Starting phenix.real_space_refine on Thu Mar 5 01:34:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nav_0397/03_2026/6nav_0397.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nav_0397/03_2026/6nav_0397.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6nav_0397/03_2026/6nav_0397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nav_0397/03_2026/6nav_0397.map" model { file = "/net/cci-nas-00/data/ceres_data/6nav_0397/03_2026/6nav_0397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nav_0397/03_2026/6nav_0397.cif" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 0.007 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: 3 Type Number sf(0) Gaussians C 11781 2.51 5 N 3045 2.21 5 O 3885 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 18711 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 891 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 891 Classifications: {'peptide': 131} Modifications used: {'COO': 1} Link IDs: {'TRANS': 130} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U Time building chain proxies: 1.46, per 1000 atoms: 0.08 Number of scatterers: 18711 At special positions: 0 Unit cell: (93.8, 93.8, 197.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 3885 8.00 N 3045 7.00 C 11781 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.52 Conformation dependent library (CDL) restraints added in 807.1 milliseconds 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4788 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 63 sheets defined 29.8% alpha, 36.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 1 through 34 removed outlier: 4.141A pdb=" N ALA A 7 " --> pdb=" O GLY A 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU A 8 " --> pdb=" O ALA A 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 15 " --> pdb=" O VAL A 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE A 16 " --> pdb=" O ILE A 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR A 33 " --> pdb=" O PHE A 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY A 34 " --> pdb=" O GLY A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU A 103 " --> pdb=" O SER A 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN A 104 " --> pdb=" O SER A 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 99 through 104' Processing helix chain 'B' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA B 7 " --> pdb=" O GLY B 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU B 8 " --> pdb=" O ALA B 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL B 15 " --> pdb=" O VAL B 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE B 16 " --> pdb=" O ILE B 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY B 34 " --> pdb=" O GLY B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU B 103 " --> pdb=" O SER B 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN B 104 " --> pdb=" O SER B 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 99 through 104' Processing helix chain 'C' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA C 7 " --> pdb=" O GLY C 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU C 8 " --> pdb=" O ALA C 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL C 15 " --> pdb=" O VAL C 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE C 16 " --> pdb=" O ILE C 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR C 33 " --> pdb=" O PHE C 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY C 34 " --> pdb=" O GLY C 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 99 through 104 removed outlier: 4.412A pdb=" N LEU C 103 " --> pdb=" O SER C 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN C 104 " --> pdb=" O SER C 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 99 through 104' Processing helix chain 'D' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA D 7 " --> pdb=" O GLY D 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU D 8 " --> pdb=" O ALA D 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL D 15 " --> pdb=" O VAL D 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE D 16 " --> pdb=" O ILE D 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY D 34 " --> pdb=" O GLY D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU D 103 " --> pdb=" O SER D 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN D 104 " --> pdb=" O SER D 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 99 through 104' Processing helix chain 'E' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA E 7 " --> pdb=" O GLY E 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU E 8 " --> pdb=" O ALA E 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL E 15 " --> pdb=" O VAL E 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE E 16 " --> pdb=" O ILE E 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU E 103 " --> pdb=" O SER E 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN E 104 " --> pdb=" O SER E 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 99 through 104' Processing helix chain 