Starting phenix.real_space_refine on Sun Feb 8 06:27:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9vyg_65452/02_2026/9vyg_65452.cif Found real_map, /net/cci-nas-00/data/ceres_data/9vyg_65452/02_2026/9vyg_65452.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9vyg_65452/02_2026/9vyg_65452.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9vyg_65452/02_2026/9vyg_65452.map" model { file = "/net/cci-nas-00/data/ceres_data/9vyg_65452/02_2026/9vyg_65452.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9vyg_65452/02_2026/9vyg_65452.cif" } resolution = 3.5 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= 0.002 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 180 5.16 5 C 25992 2.51 5 N 7037 2.21 5 O 8157 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 66 residue(s): 0.04s 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: 41366 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "B" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "C" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "D" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "E" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "F" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "G" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "H" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "I" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "J" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "K" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "L" Number of atoms: 1386 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1386 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 7, 'TRANS': 177} Chain: "M" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3431 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 426} Chain: "N" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3431 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 426} Chain: "O" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3431 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 426} Chain: "P" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3431 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 426} Chain: "Q" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3431 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 426} Chain: "R" Number of atoms: 3431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3431 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 426} Chain: "S" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 439 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "T" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 439 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "U" Number of atoms: 439 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 439 Classifications: {'peptide': 56} Link IDs: {'PTRANS': 2, 'TRANS': 53} Chain: "m" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 940 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 8, 'TRANS': 118} Chain: "n" Number of atoms: 956 Number of conformers: 1 Conformer: "" Number of residues, atoms: 129, 956 Classifications: {'peptide': 129} Link IDs: {'PTRANS': 8, 'TRANS': 120} Chain: "o" Number of atoms: 935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 935 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 8, 'TRANS': 117} Time building chain proxies: 8.94, per 1000 atoms: 0.22 Number of scatterers: 41366 At special positions: 0 Unit cell: (176.55, 162.64, 178.69, 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 180 16.00 O 8157 8.00 N 7037 7.00 C 25992 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: 3.27 Conformation dependent library (CDL) restraints added in 1.7 seconds 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9650 Finding SS restraints... Secondary structure from input PDB file: 97 helices and 102 sheets defined 23.1% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.59 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 Processing helix chain 'A' and resid 25 through 46 Processing helix chain 'A' and resid 135 through 148 removed outlier: 3.726A pdb=" N HIS A 146 " --> pdb=" O LEU A 142 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 152 Processing helix chain 'A' and resid 156 through 173 Processing helix chain 'B' and resid 3 through 15 Processing helix chain 'B' and resid 25 through 46 Processing helix chain 'B' and resid 135 through 151 removed outlier: 3.844A pdb=" N HIS B 146 " --> pdb=" O LEU B 142 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N GLU B 149 " --> pdb=" O LEU B 145 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N ALA B 150 " --> pdb=" O HIS B 146 " (cutoff:3.500A) removed outlier: 3.861A pdb=" N PHE B 151 " --> pdb=" O MET B 147 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 173 Processing helix chain 'C' and resid 3 through 15 Processing helix chain 'C' and resid 25 through 46 Processing helix chain 'C' and resid 135 through 148 removed outlier: 3.746A pdb=" N HIS C 146 " --> pdb=" O LEU C 142 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 152 Processing helix chain 'C' and resid 156 through 173 Processing helix chain 'D' and resid 3 through 15 Processing helix chain 'D' and resid 25 through 46 Processing helix chain 'D' and resid 135 through 151 removed outlier: 3.750A pdb=" N HIS D 146 " --> pdb=" O LEU D 142 " (cutoff:3.500A) removed outlier: 4.925A pdb=" N GLU D 149 " --> pdb=" O LEU D 145 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ALA D 150 " --> pdb=" O HIS D 146 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N PHE D 151 " --> pdb=" O MET D 147 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 173 removed outlier: 3.519A pdb=" N ALA D 160 " --> pdb=" O GLY D 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 15 Processing helix chain 'E' and resid 25 through 46 Processing helix chain 'E' and resid 135 through 148 removed outlier: 3.726A pdb=" N HIS E 146 " --> pdb=" O LEU E 142 " (cutoff:3.500A) Processing helix chain 'E' and resid 149 through 152 Processing helix chain 'E' and resid 156 through 173 Processing helix chain 'F' and resid 3 through 15 Processing helix chain 'F' and resid 25 through 46 Processing helix chain 'F' and resid 135 through 151 removed outlier: 3.726A pdb=" N HIS F 146 " --> pdb=" O LEU F 142 " (cutoff:3.500A) removed outlier: 4.888A pdb=" N GLU F 149 " --> pdb=" O LEU F 145 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ALA F 150 " --> pdb=" O HIS F 146 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE F 151 " --> pdb=" O MET F 147 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 173 removed outlier: 3.570A pdb=" N ALA F 160 " --> pdb=" O GLY F 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 15 Processing helix chain 'G' and resid 25 through 46 Processing helix chain 'G' and resid 135 through 148 removed outlier: 3.728A pdb=" N HIS G 146 " --> pdb=" O LEU G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 149 through 152 Processing helix chain 'G' and resid 156 through 173 Processing helix chain 'H' and resid 3 through 15 Processing helix chain 'H' and resid 25 through 46 Processing helix chain 'H' and resid 135 through 148 removed outlier: 3.751A pdb=" N HIS H 146 " --> pdb=" O LEU H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 149 through 152 Processing helix chain 'H' and resid 156 through 173 Processing helix chain 'I' and resid 3 through 15 Processing helix chain 'I' and resid 25 through 46 Processing helix chain 'I' and resid 135 through 148 removed outlier: 3.684A pdb=" N HIS I 146 " --> pdb=" O LEU I 142 " (cutoff:3.500A) Processing helix chain 'I' and resid 149 through 152 Processing helix chain 'I' and resid 156 through 173 Processing helix chain 'J' and resid 3 through 15 Processing helix chain 'J' and resid 25 through 46 Processing helix chain 'J' and resid 135 through 151 removed outlier: 3.785A pdb=" N HIS J 146 " --> pdb=" O LEU J 142 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU J 149 " --> pdb=" O LEU J 145 " (cutoff:3.500A) removed outlier: 4.260A pdb=" N ALA J 150 " --> pdb=" O HIS J 146 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N PHE J 151 " --> pdb=" O MET J 147 " (cutoff:3.500A) Processing helix chain 'J' and resid 156 through 173 Processing helix chain 'K' and resid 3 through 15 Processing helix chain 'K' and resid 25 through 46 Processing helix chain 'K' and resid 135 through 148 removed outlier: 3.738A pdb=" N HIS K 146 " --> pdb=" O LEU K 142 " (cutoff:3.500A) Processing helix chain 'K' and resid 149 through 152 Processing helix chain 'K' and resid 156 through 173 Processing helix chain 'L' and resid 3 through 15 Processing helix chain 'L' and resid 25 through 46 Processing helix chain 'L' and resid 135 through 148 removed outlier: 3.658A pdb=" N HIS L 146 " --> pdb=" O LEU L 142 " (cutoff:3.500A) Processing helix chain 'L' and resid 149 through 152 Processing helix chain 'L' and resid 156 through 173 removed outlier: 3.534A pdb=" N ALA L 160 " --> pdb=" O GLY L 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 124 through 128 Processing helix chain 'M' and resid 253 through 262 Processing helix chain 'M' and resid 311 through 315 Processing helix chain 'M' and resid 329 through 333 removed outlier: 3.737A pdb=" N GLY M 332 " --> pdb=" O SER M 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 65 through 69 removed outlier: 3.758A pdb=" N ALA N 69 " --> pdb=" O LEU N 66 " (cutoff:3.500A) Processing helix chain 'N' and resid 124 through 128 Processing helix chain 'N' and resid 253 through 262 removed outlier: 3.555A pdb=" N GLY N 262 " --> pdb=" O GLU N 258 " (cutoff:3.500A) Processing helix chain 'N' and resid 311 through 315 Processing helix chain 'N' and resid 329 through 333 removed outlier: 3.840A pdb=" N GLY N 332 " --> pdb=" O SER N 329 " (cutoff:3.500A) Processing helix chain 'N' and resid 368 through 372 removed outlier: 3.555A pdb=" N ALA N 371 " --> pdb=" O GLY N 368 " (cutoff:3.500A) removed outlier: 4.315A pdb=" N ASP N 372 " --> pdb=" O GLU N 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 368 through 372' Processing helix chain 'O' and resid 65 through 69 removed outlier: 3.689A pdb=" N ALA O 69 " --> pdb=" O LEU O 66 " (cutoff:3.500A) Processing helix chain 'O' and resid 124 through 128 Processing helix chain 'O' and resid 253 through 262 Processing helix chain 'O' and resid 311 through 315 Processing helix chain 'P' and resid 13 through 17 removed outlier: 4.160A pdb=" N LEU P 17 " --> pdb=" O ARG P 14 " (cutoff:3.500A) Processing helix chain 'P' and resid 65 through 69 removed outlier: 3.701A pdb=" N ALA P 69 " --> pdb=" O LEU P 66 " (cutoff:3.500A) Processing helix chain 'P' and resid 124 through 128 Processing helix chain 'P' and resid 253 through 262 Processing helix chain 'P' and resid 311 through 315 Processing helix chain 'P' and resid 329 through 333 removed outlier: 3.944A pdb=" N GLY P 332 " --> pdb=" O SER P 329 " (cutoff:3.500A) Processing helix chain 'P' and resid 368 through 372 removed outlier: 3.608A pdb=" N ALA P 371 " --> pdb=" O GLY P 368 " (cutoff:3.500A) removed outlier: 4.428A pdb=" N ASP P 372 " --> pdb=" O GLU P 369 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 368 through 372' Processing helix chain 'Q' and resid 13 through 17 removed outlier: 3.908A pdb=" N LEU Q 17 " --> pdb=" O ARG Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 65 through 69 removed outlier: 3.698A pdb=" N ALA Q 69 " --> pdb=" O LEU Q 66 " (cutoff:3.500A) Processing helix chain 'Q' and resid 124 through 128 Processing helix chain 'Q' and resid 253 through 262 Processing helix chain 'Q' and resid 311 through 315 Processing helix chain 'Q' and resid 329 through 333 removed outlier: 3.625A pdb=" N GLY Q 332 " --> pdb=" O SER Q 329 " (cutoff:3.500A) Processing helix chain 'Q' and resid 368 through 372 removed outlier: 4.208A pdb=" N ASP Q 372 " --> pdb=" O GLU Q 369 " (cutoff:3.500A) Processing helix chain 'R' and resid 13 through 17 removed outlier: 4.166A pdb=" N LEU R 17 " --> pdb=" O ARG R 14 " (cutoff:3.500A) Processing helix chain 'R' and resid 65 through 68 Processing helix chain 'R' and resid 124 through 128 Processing helix chain 'R' and resid 253 through 262 removed outlier: 3.571A pdb=" N GLY R 262 " --> pdb=" O GLU R 258 " (cutoff:3.500A) Processing helix chain 'R' and resid 311 through 315 Processing helix chain 'R' and resid 329 through 333 removed outlier: 3.925A pdb=" N GLY R 332 " --> pdb=" O SER R 329 " (cutoff:3.500A) Processing helix chain 'S' and resid 22 through 57 Processing helix chain 'T' and resid 22 through 58 removed outlier: 3.569A pdb=" N ALA T 55 " --> pdb=" O ALA T 51 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N VAL T 58 " --> pdb=" O LEU T 54 " (cutoff:3.500A) Processing helix chain 'U' and resid 22 through 58 Processing helix chain 'm' and resid 99 through 129 Processing helix chain 'n' and resid 15 through 20 removed outlier: 3.579A pdb=" N ALA n 20 " --> pdb=" O ASN n 17 " (cutoff:3.500A) Processing helix chain 'n' and resid 99 through 126 Processing helix chain 'o' and resid 93 through 127 removed outlier: 4.075A pdb=" N GLU o 97 " --> pdb=" O SER o 93 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ASP o 104 " --> pdb=" O ASP o 100 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N VAL o 105 " --> pdb=" O GLU o 101 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 57 removed outlier: 3.581A pdb=" N GLU A 67 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 61 through 62 removed outlier: 6.849A pdb=" N TYR A 61 " --> pdb=" O THR A 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 83 Processing sheet with id=AA4, first strand: chain 'B' and resid 53 through 57 Processing sheet with id=AA5, first strand: chain 'B' and resid 61 through 62 removed outlier: 6.862A pdb=" N TYR B 61 " --> pdb=" O THR B 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 82 through 83 Processing sheet with id=AA7, first strand: chain 'C' and resid 53 through 57 removed outlier: 6.276A pdb=" N GLU C 67 " --> pdb=" O VAL C 100 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N ILE C 102 " --> pdb=" O GLU C 67 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL C 69 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ALA C 97 " --> pdb=" O TRP C 112 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 61 through 62 removed outlier: 6.758A pdb=" N TYR C 61 " --> pdb=" O THR C 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 82 through 83 Processing sheet with id=AB1, first strand: chain 'D' and resid 53 through 57 removed outlier: 3.565A pdb=" N GLU D 67 " --> pdb=" O ALA D 98 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLU D 116 " --> pdb=" O CYS D 113 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 61 through 62 removed outlier: 6.622A pdb=" N TYR D 61 " --> pdb=" O THR D 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 82 through 83 Processing sheet with id=AB4, first strand: chain 'E' and resid 53 through 57 removed outlier: 3.774A pdb=" N GLU E 67 " --> pdb=" O ALA E 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'E' and resid 61 through 62 removed outlier: 6.722A pdb=" N TYR E 61 " --> pdb=" O THR E 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'E' and resid 82 through 83 Processing sheet with id=AB7, first strand: chain 'F' and resid 53 through 57 Processing sheet with id=AB8, first strand: chain 'F' and resid 61 through 62 removed outlier: 6.706A pdb=" N TYR F 61 " --> pdb=" O THR F 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'F' and resid 82 through 83 Processing sheet with id=AC1, first strand: chain 'G' and resid 53 through 57 removed outlier: 3.772A pdb=" N GLU G 67 " --> pdb=" O ALA G 98 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'G' and resid 61 through 62 removed outlier: 6.621A pdb=" N TYR G 61 " --> pdb=" O THR G 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC2 Processing sheet with id=AC3, first strand: chain 'G' and resid 82 through 83 Processing sheet with id=AC4, first strand: chain 'H' and resid 53 through 57 removed outlier: 6.303A pdb=" N GLU H 67 " --> pdb=" O VAL H 100 " (cutoff:3.500A) removed outlier: 7.864A pdb=" N ILE H 102 " --> pdb=" O GLU H 67 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N VAL H 69 " --> pdb=" O ILE H 102 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 61 through 62 removed outlier: 6.717A pdb=" N TYR H 61 " --> pdb=" O THR H 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'H' and resid 82 through 83 Processing sheet with id=AC7, first strand: chain 'I' and resid 53 through 57 removed outlier: 6.054A pdb=" N THR I 53 " --> pdb=" O ARG I 68 " (cutoff:3.500A) removed outlier: 7.407A pdb=" N THR I 70 " --> pdb=" O THR I 53 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N VAL I 55 " --> pdb=" O THR I 70 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU I 67 " --> pdb=" O ALA I 98 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'I' and resid 61 through 62 removed outlier: 6.711A pdb=" N TYR I 61 " --> pdb=" O THR I 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'I' and resid 82 through 83 Processing sheet with id=AD1, first strand: chain 'J' and resid 53 through 57 removed outlier: 3.536A pdb=" N GLU J 116 " --> pdb=" O CYS J 113 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'J' and resid 61 through 62 removed outlier: 6.794A pdb=" N TYR J 61 " --> pdb=" O THR J 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD2 Processing sheet with id=AD3, first strand: chain 'J' and resid 82 through 83 Processing sheet with id=AD4, first strand: chain 'K' and resid 53 through 57 removed outlier: 3.783A pdb=" N GLU K 67 " --> pdb=" O ALA K 98 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'K' and resid 61 through 62 removed outlier: 6.717A pdb=" N TYR K 61 " --> pdb=" O THR K 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD5 Processing sheet with id=AD6, first strand: chain 'K' and resid 82 through 83 Processing sheet with id=AD7, first strand: chain 'L' and resid 53 through 57 removed outlier: 6.246A pdb=" N GLU L 67 " --> pdb=" O VAL L 100 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE L 102 " --> pdb=" O GLU L 67 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N VAL L 69 " --> pdb=" O ILE L 102 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'L' and resid 61 through 62 removed outlier: 6.760A pdb=" N TYR L 61 " --> pdb=" O THR L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD8 Processing sheet with id=AD9, first strand: chain 'L' and resid 82 through 83 Processing sheet with id=AE1, first strand: chain 'M' and resid 25 through 29 removed outlier: 11.401A pdb=" N VAL M 37 " --> pdb=" O ALA M 434 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N ALA M 434 " --> pdb=" O VAL M 37 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ARG M 350 " --> pdb=" O GLY M 411 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N GLY M 411 " --> pdb=" O ARG M 350 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ASN M 352 " --> pdb=" O ALA M 409 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'M' and resid 45 through 50 removed outlier: 6.707A pdb=" N ILE M 322 " --> pdb=" O ASP M 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'M' and resid 58 through 60 removed outlier: 4.027A pdb=" N GLY M 58 " --> pdb=" O VAL M 73 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N PHE M 71 " --> pdb=" O PHE M 60 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU M 78 " --> pdb=" O LEU M 85 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'M' and resid 90 through 98 removed outlier: 4.136A pdb=" N GLY M 108 " --> pdb=" O PRO M 93 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'M' and resid 130 through 136 removed outlier: 6.617A pdb=" N LEU M 143 " --> pdb=" O THR M 131 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N VAL M 133 " --> pdb=" O ILE M 141 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N ILE M 141 " --> pdb=" O VAL M 133 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N TYR M 135 " --> pdb=" O TYR M 139 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N TYR M 139 " --> pdb=" O TYR M 135 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ARG M 144 " --> pdb=" O GLN M 149 " (cutoff:3.500A) removed outlier: 5.666A pdb=" N GLN M 149 " --> pdb=" O ARG M 144 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'M' and resid 176 through 182 removed outlier: 6.583A pdb=" N PHE M 189 " --> pdb=" O LEU M 177 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE M 179 " --> pdb=" O VAL M 187 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N VAL M 187 " --> pdb=" O ILE M 179 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N VAL M 181 " --> pdb=" O ASN M 185 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ASN M 185 " --> pdb=" O VAL M 181 " (cutoff:3.500A) removed outlier: 11.267A pdb=" N VAL M 194 " --> pdb=" O ASN M 212 " (cutoff:3.500A) removed outlier: 9.027A pdb=" N ASN M 212 " --> pdb=" O VAL M 194 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N PHE M 196 " --> pdb=" O ILE M 210 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'M' and resid 225 through 228 removed outlier: 3.554A pdb=" N VAL M 249 " --> pdb=" O ARG M 243 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'M' and resid 267 through 272 removed outlier: 3.606A pdb=" N GLU M 296 " --> pdb=" O ASP M 291 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'M' and resid 337 through 343 Processing sheet with id=AF1, first strand: chain 'N' and resid 4 through 5 removed outlier: 4.223A pdb=" N ALA N 4 " --> pdb=" O GLY N 342 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY N 342 " --> pdb=" O ALA N 4 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'N' and resid 25 through 29 removed outlier: 11.502A pdb=" N VAL N 37 " --> pdb=" O ALA N 434 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ALA N 434 " --> pdb=" O VAL N 37 " (cutoff:3.500A) removed outlier: 4.550A pdb=" N ARG N 350 " --> pdb=" O GLY N 411 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY N 411 " --> pdb=" O ARG N 350 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN N 352 " --> pdb=" O ALA N 409 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'N' and resid 45 through 50 removed outlier: 5.569A pdb=" N GLU N 47 " --> pdb=" O ARG N 324 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N ARG N 324 " --> pdb=" O GLU N 47 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ALA N 49 " --> pdb=" O ILE N 322 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'N' and resid 58 through 60 removed outlier: 3.932A pdb=" N GLY N 58 " --> pdb=" O VAL N 73 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU N 78 " --> pdb=" O LEU N 85 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'N' and resid 95 through 99 Processing sheet with id=AF6, first strand: chain 'N' and resid 130 through 136 removed outlier: 6.688A pdb=" N LEU N 143 " --> pdb=" O THR N 131 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N VAL N 133 " --> pdb=" O ILE N 141 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N ILE N 141 " --> pdb=" O VAL N 133 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N TYR N 135 " --> pdb=" O TYR N 139 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N TYR N 139 " --> pdb=" O TYR N 135 " (cutoff:3.500A) removed outlier: 5.009A pdb=" N GLN N 149 " --> pdb=" O ARG N 144 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'N' and resid 176 through 182 removed outlier: 11.112A pdb=" N VAL N 194 " --> pdb=" O ASN N 212 " (cutoff:3.500A) removed outlier: 8.798A pdb=" N ASN N 212 " --> pdb=" O VAL N 194 " (cutoff:3.500A) removed outlier: 4.945A pdb=" N PHE N 196 " --> pdb=" O ILE N 210 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'N' and resid 225 through 228 Processing sheet with id=AF9, first strand: chain 'N' and resid 267 through 272 removed outlier: 3.699A pdb=" N GLU N 296 " --> pdb=" O ASP N 291 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'O' and resid 4 through 5 removed outlier: 4.080A pdb=" N ALA O 4 " --> pdb=" O GLY O 342 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N GLY O 342 " --> pdb=" O ALA O 4 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'O' and resid 25 through 29 removed outlier: 11.494A pdb=" N VAL O 37 " --> pdb=" O ALA O 434 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ALA O 434 " --> pdb=" O VAL O 37 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'O' and resid 45 through 50 removed outlier: 6.713A pdb=" N ILE O 322 " --> pdb=" O ASP O 48 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'O' and resid 58 through 60 removed outlier: 3.829A pdb=" N GLY O 58 " --> pdb=" O VAL O 73 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N LEU O 78 " --> pdb=" O LEU O 85 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'O' and resid 95 through 99 removed outlier: 3.513A pdb=" N GLU O 102 " --> pdb=" O ILE O 99 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N ILE O 111 " --> pdb=" O VAL O 122 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'O' and resid 130 through 136 removed outlier: 4.100A pdb=" N LYS O 132 " --> pdb=" O LEU O 143 " (cutoff:3.500A) removed outlier: 5.077A pdb=" N GLN O 149 " --> pdb=" O ARG O 144 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'O' and resid 176 through 182 removed outlier: 6.744A pdb=" N PHE O 189 " --> pdb=" O LEU O 177 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE O 179 " --> pdb=" O VAL O 187 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N VAL O 187 " --> pdb=" O ILE O 179 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N VAL O 181 " --> pdb=" O ASN O 185 " (cutoff:3.500A) removed outlier: 5.643A pdb=" N ASN O 185 " --> pdb=" O VAL O 181 " (cutoff:3.500A) removed outlier: 11.317A pdb=" N VAL O 194 " --> pdb=" O ASN O 212 " (cutoff:3.500A) removed outlier: 9.059A pdb=" N ASN O 212 " --> pdb=" O VAL O 194 " (cutoff:3.500A) removed outlier: 5.310A pdb=" N PHE O 196 " --> pdb=" O ILE O 210 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'O' and resid 225 through 227 Processing sheet with id=AG9, first strand: chain 'O' and resid 267 through 272 removed outlier: 3.673A pdb=" N GLU O 296 " --> pdb=" O ASP O 291 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'O' and resid 349 through 350 Processing sheet with id=AH2, first strand: chain 'P' and resid 4 through 5 removed outlier: 4.240A pdb=" N ALA P 4 " --> pdb=" O GLY P 342 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY P 342 " --> pdb=" O ALA P 4 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'P' and resid 25 through 29 removed outlier: 11.426A pdb=" N VAL P 37 " --> pdb=" O ALA P 434 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA P 434 " --> pdb=" O VAL P 37 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'P' and resid 45 through 50 removed outlier: 5.513A pdb=" N GLU P 47 " --> pdb=" O ARG P 324 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N ARG P 324 " --> pdb=" O GLU P 47 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ALA P 49 " --> pdb=" O ILE P 322 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'P' and resid 56 through 60 removed outlier: 4.194A pdb=" N GLY P 58 " --> pdb=" O VAL P 73 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU P 78 " --> pdb=" O LEU P 85 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'P' and resid 95 through 98 Processing sheet with id=AH7, first strand: chain 'P' and resid 130 through 136 removed outlier: 6.934A pdb=" N LEU P 143 " --> pdb=" O THR P 131 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL P 133 " --> pdb=" O ILE P 141 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N ILE P 141 " --> pdb=" O VAL P 133 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N TYR P 135 " --> pdb=" O TYR P 139 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N TYR P 139 " --> pdb=" O TYR P 135 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N PHE P 140 " --> pdb=" O SER P 153 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ARG P 144 " --> pdb=" O GLN P 149 " (cutoff:3.500A) removed outlier: 5.615A pdb=" N GLN P 149 " --> pdb=" O ARG P 144 " (cutoff:3.500A) removed