier: 3.980A pdb=" N ALA p 201 " --> pdb=" O VAL p 188 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'p' and resid 215 through 221 removed outlier: 3.500A pdb=" N LEU q 238 " --> pdb=" O HIS q 278 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N HIS q 278 " --> pdb=" O LEU q 238 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 's' and resid 69 through 72 Processing sheet with id=AE7, first strand: chain 's' and resid 69 through 72 Processing sheet with id=AE8, first strand: chain 's' and resid 76 through 77 removed outlier: 6.032A pdb=" N THR s 76 " --> pdb=" O THR t 210 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N ALA t 201 " --> pdb=" O VAL t 188 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 't' and resid 215 through 221 682 hydrogen bonds defined for protein. 1911 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.99 Time building geometry restraints manager: 1.87 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: 5305 1.34 - 1.46: 4550 1.46 - 1.58: 7485 1.58 - 1.70: 0 1.70 - 1.82: 60 Bond restraints: 17400 Sorted by residual: bond pdb=" CA GLU K 253 " pdb=" CB GLU K 253 " ideal model delta sigma weight residual 1.527 1.574 -0.047 2.48e-02 1.63e+03 3.60e+00 bond pdb=" CA ASP I 73 " pdb=" CB ASP I 73 " ideal model delta sigma weight residual 1.526 1.547 -0.021 1.51e-02 4.39e+03 1.86e+00 bond pdb=" CA ASP A 73 " pdb=" CB ASP A 73 " ideal model delta sigma weight residual 1.526 1.544 -0.018 1.51e-02 4.39e+03 1.48e+00 bond pdb=" CA GLU C 253 " pdb=" CB GLU C 253 " ideal model delta sigma weight residual 1.527 1.555 -0.028 2.48e-02 1.63e+03 1.25e+00 bond pdb=" CA VAL Z 198 " pdb=" CB VAL Z 198 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 1.01e+00 ... (remaining 17395 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.52: 22902 1.52 - 3.04: 773 3.04 - 4.56: 68 4.56 - 6.08: 20 6.08 - 7.60: 9 Bond angle restraints: 23772 Sorted by residual: angle pdb=" N ASP b 488 " pdb=" CA ASP b 488 " pdb=" C ASP b 488 " ideal model delta sigma weight residual 110.65 106.86 3.79 1.26e+00 6.30e-01 9.03e+00 angle pdb=" C PHE m 232 " pdb=" N LEU m 233 " pdb=" CA LEU m 233 " ideal model delta sigma weight residual 122.45 127.20 -4.75 1.78e+00 3.16e-01 7.11e+00 angle pdb=" C PHE W 232 " pdb=" N LEU W 233 " pdb=" CA LEU W 233 " ideal model delta sigma weight residual 122.45 127.19 -4.74 1.78e+00 3.16e-01 7.09e+00 angle pdb=" C PHE u 232 " pdb=" N LEU u 233 " pdb=" CA LEU u 233 " ideal model delta sigma weight residual 122.45 127.13 -4.68 1.78e+00 3.16e-01 6.92e+00 angle pdb=" N ASP v 488 " pdb=" CA ASP v 488 " pdb=" C ASP v 488 " ideal model delta sigma weight residual 110.68 107.43 3.25 1.39e+00 5.18e-01 5.48e+00 ... (remaining 23767 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.93: 9176 17.93 - 35.87: 668 35.87 - 53.80: 70 53.80 - 71.74: 27 71.74 - 89.67: 7 Dihedral angle restraints: 9948 sinusoidal: 3624 harmonic: 6324 Sorted by residual: dihedral pdb=" CA PRO G 285 " pdb=" C PRO G 285 " pdb=" N VAL G 286 " pdb=" CA VAL G 286 " ideal model delta harmonic sigma weight residual -180.00 -158.20 -21.80 0 5.00e+00 4.00e-02 1.90e+01 dihedral pdb=" CA PRO O 285 " pdb=" C PRO O 285 " pdb=" N VAL O 286 " pdb=" CA VAL O 286 " ideal model delta harmonic sigma weight residual -180.00 -158.50 -21.50 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA GLY q 284 " pdb=" C GLY q 284 " pdb=" N PRO q 285 " pdb=" CA PRO q 285 " ideal model delta harmonic sigma weight residual 180.00 159.12 20.88 0 5.00e+00 4.00e-02 1.74e+01 ... (remaining 9945 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1715 0.034 - 0.068: 602 0.068 - 0.102: 308 0.102 - 0.135: 140 0.135 - 0.169: 19 Chirality restraints: 2784 Sorted by residual: chirality pdb=" CA VAL f 476 " pdb=" N VAL f 476 " pdb=" C VAL f 476 " pdb=" CB VAL f 476 " both_signs ideal model delta sigma weight residual False 2.44 2.61 -0.17 2.00e-01 2.50e+01 7.16e-01 chirality pdb=" CB ILE P 489 " pdb=" CA ILE P 489 " pdb=" CG1 ILE P 489 " pdb=" CG2 ILE P 489 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.17 2.00e-01 2.50e+01 6.85e-01 chirality pdb=" CA VAL j 476 " pdb=" N VAL j 476 " pdb=" C VAL j 476 " pdb=" CB VAL j 476 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2781 not shown) Planarity restraints: 2952 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY O 284 " -0.036 5.00e-02 4.00e+02 5.48e-02 4.81e+00 pdb=" N PRO O 285 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO O 285 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO O 285 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 284 " 0.030 5.00e-02 4.00e+02 4.58e-02 3.36e+00 pdb=" N PRO K 285 " -0.079 5.00e-02 4.00e+02 pdb=" CA PRO K 285 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO K 285 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 284 " -0.029 5.00e-02 4.00e+02 4.39e-02 3.08e+00 pdb=" N PRO C 285 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO C 285 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 285 " -0.024 5.00e-02 4.00e+02 ... (remaining 2949 not shown) Histogram of nonbonded interaction distances: 1.04 - 1.81: 4 1.81 - 2.59: 116 2.59 - 3.36: 18392 3.36 - 4.13: 38323 4.13 - 4.90: 67670 Nonbonded interactions: 124505 Sorted by model distance: nonbonded pdb=" OD2 ASP e 255 " pdb=" OH TYR r 478 " model vdw 1.042 3.040 nonbonded pdb=" OH TYR T 478 " pdb=" OD2 ASP i 255 " model vdw 1.304 3.040 nonbonded pdb=" OD2 ASP S 255 " pdb=" OH TYR j 478 " model vdw 1.365 3.040 nonbonded pdb=" OH TYR f 478 " pdb=" OD2 ASP q 255 " model vdw 1.647 3.040 nonbonded pdb=" OH TYR T 478 " pdb=" CG ASP i 255 " model vdw 1.933 3.270 ... (remaining 124500 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' selection = chain 'I' selection = chain 'M' selection = chain 'Q' selection = chain 'U' selection = chain 'Y' selection = chain 'c' selection = chain 'g' selection = chain 'k' selection = chain 'o' selection = chain 's' } ncs_group { reference = chain 'B' selection = chain 'F' selection = chain 'J' selection = chain 'N' selection = chain 'R' selection = chain 'V' selection = chain 'Z' selection = chain 'd' selection = chain 'h' selection = chain 'l' selection = chain 'p' selection = chain 't' } ncs_group { reference = chain 'C' selection = chain 'G' selection = chain 'K' selection = chain 'O' selection = chain 'S' selection = chain 'W' selection = chain 'a' selection = chain 'e' selection = chain 'i' selection = chain 'm' selection = chain 'q' selection = chain 'u' } ncs_group { reference = chain 'D' selection = chain 'H' selection = chain 'L' selection = chain 'P' selection = chain 'T' selection = chain 'X' selection = chain 'b' selection = chain 'f' selection = chain 'j' selection = chain 'n' selection = chain 'r' selection = chain 'v' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.390 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: 0.010 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.900 Find NCS groups from input model: 0.460 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6471 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 : 0.004 0.047 17400 Z= 0.187 Angle : 0.662 7.599 23772 Z= 0.370 Chirality : 0.048 0.169 2784 Planarity : 0.005 0.055 2952 Dihedral : 12.683 89.671 5892 Min Nonbonded Distance : 1.042 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.05 % Allowed : 9.00 % Favored : 90.96 % Rotamer: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.91 (0.16), residues: 2112 helix: None (None), residues: 0 sheet: 0.41 (0.18), residues: 792 loop : -3.76 (0.11), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG a 234 TYR 0.013 0.001 TYR R 189 PHE 0.017 0.002 PHE a 240 TRP 0.008 0.001 TRP F 156 HIS 0.004 0.001 HIS S 231 Details of bonding type rmsd covalent geometry : bond 0.00392 (17400) covalent geometry : angle 0.66176 (23772) hydrogen bonds : bond 0.22133 ( 670) hydrogen