'F' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA F 7 " --> pdb=" O GLY F 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU F 8 " --> pdb=" O ALA F 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL F 15 " --> pdb=" O VAL F 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE F 16 " --> pdb=" O ILE F 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR F 33 " --> pdb=" O PHE F 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY F 34 " --> pdb=" O GLY F 30 " (cutoff:3.500A) Processing helix chain 'F' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU F 103 " --> pdb=" O SER F 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN F 104 " --> pdb=" O SER F 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 99 through 104' Processing helix chain 'G' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA G 7 " --> pdb=" O GLY G 3 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU G 8 " --> pdb=" O ALA G 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL G 15 " --> pdb=" O VAL G 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE G 16 " --> pdb=" O ILE G 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR G 33 " --> pdb=" O PHE G 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY G 34 " --> pdb=" O GLY G 30 " (cutoff:3.500A) Processing helix chain 'G' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU G 103 " --> pdb=" O SER G 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN G 104 " --> pdb=" O SER G 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 99 through 104' Processing helix chain 'H' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA H 7 " --> pdb=" O GLY H 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU H 8 " --> pdb=" O ALA H 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL H 15 " --> pdb=" O VAL H 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE H 16 " --> pdb=" O ILE H 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR H 33 " --> pdb=" O PHE H 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY H 34 " --> pdb=" O GLY H 30 " (cutoff:3.500A) Processing helix chain 'H' and resid 99 through 104 removed outlier: 4.412A pdb=" N LEU H 103 " --> pdb=" O SER H 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN H 104 " --> pdb=" O SER H 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 99 through 104' Processing helix chain 'I' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA I 7 " --> pdb=" O GLY I 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU I 8 " --> pdb=" O ALA I 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL I 15 " --> pdb=" O VAL I 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE I 16 " --> pdb=" O ILE I 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR I 33 " --> pdb=" O PHE I 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY I 34 " --> pdb=" O GLY I 30 " (cutoff:3.500A) Processing helix chain 'I' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU I 103 " --> pdb=" O SER I 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN I 104 " --> pdb=" O SER I 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 99 through 104' Processing helix chain 'J' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA J 7 " --> pdb=" O GLY J 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU J 8 " --> pdb=" O ALA J 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL J 15 " --> pdb=" O VAL J 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE J 16 " --> pdb=" O ILE J 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR J 33 " --> pdb=" O PHE J 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY J 34 " --> pdb=" O GLY J 30 " (cutoff:3.500A) Processing helix chain 'J' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU J 103 " --> pdb=" O SER J 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN J 104 " --> pdb=" O SER J 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 99 through 104' Processing helix chain 'K' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA K 7 " --> pdb=" O GLY K 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU K 8 " --> pdb=" O ALA K 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL K 15 " --> pdb=" O VAL K 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE K 16 " --> pdb=" O ILE K 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR K 33 " --> pdb=" O PHE K 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY K 34 " --> pdb=" O GLY K 30 " (cutoff:3.500A) Processing helix chain 'K' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU K 103 " --> pdb=" O SER K 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN K 104 " --> pdb=" O SER K 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 99 through 104' Processing helix chain 'L' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA L 7 " --> pdb=" O GLY L 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU L 8 " --> pdb=" O ALA L 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL L 15 " --> pdb=" O VAL L 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE L 16 " --> pdb=" O ILE L 