outlier: 5.687A pdb=" N ASP P 165 " --> pdb=" O PHE P 152 " (cutoff:3.500A) removed outlier: 11.652A pdb=" N ALA P 154 " --> pdb=" O GLY P 163 " (cutoff:3.500A) removed outlier: 12.412A pdb=" N GLY P 163 " --> pdb=" O ALA P 154 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'P' and resid 176 through 182 removed outlier: 11.058A pdb=" N VAL P 194 " --> pdb=" O ASN P 212 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N ASN P 212 " --> pdb=" O VAL P 194 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N PHE P 196 " --> pdb=" O ILE P 210 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'P' and resid 225 through 228 Processing sheet with id=AI1, first strand: chain 'P' and resid 267 through 273 Processing sheet with id=AI2, first strand: chain 'P' and resid 349 through 350 Processing sheet with id=AI3, first strand: chain 'Q' and resid 4 through 5 removed outlier: 4.047A pdb=" N ALA Q 4 " --> pdb=" O GLY Q 342 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY Q 342 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'Q' and resid 25 through 29 removed outlier: 11.596A pdb=" N VAL Q 37 " --> pdb=" O ALA Q 434 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N ALA Q 434 " --> pdb=" O VAL Q 37 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE Q 357 " --> pdb=" O THR Q 433 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N VAL Q 435 " --> pdb=" O ARG Q 355 " (cutoff:3.500A) removed outlier: 6.572A pdb=" N ARG Q 355 " --> pdb=" O VAL Q 435 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N VAL Q 437 " --> pdb=" O ARG Q 353 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ARG Q 353 " --> pdb=" O VAL Q 437 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ARG Q 350 " --> pdb=" O GLY Q 411 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLY Q 411 " --> pdb=" O ARG Q 350 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N ASN Q 352 " --> pdb=" O ALA Q 409 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Q' and resid 45 through 50 removed outlier: 6.860A pdb=" N ILE Q 322 " --> pdb=" O ASP Q 48 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Q' and resid 56 through 60 removed outlier: 4.256A pdb=" N GLY Q 58 " --> pdb=" O VAL Q 73 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU Q 78 " --> pdb=" O LEU Q 85 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Q' and resid 95 through 98 removed outlier: 4.796A pdb=" N ILE Q 111 " --> pdb=" O VAL Q 122 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'Q' and resid 130 through 136 removed outlier: 6.579A pdb=" N LEU Q 143 " --> pdb=" O THR Q 131 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N VAL Q 133 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE Q 141 " --> pdb=" O VAL Q 133 " (cutoff:3.500A) removed outlier: 4.554A pdb=" N TYR Q 135 " --> pdb=" O TYR Q 139 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N TYR Q 139 " --> pdb=" O TYR Q 135 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N PHE Q 140 " --> pdb=" O SER Q 153 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG Q 144 " --> pdb=" O GLN Q 149 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N GLN Q 149 " --> pdb=" O ARG Q 144 " (cutoff:3.500A) removed outlier: 5.493A pdb=" N ASP Q 165 " --> pdb=" O PHE Q 152 " (cutoff:3.500A) removed outlier: 11.729A pdb=" N ALA Q 154 " --> pdb=" O GLY Q 163 " (cutoff:3.500A) removed outlier: 12.264A pdb=" N GLY Q 163 " --> pdb=" O ALA Q 154 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'Q' and resid 176 through 182 removed outlier: 6.637A pdb=" N PHE Q 189 " --> pdb=" O LEU Q 177 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N ILE Q 179 " --> pdb=" O VAL Q 187 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N VAL Q 187 " --> pdb=" O ILE Q 179 " (cutoff:3.500A) removed outlier: 4.462A pdb=" N VAL Q 181 " --> pdb=" O ASN Q 185 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ASN Q 185 " --> pdb=" O VAL Q 181 " (cutoff:3.500A) removed outlier: 11.284A pdb=" N VAL Q 194 " --> pdb=" O ASN Q 212 " (cutoff:3.500A) removed outlier: 8.979A pdb=" N ASN Q 212 " --> pdb=" O VAL Q 194 " (cutoff:3.500A) removed outlier: 5.294A pdb=" N PHE Q 196 " --> pdb=" O ILE Q 210 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'Q' and resid 225 through 228 removed outlier: 3.596A pdb=" N VAL Q 249 " --> pdb=" O ARG Q 243 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'Q' and resid 267 through 272 Processing sheet with id=AJ3, first strand: chain 'R' and resid 4 through 5 removed outlier: 4.197A pdb=" N ALA R 4 " --> pdb=" O GLY R 342 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY R 342 " --> pdb=" O ALA R 4 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'R' and resid 25 through 29 removed outlier: 11.551A pdb=" N VAL R 37 " --> pdb=" O ALA R 434 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N ALA R 434 " --> pdb=" O VAL R 37 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'R' and resid 45 through 52 removed outlier: 6.862A pdb=" N ILE R 322 " --> pdb=" O ASP R 48 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N GLU R 50 " --> pdb=" O GLY R 320 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N GLY R 320 " --> pdb=" O GLU R 50 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'R' and resid 58 through 61 removed outlier: 3.677A pdb=" N GLY R 58 " --> pdb=" O VAL R 73 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N GLU R 77 " --> pdb=" O SER R 74 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU R 78 " --> pdb=" O LEU R 85 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'R' and resid 95 through 98 Processing sheet with id=AJ8, first strand: chain 'R' and resid 130 through 136 removed outlier: 4.030A pdb=" N LYS R 132 " --> pdb=" O LEU R 143 " (cutoff:3.500A) removed outlier: 5.053A pdb=" N GLN R 149 " --> pdb=" O ARG R 144 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'R' and resid 176 through 182 removed outlier: 6.695A pdb=" N PHE R 189 " --> pdb=" O LEU R 177 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ILE R 179 " --> pdb=" O VAL R 187 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL R 187 " --> pdb=" O ILE R 179 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N VAL R 181 " --> pdb=" O ASN R 185 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N ASN R 185 " --> pdb=" O VAL R 181 " (cutoff:3.500A) removed outlier: 11.047A pdb=" N VAL R 194 " --> pdb=" O ASN R 212 " (cutoff:3.500A) removed outlier: 8.790A pdb=" N ASN R 212 " --> pdb=" O VAL R 194 " (cutoff:3.500A) removed outlier: 4.972A pdb=" N PHE R 196 " --> pdb=" O ILE R 210 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'R' and resid 225 through 228 Processing sheet with id=AK2, first strand: chain 'R' and resid 267 through 272 Processing sheet with id=AK3, first strand: chain 'R' and resid 349 through 350 Processing sheet with id=AK4, first strand: chain 'm' and resid 3 through 5 Processing sheet with id=AK5, first strand: chain 'm' and resid 53 through 54 removed outlier: 7.115A pdb=" N TYR m 72 " --> pdb=" O PRO m 89 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ALA m 85 " --> pdb=" O ILE m 76 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'm' and resid 39 through 40 removed outlier: 4.551A pdb=" N VAL m 39 " --> pdb=" O LEU m 49 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'm' and resid 65 through 67 Processing sheet with id=AK8, first strand: chain 'n' and resid 4 through 5 Processing sheet with id=AK9, first strand: chain 'n' and resid 25 through 30 removed outlier: 4.014A pdb=" N ALA n 85 " --> pdb=" O ILE n 76 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'n' and resid 39 through 40 removed outlier: 4.729A pdb=" N VAL n 39 " --> pdb=" O LEU n 49 " (cutoff:3.500A) Processing sheet with id=AL2, first strand: chain 'o' and resid 53 through 54 removed outlier: 3.590A pdb=" N ALA o 85 " --> pdb=" O ILE o 76 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'o' and resid 39 through 40 removed outlier: 4.254A pdb=" N VAL o 39 " --> pdb=" O LEU o 49 " (cutoff:3.500A) 1662 hydrogen bonds defined for protein. 4506 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: 8.20 Time building geometry restraints manager: 4.36 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: 13803 1.34 - 1.46: 7166 1.46 - 1.58: 20973 1.58 - 1.70: 0 1.70 - 1.82: 273 Bond restraints: 42215 Sorted by residual: bond pdb=" N ASP n 88 " pdb=" CA ASP n 88 " ideal model delta sigma weight residual 1.463 1.490 -0.027 6.90e-03 2.10e+04 1.49e+01 bond pdb=" N GLY Q 368 " pdb=" CA GLY Q 368 " ideal model delta sigma weight residual 1.444 1.479 -0.035 9.30e-03 1.16e+04 1.44e+01 bond pdb=" C ARG M 337 " pdb=" N ARG M 338 " ideal model delta sigma weight residual 1.331 1.388 -0.057 1.51e-02 4.39e+03 1.42e+01 bond pdb=" CA SER O 41 " pdb=" CB SER O 41 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.66e-02 3.63e+03 1.42e+01 bond pdb=" N PRO M 93 " pdb=" CD PRO M 93 " ideal model delta sigma weight residual 1.473 1.520 -0.047 1.40e-02 5.10e+03 1.12e+01 ... (remaining 42210 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.12: 56319 2.12 - 4.23: 945 4.23 - 6.35: 127 6.35 - 8.46: 30 8.46 - 10.58: 5 Bond angle restraints: 57426 Sorted by residual: angle pdb=" N SER Q 329 " pdb=" CA SER Q 329 " pdb=" C SER Q 329 " ideal model delta sigma weight residual 107.69 97.74 9.95 2.01e+00 2.48e-01 2.45e+01 angle pdb=" C ASP M 75 " pdb=" CA ASP M 75 " pdb=" CB ASP M 75 " ideal model delta sigma weight residual 110.06 116.87 -6.81 1.39e+00 5.18e-01 2.40e+01 angle pdb=" N ASP M 75 " pdb=" CA ASP M 75 " pdb=" C ASP M 75 " ideal model delta sigma weight residual 110.30 103.03 7.27 1.50e+00 4.44e-01 2.35e+01 angle pdb=" N SER R 445 " pdb=" CA SER R 445 " pdb=" C SER R 445 " ideal model delta sigma weight residual 111.30 117.88 -6.58 1.36e+00 5.41e-01 2.34e+01 angle pdb=" N VAL P 351 " pdb=" CA VAL P 351 " pdb=" C VAL P 351 " ideal model delta sigma weight residual 106.85 113.56 -6.71 1.42e+00 4.96e-01 2.23e+01 ... (remaining 57421 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 21413 17.96 - 35.92: 2459 35.92 - 53.88: 614 53.88 - 71.85: 99 71.85 - 89.81: 49 Dihedral angle restraints: 24634 sinusoidal: 9391 harmonic: 15243 Sorted by residual: dihedral pdb=" N SER O 41 " pdb=" C SER O 41 " pdb=" CA SER O 41 " pdb=" CB SER O 41 " ideal model delta harmonic sigma weight residual 122.80 110.72 12.08 0 2.50e+00 1.60e-01 2.34e+01 dihedral pdb=" CA GLY Q 90 " pdb=" C GLY Q 90 " pdb=" N THR Q 91 " pdb=" CA THR Q 91 " ideal model delta harmonic sigma weight residual -180.00 -157.88 -22.12 0 5.00e+00 4.00e-02 1.96e+01 dihedral pdb=" C SER O 41 " pdb=" N SER O 41 " pdb=" CA SER O 41 " pdb=" CB SER O 41 " ideal model delta harmonic sigma weight residual -122.60 -111.79 -10.81 0 2.50e+00 1.60e-01 1.87e+01 ... (remaining 24631 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 5463 0.061 - 0.123: 816 0.123 - 0.184: 82 0.184 - 0.245: 10 0.245 - 0.307: 3 Chirality restraints: 6374 Sorted by residual: chirality pdb=" CA TYR Q 328 " pdb=" N TYR Q 328 " pdb=" C TYR Q 328 " pdb=" CB TYR Q 328 " both_signs ideal model delta sigma weight residual False 2.51 2.82 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ARG R 446 " pdb=" N ARG R 446 " pdb=" C ARG R 446 " pdb=" CB ARG R 446 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 2.02e+00 chirality pdb=" CA SER R 74 " pdb=" N SER R 74 " pdb=" C SER R 74 " pdb=" CB SER R 74 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 6371 not shown) Planarity restraints: 7613 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY M 92 " -0.072 5.00e-02 4.00e+02 1.07e-01 1.84e+01 pdb=" N PRO M 93 " 0.186 5.00e-02 4.00e+02 pdb=" CA PRO M 93 " -0.058 5.00e-02 4.00e+02 pdb=" CD PRO M 93 " -0.056 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA S 55 " -0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C ALA S 55 " 0.071 2.00e-02 2.50e+03 pdb=" O ALA S 55 " -0.027 2.00e-02 2.50e+03 pdb=" N LEU S 56 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL M 73 " 0.016 2.00e-02 2.50e+03 3.18e-02 1.01e+01 pdb=" C VAL M 73 " -0.055 2.00e-02 2.50e+03 pdb=" O VAL M 73 " 0.021 2.00e-02 2.50e+03 pdb=" N SER M 74 " 0.019 2.00e-02 2.50e+03 ... (remaining 7610 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 390 2.53 - 3.12: 30230 3.12 - 3.71: 63529 3.71 - 4.31: 92069 4.31 - 4.90: 157784 Nonbonded interactions: 344002 Sorted by model distance: nonbonded pdb=" O ASN R 244 " pdb=" OD1 ASP R 245 " model vdw 1.937 3.040 nonbonded pdb=" OD1 ASP m 78 " pdb=" N ALA m 79 " model vdw 2.176 3.120 nonbonded pdb=" OG SER O 153 " pdb=" O ASP O 157 " model vdw 2.195 3.040 nonbonded pdb=" OG1 THR P 287 " pdb=" OD1 ASN P 307 " model vdw 2.206 3.040 nonbonded pdb=" OE2 GLU P 102 " pdb=" OG SER P 113 " model vdw 2.206 3.040 ... (remaining 343997 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 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' selection = chain 'U' } ncs_group { reference = (chain 'm' and resid 2 through 127) selection = (chain 'n' and resid 2 through 127) selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.330 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 35.030 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.110 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: 0.000 Load rotamer database and sin/cos tables:1.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 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 : 0.003 0.062 42215 Z= 0.177 Angle : 0.630 10.580 57426 Z= 0.352 Chirality : 0.045 0.307 6374 Planarity : 0.005 0.118 7613 Dihedral : 16.356 89.807 14984 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 11.