bonds : angle 8.43773 ( 1911) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 695 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 692 time to evaluate : 0.670 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASN cc_start: 0.7213 (t0) cc_final: 0.6881 (p0) REVERT: B 189 TYR cc_start: 0.7220 (m-80) cc_final: 0.6973 (m-10) REVERT: I 73 ASP cc_start: 0.7356 (t70) cc_final: 0.7152 (t70) REVERT: I 89 ASN cc_start: 0.5721 (m110) cc_final: 0.5309 (t0) REVERT: J 189 TYR cc_start: 0.7295 (m-80) cc_final: 0.6982 (m-10) REVERT: J 216 SER cc_start: 0.8463 (m) cc_final: 0.8221 (t) REVERT: N 179 LEU cc_start: 0.8169 (mt) cc_final: 0.7966 (mp) REVERT: i 275 VAL cc_start: 0.8611 (t) cc_final: 0.8356 (p) REVERT: l 208 THR cc_start: 0.7894 (m) cc_final: 0.7628 (p) REVERT: Z 208 THR cc_start: 0.7959 (m) cc_final: 0.7709 (p) REVERT: a 260 TRP cc_start: 0.8165 (m100) cc_final: 0.7956 (m100) REVERT: a 266 SER cc_start: 0.8010 (t) cc_final: 0.7671 (t) outliers start: 3 outliers final: 0 residues processed: 695 average time/residue: 0.1151 time to fit residues: 125.7894 Evaluate side-chains 407 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 407 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 2.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 103 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 3.9990 chunk 149 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 161 GLN R 182 HIS R 190 HIS R 221 GLN ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 245 HIS S 293 GLN V 161 GLN V 202 HIS X 491 GLN A 72 ASN B 158 GLN F 158 GLN F 161 GLN G 243 GLN G 293 GLN J 161 GLN J 182 HIS J 202 HIS K 236 GLN K 293 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 212 GLN O 243 GLN O 293 GLN h 161 GLN h 182 HIS h 190 HIS h 202 HIS i 243 GLN l 202 HIS ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** n 491 GLN ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 190 HIS Z 202 HIS ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 182 HIS d 190 HIS e 289 GLN f 491 GLN p 161 GLN p 190 HIS p 221 GLN q 245 HIS t 161 GLN t 202 HIS ** v 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 42 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.175769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.122821 restraints weight = 26549.997| |-----------------------------------------------------------------------------| r_work (start): 0.3686 rms_B_bonded: 3.90 r_work: 0.3517 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.4327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.085 17400 Z= 0.317 Angle : 0.813 11.251 23772 Z= 0.415 Chirality : 0.051 0.204 2784 Planarity : 0.006 0.055 2952 Dihedral : 5.902 24.287 2352 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.80 % Favored : 90.20 % Rotamer: Outliers : 6.36 % Allowed : 16.93 % Favored : 76.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.45 (0.16), residues: 2112 helix: None (None), residues: 0 sheet: 0.68 (0.17), residues: 852 loop : -3.59 (0.12), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG a 234 TYR 0.024 0.002 TYR H 478 PHE 0.030 0.003 PHE Z 207 TRP 0.017 0.002 TRP C 260 HIS 0.009 0.002 HIS a 278 Details of bonding type rmsd covalent geometry : bond 0.00729 (17400) covalent geometry : angle 0.81276 (23772) hydrogen bonds : bond 0.04703 ( 670) hydrogen bonds : angle 6.13254 ( 1911) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 432 time to evaluate : 0.690 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: S 236 GLN cc_start: 0.8131 (OUTLIER) cc_final: 0.7838 (tt0) REVERT: S 266 SER cc_start: 0.8279 (m) cc_final: 0.7995 (p) REVERT: U 84 PHE cc_start: 0.7404 (m-80) cc_final: 0.7149 (m-80) REVERT: V 185 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8471 (pm20) REVERT: W 289 GLN cc_start: 0.7993 (mp-120) cc_final: 0.7754 (mp-120) REVERT: B 178 MET cc_start: 0.8171 (mpp) cc_final: 0.7818 (mmm) REVERT: B 189 TYR cc_start: 0.8309 (m-80) cc_final: 0.7770 (m-10) REVERT: E 69 LYS cc_start: 0.7284 (mtmm) cc_final: 0.7048 (pttm) REVERT: F 159 TYR cc_start: 0.8643 (m-80) cc_final: 0.8283 (m-80) REVERT: I 69 LYS cc_start: 0.6695 (mppt) cc_final: 0.6126 (mppt) REVERT: I 89 ASN cc_start: 0.6252 (m110) cc_final: 0.5960 (t0) REVERT: J 189 TYR cc_start: 0.8320 (m-80) cc_final: 0.7838 (m-10) REVERT: h 191 ARG cc_start: 0.6190 (tpp80) cc_final: 0.5737 (ptm160) REVERT: i 236 GLN cc_start: 0.7778 (mm-40) cc_final: 0.7546 (mm-40) REVERT: i 268 THR cc_start: 0.8983 (m) cc_final: 0.8766 (p) REVERT: m 261 ASP cc_start: 0.8014 (t0) cc_final: 0.7771 (t0) REVERT: m 266 SER cc_start: 0.8129 (t) cc_final: 0.7765 (t) REVERT: Y 69 LYS cc_start: 0.7201 (tppt) cc_final: 0.6797 (tppt) REVERT: a 266 SER cc_start: 0.8239 (t) cc_final: 0.7999 (t) REVERT: d 155 THR cc_start: 0.8631 (OUTLIER) cc_final: 0.8397 (m) REVERT: e 232 PHE cc_start: 0.5662 (m-80) cc_final: 0.5350 (m-80) REVERT: e 236 GLN cc_start: 0.6371 (tt0) cc_final: 0.6019 (tt0) REVERT: e 253 GLU cc_start: 0.8006 (mm-30) cc_final: 0.7749 (mp0) REVERT: e 281 LEU cc_start: 0.8133 (mt) cc_final: 0.6900 (mt) REVERT: q 236 GLN cc_start: 0.8090 (OUTLIER) cc_final: 0.7685 (tt0) REVERT: q 266 SER cc_start: 0.8468 (m) cc_final: 0.8147 (p) REVERT: s 84 PHE cc_start: 0.7402 (m-80) cc_final: 0.7151 (m-80) REVERT: t 185 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8445 (pm20) REVERT: u 289 GLN cc_start: 0.7945 (mp-120) cc_final: 0.7717 (mp-120) outliers start: 119 outliers final: 88 residues processed: 500 average time/residue: 0.1206 time to fit residues: 94.3747 Evaluate side-chains 459 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 366 time to evaluate : 0.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain S residue 236 GLN Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 268 THR Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 277 THR Chi-restraints excluded: chain W residue 279 THR Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain X residue 486 THR Chi-restraints excluded: chain X residue 487 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 183 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 183 THR Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain K residue 233 LEU Chi-restraints excluded: chain K residue 286 VAL Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain g residue 86 ILE Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 163 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 184 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 239 THR Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain i residue 292 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 78 ILE Chi-restraints excluded: chain l residue 210 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 257 SER Chi-restraints excluded: chain m residue 268 THR Chi-restraints excluded: chain m residue 277 THR Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 150 VAL Chi-restraints excluded: chain Z residue 172 ILE Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 188 VAL Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 218 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain a residue 257 SER Chi-restraints excluded: chain a residue 277 THR Chi-restraints excluded: chain b residue 476 VAL Chi-restraints excluded: chain c residue 88 LEU Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain o residue 72 ASN Chi-restraints excluded: chain p residue 151 TYR Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 204 SER Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain q residue 236 GLN Chi-restraints excluded: chain q residue 238 LEU Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Chi-restraints excluded: chain u residue 277 THR Chi-restraints excluded: chain u residue 279 THR Chi-restraints excluded: chain u residue 281 LEU Chi-restraints excluded: chain v residue 486 THR Chi-restraints excluded: chain v residue 487 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 15 optimal weight: 0.9980 chunk 190 optimal weight: 10.0000 chunk 166 optimal weight: 8.9990 chunk 185 optimal weight: 0.0070 chunk 147 optimal weight: 0.6980 chunk 163 optimal weight: 8.9990 chunk 176 optimal weight: 20.0000 chunk 165 optimal weight: 9.9990 chunk 2 optimal weight: 3.9990 chunk 136 optimal weight: 1.9990 chunk 157 optimal weight: 5.