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR L 33 " --> pdb=" O PHE L 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY L 34 " --> pdb=" O GLY L 30 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU L 103 " --> pdb=" O SER L 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN L 104 " --> pdb=" O SER L 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 99 through 104' Processing helix chain 'M' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA M 7 " --> pdb=" O GLY M 3 " (cutoff:3.500A) removed outlier: 4.809A pdb=" N LEU M 8 " --> pdb=" O ALA M 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL M 15 " --> pdb=" O VAL M 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE M 16 " --> pdb=" O ILE M 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR M 33 " --> pdb=" O PHE M 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY M 34 " --> pdb=" O GLY M 30 " (cutoff:3.500A) Processing helix chain 'M' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU M 103 " --> pdb=" O SER M 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN M 104 " --> pdb=" O SER M 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 99 through 104' Processing helix chain 'N' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA N 7 " --> pdb=" O GLY N 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU N 8 " --> pdb=" O ALA N 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL N 15 " --> pdb=" O VAL N 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE N 16 " --> pdb=" O ILE N 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR N 33 " --> pdb=" O PHE N 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY N 34 " --> pdb=" O GLY N 30 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 104 removed outlier: 4.412A pdb=" N LEU N 103 " --> pdb=" O SER N 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN N 104 " --> pdb=" O SER N 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 99 through 104' Processing helix chain 'O' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA O 7 " --> pdb=" O GLY O 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU O 8 " --> pdb=" O ALA O 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL O 15 " --> pdb=" O VAL O 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE O 16 " --> pdb=" O ILE O 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR O 33 " --> pdb=" O PHE O 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY O 34 " --> pdb=" O GLY O 30 " (cutoff:3.500A) Processing helix chain 'O' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU O 103 " --> pdb=" O SER O 99 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLN O 104 " --> pdb=" O SER O 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 99 through 104' Processing helix chain 'P' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA P 7 " --> pdb=" O GLY P 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU P 8 " --> pdb=" O ALA P 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL P 15 " --> pdb=" O VAL P 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE P 16 " --> pdb=" O ILE P 12 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N THR P 33 " --> pdb=" O PHE P 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY P 34 " --> pdb=" O GLY P 30 " (cutoff:3.500A) Processing helix chain 'P' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU P 103 " --> pdb=" O SER P 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN P 104 " --> pdb=" O SER P 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 99 through 104' Processing helix chain 'Q' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA Q 7 " --> pdb=" O GLY Q 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU Q 8 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL Q 15 " --> pdb=" O VAL Q 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE Q 16 " --> pdb=" O ILE Q 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR Q 33 " --> pdb=" O PHE Q 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY Q 34 " --> pdb=" O GLY Q 30 " (cutoff:3.500A) Processing helix chain 'Q' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU Q 103 " --> pdb=" O SER Q 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN Q 104 " --> pdb=" O SER Q 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 99 through 104' Processing helix chain 'R' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA R 7 " --> pdb=" O GLY R 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU R 8 " --> pdb=" O ALA R 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL R 15 " --> pdb=" O VAL R 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE R 16 " --> pdb=" O ILE R 12 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N THR R 33 " --> pdb=" O PHE R 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY R 34 " --> pdb=" O GLY R 30 " (cutoff:3.500A) Processing helix chain 'R' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU R 103 " --> pdb=" O SER R 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN R 104 " --> pdb=" O