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.90 % Allowed : 27.73 % Favored : 70.37 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.12), residues: 5392 helix: 2.86 (0.17), residues: 1034 sheet: 0.68 (0.15), residues: 1057 loop : -0.28 (0.11), residues: 3301 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG K 5 TYR 0.030 0.001 TYR O 328 PHE 0.009 0.001 PHE N 71 TRP 0.020 0.001 TRP N 323 HIS 0.002 0.000 HIS R 422 Details of bonding type rmsd covalent geometry : bond 0.00315 (42215) covalent geometry : angle 0.63048 (57426) hydrogen bonds : bond 0.11288 ( 1662) hydrogen bonds : angle 4.63228 ( 4506) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1344 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1263 time to evaluate : 1.540 Fit side-chains revert: symmetry clash REVERT: A 127 ASP cc_start: 0.8625 (m-30) cc_final: 0.8327 (m-30) REVERT: E 127 ASP cc_start: 0.8765 (m-30) cc_final: 0.8561 (m-30) REVERT: E 158 MET cc_start: 0.8853 (mmm) cc_final: 0.8285 (mmm) REVERT: J 127 ASP cc_start: 0.8653 (m-30) cc_final: 0.8322 (m-30) REVERT: M 258 GLU cc_start: 0.8109 (mt-10) cc_final: 0.7875 (mt-10) REVERT: N 243 ARG cc_start: 0.8706 (ttp80) cc_final: 0.8497 (ttp-170) REVERT: N 274 GLU cc_start: 0.8372 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: N 323 TRP cc_start: 0.7838 (m100) cc_final: 0.7313 (m100) REVERT: O 76 ASP cc_start: 0.7740 (m-30) cc_final: 0.7481 (p0) REVERT: Q 258 GLU cc_start: 0.8193 (tt0) cc_final: 0.7979 (mt-10) REVERT: Q 336 GLU cc_start: 0.8800 (tt0) cc_final: 0.8593 (tt0) REVERT: Q 410 LEU cc_start: 0.8922 (OUTLIER) cc_final: 0.8416 (mm) REVERT: R 299 GLU cc_start: 0.8747 (tt0) cc_final: 0.8538 (tt0) outliers start: 81 outliers final: 62 residues processed: 1319 average time/residue: 0.2483 time to fit residues: 530.9446 Evaluate side-chains 1260 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 1196 time to evaluate : 1.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 182 SER Chi-restraints excluded: chain B residue 137 MET Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 71 VAL Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain E residue 153 THR Chi-restraints excluded: chain E residue 171 SER Chi-restraints excluded: chain F residue 132 SER Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain I residue 6 ASP Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 53 THR Chi-restraints excluded: chain J residue 153 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain K residue 171 SER Chi-restraints excluded: chain K residue 182 SER Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 77 THR Chi-restraints excluded: chain M residue 53 THR Chi-restraints excluded: chain M residue 118 THR Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 344 THR Chi-restraints excluded: chain M residue 389 ILE Chi-restraints excluded: chain M residue 436 THR Chi-restraints excluded: chain N residue 95 SER Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain P residue 46 VAL Chi-restraints excluded: chain P residue 95 SER Chi-restraints excluded: chain P residue 174 ASP Chi-restraints excluded: chain P residue 192 GLN Chi-restraints excluded: chain P residue 228 ILE Chi-restraints excluded: chain P residue 263 SER Chi-restraints excluded: chain P residue 336 GLU Chi-restraints excluded: chain P residue 389 ILE Chi-restraints excluded: chain P residue 414 ASP Chi-restraints excluded: chain Q residue 53 THR Chi-restraints excluded: chain Q residue 95 SER Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 344 THR Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 95 SER Chi-restraints excluded: chain R residue 263 SER Chi-restraints excluded: chain R residue 336 GLU Chi-restraints excluded: chain R residue 412 LEU Chi-restraints excluded: chain R residue 446 ARG Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain m residue 74 CYS Chi-restraints excluded: chain m residue 93 SER Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain n residue 119 SER Chi-restraints excluded: chain o residue 101 GLU Chi-restraints excluded: chain o residue 121 THR Chi-restraints excluded: chain o residue 126 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 394 optimal weight: 0.9980 chunk 430 optimal weight: 6.9990 chunk 41 optimal weight: 6.9990 chunk 265 optimal weight: 4.9990 chunk 523 optimal weight: 5.9990 chunk 497 optimal weight: 5.9990 chunk 414 optimal weight: 9.9990 chunk 310 optimal weight: 4.9990 chunk 488 optimal weight: 6.9990 chunk 366 optimal weight: 6.9990 chunk 223 optimal weight: 2.9990 overall best weight: 3.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN B 106 ASN ** B 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 37 GLN E 37 GLN ** F 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 385 ASN P 211 GLN Q 16 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 365 ASN R 40 GLN R 192 GLN ** R 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** n 82 ASN ** o 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.087738 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2537 r_free = 0.2537 target = 0.071730 restraints weight = 71685.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2591 r_free = 0.2591 target = 0.074690 restraints weight = 32881.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.076611 restraints weight = 19450.296| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.077862 restraints weight = 13348.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.078695 restraints weight = 10078.332| |-----------------------------------------------------------------------------| r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.1469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.069 42215 Z= 0.369 Angle : 0.658 10.146 57426 Z= 0.339 Chirality : 0.047 0.189 6374 Planarity : 0.005 0.069 7613 Dihedral : 5.409 57.926 6027 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 4.48 % Allowed : 22.42 % Favored : 73.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.11), residues: 5392 helix: 2.45 (0.16), residues: 1046 sheet: 0.63 (0.16), residues: 918 loop : -0.38 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG J 134 TYR 0.020 0.002 TYR F 40 PHE 0.019 0.002 PHE I 49 TRP 0.014 0.002 TRP K 43 HIS 0.006 0.001 HIS R 276 Details of bonding type rmsd covalent geometry : bond 0.00855 (42215) covalent geometry : angle 0.65835 (57426) hydrogen bonds : bond 0.04339 ( 1662) hydrogen bonds : angle 4.30044 ( 4506) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1392 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 191 poor density : 1201 time to evaluate : 1.331 Fit side-chains REVERT: A 94 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.7659 (mmp-170) REVERT: A 124 THR cc_start: 0.8864 (m) cc_final: 0.8582 (p) REVERT: A 127 ASP cc_start: 0.8332 (m-30) cc_final: 0.7871 (m-30) REVERT: B 101 GLU cc_start: 0.7971 (tt0) cc_final: 0.7744 (tt0) REVERT: B 103 ASN cc_start: 0.8700 (t0) cc_final: 0.8265 (m-40) REVERT: B 135 ASP cc_start: 0.8391 (t0) cc_final: 0.8045 (t0) REVERT: C 165 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7972 (tt0) REVERT: D 186 TYR cc_start: 0.8251 (OUTLIER) cc_final: 0.7630 (m-80) REVERT: E 25 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.8518 (mmtp) REVERT: E 65 GLU cc_start: 0.9052 (OUTLIER) cc_final: 0.8851 (mt-10) REVERT: G 72 ASP cc_start: 0.7231 (p0) cc_final: 0.7022 (p0) REVERT: H 22 LYS cc_start: 0.8791 (OUTLIER) cc_final: 0.8122 (mttm) REVERT: I 96 LEU cc_start: 0.9326 (OUTLIER) cc_final: 0.9109 (mm) REVERT: J 10 ARG cc_start: 0.9005 (OUTLIER) cc_final: 0.7869 (mmp80) REVERT: J 83 GLU cc_start: 0.8181 (OUTLIER) cc_final: 0.7846 (tp30) REVERT: J 101 GLU cc_start: 0.7883 (tt0) cc_final: 0.7609 (tt0) REVERT: M 245 ASP cc_start: 0.8386 (t0) cc_final: 0.8175 (t0) REVERT: N 149 GLN cc_start: 0.8640 (OUTLIER) cc_final: 0.8064 (mm110) REVERT: N 274 GLU cc_start: 0.7875 (OUTLIER) cc_final: 0.7606 (pt0) REVERT: N 277 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.8835 (mmtm) REVERT: N 314 MET cc_start: 0.8663 (mmt) cc_final: 0.8199 (mmt) REVERT: N 406 GLU cc_start: 0.8039 (tt0) cc_final: 0.7833 (tt0) REVERT: N 440 GLU cc_start: 0.7423 (mt-10) cc_final: 0.7198 (mt-10) REVERT: O 149 GLN cc_start: 0.8517 (mt0) cc_final: 0.8294 (mt0) REVERT: P 403 GLN cc_start: 0.9160 (OUTLIER) cc_final: 0.7674 (tm-30) REVERT: Q 61 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.7757 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8358 (t0) cc_final: 0.8088 (t0) REVERT: Q 301 GLN cc_start: 0.9153 (mt0) cc_final: 0.8905 (mt0) REVERT: Q 372 ASP cc_start: 0.8707 (t0) cc_final: 0.8386 (t0) REVERT: R 102 GLU cc_start: 0.8318 (OUTLIER) cc_final: 0.8074 (tt0) REVERT: R 446 ARG cc_start: 0.8875 (ptp-110) cc_final: 0.8285 (ptp-110) REVERT: S 39 ASP cc_start: 0.7968 (t70) cc_final: 0.7590 (t0) REVERT: T 36 LEU cc_start: 0.8891 (OUTLIER) cc_final: 0.8593 (mm) REVERT: T 39 ASP cc_start: 0.7750 (t0) cc_final: 0.7502 (t0) REVERT: U 39 ASP cc_start: 0.7792 (t0) cc_final: 0.7236 (t0) REVERT: m 78 ASP cc_start: 0.8125 (t0) cc_final: 0.7812 (t0) REVERT: m 100 ASP cc_start: 0.8604 (p0) cc_final: 0.8403 (p0) REVERT: m 101 GLU cc_start: 0.8683 (mp0) cc_final: 0.8483 (mp0) REVERT: n 60 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8758 (mmmm) REVERT: n 107 ASP cc_start: 0.9194 (p0) cc_final: 0.8981 (p0) REVERT: o 37 GLN cc_start: 0.8807 (OUTLIER) cc_final: 0.7330 (mp10) REVERT: o 110 GLU cc_start: 0.8705 (tp30) cc_final: 0.8297 (tp30) REVERT: o 113 ARG cc_start: 0.8565 (tmm-80) cc_final: 0.8256 (tmm-80) outliers start: 191 outliers final: 117 residues processed: 1275 average time/residue: 0.2485 time to fit residues: 516.0392 Evaluate side-chains 1302 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 134 poor density : 1168 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 VAL Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 177 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 121 SER Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain D residue 186 TYR Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 65 GLU Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 147 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 118 GLN Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 64 LYS Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 153 THR Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 10 ARG Chi-restraints excluded: chain J residue 25 LYS Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 176 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 3 THR Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 118 GLN Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 389 ILE Chi-restraints excluded: chain M residue 391 GLU Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 149 GLN Chi-restraints excluded: chain N residue 230 ASN Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 310 CYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 410 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 171 SER Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 270 LEU Chi-restraints excluded: chain O residue 336 GLU Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain O residue 412 LEU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 228 ILE Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 326 GLU Chi-restraints excluded: chain P residue 403 GLN Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 77 GLU Chi-restraints excluded: chain Q residue 136 SER Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 270 LEU Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 292 ILE Chi-restraints excluded: chain Q residue 359 GLU Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 389 ILE Chi-restraints excluded: chain Q residue 410 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 40 GLN Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 375 ILE Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 23 THR Chi-restraints excluded: chain S residue 32 THR Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 33 VAL Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 23 THR Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain m residue 33 THR Chi-restraints excluded: chain m residue 105 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 87 SER Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 334 optimal weight: 0.8980 chunk 88 optimal weight: 3.9990 chunk 30 optimal weight: 0.0970 chunk 63 optimal weight: 0.9990 chunk 358 optimal weight: 0.8980 chunk 529 optimal weight: 1.9990 chunk 452 optimal weight: 6.9990 chunk 277 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 320 optimal weight: 0.0030 chunk 127 optimal weight: 1.9990 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 GLN B 30 GLN B 106 ASN B 118 GLN C 37 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 37 GLN F 37 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN H 118 GLN I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 385 ASN R 192 GLN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.092405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2619 r_free = 0.2619 target = 0.076432 restraints weight = 69994.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2675 r_free = 0.2675 target = 0.079485 restraints weight = 32029.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.081483 restraints weight = 18722.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.082765 restraints weight = 12740.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.083600 restraints weight = 9549.861| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 42215 Z= 0.103 Angle : 0.514 8.853 57426 Z= 0.269 Chirality : 0.042 0.150 6374 Planarity : 0.004 0.057 7613 Dihedral : 4.335 45.768 5953 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.36 % Allowed : 23.20 % Favored : 73.