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 236 GLN S 293 GLN W 293 GLN G 243 GLN J 202 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 HIS q 236 GLN u 293 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.166888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.114571 restraints weight = 26810.678| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.85 r_work: 0.3544 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.4972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 17400 Z= 0.212 Angle : 0.676 11.001 23772 Z= 0.343 Chirality : 0.047 0.179 2784 Planarity : 0.005 0.059 2952 Dihedral : 5.272 24.172 2352 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 5.24 % Allowed : 20.78 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.16), residues: 2112 helix: None (None), residues: 0 sheet: 0.88 (0.17), residues: 828 loop : -3.25 (0.13), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG i 234 TYR 0.015 0.001 TYR d 151 PHE 0.020 0.002 PHE Z 207 TRP 0.010 0.002 TRP l 153 HIS 0.021 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00490 (17400) covalent geometry : angle 0.67568 (23772) hydrogen bonds : bond 0.04029 ( 670) hydrogen bonds : angle 5.52149 ( 1911) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 406 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 84 PHE cc_start: 0.7432 (m-80) cc_final: 0.6996 (m-80) REVERT: S 236 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7587 (tt0) REVERT: S 243 GLN cc_start: 0.5012 (mm-40) cc_final: 0.4657 (mm-40) REVERT: U 84 PHE cc_start: 0.7407 (m-80) cc_final: 0.6844 (m-80) REVERT: V 185 GLU cc_start: 0.8687 (pt0) cc_final: 0.8418 (pm20) REVERT: B 178 MET cc_start: 0.8134 (mpp) cc_final: 0.7755 (mmm) REVERT: B 189 TYR cc_start: 0.8322 (m-80) cc_final: 0.7837 (m-10) REVERT: E 69 LYS cc_start: 0.7057 (mtmm) cc_final: 0.6751 (pttm) REVERT: F 159 TYR cc_start: 0.8657 (m-80) cc_final: 0.8416 (m-80) REVERT: G 233 LEU cc_start: 0.6668 (OUTLIER) cc_final: 0.6452 (mp) REVERT: H 488 ASP cc_start: 0.6755 (m-30) cc_final: 0.6197 (p0) REVERT: I 69 LYS cc_start: 0.6703 (mppt) cc_final: 0.6189 (mppt) REVERT: N 179 LEU cc_start: 0.8303 (mt) cc_final: 0.8070 (mp) REVERT: h 191 ARG cc_start: 0.6362 (tpp80) cc_final: 0.5917 (ptm160) REVERT: h 197 TYR cc_start: 0.7853 (m-80) cc_final: 0.7377 (m-80) REVERT: i 268 THR cc_start: 0.9009 (m) cc_final: 0.8694 (p) REVERT: m 261 ASP cc_start: 0.8148 (t0) cc_final: 0.7867 (t0) REVERT: q 236 GLN cc_start: 0.7920 (OUTLIER) cc_final: 0.7572 (tt0) REVERT: q 243 GLN cc_start: 0.5075 (mm-40) cc_final: 0.4755 (mm-40) REVERT: q 266 SER cc_start: 0.8394 (m) cc_final: 0.8179 (p) REVERT: s 84 PHE cc_start: 0.7402 (m-80) cc_final: 0.6830 (m-80) REVERT: t 185 GLU cc_start: 0.8687 (pt0) cc_final: 0.8418 (pm20) outliers start: 98 outliers final: 75 residues processed: 472 average time/residue: 0.1195 time to fit residues: 88.8419 Evaluate side-chains 437 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 359 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 72 ASN Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain S residue 236 GLN Chi-restraints excluded: chain S residue 268 THR Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 198 VAL Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain K residue 276 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 184 MET Chi-restraints excluded: chain h residue 194 SER Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain i residue 292 LEU Chi-restraints excluded: chain k residue 66 VAL Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 83 SER Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 210 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 257 SER Chi-restraints excluded: chain m residue 268 THR Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Z residue 150 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain b residue 476 VAL Chi-restraints excluded: chain c residue 88 LEU Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain o residue 72 ASN Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 204 SER Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain q residue 236 GLN Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 279 THR Chi-restraints excluded: chain t residue 217 VAL Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Chi-restraints excluded: chain u residue 281 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 67 optimal weight: 2.9990 chunk 131 optimal weight: 3.9990 chunk 29 optimal weight: 8.9990 chunk 81 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 5 optimal weight: 20.0000 chunk 166 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 85 optimal weight: 0.6980 chunk 155 optimal weight: 3.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 HIS R 212 GLN R 221 GLN ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 278 HIS ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 243 GLN h 221 GLN i 236 GLN i 243 GLN ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 293 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN p 221 GLN u 278 HIS ** u 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.163623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.111897 restraints weight = 27075.239| |-----------------------------------------------------------------------------| r_work (start): 0.3658 rms_B_bonded: 3.84 r_work: 0.3495 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 17400 Z= 0.275 Angle : 0.733 15.871 23772 Z= 0.368 Chirality : 0.049 0.216 2784 Planarity : 0.005 0.052 2952 Dihedral : 5.597 24.213 2352 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 11.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.09 % Favored : 89.91 % Rotamer: Outliers : 6.94 % Allowed : 21.47 % Favored : 71.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.16), residues: 2112 helix: None (None), residues: 0 sheet: 0.70 (0.17), residues: 840 loop : -3.32 (0.13), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 195 TYR 0.017 0.002 TYR d 151 PHE 0.032 0.003 PHE n 483 TRP 0.010 0.002 TRP B 153 HIS 0.013 0.001 HIS p 182 Details of bonding type rmsd covalent geometry : bond 0.00636 (17400) covalent geometry : angle 0.73296 (23772) hydrogen bonds : bond 0.04076 ( 670) hydrogen bonds : angle 5.72282 ( 1911) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 130 poor density : 380 time to evaluate : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: U 84 PHE cc_start: 0.7447 (m-80) cc_final: 0.6822 (m-80) REVERT: V 185 GLU cc_start: 0.8708 (pt0) cc_final: 0.8350 (pm20) REVERT: B 178 MET cc_start: 0.8074 (mpp) cc_final: 0.7747 (mmm) REVERT: B 189 TYR cc_start: 0.8467 (m-80) cc_final: 0.8147 (m-10) REVERT: D 489 ILE cc_start: 0.8381 (OUTLIER) cc_final: 0.7789 (mm) REVERT: F 159 TYR cc_start: 0.8623 (m-80) cc_final: 0.8384 (m-80) REVERT: G 233 LEU cc_start: 0.6805 (mt) cc_final: 0.6593 (mp) REVERT: I 69 LYS cc_start: 0.6800 (mppt) cc_final: 0.6279 (mppt) REVERT: K 243 GLN cc_start: 0.8539 (mm-40) cc_final: 0.7940 (tm-30) REVERT: N 179 LEU cc_start: 0.8389 (mt) cc_final: 0.8176 (mp) REVERT: h 191 ARG cc_start: 0.6396 (tpp80) cc_final: 0.5632 (ttm170) REVERT: h 197 TYR cc_start: 0.7909 (m-80) cc_final: 0.7355 (m-80) REVERT: i 268 THR cc_start: 0.9048 (m) cc_final: 0.8730 (p) REVERT: j 487 LEU cc_start: 0.6358 (OUTLIER) cc_final: 0.5935 (pp) REVERT: k 69 LYS cc_start: 0.7138 (pttm) cc_final: 0.6449 (tppt) REVERT: l 155 THR cc_start: 0.7570 (t) cc_final: 