SER R 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 99 through 104' Processing helix chain 'S' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA S 7 " --> pdb=" O GLY S 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU S 8 " --> pdb=" O ALA S 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL S 15 " --> pdb=" O VAL S 11 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE S 16 " --> pdb=" O ILE S 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR S 33 " --> pdb=" O PHE S 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY S 34 " --> pdb=" O GLY S 30 " (cutoff:3.500A) Processing helix chain 'S' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU S 103 " --> pdb=" O SER S 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN S 104 " --> pdb=" O SER S 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 99 through 104' Processing helix chain 'T' and resid 2 through 34 removed outlier: 4.142A pdb=" N ALA T 7 " --> pdb=" O GLY T 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU T 8 " --> pdb=" O ALA T 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL T 15 " --> pdb=" O VAL T 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE T 16 " --> pdb=" O ILE T 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR T 33 " --> pdb=" O PHE T 29 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLY T 34 " --> pdb=" O GLY T 30 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLN T 104 " --> pdb=" O SER T 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 99 through 104' Processing helix chain 'U' and resid 2 through 34 removed outlier: 4.141A pdb=" N ALA U 7 " --> pdb=" O GLY U 3 " (cutoff:3.500A) removed outlier: 4.808A pdb=" N LEU U 8 " --> pdb=" O ALA U 4 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL U 15 " --> pdb=" O VAL U 11 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ILE U 16 " --> pdb=" O ILE U 12 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR U 33 " --> pdb=" O PHE U 29 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N GLY U 34 " --> pdb=" O GLY U 30 " (cutoff:3.500A) Processing helix chain 'U' and resid 99 through 104 removed outlier: 4.413A pdb=" N LEU U 103 " --> pdb=" O SER U 99 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLN U 104 " --> pdb=" O SER U 100 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 99 through 104' Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 77 Processing sheet with id=AA3, first strand: chain 'A' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY A 68 " --> pdb=" O GLN A 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR A 45 " --> pdb=" O LYS A 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR A 52 " --> pdb=" O SER A 47 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA5, first strand: chain 'B' and resid 74 through 77 Processing sheet with id=AA6, first strand: chain 'B' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY B 68 " --> pdb=" O GLN B 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR B 45 " --> pdb=" O LYS B 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR B 52 " --> pdb=" O SER B 47 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 38 through 40 Processing sheet with id=AA8, first strand: chain 'C' and resid 74 through 77 Processing sheet with id=AA9, first strand: chain 'C' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY C 68 " --> pdb=" O GLN C 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR C 45 " --> pdb=" O LYS C 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR C 52 " --> pdb=" O SER C 47 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 38 through 40 Processing sheet with id=AB2, first strand: chain 'D' and resid 74 through 77 Processing sheet with id=AB3, first strand: chain 'D' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY D 68 " --> pdb=" O GLN D 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR D 45 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR D 52 " --> pdb=" O SER D 47 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 38 through 40 Processing sheet with id=AB5, first strand: chain 'E' and resid 74 through 77 Processing sheet with id=AB6, first strand: chain 'E' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY E 68 " --> pdb=" O GLN E 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR E 45 " --> pdb=" O LYS E 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR E 52 " --> pdb=" O SER E 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 38 through 40 Processing sheet with id=AB8, first strand: chain 'F' and resid 74 through 77 Processing sheet with id=AB9, first strand: chain 'F' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY F 68 " --> pdb=" O GLN F 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR F 45 " --> pdb=" O LYS F 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR F 52 " --> pdb=" O SER F 47 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 38 through 40 Processing sheet with id=AC2, first strand: chain 'G' and resid 74 through 77 Processing