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.74 (0.12), residues: 5392 helix: 2.73 (0.16), residues: 1046 sheet: 0.61 (0.15), residues: 1008 loop : -0.26 (0.11), residues: 3338 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG n 113 TYR 0.016 0.001 TYR P 156 PHE 0.009 0.001 PHE Q 232 TRP 0.009 0.001 TRP L 117 HIS 0.001 0.000 HIS M 422 Details of bonding type rmsd covalent geometry : bond 0.00235 (42215) covalent geometry : angle 0.51353 (57426) hydrogen bonds : bond 0.03151 ( 1662) hydrogen bonds : angle 3.95742 ( 4506) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1383 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 1240 time to evaluate : 1.635 Fit side-chains revert: symmetry clash REVERT: A 94 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.7604 (mmp-170) REVERT: A 124 THR cc_start: 0.8910 (m) cc_final: 0.8403 (p) REVERT: A 127 ASP cc_start: 0.8338 (m-30) cc_final: 0.7821 (m-30) REVERT: B 103 ASN cc_start: 0.8610 (t0) cc_final: 0.8194 (m-40) REVERT: C 165 GLN cc_start: 0.8151 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: D 48 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8210 (tpp) REVERT: E 25 LYS cc_start: 0.8868 (OUTLIER) cc_final: 0.8597 (mmtp) REVERT: G 41 ASP cc_start: 0.8463 (m-30) cc_final: 0.8236 (m-30) REVERT: H 94 ARG cc_start: 0.8850 (OUTLIER) cc_final: 0.8373 (mmt90) REVERT: H 135 ASP cc_start: 0.8646 (t0) cc_final: 0.8403 (t0) REVERT: I 14 MET cc_start: 0.8837 (mmm) cc_final: 0.8530 (mmm) REVERT: I 137 MET cc_start: 0.9044 (mmm) cc_final: 0.8814 (mmp) REVERT: J 37 GLN cc_start: 0.8755 (tp40) cc_final: 0.8507 (tp-100) REVERT: M 156 TYR cc_start: 0.8488 (m-80) cc_final: 0.7914 (m-80) REVERT: M 245 ASP cc_start: 0.8274 (t0) cc_final: 0.8041 (t0) REVERT: M 336 GLU cc_start: 0.8329 (tt0) cc_final: 0.8093 (tt0) REVERT: N 274 GLU cc_start: 0.7782 (OUTLIER) cc_final: 0.7253 (pt0) REVERT: N 277 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.8783 (mmtm) REVERT: N 296 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7587 (mt-10) REVERT: N 314 MET cc_start: 0.8605 (mmt) cc_final: 0.8226 (mmt) REVERT: N 355 ARG cc_start: 0.8535 (mtt180) cc_final: 0.8278 (mtt180) REVERT: O 314 MET cc_start: 0.8798 (mmt) cc_final: 0.8508 (mmt) REVERT: O 377 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8349 (tmm) REVERT: Q 61 ARG cc_start: 0.8623 (OUTLIER) cc_final: 0.7656 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8334 (t0) cc_final: 0.8040 (t0) REVERT: Q 277 LYS cc_start: 0.9449 (OUTLIER) cc_final: 0.8860 (mmtm) REVERT: Q 301 GLN cc_start: 0.9122 (mt0) cc_final: 0.8915 (mt0) REVERT: Q 355 ARG cc_start: 0.8949 (mtm-85) cc_final: 0.8504 (mtt180) REVERT: R 102 GLU cc_start: 0.8319 (OUTLIER) cc_final: 0.8007 (tp30) REVERT: S 39 ASP cc_start: 0.8194 (t70) cc_final: 0.7475 (t0) REVERT: T 39 ASP cc_start: 0.7774 (t0) cc_final: 0.7304 (t0) REVERT: U 39 ASP cc_start: 0.7843 (t0) cc_final: 0.6987 (t0) REVERT: m 78 ASP cc_start: 0.8123 (t0) cc_final: 0.7870 (t0) REVERT: m 101 GLU cc_start: 0.8656 (mp0) cc_final: 0.8400 (mp0) REVERT: m 113 ARG cc_start: 0.8382 (tmm-80) cc_final: 0.8052 (tmm-80) REVERT: o 37 GLN cc_start: 0.8694 (OUTLIER) cc_final: 0.8244 (mt0) REVERT: o 110 GLU cc_start: 0.8745 (tp30) cc_final: 0.8078 (tp30) REVERT: o 113 ARG cc_start: 0.8515 (tmm-80) cc_final: 0.8262 (tmm-80) outliers start: 143 outliers final: 83 residues processed: 1293 average time/residue: 0.2433 time to fit residues: 511.8936 Evaluate side-chains 1292 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 1197 time to evaluate : 1.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 48 MET Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 118 GLN Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 273 ASP Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 441 LEU Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 336 GLU Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain O residue 377 MET Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 191 THR Chi-restraints excluded: chain P residue 228 ILE Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 277 LYS Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 362 THR Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 436 THR Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 30 GLN Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain n residue 25 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 80 ASP Chi-restraints excluded: chain n residue 94 ILE Chi-restraints excluded: chain n residue 96 ASP Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 77 optimal weight: 2.9990 chunk 166 optimal weight: 3.9990 chunk 358 optimal weight: 5.9990 chunk 138 optimal weight: 0.3980 chunk 341 optimal weight: 2.9990 chunk 194 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 136 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 133 optimal weight: 5.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN B 106 ASN C 37 GLN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 37 GLN D 118 GLN E 37 GLN F 37 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN ** P 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 385 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 GLN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.088526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2552 r_free = 0.2552 target = 0.072590 restraints weight = 70997.531| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2606 r_free = 0.2606 target = 0.075542 restraints weight = 32606.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2639 r_free = 0.2639 target = 0.077494 restraints weight = 19258.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2662 r_free = 0.2662 target = 0.078742 restraints weight = 13224.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.079584 restraints weight = 9991.165| |-----------------------------------------------------------------------------| r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 42215 Z= 0.273 Angle : 0.583 8.364 57426 Z= 0.300 Chirality : 0.045 0.194 6374 Planarity : 0.005 0.063 7613 Dihedral : 4.515 59.112 5943 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 4.23 % Allowed : 22.00 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.48 (0.11), residues: 5392 helix: 2.62 (0.16), residues: 1046 sheet: 0.26 (0.15), residues: 1038 loop : -0.41 (0.11), residues: 3308 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 431 TYR 0.017 0.002 TYR I 40 PHE 0.015 0.002 PHE I 49 TRP 0.008 0.001 TRP R 150 HIS 0.003 0.001 HIS N 276 Details of bonding type rmsd covalent geometry : bond 0.00637 (42215) covalent geometry : angle 0.58317 (57426) hydrogen bonds : bond 0.03834 ( 1662) hydrogen bonds : angle 4.10893 ( 4506) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1381 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 180 poor density : 1201 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 28 GLU cc_start: 0.8985 (mt-10) cc_final: 0.8783 (mt-10) REVERT: A 72 ASP cc_start: 0.8481 (t0) cc_final: 0.7958 (t0) REVERT: A 94 ARG cc_start: 0.9114 (OUTLIER) cc_final: 0.7701 (mmp-170) REVERT: A 124 THR cc_start: 0.8804 (m) cc_final: 0.8296 (p) REVERT: A 127 ASP cc_start: 0.8319 (m-30) cc_final: 0.7768 (m-30) REVERT: B 101 GLU cc_start: 0.7884 (tt0) cc_final: 0.7567 (tt0) REVERT: B 103 ASN cc_start: 0.8696 (t0) cc_final: 0.8279 (m-40) REVERT: B 135 ASP cc_start: 0.8481 (t0) cc_final: 0.8178 (t0) REVERT: C 165 GLN cc_start: 0.8234 (OUTLIER) cc_final: 0.7971 (tt0) REVERT: D 133 LYS cc_start: 0.9200 (OUTLIER) cc_final: 0.8998 (mtmm) REVERT: E 25 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8607 (mmtp) REVERT: E 37 GLN cc_start: 0.8723 (tp40) cc_final: 0.8462 (tp-100) REVERT: E 68 ARG cc_start: 0.8740 (OUTLIER) cc_final: 0.7890 (ttm170) REVERT: F 28 GLU cc_start: 0.8986 (mt-10) cc_final: 0.8784 (mt-10) REVERT: H 94 ARG cc_start: 0.8964 (OUTLIER) cc_final: 0.8424 (mmt90) REVERT: H 135 ASP cc_start: 0.8711 (t0) cc_final: 0.8435 (t0) REVERT: I 37 GLN cc_start: 0.8834 (tp40) cc_final: 0.8630 (tp-100) REVERT: J 37 GLN cc_start: 0.8864 (tp40) cc_final: 0.8479 (tp-100) REVERT: J 101 GLU cc_start: 0.7890 (tt0) cc_final: 0.7599 (tt0) REVERT: K 30 GLN cc_start: 0.8922 (OUTLIER) cc_final: 0.8227 (tm-30) REVERT: K 72 ASP cc_start: 0.8023 (t0) cc_final: 0.7818 (t0) REVERT: L 30 GLN cc_start: 0.9361 (tp40) cc_final: 0.9035 (tp40) REVERT: M 245 ASP cc_start: 0.8403 (t0) cc_final: 0.8143 (t0) REVERT: M 406 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8118 (tt0) REVERT: N 274 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7511 (pt0) REVERT: N 277 LYS cc_start: 0.9433 (OUTLIER) cc_final: 0.8777 (mmtm) REVERT: N 296 GLU cc_start: 0.8055 (mt-10) cc_final: 0.7636 (mt-10) REVERT: N 314 MET cc_start: 0.8672 (mmt) cc_final: 0.8292 (mmt) REVERT: O 61 ARG cc_start: 0.8623 (mmm-85) cc_final: 0.8423 (mmm-85) REVERT: O 149 GLN cc_start: 0.8455 (mt0) cc_final: 0.8211 (mt0) REVERT: O 314 MET cc_start: 0.8804 (mmt) cc_final: 0.8480 (mmt) REVERT: P 43 LYS cc_start: 0.9438 (OUTLIER) cc_final: 0.8748 (mmmt) REVERT: Q 12 ARG cc_start: 0.8246 (ttt180) cc_final: 0.7840 (ttt90) REVERT: Q 61 ARG cc_start: 0.8677 (OUTLIER) cc_final: 0.7855 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8428 (t0) cc_final: 0.8080 (t0) REVERT: Q 301 GLN cc_start: 0.9083 (mt0) cc_final: 0.8818 (mt0) REVERT: Q 350 ARG cc_start: 0.9189 (ttm-80) cc_final: 0.8734 (ttm-80) REVERT: Q 355 ARG cc_start: 0.8981 (mtm-85) cc_final: 0.8616 (mtt180) REVERT: Q 359 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7775 (tt0) REVERT: Q 393 GLU cc_start: 0.7428 (mm-30) cc_final: 0.7207 (mm-30) REVERT: Q 429 SER cc_start: 0.9329 (OUTLIER) cc_final: 0.9085 (t) REVERT: R 50 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7938 (tp30) REVERT: R 102 GLU cc_start: 0.8331 (OUTLIER) cc_final: 0.8044 (tt0) REVERT: R 217 GLN cc_start: 0.9315 (mp10) cc_final: 0.8965 (mp10) REVERT: R 385 ASN cc_start: 0.9097 (m-40) cc_final: 0.8824 (m110) REVERT: R 406 GLU cc_start: 0.8423 (tt0) cc_final: 0.8103 (tt0) REVERT: S 39 ASP cc_start: 0.8027 (t70) cc_final: 0.7156 (t0) REVERT: T 39 ASP cc_start: 0.7624 (t0) cc_final: 0.6805 (t0) REVERT: U 39 ASP cc_start: 0.7864 (t0) cc_final: 0.6582 (t0) REVERT: m 78 ASP cc_start: 0.8206 (t0) cc_final: 0.7966 (t0) REVERT: m 101 GLU cc_start: 0.8733 (mp0) cc_final: 0.8433 (mp0) REVERT: n 107 ASP cc_start: 0.9178 (p0) cc_final: 0.8939 (p0) REVERT: o 37 GLN cc_start: 0.8781 (OUTLIER) cc_final: 0.8199 (mt0) REVERT: o 75 TYR cc_start: 0.8868 (t80) cc_final: 0.7739 (t80) REVERT: o 93 SER cc_start: 0.9130 (OUTLIER) cc_final: 0.8777 (p) REVERT: o 110 GLU cc_start: 0.8716 (tp30) cc_final: 0.8006 (tp30) REVERT: o 113 ARG cc_start: 0.8537 (tmm-80) cc_final: 0.8307 (tmm-80) outliers start: 180 outliers final: 117 residues processed: 1273 average time/residue: 0.2446 time to fit residues: 506.8867 Evaluate side-chains 1325 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 1190 time to evaluate : 1.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 176 SER Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 133 LYS Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 118 GLN Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 25 LYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 176 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 55 VAL Chi-restraints excluded: chain K residue 96 LEU Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 132 LYS Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain M residue 410 LEU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 310 CYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 441 LEU Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 118 THR Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 336 GLU Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain O residue 436 THR Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 43 LYS Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 228 ILE Chi-restraints excluded: chain P residue 229 ASP Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 77 GLU Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 254 ASP Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 359 GLU Chi-restraints excluded: chain Q residue 389 ILE Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain Q residue 429 SER Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 50 GLU Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 179 ILE Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 23 THR Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain n residue 39 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 93 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 390 optimal weight: 1.9990 chunk 440 optimal weight: 5.9990 chunk 301 optimal weight: 0.0270 chunk 354 optimal weight: 5.9990 chunk 180 optimal weight: 0.8980 chunk 90 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 77 optimal weight: 2.9990 chunk 268 optimal weight: 4.9990 chunk 498 optimal weight: 2.9990 chunk 122 optimal weight: 5.9990 overall best weight: 1.3844 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 118 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 385 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 GLN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 30 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.090338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.074346 restraints weight = 70165.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2637 r_free = 0.2637 target = 0.077372 restraints weight = 32016.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2671 r_free = 0.2671 target = 0.079377 restraints weight = 18762.314| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.080620 restraints weight = 12822.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.081459 restraints weight = 9555.274| |-----------------------------------------------------------------------------| r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.1653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 42215 Z= 0.152 Angle : 0.529 11.009 57426 Z= 0.274 Chirality : 0.043 0.167 6374 Planarity : 0.004 0.059 7613 Dihedral : 4.346 47.366 5943 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.57 % Allowed : 22.66 % Favored : 73.