0.7368 (t) REVERT: m 261 ASP cc_start: 0.8289 (t0) cc_final: 0.7985 (t0) REVERT: d 197 TYR cc_start: 0.7976 (m-80) cc_final: 0.7550 (m-80) REVERT: d 211 ASP cc_start: 0.8841 (p0) cc_final: 0.8576 (p0) REVERT: o 84 PHE cc_start: 0.7504 (m-80) cc_final: 0.7163 (m-80) REVERT: p 155 THR cc_start: 0.6497 (OUTLIER) cc_final: 0.6260 (t) REVERT: p 184 MET cc_start: 0.4613 (tpt) cc_final: 0.4311 (tpt) REVERT: s 84 PHE cc_start: 0.7447 (m-80) cc_final: 0.6814 (m-80) REVERT: t 185 GLU cc_start: 0.8708 (pt0) cc_final: 0.8349 (pm20) outliers start: 130 outliers final: 98 residues processed: 476 average time/residue: 0.1149 time to fit residues: 87.0022 Evaluate side-chains 452 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 351 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 268 THR Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 277 THR Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 281 LEU Chi-restraints excluded: chain K residue 286 VAL Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 171 SER Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 239 THR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 163 LEU Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 184 MET Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain i residue 292 LEU Chi-restraints excluded: chain j residue 485 VAL Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 83 SER Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 198 VAL Chi-restraints excluded: chain l residue 210 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 268 THR Chi-restraints excluded: chain m residue 286 VAL Chi-restraints excluded: chain n residue 476 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain b residue 476 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain o residue 72 ASN Chi-restraints excluded: chain p residue 151 TYR Chi-restraints excluded: chain p residue 155 THR Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 204 SER Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain p residue 219 VAL Chi-restraints excluded: chain q residue 238 LEU Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain r residue 485 VAL Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Chi-restraints excluded: chain u residue 277 THR Chi-restraints excluded: chain u residue 281 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 44 optimal weight: 0.9980 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 152 optimal weight: 0.6980 chunk 83 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 33 optimal weight: 2.9990 chunk 129 optimal weight: 2.9990 chunk 143 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 HIS ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** i 236 GLN i 243 GLN l 161 GLN ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 293 GLN d 212 GLN p 182 HIS q 236 GLN ** u 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.166808 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3754 r_free = 0.3754 target = 0.114633 restraints weight = 26790.521| |-----------------------------------------------------------------------------| r_work (start): 0.3704 rms_B_bonded: 3.89 r_work: 0.3544 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.5746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 17400 Z= 0.144 Angle : 0.647 11.116 23772 Z= 0.322 Chirality : 0.046 0.209 2784 Planarity : 0.004 0.052 2952 Dihedral : 4.943 23.907 2352 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 5.29 % Allowed : 24.09 % Favored : 70.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.92 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 0.97 (0.17), residues: 840 loop : -3.13 (0.13), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG a 234 TYR 0.013 0.001 TYR e 258 PHE 0.020 0.002 PHE R 149 TRP 0.012 0.001 TRP V 153 HIS 0.007 0.001 HIS R 182 Details of bonding type rmsd covalent geometry : bond 0.00337 (17400) covalent geometry : angle 0.64736 (23772) hydrogen bonds : bond 0.03351 ( 670) hydrogen bonds : angle 5.23037 ( 1911) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 479 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 380 time to evaluate : 0.653 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: Q 84 PHE cc_start: 0.7675 (m-80) cc_final: 0.7233 (m-80) REVERT: R 153 TRP cc_start: 0.7771 (m100) cc_final: 0.7351 (m100) REVERT: R 184 MET cc_start: 0.4635 (tpt) cc_final: 0.4277 (tpp) REVERT: V 185 GLU cc_start: 0.8642 (OUTLIER) cc_final: 0.8234 (pm20) REVERT: B 178 MET cc_start: 0.8118 (mpp) cc_final: 0.7765 (mmm) REVERT: B 189 TYR cc_start: 0.8417 (m-80) cc_final: 0.7902 (m-10) REVERT: C 243 GLN cc_start: 0.8519 (tp40) cc_final: 0.7395 (mp10) REVERT: D 489 ILE cc_start: 0.8237 (OUTLIER) cc_final: 0.7598 (mm) REVERT: F 159 TYR cc_start: 0.8675 (m-80) cc_final: 0.8455 (m-80) REVERT: G 233 LEU cc_start: 0.6533 (OUTLIER) cc_final: 0.6290 (mp) REVERT: H 488 ASP cc_start: 0.6814 (m-30) cc_final: 0.6302 (p0) REVERT: I 69 LYS cc_start: 0.6662 (mppt) cc_final: 0.6191 (mppt) REVERT: L 487 LEU cc_start: 0.8995 (mt) cc_final: 0.8758 (mp) REVERT: N 179 LEU cc_start: 0.8317 (mt) cc_final: 0.8099 (mp) REVERT: h 191 ARG cc_start: 0.6390 (tpp80) cc_final: 0.6038 (ptm160) REVERT: h 197 TYR cc_start: 0.7587 (m-80) cc_final: 0.7283 (m-80) REVERT: i 268 THR cc_start: 0.8975 (m) cc_final: 0.8702 (p) REVERT: j 487 LEU cc_start: 0.6348 (OUTLIER) cc_final: 0.6047 (pp) REVERT: m 261 ASP cc_start: 0.8217 (t0) cc_final: 0.7935 (t0) REVERT: a 236 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8158 (tp40) REVERT: f 491 GLN cc_start: 0.6444 (mm110) cc_final: 0.5777 (mp10) REVERT: p 153 TRP cc_start: 0.7768 (m100) cc_final: 0.7411 (m100) REVERT: p 155 THR cc_start: 0.6442 (OUTLIER) cc_final: 0.6173 (t) REVERT: p 184 MET cc_start: 0.4668 (tpt) cc_final: 0.4331 (tpt) REVERT: t 185 GLU cc_start: 0.8649 (OUTLIER) cc_final: 0.8237 (pm20) outliers start: 99 outliers final: 79 residues processed: 447 average time/residue: 0.1167 time to fit residues: 82.2715 Evaluate side-chains 434 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 349 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 151 TYR Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 268 THR Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain C residue 287 THR Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 191 ARG Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 184 MET Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain j residue 485 VAL Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 83 SER Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 268 THR Chi-restraints excluded: chain n residue 476 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 150 VAL Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain b residue 476 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain c residue 88 LEU Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain p residue 155 THR Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 204 SER Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain p residue 219 VAL Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain r residue 485 VAL Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain t residue 217 VAL Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 178 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 138 optimal weight: 0.7980 chunk 161 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 142 optimal weight: 6.9990 chunk 137 optimal weight: 3.9990 chunk 106 optimal weight: 0.9980 chunk 177 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 144 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 182 HIS ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 243 GLN J 202 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 243 GLN i 236 GLN i 243 GLN m 235 ASN ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** f 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** p 182 HIS p 212 GLN ** u 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.162889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.111709 restraints weight = 26917.300| |-----------------------------------------------------------------------------| r_work (start): 0.3652 rms_B_bonded: 3.79 r_work: 0.3489 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.6129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 17400 Z= 0.254 Angle : 0.719 10.780 23772 Z= 0.362 Chirality : 0.048 0.195 2784 Planarity : 0.005 0.052 2952 Dihedral : 5.406 24.183 2352 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.23 % Favored : 89.77 % Rotamer: Outliers : 6.46 % Allowed : 24.20 % Favored : 69.