sheet with id=AC3, first strand: chain 'G' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY G 68 " --> pdb=" O GLN G 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR G 45 " --> pdb=" O LYS G 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR G 52 " --> pdb=" O SER G 47 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 38 through 40 Processing sheet with id=AC5, first strand: chain 'H' and resid 74 through 77 Processing sheet with id=AC6, first strand: chain 'H' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY H 68 " --> pdb=" O GLN H 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR H 45 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR H 52 " --> pdb=" O SER H 47 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 38 through 40 Processing sheet with id=AC8, first strand: chain 'I' and resid 74 through 77 Processing sheet with id=AC9, first strand: chain 'I' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY I 68 " --> pdb=" O GLN I 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR I 45 " --> pdb=" O LYS I 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR I 52 " --> pdb=" O SER I 47 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 38 through 40 Processing sheet with id=AD2, first strand: chain 'J' and resid 74 through 77 Processing sheet with id=AD3, first strand: chain 'J' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY J 68 " --> pdb=" O GLN J 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR J 45 " --> pdb=" O LYS J 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR J 52 " --> pdb=" O SER J 47 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 38 through 40 Processing sheet with id=AD5, first strand: chain 'K' and resid 74 through 77 Processing sheet with id=AD6, first strand: chain 'K' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY K 68 " --> pdb=" O GLN K 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR K 45 " --> pdb=" O LYS K 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR K 52 " --> pdb=" O SER K 47 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 38 through 40 Processing sheet with id=AD8, first strand: chain 'L' and resid 74 through 77 Processing sheet with id=AD9, first strand: chain 'L' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY L 68 " --> pdb=" O GLN L 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR L 45 " --> pdb=" O LYS L 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR L 52 " --> pdb=" O SER L 47 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'M' and resid 38 through 40 Processing sheet with id=AE2, first strand: chain 'M' and resid 74 through 77 Processing sheet with id=AE3, first strand: chain 'M' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY M 68 " --> pdb=" O GLN M 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR M 45 " --> pdb=" O LYS M 54 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N THR M 52 " --> pdb=" O SER M 47 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'N' and resid 38 through 40 Processing sheet with id=AE5, first strand: chain 'N' and resid 74 through 77 Processing sheet with id=AE6, first strand: chain 'N' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY N 68 " --> pdb=" O GLN N 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR N 45 " --> pdb=" O LYS N 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR N 52 " --> pdb=" O SER N 47 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'O' and resid 38 through 40 Processing sheet with id=AE8, first strand: chain 'O' and resid 74 through 77 Processing sheet with id=AE9, first strand: chain 'O' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY O 68 " --> pdb=" O GLN O 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR O 45 " --> pdb=" O LYS O 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR O 52 " --> pdb=" O SER O 47 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'P' and resid 38 through 40 Processing sheet with id=AF2, first strand: chain 'P' and resid 74 through 77 Processing sheet with id=AF3, first strand: chain 'P' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY P 68 " --> pdb=" O GLN P 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR P 45 " --> pdb=" O LYS P 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR P 52 " --> pdb=" O SER P 47 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Q' and resid 38 through 40 Processing sheet with id=AF5, first strand: chain 'Q' and resid 74 through 77 Processing sheet with id=AF6, first strand: chain 'Q' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY Q 68 " --> pdb=" O GLN Q 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR Q 45 " --> pdb=" O LYS Q 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR Q 52 " --> pdb=" O SER Q 47 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'R' and resid 38 through 40 Processing sheet with id=AF8, first strand: chain 'R' and resid 74 through 77 Processing sheet with id=AF9, first strand: chain 'R' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY R 68 " --> pdb=" O GLN R 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR R 45 " --> pdb=" O LYS R 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR R 52 " --> pdb=" O SER R 47 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'S' and resid 38 through 40 Processing sheet with id=AG2, first strand: chain 'S' and resid 74 through 77 Processing sheet with id=AG3, first strand: chain 'S' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY S 68 " --> pdb=" O GLN S 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR S 45 " --> pdb=" O LYS S 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR S 52 " --> pdb=" O SER S 47 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'T' and resid 38 through 40 Processing sheet with id=AG5, first strand: chain 'T' and resid 74 through 77 Processing sheet with id=AG6, first strand: chain 'T' and resid 74 through 77 removed outlier: 3.536A pdb=" N GLY T 68 " --> pdb=" O GLN T 116 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N THR T 45 " --> pdb=" O LYS T 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR T 52 " --> pdb=" O SER T 47 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'U' and resid 38 through 40 Processing sheet with id=AG8, first strand: chain 'U' and resid 74 through 77 Processing sheet with id=AG9, first strand: chain 'U' and resid 74 through 77 removed outlier: 3.537A pdb=" N GLY U 68 " --> pdb=" O GLN U 116 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N THR U 45 " --> pdb=" O LYS U 54 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N THR U 52 " --> pdb=" O SER U 47 " (cutoff:3.500A) 1093 hydrogen bonds defined for protein. 3027 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: 3.25 Time building geometry restraints manager: 2.02 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.29: 3024 1.29 - 1.36: 2982 1.36 - 1.42: 1050 1.42 - 1.49: 3255 1.49 - 1.56: 8484 Bond restraints: 18795 Sorted by residual: bond pdb=" CA THR F 90 " pdb=" CB THR F 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.04e+00 bond pdb=" CA THR T 90 " pdb=" CB THR T 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" CA THR L 90 " pdb=" CB THR L 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" CA THR H 90 " pdb=" CB THR H 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.02e+00 bond pdb=" CA THR O 90 " pdb=" CB THR O 90 " ideal model delta sigma weight residual 1.530 1.554 -0.024 1.69e-02 3.50e+03 2.00e+00 ... (remaining 18790 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.51: 24028 1.51 - 3.02: 1403 3.02 - 4.53: 161 4.53 - 6.03: 70 6.03 - 7.54: 42 Bond angle restraints: 25704 Sorted by residual: angle pdb=" C SER R 89 " pdb=" N THR R 90 " pdb=" CA THR R 90 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C SER E 89 " pdb=" N THR E 90 " pdb=" CA THR E 90 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C SER H 89 " pdb=" N THR H 90 " pdb=" CA THR H 90 " ideal model delta sigma weight residual 121.54 128.26 -6.72 1.91e+00 2.74e-01 1.24e+01 angle pdb=" C SER C 89 " pdb=" N THR C 90 " pdb=" CA THR C 90 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 angle pdb=" C SER T 89 " pdb=" N THR T 90 " pdb=" CA THR T 90 " ideal model delta sigma weight residual 121.54 128.25 -6.71 1.91e+00 2.74e-01 1.23e+01 ... (remaining 25699 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.10: 10227 11.10 - 22.21: 441 22.21 - 33.31: 126 33.31 - 44.42: 42 44.42 - 55.52: 21 Dihedral angle restraints: 10857 sinusoidal: 3318 harmonic: 7539 Sorted by residual: dihedral pdb=" CA GLN Q 88 " pdb=" C GLN Q 88 " pdb=" N SER Q 89 " pdb=" CA SER Q 89 " ideal model delta harmonic sigma weight residual -180.00 -124.48 -55.52 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLN O 88 " pdb=" C GLN O 88 " pdb=" N SER O 89 " pdb=" CA SER O 89 " ideal model delta harmonic sigma weight residual -180.00 -124.50 -55.50 0 5.00e+00 4.00e-02 1.23e+02 dihedral pdb=" CA GLN I 88 " pdb=" C GLN I 88 " pdb=" N SER I 89 " pdb=" CA SER I 89 " ideal model delta harmonic sigma weight residual -180.00 -124.51 -55.49 0 5.00e+00 4.00e-02 1.23e+02 ... (remaining 10854 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 2486 0.046 - 0.091: 840 0.091 - 0.137: 307 0.137 - 0.182: 42 0.182 - 0.228: 21 Chirality restraints: 3696 Sorted by residual: chirality pdb=" CB ILE C 71 " pdb=" CA ILE C 71 " pdb=" CG1 ILE C 71 " pdb=" CG2 ILE C 71 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB ILE N 71 " pdb=" CA ILE N 71 " pdb=" CG1 ILE N 71 " pdb=" CG2 ILE N 71 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.29e+00 ... (remaining 3693 not shown) Planarity restraints: 3108 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 89 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C SER E 89 " 0.029 2.00e-02 2.50e+03 pdb=" O SER E 89 " -0.011 2.00e-02 2.50e+03 pdb=" N THR E 90 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER L 89 " 0.008 2.00e-02 2.50e+03 1.66e-02 2.74e+00 pdb=" C SER L 89 " -0.029 2.00e-02 2.50e+03 pdb=" O SER L 89 " 0.011 2.00e-02 2.50e+03 pdb=" N THR L 90 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN N 88 " 0.008 2.00e-02 2.50e+03 1.65e-02 2.72e+00 pdb=" C GLN N 88 " -0.029 2.00e-02 2.50e+03 pdb=" O GLN N 88 " 0.011 2.00e-02 2.50e+03 pdb=" N SER N 89 " 0.010 2.00e-02 2.50e+03 ... (remaining 3105 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.78: 3660 2.78 - 3.31: 17111 3.31 - 3.84: 30074 3.84 - 4.37: 31846 4.37 - 4.90: 61367 Nonbonded interactions: 144058 Sorted by model distance: nonbonded pdb=" OG SER M 14 " pdb=" OG1 THR S 6 " model vdw 2.245 3.040 nonbonded pdb=" OG1 THR L 6 " pdb=" OG SER R 14 " model vdw 2.245 3.040 nonbonded pdb=" OG SER B 14 " pdb=" OG1 THR E 6 " model vdw 2.245 3.040 nonbonded pdb=" OG SER I 14 " pdb=" OG1 THR O 6 " model vdw 2.245 3.040 nonbonded pdb=" OG SER K 14 " pdb=" OG1 THR Q 6 " model vdw 2.245 3.040 ... (remaining 144053 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: 0.06 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' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } 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: 3.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.040 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 18795 Z= 0.234 Angle : 0.823 7.543 25704 Z= 0.454 Chirality : 0.055 0.228 3696 Planarity : 0.005 0.017 3108 Dihedral : 8.772 55.521 6069 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.14), residues: 2709 helix: -1.01 (0.17), residues: 651 sheet: -2.40 (0.18), residues: 714 loop : -2.14 (0.14), residues: 1344 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.021 0.005 TYR P 91 PHE 0.024 0.004 PHE E 29 Details of bonding type rmsd covalent geometry : bond 0.00502 (18795) covalent geometry : angle 0.82301 (25704) hydrogen bonds : bond 0.11289 ( 1009) hydrogen bonds : angle 5.48383 ( 3027) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 346 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 346 time to evaluate : 0.666 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8673 (pp30) cc_final: 0.8124 (pp30) REVERT: A 81 GLN cc_start: 0.7381 (mp10) cc_final: 0.6621 (tp40) REVERT: B 81 GLN cc_start: 0.7139 (mp10) cc_final: 0.6811 (tp-100) REVERT: C 59 ASN cc_start: 0.8729 (t0) cc_final: 0.8431 (t0) REVERT: C 81 GLN cc_start: 0.7452 (mp10) cc_final: 0.7013 (mp10) REVERT: C 121 GLN cc_start: 0.8718 (tt0) cc_final: 0.8429 (tt0) REVERT: C 124 THR cc_start: 0.8838 (p) cc_final: 0.8567 (p) REVERT: D 60 THR cc_start: 0.8459 (p) cc_final: 0.8196 (t) REVERT: E 40 GLN cc_start: 0.8286 (tt0) cc_final: 0.7629 (tt0) REVERT: E 59 ASN cc_start: 0.8665 (t0) cc_final: 0.8420 (t0) REVERT: F 59 ASN cc_start: 0.8839 (t0) cc_final: 0.8547 (t0) REVERT: F 81 GLN cc_start: 0.7283 (mp10) cc_final: 0.7082 (mm-40) REVERT: F 124 THR cc_start: 0.8608 (p) cc_final: 0.8364 (p) REVERT: G 81 GLN cc_start: 0.7311 (mp10) cc_final: 0.6839 (mp10) REVERT: G 124 THR cc_start: 0.8641 (p) cc_final: 0.8423 (p) REVERT: H 21 VAL cc_start: 0.9122 (t) cc_final: 0.8883 (p) REVERT: H 40 GLN cc_start: 0.8465 (tt0) cc_final: 0.7932 (tt0) REVERT: H 59 ASN cc_start: 0.8731 (t0) cc_final: 0.8332 (t0) REVERT: H 81 GLN cc_start: 0.6837 (mp10) cc_final: 0.6614 (mm-40) REVERT: I 81 GLN cc_start: 0.7633 (mp10) cc_final: 0.6936 (mm-40) REVERT: J 59 ASN cc_start: 0.8847 (t0) cc_final: 0.8576 (t0) REVERT: J 81 GLN cc_start: 0.6673 (mp10) cc_final: 0.6326 (tp-100) REVERT: J 124 THR cc_start: 0.8597 (p) cc_final: 0.8326 (p) REVERT: K 81 GLN cc_start: 0.7540 (mp10) cc_final: 0.7051 (tp-100) REVERT: L 29 PHE cc_start: 0.7751 (t80) cc_final: 0.7510 (t80) REVERT: L 59 ASN cc_start: 0.8679 (t0) cc_final: 0.8131 (t0) REVERT: M 81 GLN cc_start: 0.7700 (mp10) cc_final: 0.6707 (tp40) REVERT: O 81 GLN cc_start: 0.7707 (mp10) cc_final: 0.7461 (mm-40) REVERT: P 29 PHE cc_start: 0.7631 (t80) cc_final: 0.7320 (t80) REVERT: P 40 GLN cc_start: 0.8844 (tt0) cc_final: 0.8344 (tt0) REVERT: Q 8 LEU cc_start: 0.7866 (tp) cc_final: 0.6309 (tp) REVERT: Q 81 GLN cc_start: 0.7781 (mp10) cc_final: 0.7339 (tp-100) REVERT: T 29 PHE cc_start: 0.7954 (t80) cc_final: 0.7680 (t80) REVERT: U 8 LEU cc_start: 0.7587 (tp) cc_final: 0.6081 (tp) outliers start: 0 outliers final: 0 residues processed: 346 average time/residue: 0.0994 time to fit residues: 58.4843 Evaluate side-chains 137 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 137 time to evaluate : 0.616 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 197 optimal weight: 0.2980 chunk 215 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 chunk 261 optimal weight: 2.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 0.9980 chunk 183 optimal weight: 2.9990 chunk 111 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN D 121 GLN E 121 GLN F 121 GLN G 40 GLN G 88 GLN I 40 GLN I 88 GLN I 121 GLN K 40 GLN L 88 GLN M 59 ASN ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN O 88 GLN Q 40 GLN Q 59 ASN R 40 GLN S 88 GLN Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.080417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.071255 restraints weight = 45283.