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.55 (0.12), residues: 5392 helix: 2.72 (0.16), residues: 1046 sheet: 0.18 (0.14), residues: 1068 loop : -0.33 (0.11), residues: 3278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 431 TYR 0.019 0.001 TYR o 75 PHE 0.009 0.001 PHE J 166 TRP 0.007 0.001 TRP Q 390 HIS 0.002 0.000 HIS O 276 Details of bonding type rmsd covalent geometry : bond 0.00354 (42215) covalent geometry : angle 0.52915 (57426) hydrogen bonds : bond 0.03329 ( 1662) hydrogen bonds : angle 3.99570 ( 4506) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1357 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 152 poor density : 1205 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8913 (mt-10) REVERT: A 72 ASP cc_start: 0.8415 (t0) cc_final: 0.7876 (t0) REVERT: A 94 ARG cc_start: 0.9087 (OUTLIER) cc_final: 0.7682 (mmp-170) REVERT: A 118 GLN cc_start: 0.8802 (pt0) cc_final: 0.8495 (pt0) REVERT: A 124 THR cc_start: 0.8784 (m) cc_final: 0.8205 (p) REVERT: A 127 ASP cc_start: 0.8316 (m-30) cc_final: 0.7740 (m-30) REVERT: B 103 ASN cc_start: 0.8682 (t0) cc_final: 0.8267 (m-40) REVERT: C 165 GLN cc_start: 0.8191 (OUTLIER) cc_final: 0.7961 (tt0) REVERT: E 25 LYS cc_start: 0.8943 (OUTLIER) cc_final: 0.8595 (mmtp) REVERT: E 37 GLN cc_start: 0.8693 (tp40) cc_final: 0.8466 (tp-100) REVERT: E 68 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.7892 (ttm170) REVERT: H 22 LYS cc_start: 0.8808 (OUTLIER) cc_final: 0.8126 (mttm) REVERT: H 94 ARG cc_start: 0.8930 (OUTLIER) cc_final: 0.8406 (mmt90) REVERT: H 135 ASP cc_start: 0.8667 (t0) cc_final: 0.8361 (t0) REVERT: I 14 MET cc_start: 0.8854 (mmm) cc_final: 0.8567 (mmm) REVERT: J 101 GLU cc_start: 0.7907 (tt0) cc_final: 0.7609 (tt0) REVERT: K 30 GLN cc_start: 0.8873 (OUTLIER) cc_final: 0.8254 (tm-30) REVERT: K 72 ASP cc_start: 0.8028 (t0) cc_final: 0.7745 (t0) REVERT: M 228 ILE cc_start: 0.9278 (OUTLIER) cc_final: 0.9070 (pp) REVERT: M 245 ASP cc_start: 0.8318 (t0) cc_final: 0.8042 (t0) REVERT: N 274 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7502 (pt0) REVERT: N 277 LYS cc_start: 0.9405 (OUTLIER) cc_final: 0.8756 (mmtm) REVERT: N 296 GLU cc_start: 0.8010 (mm-30) cc_final: 0.7535 (mt-10) REVERT: N 314 MET cc_start: 0.8607 (mmt) cc_final: 0.8332 (mmt) REVERT: O 61 ARG cc_start: 0.8601 (mmm-85) cc_final: 0.8355 (mmm-85) REVERT: O 314 MET cc_start: 0.8775 (mmt) cc_final: 0.8443 (mmt) REVERT: Q 61 ARG cc_start: 0.8635 (OUTLIER) cc_final: 0.7830 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8434 (t0) cc_final: 0.8076 (t0) REVERT: Q 277 LYS cc_start: 0.9484 (OUTLIER) cc_final: 0.8750 (mmtm) REVERT: Q 301 GLN cc_start: 0.9036 (mt0) cc_final: 0.8795 (mt0) REVERT: Q 355 ARG cc_start: 0.8944 (mtm-85) cc_final: 0.8614 (mtt180) REVERT: Q 393 GLU cc_start: 0.7413 (mm-30) cc_final: 0.7201 (mm-30) REVERT: R 102 GLU cc_start: 0.8337 (OUTLIER) cc_final: 0.7995 (tp30) REVERT: R 385 ASN cc_start: 0.9064 (m-40) cc_final: 0.8691 (m110) REVERT: R 406 GLU cc_start: 0.8396 (tt0) cc_final: 0.8068 (tt0) REVERT: S 39 ASP cc_start: 0.8015 (t70) cc_final: 0.6911 (t0) REVERT: T 39 ASP cc_start: 0.7674 (t0) cc_final: 0.6828 (t0) REVERT: U 24 GLN cc_start: 0.9101 (tt0) cc_final: 0.8630 (tt0) REVERT: U 39 ASP cc_start: 0.7853 (t0) cc_final: 0.6443 (t0) REVERT: m 100 ASP cc_start: 0.8629 (p0) cc_final: 0.8350 (p0) REVERT: n 13 MET cc_start: 0.8620 (mmt) cc_final: 0.8206 (mmt) REVERT: n 107 ASP cc_start: 0.9181 (p0) cc_final: 0.8912 (p0) REVERT: o 37 GLN cc_start: 0.8753 (OUTLIER) cc_final: 0.8275 (mt0) REVERT: o 75 TYR cc_start: 0.8474 (t80) cc_final: 0.7999 (t80) REVERT: o 93 SER cc_start: 0.9132 (OUTLIER) cc_final: 0.8752 (p) outliers start: 152 outliers final: 108 residues processed: 1256 average time/residue: 0.2440 time to fit residues: 499.0147 Evaluate side-chains 1303 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1179 time to evaluate : 1.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 176 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 118 GLN Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 89 LEU Chi-restraints excluded: chain F residue 118 GLN Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 176 SER Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 25 LYS Chi-restraints excluded: chain J residue 89 LEU Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 176 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 55 VAL Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 165 GLN Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 228 ILE Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 292 ILE Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 271 LEU Chi-restraints excluded: chain N residue 274 GLU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 310 CYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain N residue 441 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 72 VAL Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 336 GLU Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 254 ASP Chi-restraints excluded: chain Q residue 277 LYS Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 12 ARG Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 102 GLU Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 243 ARG Chi-restraints excluded: chain R residue 247 VAL Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 50 LEU Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 36 LEU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain n residue 25 LYS Chi-restraints excluded: chain n residue 39 VAL Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 87 SER Chi-restraints excluded: chain n residue 96 ASP Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 93 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 375 optimal weight: 3.9990 chunk 250 optimal weight: 0.8980 chunk 119 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 chunk 133 optimal weight: 0.2980 chunk 334 optimal weight: 0.0570 chunk 130 optimal weight: 3.9990 chunk 158 optimal weight: 0.9990 chunk 527 optimal weight: 6.9990 chunk 108 optimal weight: 0.9990 chunk 307 optimal weight: 0.0970 overall best weight: 0.4696 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN D 37 GLN F 37 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 37 GLN I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 149 GLN O 301 GLN P 244 ASN P 385 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 GLN T 27 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.093921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2648 r_free = 0.2648 target = 0.078062 restraints weight = 69779.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.081087 restraints weight = 31799.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.083098 restraints weight = 18688.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.084342 restraints weight = 12691.188| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2773 r_free = 0.2773 target = 0.085184 restraints weight = 9522.783| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 42215 Z= 0.093 Angle : 0.501 8.133 57426 Z= 0.261 Chirality : 0.042 0.143 6374 Planarity : 0.004 0.055 7613 Dihedral : 4.011 37.003 5940 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.91 % Allowed : 23.29 % Favored : 73.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5392 helix: 2.89 (0.16), residues: 1046 sheet: 0.78 (0.16), residues: 918 loop : -0.23 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG n 113 TYR 0.017 0.001 TYR C 56 PHE 0.009 0.001 PHE M 232 TRP 0.008 0.001 TRP M 390 HIS 0.002 0.000 HIS M 422 Details of bonding type rmsd covalent geometry : bond 0.00214 (42215) covalent geometry : angle 0.50053 (57426) hydrogen bonds : bond 0.02884 ( 1662) hydrogen bonds : angle 3.82607 ( 4506) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1351 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 1227 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8397 (t0) cc_final: 0.7841 (t0) REVERT: A 118 GLN cc_start: 0.8775 (OUTLIER) cc_final: 0.8437 (pt0) REVERT: A 124 THR cc_start: 0.8731 (m) cc_final: 0.7983 (p) REVERT: A 127 ASP cc_start: 0.8381 (m-30) cc_final: 0.7766 (m-30) REVERT: B 101 GLU cc_start: 0.7808 (tt0) cc_final: 0.7469 (tt0) REVERT: B 103 ASN cc_start: 0.8660 (t0) cc_final: 0.8308 (m-40) REVERT: C 65 GLU cc_start: 0.8668 (mt-10) cc_final: 0.8374 (mt-10) REVERT: C 165 GLN cc_start: 0.8146 (OUTLIER) cc_final: 0.7935 (tt0) REVERT: E 37 GLN cc_start: 0.8585 (tp40) cc_final: 0.8378 (tp-100) REVERT: H 94 ARG cc_start: 0.8797 (OUTLIER) cc_final: 0.8349 (mmt90) REVERT: H 135 ASP cc_start: 0.8570 (t0) cc_final: 0.8172 (t0) REVERT: I 14 MET cc_start: 0.8849 (mmm) cc_final: 0.8551 (mmm) REVERT: J 72 ASP cc_start: 0.8068 (t0) cc_final: 0.7752 (t0) REVERT: J 101 GLU cc_start: 0.7874 (tt0) cc_final: 0.7582 (tt0) REVERT: K 72 ASP cc_start: 0.7983 (t0) cc_final: 0.7601 (t0) REVERT: M 245 ASP cc_start: 0.8293 (t0) cc_final: 0.8026 (t0) REVERT: M 336 GLU cc_start: 0.8343 (tt0) cc_final: 0.8083 (tt0) REVERT: N 274 GLU cc_start: 0.7764 (pt0) cc_final: 0.7528 (pt0) REVERT: N 277 LYS cc_start: 0.9377 (OUTLIER) cc_final: 0.8705 (mmtm) REVERT: N 296 GLU cc_start: 0.8009 (mm-30) cc_final: 0.7504 (mt-10) REVERT: N 381 ASP cc_start: 0.7846 (p0) cc_final: 0.7643 (p0) REVERT: N 445 SER cc_start: 0.9317 (t) cc_final: 0.9075 (t) REVERT: O 61 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8367 (mmm-85) REVERT: O 314 MET cc_start: 0.8714 (mmt) cc_final: 0.8269 (mmt) REVERT: Q 61 ARG cc_start: 0.8629 (OUTLIER) cc_final: 0.7670 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8452 (t0) cc_final: 0.8111 (t0) REVERT: Q 277 LYS cc_start: 0.9458 (OUTLIER) cc_final: 0.8504 (mmtm) REVERT: R 406 GLU cc_start: 0.8389 (tt0) cc_final: 0.8077 (tt0) REVERT: S 39 ASP cc_start: 0.7988 (t70) cc_final: 0.6792 (t0) REVERT: T 39 ASP cc_start: 0.7704 (t0) cc_final: 0.6807 (t0) REVERT: T 50 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8291 (mp) REVERT: U 39 ASP cc_start: 0.7855 (t0) cc_final: 0.6357 (t0) REVERT: m 78 ASP cc_start: 0.7885 (t0) cc_final: 0.7587 (t0) REVERT: m 100 ASP cc_start: 0.8620 (p0) cc_final: 0.8380 (p0) REVERT: m 101 GLU cc_start: 0.8720 (mp0) cc_final: 0.8495 (mp0) REVERT: n 77 GLU cc_start: 0.8041 (tp30) cc_final: 0.7838 (tp30) REVERT: n 107 ASP cc_start: 0.9154 (p0) cc_final: 0.8891 (p0) REVERT: o 37 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8320 (mt0) REVERT: o 93 SER cc_start: 0.9154 (OUTLIER) cc_final: 0.8950 (p) outliers start: 124 outliers final: 71 residues processed: 1269 average time/residue: 0.2399 time to fit residues: 495.9924 Evaluate side-chains 1275 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 1194 time to evaluate : 1.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 121 SER Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 118 GLN Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 228 ILE Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 301 GLN Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 77 GLU Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 277 LYS Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain n residue 25 LYS Chi-restraints excluded: chain n residue 42 SER Chi-restraints excluded: chain n residue 80 ASP Chi-restraints excluded: chain n residue 94 ILE Chi-restraints excluded: chain n residue 96 ASP Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 93 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 516 optimal weight: 0.0070 chunk 520 optimal weight: 0.6980 chunk 129 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 168 optimal weight: 5.9990 chunk 307 optimal weight: 3.9990 chunk 192 optimal weight: 5.9990 chunk 209 optimal weight: 0.6980 chunk 220 optimal weight: 0.2980 chunk 35 optimal weight: 0.8980 chunk 412 optimal weight: 1.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 37 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 37 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN P 385 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 GLN T 27 ASN ** T 30 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 = 0.2930 r_free = 0.2930 target = 0.093716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2645 r_free = 0.2645 target = 0.077833 restraints weight = 69559.992| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.080888 restraints weight = 31696.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2732 r_free = 0.2732 target = 0.082906 restraints weight = 18514.945| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.084117 restraints weight = 12562.001| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.084946 restraints weight = 9476.998| |-----------------------------------------------------------------------------| r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 42215 Z= 0.097 Angle : 0.502 7.847 57426 Z= 0.261 Chirality : 0.042 0.207 6374 Planarity : 0.004 0.055 7613 Dihedral : 3.885 38.377 5935 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.51 % Allowed : 23.74 % Favored : 73.