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.06 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 0.80 (0.17), residues: 840 loop : -3.16 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 195 TYR 0.019 0.002 TYR i 258 PHE 0.038 0.002 PHE b 483 TRP 0.012 0.002 TRP V 160 HIS 0.012 0.001 HIS p 182 Details of bonding type rmsd covalent geometry : bond 0.00587 (17400) covalent geometry : angle 0.71883 (23772) hydrogen bonds : bond 0.03781 ( 670) hydrogen bonds : angle 5.55571 ( 1911) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 471 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 121 poor density : 350 time to evaluate : 0.668 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: R 153 TRP cc_start: 0.7632 (m100) cc_final: 0.7252 (m100) REVERT: R 184 MET cc_start: 0.4714 (tpt) cc_final: 0.4371 (tpt) REVERT: V 160 TRP cc_start: 0.6326 (m-90) cc_final: 0.5977 (m100) REVERT: V 185 GLU cc_start: 0.8688 (OUTLIER) cc_final: 0.8237 (pm20) REVERT: B 178 MET cc_start: 0.8099 (mpp) cc_final: 0.7773 (mmm) REVERT: B 189 TYR cc_start: 0.8509 (m-80) cc_final: 0.8193 (m-10) REVERT: C 243 GLN cc_start: 0.8545 (tp40) cc_final: 0.7402 (mp10) REVERT: D 489 ILE cc_start: 0.8463 (OUTLIER) cc_final: 0.7850 (mm) REVERT: F 159 TYR cc_start: 0.8629 (m-80) cc_final: 0.8377 (m-80) REVERT: G 233 LEU cc_start: 0.6717 (OUTLIER) cc_final: 0.6471 (mp) REVERT: H 488 ASP cc_start: 0.6911 (m-30) cc_final: 0.6355 (p0) REVERT: J 189 TYR cc_start: 0.8598 (m-10) cc_final: 0.8258 (m-10) REVERT: O 231 HIS cc_start: 0.6439 (OUTLIER) cc_final: 0.6100 (p90) REVERT: h 191 ARG cc_start: 0.6460 (tpp80) cc_final: 0.5761 (ttm170) REVERT: i 268 THR cc_start: 0.9014 (m) cc_final: 0.8700 (p) REVERT: j 487 LEU cc_start: 0.6356 (OUTLIER) cc_final: 0.5934 (pp) REVERT: k 69 LYS cc_start: 0.7460 (pttm) cc_final: 0.6692 (tptt) REVERT: m 261 ASP cc_start: 0.8297 (t0) cc_final: 0.7978 (t0) REVERT: a 236 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8182 (tp40) REVERT: d 184 MET cc_start: 0.7590 (tpp) cc_final: 0.7061 (tpt) REVERT: d 197 TYR cc_start: 0.7997 (m-80) cc_final: 0.7523 (m-80) REVERT: f 491 GLN cc_start: 0.6220 (mm110) cc_final: 0.5746 (mp10) REVERT: o 84 PHE cc_start: 0.7636 (m-80) cc_final: 0.7392 (m-80) REVERT: p 184 MET cc_start: 0.4938 (tpt) cc_final: 0.4620 (tpt) REVERT: t 160 TRP cc_start: 0.6327 (m-90) cc_final: 0.5979 (m100) REVERT: t 185 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8262 (pm20) outliers start: 121 outliers final: 97 residues processed: 431 average time/residue: 0.1097 time to fit residues: 75.5583 Evaluate side-chains 443 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 340 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 268 THR Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 485 VAL Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 277 THR Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain D residue 489 ILE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 183 THR Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 239 THR Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 286 VAL Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 183 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 231 HIS Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 163 LEU Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 184 MET Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain i residue 292 LEU Chi-restraints excluded: chain j residue 485 VAL Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain k residue 83 SER Chi-restraints excluded: chain k residue 86 ILE Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 210 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 253 GLU Chi-restraints excluded: chain m residue 268 THR Chi-restraints excluded: chain n residue 476 VAL Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain b residue 476 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 162 VAL Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 194 SER Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain e residue 268 THR Chi-restraints excluded: chain e residue 275 VAL Chi-restraints excluded: chain p residue 204 SER Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain p residue 219 VAL Chi-restraints excluded: chain q residue 238 LEU Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 279 THR Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain r residue 485 VAL Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain t residue 217 VAL Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Chi-restraints excluded: chain u residue 277 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 112 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 146 optimal weight: 0.5980 chunk 173 optimal weight: 0.9980 chunk 127 optimal weight: 1.9990 chunk 97 optimal weight: 0.7980 chunk 54 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 chunk 189 optimal weight: 2.9990 chunk 152 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 ASN ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS K 243 GLN ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.165415 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.113733 restraints weight = 26246.709| |-----------------------------------------------------------------------------| r_work (start): 0.3709 rms_B_bonded: 3.84 r_work: 0.3545 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.3545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.6200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17400 Z= 0.142 Angle : 0.644 10.566 23772 Z= 0.320 Chirality : 0.047 0.187 2784 Planarity : 0.004 0.051 2952 Dihedral : 4.817 22.561 2352 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 5.29 % Allowed : 25.53 % Favored : 69.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 1.02 (0.18), residues: 840 loop : -3.00 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG q 272 TYR 0.009 0.001 TYR K 258 PHE 0.026 0.002 PHE J 149 TRP 0.016 0.002 TRP p 156 HIS 0.006 0.001 HIS W 278 Details of bonding type rmsd covalent geometry : bond 0.00332 (17400) covalent geometry : angle 0.64396 (23772) hydrogen bonds : bond 0.03168 ( 670) hydrogen bonds : angle 5.08453 ( 1911) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 365 time to evaluate : 0.670 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: R 153 TRP cc_start: 0.7585 (m100) cc_final: 0.7089 (m100) REVERT: R 184 MET cc_start: 0.4858 (tpt) cc_final: 0.4336 (tpp) REVERT: V 160 TRP cc_start: 0.6363 (m-90) cc_final: 0.6020 (m100) REVERT: V 185 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8303 (pm20) REVERT: W 261 ASP cc_start: 0.8881 (t0) cc_final: 0.8664 (t0) REVERT: W 289 GLN cc_start: 0.8682 (tt0) cc_final: 0.7960 (mp10) REVERT: B 178 MET cc_start: 0.8066 (mpp) cc_final: 0.7745 (mmm) REVERT: B 189 TYR cc_start: 0.8490 (m-80) cc_final: 0.7983 (m-10) REVERT: C 243 GLN cc_start: 0.8523 (tp40) cc_final: 0.7426 (mp10) REVERT: G 233 LEU cc_start: 0.6477 (OUTLIER) cc_final: 0.6222 (mp) REVERT: H 488 ASP cc_start: 0.6681 (m-30) cc_final: 0.6328 (p0) REVERT: J 189 TYR cc_start: 0.8658 (m-10) cc_final: 0.8376 (m-10) REVERT: J 197 TYR cc_start: 0.7834 (OUTLIER) cc_final: 0.6156 (t80) REVERT: K 287 THR cc_start: 0.8419 (OUTLIER) cc_final: 0.8187 (t) REVERT: h 191 ARG cc_start: 0.6394 (tpp80) cc_final: 0.5471 (ttp-170) REVERT: i 268 THR cc_start: 0.8967 (m) cc_final: 0.8689 (p) REVERT: i 281 LEU cc_start: 0.6969 (mm) cc_final: 0.6345 (mt) REVERT: j 487 LEU cc_start: 0.6317 (OUTLIER) cc_final: 0.6002 (pp) REVERT: k 69 LYS cc_start: 0.7330 (pttm) cc_final: 0.6650 (tptt) REVERT: m 261 ASP cc_start: 0.8239 (t0) cc_final: 0.7978 (t0) REVERT: a 236 GLN cc_start: 0.8560 (mm-40) cc_final: 0.8166 (tp40) REVERT: f 491 GLN cc_start: 0.6209 (mm110) cc_final: 0.5776 (mp10) REVERT: o 84 PHE cc_start: 0.7539 (m-80) cc_final: 0.7332 (m-80) REVERT: p 184 MET cc_start: 0.4677 (tpt) cc_final: 0.4376 (tpt) REVERT: t 160 TRP cc_start: 0.6360 (m-90) cc_final: 0.6020 (m100) REVERT: t 185 GLU cc_start: 0.8734 (OUTLIER) cc_final: 0.8281 (pm20) REVERT: u 289 GLN cc_start: 0.8691 (tt0) cc_final: 0.7979 (mp10) outliers start: 99 outliers final: 80 residues processed: 434 average time/residue: 0.1113 time to fit residues: 77.0533 Evaluate side-chains 429 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 343 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 204 SER Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 485 VAL Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain K residue 277 THR Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain i residue 275 VAL Chi-restraints excluded: chain j residue 485 VAL Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 256 LEU Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 168 SER Chi-restraints excluded: chain Z residue 171 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain b residue 476 VAL Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 162 VAL Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain e residue 275 VAL Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 204 SER Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain p residue 219 VAL Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain r residue 485 VAL Chi-restraints excluded: chain t residue 162 VAL Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain t residue 217 VAL Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 180 optimal weight: 9.9990 chunk 134 optimal weight: 0.2980 chunk 18 optimal weight: 6.9990 chunk 2 optimal weight: 20.0000 chunk 161 optimal weight: 9.9990 chunk 46 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 88 optimal weight: 0.6980 chunk 184 optimal weight: 0.6980 chunk 11 optimal weight: 3.9990 chunk 164 optimal weight: 4.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 212 GLN ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS K 231 HIS i 236 GLN i 243 GLN ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** p 212 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.167204 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.115508 restraints weight = 26271.645| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 3.83 r_work: 0.3564 rms_B_bonded: 3.78 restraints_weight: 0.5000 r_work (final): 0.3564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.6324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 17400 Z= 0.130 Angle : 0.637 10.543 23772 Z= 0.315 Chirality : 0.047 0.214 2784 Planarity : 0.004 0.047 2952 Dihedral : 4.718 21.541 2352 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.90 % Favored : 91.10 % Rotamer: Outliers : 5.07 % Allowed : 26.66 % Favored : 68.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 1.18 (0.18), residues: 840 loop : -2.92 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG S 272 TYR 0.013 0.001 TYR i 258 PHE 0.034 0.002 PHE b 483 TRP 0.012 0.001 TRP l 153 HIS 0.005 0.001 HIS W 278 Details of bonding type rmsd covalent geometry : bond 0.00304 (17400) covalent geometry : angle 0.63652 (23772) hydrogen bonds : bond 0.03035 ( 670) hydrogen bonds : angle 4.92405 ( 1911) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 461 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 366 time to evaluate : 0.652 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 153 TRP cc_start: 0.7599 (m100) cc_final: 0.7113 (m100) REVERT: R 184 MET cc_start: 0.4639 (tpt) cc_final: 0.4233 (tpp) REVERT: S 272 ARG cc_start: 0.7380 (mtt-85) cc_final: 0.7063 (mtt-85) REVERT: V 160 TRP cc_start: 0.6395 (m-90) cc_final: 0.6055 (m100) REVERT: V 183 THR cc_start: 0.8256 (p) cc_final: 0.8028 (p) REVERT: V 184 MET cc_start: 0.8462 (tpp) cc_final: 0.7922 (tpp) REVERT: V 185 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: W 261 ASP cc_start: 0.8868 (t0) cc_final: 0.8641 (t0) REVERT: W 289 GLN cc_start: 0.8659 (tt0) cc_final: 0.7939 (mp10) REVERT: B 178 MET cc_start: 0.8018 (mpp) cc_final: 0.7709 (mmm) REVERT: B 189 TYR cc_start: 0.8463 (m-80) cc_final: 0.7954 (m-10) REVERT: C 243 GLN cc_start: 0.8493 (tp40) cc_final: 0.7431 (mp10) REVERT: G 233 LEU cc_start: 0.6456 (OUTLIER) cc_final: 0.6207 (mp) REVERT: H 488 ASP cc_start: 0.6564 (m-30) cc_final: 0.6236 (p0) REVERT: I 73 ASP cc_start: 0.7582 (t70) cc_final: 0.7364 (t70) REVERT: J 189 TYR cc_start: 0.8619 (m-10) cc_final: 0.8279 (m-10) REVERT: J 197 TYR cc_start: 0.7724 (OUTLIER) cc_final: 0.6194 (t80) REVERT: K 287 THR cc_start: 0.8408 (OUTLIER) cc_final: 0.8169 (t) REVERT: L 487 LEU cc_start: 0.8974 (mt) cc_final: 0.8767 (mp) REVERT: h 191 ARG cc_start: 0.6387 (tpp80) cc_final: 0.5312 (ttm-80) REVERT: i 268 THR cc_start: 0.8931 (m) cc_final: 0.8629 (p) REVERT: i 281 LEU cc_start: 0.7026 (mm) cc_final: 0.6394 (mt) REVERT: j 487 LEU cc_start: 0.6169 (OUTLIER) cc_final: 0.5850 (pp) REVERT: k 69 LYS cc_start: 0.7314 (pttm) cc_final: 0.6642 (tptt) REVERT: m 238 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8989 (mt) REVERT: m 261 ASP cc_start: 0.8189 (t0) cc_final: 0.7938 (t0) REVERT: a 236 GLN cc_start: 0.8573 (mm-40) cc_final: 0.8288 (tp40) REVERT: f 491 GLN cc_start: 0.5887 (mm110) cc_final: 0.5492 (mp10) REVERT: o 84 PHE cc_start: 0.7399 (m-80) cc_final: 0.7191 (m-80) REVERT: p 153 TRP cc_start: 0.7639 (m100) cc_final: 0.7240 (m100) REVERT: t 160 TRP cc_start: 0.6379 (m-90) cc_final: 0.6042 (m100) REVERT: t 183 THR cc_start: 0.8255 (p) cc_final: 0.8025 (p) REVERT: t 184 MET cc_start: 0.8481 (tpp) cc_final: 0.7954 (tpp) REVERT: t 185 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8539 (pm20) REVERT: u 261 ASP cc_start: 0.8855 (t0) cc_final: 0.8649 (t0) REVERT: u 289 GLN cc_start: 0.8667 (tt0) cc_final: 0.7952 (mp10) outliers start: 95 outliers final: 77 residues processed: 430 average time/residue: 0.1030 time to fit residues: 70.4571 Evaluate side-chains 433 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 349 time to evaluate : 0.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 485 VAL Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain F residue 222 LEU Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain K residue 286 VAL Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 236 GLN Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 238 LEU Chi-restraints excluded: chain m residue 253 GLU Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 150 VAL Chi-restraints excluded: chain Z residue 168 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 205 SER Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 162 VAL Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain e residue 268 THR Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain q residue 238 LEU Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain t residue 162 VAL Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain t residue 217 VAL Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 117 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 172 optimal weight: 0.6980 chunk 82 optimal weight: 2.9990 chunk 87 optimal weight: 4.9990 chunk 190 optimal weight: 2.9990 chunk 3 optimal weight: 7.9990 chunk 72 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 69 optimal weight: 0.9990 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 243 GLN ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** h 158 GLN ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.163790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.112301 restraints weight = 26402.426| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 3.80 r_work: 0.3496 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.6505 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.092 17400 Z= 0.228 Angle : 0.708 11.198 23772 Z= 0.355 Chirality : 0.048 0.219 2784 Planarity : 0.005 0.055 2952 Dihedral : 5.234 23.280 2352 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.04 % Favored : 89.96 % Rotamer: Outliers : 5.72 % Allowed : 25.91 % Favored : 68.