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.12), residues: 5392 helix: 2.95 (0.16), residues: 1046 sheet: 0.82 (0.16), residues: 918 loop : -0.21 (0.11), residues: 3428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 7 TYR 0.017 0.001 TYR C 56 PHE 0.012 0.001 PHE O 300 TRP 0.008 0.001 TRP N 150 HIS 0.002 0.000 HIS R 422 Details of bonding type rmsd covalent geometry : bond 0.00224 (42215) covalent geometry : angle 0.50198 (57426) hydrogen bonds : bond 0.02859 ( 1662) hydrogen bonds : angle 3.76220 ( 4506) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1324 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1217 time to evaluate : 1.615 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 94 ARG cc_start: 0.8991 (OUTLIER) cc_final: 0.7559 (mmp-170) REVERT: A 124 THR cc_start: 0.8666 (m) cc_final: 0.7825 (p) REVERT: A 127 ASP cc_start: 0.8310 (m-30) cc_final: 0.7650 (m-30) REVERT: B 101 GLU cc_start: 0.7816 (tt0) cc_final: 0.7477 (tt0) REVERT: B 103 ASN cc_start: 0.8687 (t0) cc_final: 0.8295 (m-40) REVERT: C 65 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8405 (mt-10) REVERT: C 165 GLN cc_start: 0.8182 (OUTLIER) cc_final: 0.7937 (tt0) REVERT: E 37 GLN cc_start: 0.8574 (tp40) cc_final: 0.8358 (tp-100) REVERT: H 94 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.8318 (mmt90) REVERT: H 135 ASP cc_start: 0.8539 (t0) cc_final: 0.8134 (t0) REVERT: I 14 MET cc_start: 0.8850 (mmm) cc_final: 0.8577 (mmm) REVERT: I 158 MET cc_start: 0.8235 (mmm) cc_final: 0.8016 (mmm) REVERT: J 72 ASP cc_start: 0.8061 (t0) cc_final: 0.7737 (t0) REVERT: J 101 GLU cc_start: 0.7906 (tt0) cc_final: 0.7595 (tt0) REVERT: K 72 ASP cc_start: 0.7967 (t0) cc_final: 0.7542 (t0) REVERT: K 158 MET cc_start: 0.7831 (mmm) cc_final: 0.7493 (mmm) REVERT: M 245 ASP cc_start: 0.8254 (t0) cc_final: 0.7983 (t0) REVERT: N 277 LYS cc_start: 0.9388 (OUTLIER) cc_final: 0.8687 (mmtm) REVERT: N 296 GLU cc_start: 0.8048 (mm-30) cc_final: 0.7528 (mt-10) REVERT: N 381 ASP cc_start: 0.7872 (p0) cc_final: 0.7670 (p0) REVERT: O 61 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.8338 (mmm-85) REVERT: O 277 LYS cc_start: 0.9397 (mmtm) cc_final: 0.9117 (mmtm) REVERT: O 314 MET cc_start: 0.8693 (mmt) cc_final: 0.8252 (mmt) REVERT: Q 61 ARG cc_start: 0.8597 (OUTLIER) cc_final: 0.7712 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8462 (t0) cc_final: 0.8133 (t0) REVERT: R 406 GLU cc_start: 0.8403 (tt0) cc_final: 0.8082 (tt0) REVERT: R 446 ARG cc_start: 0.8463 (ptp-110) cc_final: 0.7905 (ptp-110) REVERT: S 39 ASP cc_start: 0.7914 (t70) cc_final: 0.6708 (t0) REVERT: T 20 ARG cc_start: 0.8897 (mpp80) cc_final: 0.8655 (mpp80) REVERT: T 39 ASP cc_start: 0.7694 (t0) cc_final: 0.6798 (t0) REVERT: T 50 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8326 (mp) REVERT: U 39 ASP cc_start: 0.7820 (t0) cc_final: 0.6396 (t0) REVERT: m 60 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8959 (tptm) REVERT: m 78 ASP cc_start: 0.7951 (t0) cc_final: 0.7671 (t0) REVERT: m 101 GLU cc_start: 0.8683 (mp0) cc_final: 0.8449 (mp0) REVERT: m 113 ARG cc_start: 0.8509 (tmm-80) cc_final: 0.7900 (tmm-80) REVERT: n 72 TYR cc_start: 0.9133 (m-80) cc_final: 0.8878 (m-80) REVERT: n 107 ASP cc_start: 0.9152 (p0) cc_final: 0.8896 (p0) REVERT: o 37 GLN cc_start: 0.8652 (OUTLIER) cc_final: 0.8307 (mt0) REVERT: o 93 SER cc_start: 0.9149 (OUTLIER) cc_final: 0.8808 (p) outliers start: 107 outliers final: 73 residues processed: 1253 average time/residue: 0.2403 time to fit residues: 492.5199 Evaluate side-chains 1268 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 1185 time to evaluate : 1.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain E residue 39 LEU Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 155 ILE Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 118 GLN Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 118 GLN Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 96 LEU Chi-restraints excluded: chain J residue 118 GLN Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 77 GLU Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 254 ASP Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 243 ARG Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 436 THR Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain m residue 60 LYS Chi-restraints excluded: chain n residue 25 LYS Chi-restraints excluded: chain n residue 80 ASP Chi-restraints excluded: chain n residue 94 ILE Chi-restraints excluded: chain n residue 96 ASP Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Chi-restraints excluded: chain o residue 93 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 514 optimal weight: 3.9990 chunk 491 optimal weight: 2.9990 chunk 360 optimal weight: 0.2980 chunk 96 optimal weight: 3.9990 chunk 363 optimal weight: 7.9990 chunk 390 optimal weight: 6.9990 chunk 393 optimal weight: 6.9990 chunk 437 optimal weight: 5.9990 chunk 464 optimal weight: 3.9990 chunk 76 optimal weight: 0.9980 chunk 231 optimal weight: 8.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 37 GLN ** F 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 126 ASN K 165 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN P 385 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 301 GLN R 192 GLN ** T 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.089328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2563 r_free = 0.2563 target = 0.073324 restraints weight = 70663.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.076278 restraints weight = 32350.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2650 r_free = 0.2650 target = 0.078231 restraints weight = 19121.077| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2673 r_free = 0.2673 target = 0.079493 restraints weight = 13075.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.080324 restraints weight = 9888.996| |-----------------------------------------------------------------------------| r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8622 moved from start: 0.1793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 42215 Z= 0.237 Angle : 0.576 8.298 57426 Z= 0.296 Chirality : 0.044 0.216 6374 Planarity : 0.005 0.086 7613 Dihedral : 4.239 40.067 5935 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 3.08 % Allowed : 23.43 % Favored : 73.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.76 (0.12), residues: 5392 helix: 2.79 (0.16), residues: 1046 sheet: 0.82 (0.17), residues: 828 loop : -0.27 (0.11), residues: 3518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 5 TYR 0.020 0.002 TYR D 40 PHE 0.012 0.001 PHE I 49 TRP 0.008 0.001 TRP Q 234 HIS 0.003 0.001 HIS O 276 Details of bonding type rmsd covalent geometry : bond 0.00553 (42215) covalent geometry : angle 0.57634 (57426) hydrogen bonds : bond 0.03616 ( 1662) hydrogen bonds : angle 4.00250 ( 4506) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1322 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 1191 time to evaluate : 1.735 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8359 (t0) cc_final: 0.7758 (t0) REVERT: A 94 ARG cc_start: 0.9055 (OUTLIER) cc_final: 0.7701 (mmp-170) REVERT: A 124 THR cc_start: 0.8734 (OUTLIER) cc_final: 0.8041 (p) REVERT: A 127 ASP cc_start: 0.8353 (m-30) cc_final: 0.7757 (m-30) REVERT: B 37 GLN cc_start: 0.8805 (tp40) cc_final: 0.8438 (tp-100) REVERT: B 101 GLU cc_start: 0.7926 (tt0) cc_final: 0.7585 (tt0) REVERT: B 103 ASN cc_start: 0.8739 (t0) cc_final: 0.8317 (m-40) REVERT: C 165 GLN cc_start: 0.8226 (OUTLIER) cc_final: 0.7988 (tt0) REVERT: E 25 LYS cc_start: 0.8917 (OUTLIER) cc_final: 0.8653 (mmtp) REVERT: E 37 GLN cc_start: 0.8704 (tp40) cc_final: 0.8415 (tp-100) REVERT: E 68 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8003 (ttm170) REVERT: E 94 ARG cc_start: 0.9005 (mmt180) cc_final: 0.8736 (mmt180) REVERT: H 22 LYS cc_start: 0.8844 (OUTLIER) cc_final: 0.8152 (mttm) REVERT: H 94 ARG cc_start: 0.8934 (OUTLIER) cc_final: 0.8367 (mmt90) REVERT: H 135 ASP cc_start: 0.8697 (t0) cc_final: 0.8383 (t0) REVERT: I 14 MET cc_start: 0.8890 (mmm) cc_final: 0.8590 (mmm) REVERT: I 72 ASP cc_start: 0.8491 (t0) cc_final: 0.7812 (t0) REVERT: J 72 ASP cc_start: 0.8097 (t0) cc_final: 0.7809 (t0) REVERT: J 101 GLU cc_start: 0.7946 (tt0) cc_final: 0.7648 (tt0) REVERT: K 72 ASP cc_start: 0.8059 (t0) cc_final: 0.7665 (t0) REVERT: M 245 ASP cc_start: 0.8395 (t0) cc_final: 0.8064 (t0) REVERT: N 277 LYS cc_start: 0.9423 (OUTLIER) cc_final: 0.8714 (mmtm) REVERT: N 296 GLU cc_start: 0.8055 (mm-30) cc_final: 0.7566 (mm-30) REVERT: N 381 ASP cc_start: 0.8090 (p0) cc_final: 0.7803 (p0) REVERT: O 61 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8411 (mmm-85) REVERT: O 314 MET cc_start: 0.8797 (mmt) cc_final: 0.8463 (mmt) REVERT: O 318 GLU cc_start: 0.7942 (tm-30) cc_final: 0.7682 (tm-30) REVERT: P 168 THR cc_start: 0.8814 (OUTLIER) cc_final: 0.8597 (p) REVERT: P 403 GLN cc_start: 0.9144 (OUTLIER) cc_final: 0.7504 (tm-30) REVERT: Q 61 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.7831 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8440 (t0) cc_final: 0.8115 (t0) REVERT: R 217 GLN cc_start: 0.9305 (mp10) cc_final: 0.9027 (mp10) REVERT: R 406 GLU cc_start: 0.8473 (tt0) cc_final: 0.8150 (tt0) REVERT: S 39 ASP cc_start: 0.7925 (t70) cc_final: 0.6650 (t0) REVERT: T 39 ASP cc_start: 0.7521 (t0) cc_final: 0.6823 (t0) REVERT: T 50 LEU cc_start: 0.8833 (OUTLIER) cc_final: 0.8310 (mp) REVERT: U 39 ASP cc_start: 0.7745 (t0) cc_final: 0.6477 (t0) REVERT: m 60 LYS cc_start: 0.9176 (OUTLIER) cc_final: 0.8882 (tptm) REVERT: m 78 ASP cc_start: 0.8027 (t0) cc_final: 0.7699 (t0) REVERT: m 101 GLU cc_start: 0.8778 (mp0) cc_final: 0.8510 (mp0) REVERT: m 110 GLU cc_start: 0.8588 (tp30) cc_final: 0.8224 (tp30) REVERT: m 113 ARG cc_start: 0.8471 (tmm-80) cc_final: 0.8137 (tmm-80) REVERT: n 77 GLU cc_start: 0.8093 (tp30) cc_final: 0.7889 (tp30) REVERT: n 107 ASP cc_start: 0.9155 (p0) cc_final: 0.8890 (p0) REVERT: o 37 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8273 (mt0) REVERT: o 110 GLU cc_start: 0.8609 (tp30) cc_final: 0.7964 (tp30) REVERT: o 113 ARG cc_start: 0.8532 (tmm-80) cc_final: 0.8197 (tmm-80) outliers start: 131 outliers final: 89 residues processed: 1242 average time/residue: 0.2639 time to fit residues: 534.7656 Evaluate side-chains 1283 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 1179 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 124 THR Chi-restraints excluded: chain C residue 153 THR Chi-restraints excluded: chain C residue 155 ILE Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 68 ARG Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 153 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 22 LYS Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain H residue 180 ASP Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 169 SER Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 310 CYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain N residue 345 LEU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 61 ARG Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 192 GLN Chi-restraints excluded: chain P residue 403 GLN Chi-restraints excluded: chain Q residue 27 VAL Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 254 ASP Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 424 MET Chi-restraints excluded: chain R residue 436 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 32 THR Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain m residue 60 LYS Chi-restraints excluded: chain n residue 87 SER Chi-restraints excluded: chain n residue 94 ILE Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 302 optimal weight: 0.7980 chunk 515 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 38 optimal weight: 0.5980 chunk 91 optimal weight: 1.9990 chunk 451 optimal weight: 8.9990 chunk 150 optimal weight: 3.9990 chunk 393 optimal weight: 5.9990 chunk 218 optimal weight: 0.8980 chunk 174 optimal weight: 0.6980 chunk 517 optimal weight: 6.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 GLN B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 37 GLN H 118 GLN I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN P 385 ASN R 192 GLN T 27 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.091593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2605 r_free = 0.2605 target = 0.075611 restraints weight = 69918.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2658 r_free = 0.2658 target = 0.078594 restraints weight = 31899.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.080598 restraints weight = 18799.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2715 r_free = 0.2715 target = 0.081870 restraints weight = 12824.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2730 r_free = 0.2730 target = 0.082674 restraints weight = 9625.382| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 42215 Z= 0.125 Angle : 0.534 8.396 57426 Z= 0.276 Chirality : 0.043 0.169 6374 Planarity : 0.004 0.059 7613 Dihedral : 4.096 40.168 5935 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.51 % Allowed : 24.28 % Favored : 73.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.12), residues: 5392 helix: 2.86 (0.16), residues: 1046 sheet: 0.71 (0.17), residues: 858 loop : -0.22 (0.11), residues: 3488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG U 7 TYR 0.019 0.001 TYR K 56 PHE 0.011 0.001 PHE P 232 TRP 0.008 0.001 TRP N 150 HIS 0.002 0.000 HIS O 276 Details of bonding type rmsd covalent geometry : bond 0.00293 (42215) covalent geometry : angle 0.53359 (57426) hydrogen bonds : bond 0.03121 ( 1662) hydrogen bonds : angle 3.89950 ( 4506) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1297 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 1190 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8263 (t0) cc_final: 0.7849 (t0) REVERT: A 94 ARG cc_start: 0.9028 (OUTLIER) cc_final: 0.7615 (mmp-170) REVERT: A 124 THR cc_start: 0.8689 (OUTLIER) cc_final: 0.7899 (p) REVERT: A 127 ASP cc_start: 0.8331 (m-30) cc_final: 0.7707 (m-30) REVERT: B 103 ASN cc_start: 0.8745 (t0) cc_final: 0.8333 (m-40) REVERT: C 65 GLU cc_start: 0.8766 (mt-10) cc_final: 0.8524 (mt-10) REVERT: C 165 GLN cc_start: 0.8170 (OUTLIER) cc_final: 0.7933 (tt0) REVERT: E 25 LYS cc_start: 0.8895 (OUTLIER) cc_final: 0.8672 (mmtp) REVERT: E 37 GLN cc_start: 0.8573 (tp40) cc_final: 0.8366 (tp-100) REVERT: H 94 ARG cc_start: 0.8835 (OUTLIER) cc_final: 0.8313 (mmt90) REVERT: H 135 ASP cc_start: 0.8581 (t0) cc_final: 0.8247 (t0) REVERT: I 14 MET cc_start: 0.8883 (mmm) cc_final: 0.8596 (mmm) REVERT: I 72 ASP cc_start: 0.8445 (t0) cc_final: 0.7777 (t0) REVERT: I 158 MET cc_start: 0.8197 (mmm) cc_final: 0.7962 (mmm) REVERT: J 72 ASP cc_start: 0.8055 (t0) cc_final: 0.7745 (t0) REVERT: J 101 GLU cc_start: 0.7909 (tt0) cc_final: 0.7613 (tt0) REVERT: K 30 GLN cc_start: 0.8891 (OUTLIER) cc_final: 0.8229 (tm-30) REVERT: K 72 ASP cc_start: 0.8029 (t0) cc_final: 0.7625 (t0) REVERT: L 14 MET cc_start: 0.8636 (mmm) cc_final: 0.8417 (mmm) REVERT: M 245 ASP cc_start: 0.8356 (t0) cc_final: 0.8037 (t0) REVERT: N 277 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8697 (mmtm) REVERT: N 296 GLU cc_start: 0.8037 (mm-30) cc_final: 0.7534 (mm-30) REVERT: N 381 ASP cc_start: 0.7946 (p0) cc_final: 0.7712 (p0) REVERT: O 314 MET cc_start: 0.8753 (mmt) cc_final: 0.8452 (mmt) REVERT: O 318 GLU cc_start: 0.7880 (tm-30) cc_final: 0.7613 (tm-30) REVERT: P 168 THR cc_start: 0.8781 (OUTLIER) cc_final: 0.8567 (p) REVERT: P 403 GLN cc_start: 0.9117 (OUTLIER) cc_final: 0.7458 (tm-30) REVERT: Q 61 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.7725 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8467 (t0) cc_final: 0.8127 (t0) REVERT: R 406 GLU cc_start: 0.8429 (tt0) cc_final: 0.8126 (tt0) REVERT: S 39 ASP cc_start: 0.8009 (t70) cc_final: 0.6716 (t0) REVERT: T 39 ASP cc_start: 0.7643 (t0) cc_final: 0.6782 (t0) REVERT: T 50 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8263 (mp) REVERT: U 24 GLN cc_start: 0.9086 (tt0) cc_final: 0.8616 (tt0) REVERT: U 39 ASP cc_start: 0.7730 (t0) cc_final: 0.6270 (t0) REVERT: m 60 LYS cc_start: 0.9151 (OUTLIER) cc_final: 0.8885 (tptm) REVERT: m 78 ASP cc_start: 0.8006 (t0) cc_final: 0.7679 (t0) REVERT: m 101 GLU cc_start: 0.8721 (mp0) cc_final: 0.8444 (mp0) REVERT: m 110 GLU cc_start: 0.8610 (tp30) cc_final: 0.8241 (tp30) REVERT: m 113 ARG cc_start: 0.8511 (tmm-80) cc_final: 0.8218 (tmm-80) REVERT: n 107 ASP cc_start: 0.9156 (p0) cc_final: 0.8913 (p0) REVERT: o 37 GLN cc_start: 0.8719 (OUTLIER) cc_final: 0.8275 (mt0) outliers start: 107 outliers final: 79 residues processed: 1227 average time/residue: 0.2624 time to fit residues: 525.7388 Evaluate side-chains 1270 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 1178 time to evaluate : 1.