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.78 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 1.01 (0.18), residues: 840 loop : -2.99 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG J 195 TYR 0.020 0.001 TYR e 258 PHE 0.021 0.002 PHE D 483 TRP 0.010 0.002 TRP l 153 HIS 0.006 0.001 HIS u 278 Details of bonding type rmsd covalent geometry : bond 0.00535 (17400) covalent geometry : angle 0.70760 (23772) hydrogen bonds : bond 0.03485 ( 670) hydrogen bonds : angle 5.31719 ( 1911) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 450 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 343 time to evaluate : 0.721 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 153 TRP cc_start: 0.7734 (m100) cc_final: 0.7365 (m100) REVERT: V 160 TRP cc_start: 0.6305 (m-90) cc_final: 0.5957 (m100) REVERT: V 183 THR cc_start: 0.8268 (p) cc_final: 0.7792 (p) REVERT: V 184 MET cc_start: 0.8473 (tpp) cc_final: 0.7970 (tpp) REVERT: V 185 GLU cc_start: 0.8732 (OUTLIER) cc_final: 0.8278 (pm20) REVERT: W 261 ASP cc_start: 0.8888 (t0) cc_final: 0.8687 (t0) REVERT: W 289 GLN cc_start: 0.8647 (tt0) cc_final: 0.7942 (mp10) REVERT: B 178 MET cc_start: 0.8085 (mpp) cc_final: 0.7797 (mmm) REVERT: B 189 TYR cc_start: 0.8613 (m-80) cc_final: 0.8246 (m-10) REVERT: C 243 GLN cc_start: 0.8524 (tp40) cc_final: 0.7377 (mp10) REVERT: G 233 LEU cc_start: 0.6667 (OUTLIER) cc_final: 0.6418 (mp) REVERT: H 488 ASP cc_start: 0.6750 (m-30) cc_final: 0.6298 (p0) REVERT: J 189 TYR cc_start: 0.8686 (m-10) cc_final: 0.8291 (m-10) REVERT: J 197 TYR cc_start: 0.7728 (OUTLIER) cc_final: 0.6034 (t80) REVERT: K 287 THR cc_start: 0.8470 (OUTLIER) cc_final: 0.8223 (t) REVERT: h 191 ARG cc_start: 0.6445 (tpp80) cc_final: 0.5340 (ttm-80) REVERT: i 268 THR cc_start: 0.8973 (m) cc_final: 0.8662 (p) REVERT: i 281 LEU cc_start: 0.7379 (mm) cc_final: 0.6822 (mt) REVERT: j 487 LEU cc_start: 0.6306 (OUTLIER) cc_final: 0.5906 (pp) REVERT: m 238 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8930 (mt) REVERT: m 261 ASP cc_start: 0.8316 (t0) cc_final: 0.8033 (t0) REVERT: a 236 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8125 (tp40) REVERT: d 197 TYR cc_start: 0.7979 (m-80) cc_final: 0.7539 (m-80) REVERT: o 84 PHE cc_start: 0.7354 (m-80) cc_final: 0.6918 (m-80) REVERT: p 153 TRP cc_start: 0.7717 (m100) cc_final: 0.7192 (m100) REVERT: p 184 MET cc_start: 0.4636 (tpt) cc_final: 0.4237 (tpp) REVERT: t 160 TRP cc_start: 0.6304 (m-90) cc_final: 0.5956 (m100) REVERT: t 183 THR cc_start: 0.8298 (p) cc_final: 0.7839 (p) REVERT: t 184 MET cc_start: 0.8483 (tpp) cc_final: 0.7981 (tpp) REVERT: t 185 GLU cc_start: 0.8701 (OUTLIER) cc_final: 0.8254 (pm20) REVERT: u 289 GLN cc_start: 0.8655 (tt0) cc_final: 0.7947 (mp10) outliers start: 107 outliers final: 86 residues processed: 422 average time/residue: 0.1096 time to fit residues: 73.4966 Evaluate side-chains 424 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 331 time to evaluate : 0.662 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain R residue 219 VAL Chi-restraints excluded: chain S residue 238 LEU Chi-restraints excluded: chain S residue 268 THR Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 485 VAL Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 268 THR Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 76 THR Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain B residue 218 SER Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain C residue 286 VAL Chi-restraints excluded: chain D residue 475 CYS Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain G residue 268 THR Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain J residue 217 VAL Chi-restraints excluded: chain J residue 218 SER Chi-restraints excluded: chain K residue 286 VAL Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain g residue 88 LEU Chi-restraints excluded: chain h residue 149 PHE Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain i residue 259 THR Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain m residue 238 LEU Chi-restraints excluded: chain m residue 253 GLU Chi-restraints excluded: chain m residue 268 THR Chi-restraints excluded: chain m residue 279 THR Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 168 SER Chi-restraints excluded: chain Z residue 171 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 183 THR Chi-restraints excluded: chain Z residue 198 VAL Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 162 VAL Chi-restraints excluded: chain d residue 183 THR Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain e residue 268 THR Chi-restraints excluded: chain e residue 275 VAL Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain p residue 219 VAL Chi-restraints excluded: chain q residue 238 LEU Chi-restraints excluded: chain q residue 268 THR Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain r residue 485 VAL Chi-restraints excluded: chain t residue 162 VAL Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain u residue 268 THR Chi-restraints excluded: chain u residue 276 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 95 optimal weight: 0.7980 chunk 70 optimal weight: 0.8980 chunk 31 optimal weight: 0.3980 chunk 25 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 135 optimal weight: 0.4980 chunk 74 optimal weight: 0.9990 chunk 146 optimal weight: 0.6980 chunk 68 optimal weight: 1.9990 chunk 84 optimal weight: 0.0980 chunk 137 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 491 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** i 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 243 GLN ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.167092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3781 r_free = 0.3781 target = 0.115940 restraints weight = 26786.995| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 3.91 r_work: 0.3579 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3579 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.6554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17400 Z= 0.124 Angle : 0.655 12.838 23772 Z= 0.322 Chirality : 0.047 0.222 2784 Planarity : 0.004 0.052 2952 Dihedral : 4.744 21.608 2352 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.33 % Favored : 91.67 % Rotamer: Outliers : 4.06 % Allowed : 27.88 % Favored : 68.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.57 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 1.18 (0.18), residues: 840 loop : -2.86 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG m 272 TYR 0.017 0.001 TYR e 258 PHE 0.028 0.002 PHE b 483 TRP 0.020 0.001 TRP V 153 HIS 0.004 0.001 HIS W 278 Details of bonding type rmsd covalent geometry : bond 0.00291 (17400) covalent geometry : angle 0.65515 (23772) hydrogen bonds : bond 0.02945 ( 670) hydrogen bonds : angle 4.96059 ( 1911) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4224 Ramachandran restraints generated. 2112 Oldfield, 0 Emsley, 2112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 357 time to evaluate : 0.634 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 153 TRP cc_start: 0.7820 (m100) cc_final: 0.7399 (m100) REVERT: R 184 MET cc_start: 0.4443 (tpt) cc_final: 0.4092 (tpp) REVERT: V 160 TRP cc_start: 0.6257 (m-90) cc_final: 0.5917 (m100) REVERT: V 183 THR cc_start: 0.8375 (p) cc_final: 0.7956 (p) REVERT: V 184 MET cc_start: 0.8492 (tpp) cc_final: 0.7959 (tpp) REVERT: V 185 GLU cc_start: 0.8760 (OUTLIER) cc_final: 0.8361 (pm20) REVERT: W 261 ASP cc_start: 0.8840 (t0) cc_final: 0.8622 (t0) REVERT: W 289 GLN cc_start: 0.8600 (tt0) cc_final: 0.7900 (mp10) REVERT: B 178 MET cc_start: 0.8043 (mpp) cc_final: 0.7727 (mmm) REVERT: B 189 TYR cc_start: 0.8516 (m-80) cc_final: 0.8021 (m-10) REVERT: B 216 SER cc_start: 0.8265 (t) cc_final: 0.8005 (m) REVERT: C 243 GLN cc_start: 0.8487 (tp40) cc_final: 0.7410 (mp10) REVERT: G 233 LEU cc_start: 0.6404 (OUTLIER) cc_final: 0.6157 (mp) REVERT: H 488 ASP cc_start: 0.6536 (m-30) cc_final: 0.6295 (p0) REVERT: J 189 TYR cc_start: 0.8567 (m-10) cc_final: 0.8209 (m-10) REVERT: J 197 TYR cc_start: 0.7496 (OUTLIER) cc_final: 0.6148 (t80) REVERT: K 287 THR cc_start: 0.8378 (OUTLIER) cc_final: 0.8160 (t) REVERT: P 488 ASP cc_start: 0.6006 (p0) cc_final: 0.5697 (p0) REVERT: h 191 ARG cc_start: 0.6375 (tpp80) cc_final: 0.5305 (ttm-80) REVERT: i 268 THR cc_start: 0.8942 (m) cc_final: 0.8697 (p) REVERT: i 281 LEU cc_start: 0.7134 (mm) cc_final: 0.6533 (mt) REVERT: j 487 LEU cc_start: 0.6326 (OUTLIER) cc_final: 0.5798 (pp) REVERT: j 488 ASP cc_start: 0.6946 (p0) cc_final: 0.5961 (m-30) REVERT: k 69 LYS cc_start: 0.7427 (pttm) cc_final: 0.6704 (tptt) REVERT: l 158 GLN cc_start: 0.7772 (mt0) cc_final: 0.7559 (mt0) REVERT: m 261 ASP cc_start: 0.8213 (t0) cc_final: 0.7981 (t0) REVERT: a 236 GLN cc_start: 0.8558 (mm-40) cc_final: 0.8279 (tp40) REVERT: e 234 ARG cc_start: 0.7609 (ttm170) cc_final: 0.6843 (ttm170) REVERT: f 491 GLN cc_start: 0.5758 (mm110) cc_final: 0.4712 (mp10) REVERT: o 84 PHE cc_start: 0.7337 (m-80) cc_final: 0.6865 (m-80) REVERT: p 153 TRP cc_start: 0.7788 (m100) cc_final: 0.7361 (m100) REVERT: p 184 MET cc_start: 0.4512 (tpt) cc_final: 0.4116 (tpp) REVERT: t 160 TRP cc_start: 0.6263 (m-90) cc_final: 0.5921 (m100) REVERT: t 183 THR cc_start: 0.8363 (p) cc_final: 0.7941 (p) REVERT: t 184 MET cc_start: 0.8497 (tpp) cc_final: 0.7964 (tpp) REVERT: t 185 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8355 (pm20) REVERT: u 289 GLN cc_start: 0.8609 (tt0) cc_final: 0.7907 (mp10) outliers start: 76 outliers final: 60 residues processed: 411 average time/residue: 0.1131 time to fit residues: 73.1538 Evaluate side-chains 413 residues out of total 1872 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 347 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 168 SER Chi-restraints excluded: chain R residue 182 HIS Chi-restraints excluded: chain R residue 217 VAL Chi-restraints excluded: chain S residue 279 THR Chi-restraints excluded: chain S residue 281 LEU Chi-restraints excluded: chain S residue 298 LEU Chi-restraints excluded: chain T residue 485 VAL Chi-restraints excluded: chain V residue 162 VAL Chi-restraints excluded: chain V residue 185 GLU Chi-restraints excluded: chain V residue 217 VAL Chi-restraints excluded: chain W residue 276 VAL Chi-restraints excluded: chain W residue 281 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain B residue 163 LEU Chi-restraints excluded: chain B residue 167 VAL Chi-restraints excluded: chain B residue 186 VAL Chi-restraints excluded: chain B residue 187 THR Chi-restraints excluded: chain B residue 200 LEU Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 276 VAL Chi-restraints excluded: chain E residue 71 SER Chi-restraints excluded: chain G residue 233 LEU Chi-restraints excluded: chain I residue 88 LEU Chi-restraints excluded: chain J residue 163 LEU Chi-restraints excluded: chain J residue 167 VAL Chi-restraints excluded: chain J residue 186 VAL Chi-restraints excluded: chain J residue 187 THR Chi-restraints excluded: chain J residue 194 SER Chi-restraints excluded: chain J residue 197 TYR Chi-restraints excluded: chain J residue 200 LEU Chi-restraints excluded: chain K residue 287 THR Chi-restraints excluded: chain L residue 490 VAL Chi-restraints excluded: chain N residue 170 LEU Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 268 THR Chi-restraints excluded: chain h residue 155 THR Chi-restraints excluded: chain h residue 170 LEU Chi-restraints excluded: chain h residue 183 THR Chi-restraints excluded: chain h residue 210 THR Chi-restraints excluded: chain i residue 244 LEU Chi-restraints excluded: chain j residue 487 LEU Chi-restraints excluded: chain k residue 70 VAL Chi-restraints excluded: chain l residue 152 VAL Chi-restraints excluded: chain l residue 181 THR Chi-restraints excluded: chain l residue 183 THR Chi-restraints excluded: chain l residue 220 SER Chi-restraints excluded: chain Y residue 70 VAL Chi-restraints excluded: chain Y residue 83 SER Chi-restraints excluded: chain Z residue 171 SER Chi-restraints excluded: chain Z residue 181 THR Chi-restraints excluded: chain Z residue 220 SER Chi-restraints excluded: chain a residue 238 LEU Chi-restraints excluded: chain c residue 86 ILE Chi-restraints excluded: chain d residue 155 THR Chi-restraints excluded: chain d residue 162 VAL Chi-restraints excluded: chain d residue 210 THR Chi-restraints excluded: chain e residue 268 THR Chi-restraints excluded: chain e residue 275 VAL Chi-restraints excluded: chain p residue 168 SER Chi-restraints excluded: chain p residue 182 HIS Chi-restraints excluded: chain p residue 217 VAL Chi-restraints excluded: chain q residue 238 LEU Chi-restraints excluded: chain q residue 298 LEU Chi-restraints excluded: chain t residue 162 VAL Chi-restraints excluded: chain t residue 185 GLU Chi-restraints excluded: chain u residue 268 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 192 random chunks: chunk 179 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 148 optimal weight: 5.9990 chunk 167 optimal weight: 6.9990 chunk 174 optimal weight: 5.9990 chunk 6 optimal weight: 20.0000 chunk 126 optimal weight: 3.9990 chunk 157 optimal weight: 6.9990 chunk 13 optimal weight: 6.9990 chunk 53 optimal weight: 0.6980 chunk 64 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 202 HIS ** M 72 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 236 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** p 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** q 243 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.161237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.113266 restraints weight = 26572.586| |-----------------------------------------------------------------------------| r_work (start): 0.3650 rms_B_bonded: 4.02 r_work: 0.3445 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 17400 Z= 0.382 Angle : 0.838 12.616 23772 Z= 0.427 Chirality : 0.053 0.251 2784 Planarity : 0.006 0.055 2952 Dihedral : 6.002 26.275 2352 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 14.69 Ramachandran Plot: Outliers : 0.05 % Allowed : 12.17 % Favored : 87.78 % Rotamer: Outliers : 5.34 % Allowed : 26.76 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.07 (0.17), residues: 2112 helix: None (None), residues: 0 sheet: 0.67 (0.18), residues: 840 loop : -3.07 (0.14), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG F 191 TYR 0.022 0.002 TYR e 258 PHE 0.027 0.003 PHE B 207 TRP 0.015 0.003 TRP F 160 HIS 0.010 0.002 HIS u 278 Details of bonding type rmsd covalent geometry : bond 0.00887 (17400) covalent geometry : angle 0.83838 (23772) hydrogen bonds : bond 0.04316 ( 670) hydrogen bonds : angle 5.98598 ( 1911) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5321.34 seconds wall clock time: 91 minutes 40.64 seconds (5500.64 seconds total)