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 39 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 39 LEU Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 403 GLN Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 254 ASP Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 424 MET Chi-restraints excluded: chain R residue 436 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain m residue 60 LYS Chi-restraints excluded: chain n residue 25 LYS Chi-restraints excluded: chain n residue 39 VAL Chi-restraints excluded: chain n residue 94 ILE Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 184 optimal weight: 0.6980 chunk 183 optimal weight: 0.7980 chunk 175 optimal weight: 2.9990 chunk 372 optimal weight: 4.9990 chunk 207 optimal weight: 0.8980 chunk 373 optimal weight: 5.9990 chunk 394 optimal weight: 3.9990 chunk 435 optimal weight: 2.9990 chunk 227 optimal weight: 1.9990 chunk 367 optimal weight: 2.9990 chunk 299 optimal weight: 7.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 37 GLN I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 385 ASN ** Q 217 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 192 GLN T 27 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.091385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2601 r_free = 0.2601 target = 0.075469 restraints weight = 69682.916| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2656 r_free = 0.2656 target = 0.078482 restraints weight = 31834.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.080470 restraints weight = 18692.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.081744 restraints weight = 12744.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.082546 restraints weight = 9560.060| |-----------------------------------------------------------------------------| r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.1781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 42215 Z= 0.159 Angle : 0.551 8.335 57426 Z= 0.284 Chirality : 0.043 0.208 6374 Planarity : 0.004 0.057 7613 Dihedral : 4.123 41.045 5935 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 2.49 % Allowed : 24.35 % Favored : 73.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.12), residues: 5392 helix: 2.84 (0.16), residues: 1047 sheet: 0.70 (0.17), residues: 858 loop : -0.22 (0.11), residues: 3487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG N 431 TYR 0.023 0.001 TYR D 40 PHE 0.009 0.001 PHE Q 232 TRP 0.008 0.001 TRP N 150 HIS 0.002 0.000 HIS O 276 Details of bonding type rmsd covalent geometry : bond 0.00373 (42215) covalent geometry : angle 0.55112 (57426) hydrogen bonds : bond 0.03260 ( 1662) hydrogen bonds : angle 3.91719 ( 4506) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10784 Ramachandran restraints generated. 5392 Oldfield, 0 Emsley, 5392 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1288 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 1182 time to evaluate : 1.644 Fit side-chains revert: symmetry clash REVERT: A 72 ASP cc_start: 0.8277 (t0) cc_final: 0.7647 (t0) REVERT: A 94 ARG cc_start: 0.9035 (OUTLIER) cc_final: 0.7632 (mmp-170) REVERT: A 124 THR cc_start: 0.8714 (OUTLIER) cc_final: 0.7999 (p) REVERT: A 127 ASP cc_start: 0.8313 (m-30) cc_final: 0.7688 (m-30) REVERT: B 37 GLN cc_start: 0.8745 (tp40) cc_final: 0.8429 (tp-100) REVERT: B 101 GLU cc_start: 0.7899 (tt0) cc_final: 0.7526 (tt0) REVERT: B 103 ASN cc_start: 0.8739 (t0) cc_final: 0.8332 (m-40) REVERT: C 65 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8565 (mt-10) REVERT: C 165 GLN cc_start: 0.8184 (OUTLIER) cc_final: 0.7923 (tt0) REVERT: E 25 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8656 (mmtp) REVERT: E 37 GLN cc_start: 0.8609 (tp40) cc_final: 0.8359 (tp-100) REVERT: H 94 ARG cc_start: 0.8833 (OUTLIER) cc_final: 0.8295 (mmt90) REVERT: H 135 ASP cc_start: 0.8636 (t0) cc_final: 0.8277 (t0) REVERT: I 14 MET cc_start: 0.8884 (mmm) cc_final: 0.8614 (mmm) REVERT: I 72 ASP cc_start: 0.8462 (t0) cc_final: 0.7799 (t0) REVERT: I 158 MET cc_start: 0.8193 (mmm) cc_final: 0.7976 (mmm) REVERT: J 72 ASP cc_start: 0.8079 (t0) cc_final: 0.7768 (t0) REVERT: J 101 GLU cc_start: 0.7915 (tt0) cc_final: 0.7610 (tt0) REVERT: K 30 GLN cc_start: 0.8910 (OUTLIER) cc_final: 0.8241 (tm-30) REVERT: K 72 ASP cc_start: 0.8032 (t0) cc_final: 0.7660 (t0) REVERT: M 245 ASP cc_start: 0.8378 (t0) cc_final: 0.8045 (t0) REVERT: N 277 LYS cc_start: 0.9390 (OUTLIER) cc_final: 0.8695 (mmtm) REVERT: N 296 GLU cc_start: 0.8066 (mm-30) cc_final: 0.7571 (mm-30) REVERT: N 381 ASP cc_start: 0.7984 (p0) cc_final: 0.7751 (p0) REVERT: O 100 GLU cc_start: 0.7498 (mp0) cc_final: 0.7256 (mp0) REVERT: O 314 MET cc_start: 0.8758 (mmt) cc_final: 0.8447 (mmt) REVERT: O 355 ARG cc_start: 0.8560 (mtm-85) cc_final: 0.8285 (mtt-85) REVERT: P 168 THR cc_start: 0.8787 (OUTLIER) cc_final: 0.8578 (p) REVERT: P 403 GLN cc_start: 0.9129 (OUTLIER) cc_final: 0.7482 (tm-30) REVERT: Q 61 ARG cc_start: 0.8624 (OUTLIER) cc_final: 0.7737 (tmm-80) REVERT: Q 245 ASP cc_start: 0.8471 (t0) cc_final: 0.8147 (t0) REVERT: R 217 GLN cc_start: 0.9278 (mp10) cc_final: 0.9018 (mp10) REVERT: R 406 GLU cc_start: 0.8453 (tt0) cc_final: 0.8125 (tt0) REVERT: S 39 ASP cc_start: 0.8001 (t70) cc_final: 0.6709 (t0) REVERT: T 39 ASP cc_start: 0.7680 (t0) cc_final: 0.6783 (t0) REVERT: T 50 LEU cc_start: 0.8793 (OUTLIER) cc_final: 0.8259 (mp) REVERT: U 24 GLN cc_start: 0.9103 (tt0) cc_final: 0.8624 (tt0) REVERT: U 39 ASP cc_start: 0.7709 (t0) cc_final: 0.6292 (t0) REVERT: m 60 LYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8897 (tptm) REVERT: m 78 ASP cc_start: 0.8024 (t0) cc_final: 0.7686 (t0) REVERT: m 101 GLU cc_start: 0.8729 (mp0) cc_final: 0.8450 (mp0) REVERT: m 110 GLU cc_start: 0.8603 (tp30) cc_final: 0.8191 (tp30) REVERT: m 113 ARG cc_start: 0.8544 (tmm-80) cc_final: 0.7893 (tmm-80) REVERT: n 107 ASP cc_start: 0.9143 (p0) cc_final: 0.8873 (p0) REVERT: o 37 GLN cc_start: 0.8752 (OUTLIER) cc_final: 0.8295 (mt0) REVERT: o 110 GLU cc_start: 0.8576 (tp30) cc_final: 0.7941 (tp30) REVERT: o 113 ARG cc_start: 0.8570 (tmm-80) cc_final: 0.8216 (tmm-80) outliers start: 106 outliers final: 86 residues processed: 1221 average time/residue: 0.2693 time to fit residues: 538.0715 Evaluate side-chains 1274 residues out of total 4259 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 1175 time to evaluate : 1.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 ARG Chi-restraints excluded: chain A residue 118 GLN Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 137 MET Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 184 VAL Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 165 GLN Chi-restraints excluded: chain D residue 39 LEU Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain D residue 116 GLU Chi-restraints excluded: chain D residue 121 SER Chi-restraints excluded: chain D residue 169 SER Chi-restraints excluded: chain E residue 25 LYS Chi-restraints excluded: chain E residue 124 THR Chi-restraints excluded: chain E residue 137 MET Chi-restraints excluded: chain E residue 164 LEU Chi-restraints excluded: chain E residue 169 SER Chi-restraints excluded: chain E residue 174 LEU Chi-restraints excluded: chain F residue 54 ASP Chi-restraints excluded: chain F residue 164 LEU Chi-restraints excluded: chain F residue 169 SER Chi-restraints excluded: chain G residue 33 LEU Chi-restraints excluded: chain G residue 124 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 184 VAL Chi-restraints excluded: chain H residue 87 THR Chi-restraints excluded: chain H residue 94 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 169 SER Chi-restraints excluded: chain I residue 55 VAL Chi-restraints excluded: chain I residue 171 SER Chi-restraints excluded: chain I residue 176 SER Chi-restraints excluded: chain J residue 121 SER Chi-restraints excluded: chain J residue 164 LEU Chi-restraints excluded: chain J residue 169 SER Chi-restraints excluded: chain J residue 180 ASP Chi-restraints excluded: chain K residue 30 GLN Chi-restraints excluded: chain K residue 128 GLU Chi-restraints excluded: chain K residue 164 LEU Chi-restraints excluded: chain L residue 121 SER Chi-restraints excluded: chain L residue 169 SER Chi-restraints excluded: chain M residue 27 VAL Chi-restraints excluded: chain M residue 171 SER Chi-restraints excluded: chain M residue 268 LEU Chi-restraints excluded: chain M residue 270 LEU Chi-restraints excluded: chain M residue 406 GLU Chi-restraints excluded: chain M residue 445 SER Chi-restraints excluded: chain N residue 27 VAL Chi-restraints excluded: chain N residue 179 ILE Chi-restraints excluded: chain N residue 247 VAL Chi-restraints excluded: chain N residue 270 LEU Chi-restraints excluded: chain N residue 277 LYS Chi-restraints excluded: chain N residue 336 GLU Chi-restraints excluded: chain O residue 27 VAL Chi-restraints excluded: chain O residue 179 ILE Chi-restraints excluded: chain O residue 359 GLU Chi-restraints excluded: chain P residue 27 VAL Chi-restraints excluded: chain P residue 61 ARG Chi-restraints excluded: chain P residue 155 LEU Chi-restraints excluded: chain P residue 168 THR Chi-restraints excluded: chain P residue 247 VAL Chi-restraints excluded: chain P residue 403 GLN Chi-restraints excluded: chain Q residue 61 ARG Chi-restraints excluded: chain Q residue 171 SER Chi-restraints excluded: chain Q residue 192 GLN Chi-restraints excluded: chain Q residue 200 THR Chi-restraints excluded: chain Q residue 231 SER Chi-restraints excluded: chain Q residue 254 ASP Chi-restraints excluded: chain Q residue 281 LEU Chi-restraints excluded: chain Q residue 414 ASP Chi-restraints excluded: chain R residue 62 LYS Chi-restraints excluded: chain R residue 200 THR Chi-restraints excluded: chain R residue 270 LEU Chi-restraints excluded: chain R residue 271 LEU Chi-restraints excluded: chain R residue 424 MET Chi-restraints excluded: chain R residue 436 THR Chi-restraints excluded: chain R residue 441 LEU Chi-restraints excluded: chain S residue 8 LEU Chi-restraints excluded: chain S residue 36 LEU Chi-restraints excluded: chain S residue 46 ILE Chi-restraints excluded: chain S residue 54 LEU Chi-restraints excluded: chain T residue 50 LEU Chi-restraints excluded: chain U residue 8 LEU Chi-restraints excluded: chain U residue 36 LEU Chi-restraints excluded: chain U residue 50 LEU Chi-restraints excluded: chain U residue 54 LEU Chi-restraints excluded: chain m residue 4 GLN Chi-restraints excluded: chain m residue 60 LYS Chi-restraints excluded: chain n residue 25 LYS Chi-restraints excluded: chain n residue 39 VAL Chi-restraints excluded: chain n residue 94 ILE Chi-restraints excluded: chain n residue 100 ASP Chi-restraints excluded: chain n residue 101 GLU Chi-restraints excluded: chain o residue 37 GLN Chi-restraints excluded: chain o residue 41 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 531 random chunks: chunk 250 optimal weight: 0.7980 chunk 385 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 449 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 340 optimal weight: 3.9990 chunk 123 optimal weight: 0.5980 chunk 427 optimal weight: 0.8980 chunk 354 optimal weight: 9.9990 chunk 353 optimal weight: 0.9980 chunk 317 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 106 ASN ** C 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 30 GLN F 37 GLN I 37 GLN ** I 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 30 GLN ** L 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 192 GLN P 385 ASN Q 230 ASN ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.093058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2632 r_free = 0.2632 target = 0.077157 restraints weight = 69999.911| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.080179 restraints weight = 31883.566| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.082180 restraints weight = 18720.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.083443 restraints weight = 12748.977| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.084260 restraints weight = 9549.587| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 42215 Z= 0.113 Angle : 0.533 8.966 57426 Z= 0.275 Chirality : 0.042 0.194 6374 Planarity : 0.004 0.055 7613 Dihedral : 4.014 43.578 5935 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 5.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.39 % Allowed : 24.65 % Favored : 72.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.12), residues: 5392 helix: 2.89 (0.16), residues: 1047 sheet: 0.73 (0.17), residues: 858 loop : -0.19 (0.11), residues: 3487 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG U 7 TYR 0.023 0.001 TYR D 40 PHE 0.011 0.001 PHE R 233 TRP 0.008 0.001 TRP N 150 HIS 0.002 0.000 HIS O 276 Details of bonding type rmsd covalent geometry : bond 0.00263 (42215) covalent geometry : angle 0.53337 (57426) hydrogen bonds : bond 0.02997 ( 1662) hydrogen bonds : angle 3.84607 ( 4506) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9282.16 seconds wall clock time: 159 minutes 57.60 seconds (9597.60 seconds total)