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.073201 restraints weight = 27250.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074587 restraints weight = 18313.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.075557 restraints weight = 13380.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.076219 restraints weight = 10413.631| |-----------------------------------------------------------------------------| r_work (final): 0.3045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 18795 Z= 0.129 Angle : 0.530 8.497 25704 Z= 0.290 Chirality : 0.042 0.133 3696 Planarity : 0.002 0.015 3108 Dihedral : 5.229 40.486 2772 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.16), residues: 2709 helix: 1.52 (0.19), residues: 651 sheet: -2.24 (0.17), residues: 819 loop : -1.71 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR M 91 PHE 0.028 0.002 PHE A 29 Details of bonding type rmsd covalent geometry : bond 0.00287 (18795) covalent geometry : angle 0.53039 (25704) hydrogen bonds : bond 0.02555 ( 1009) hydrogen bonds : angle 4.10959 ( 3027) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.650 Fit side-chains REVERT: A 21 VAL cc_start: 0.8918 (t) cc_final: 0.8652 (p) REVERT: A 81 GLN cc_start: 0.7330 (mp10) cc_final: 0.6873 (mm-40) REVERT: C 81 GLN cc_start: 0.7395 (mp10) cc_final: 0.7075 (mp10) REVERT: C 121 GLN cc_start: 0.8513 (tt0) cc_final: 0.8262 (tt0) REVERT: D 35 GLN cc_start: 0.8724 (pp30) cc_final: 0.7861 (pp30) REVERT: D 59 ASN cc_start: 0.8771 (t0) cc_final: 0.8368 (t0) REVERT: D 60 THR cc_start: 0.8258 (p) cc_final: 0.7973 (t) REVERT: E 40 GLN cc_start: 0.8344 (tt0) cc_final: 0.7877 (tt0) REVERT: E 59 ASN cc_start: 0.8670 (t0) cc_final: 0.8256 (t0) REVERT: E 81 GLN cc_start: 0.7246 (mp10) cc_final: 0.6977 (mp10) REVERT: G 81 GLN cc_start: 0.7475 (mp10) cc_final: 0.6940 (mp10) REVERT: H 40 GLN cc_start: 0.8505 (tt0) cc_final: 0.8099 (tt0) REVERT: H 59 ASN cc_start: 0.8884 (t0) cc_final: 0.8674 (t0) REVERT: I 59 ASN cc_start: 0.8806 (t0) cc_final: 0.8565 (t0) REVERT: I 81 GLN cc_start: 0.7554 (mp10) cc_final: 0.6926 (mm-40) REVERT: K 81 GLN cc_start: 0.7545 (mp10) cc_final: 0.7198 (mm-40) REVERT: L 29 PHE cc_start: 0.7604 (t80) cc_final: 0.7390 (t80) REVERT: L 59 ASN cc_start: 0.8713 (t0) cc_final: 0.8393 (t0) REVERT: L 71 ILE cc_start: 0.9131 (tt) cc_final: 0.8796 (pt) REVERT: L 91 TYR cc_start: 0.8126 (m-80) cc_final: 0.7926 (m-80) REVERT: M 81 GLN cc_start: 0.7700 (mp10) cc_final: 0.6857 (tp40) REVERT: O 81 GLN cc_start: 0.7886 (mp10) cc_final: 0.7538 (mm-40) REVERT: O 91 TYR cc_start: 0.7000 (m-80) cc_final: 0.6754 (m-80) REVERT: P 40 GLN cc_start: 0.9035 (tt0) cc_final: 0.8616 (tt0) outliers start: 0 outliers final: 0 residues processed: 196 average time/residue: 0.0995 time to fit residues: 33.2817 Evaluate side-chains 105 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 188 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 58 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 194 optimal weight: 3.9990 chunk 118 optimal weight: 0.5980 chunk 252 optimal weight: 5.9990 chunk 46 optimal weight: 0.0970 chunk 206 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN C 88 GLN F 88 GLN G 40 GLN G 88 GLN H 88 GLN H 121 GLN I 40 GLN J 81 GLN K 40 GLN M 88 GLN N 88 GLN U 121 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.079824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.070657 restraints weight = 46060.425| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072579 restraints weight = 27662.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.073961 restraints weight = 18653.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074868 restraints weight = 13601.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.075591 restraints weight = 10697.520| |-----------------------------------------------------------------------------| r_work (final): 0.3031 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.2516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 18795 Z= 0.121 Angle : 0.516 8.001 25704 Z= 0.281 Chirality : 0.042 0.164 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.678 34.019 2772 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.11 (0.17), residues: 2709 helix: 2.54 (0.20), residues: 651 sheet: -2.11 (0.17), residues: 819 loop : -1.52 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR A 91 PHE 0.034 0.002 PHE C 29 Details of bonding type rmsd covalent geometry : bond 0.00264 (18795) covalent geometry : angle 0.51579 (25704) hydrogen bonds : bond 0.02608 ( 1009) hydrogen bonds : angle 3.95065 ( 3027) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.557 Fit side-chains REVERT: A 81 GLN cc_start: 0.7285 (mp10) cc_final: 0.6802 (mm-40) REVERT: C 81 GLN cc_start: 0.7437 (mp10) cc_final: 0.6936 (mm-40) REVERT: D 35 GLN cc_start: 0.8709 (pp30) cc_final: 0.7720 (pp30) REVERT: D 40 GLN cc_start: 0.8181 (tt0) cc_final: 0.7621 (tt0) REVERT: D 59 ASN cc_start: 0.8683 (t0) cc_final: 0.8293 (t0) REVERT: E 40 GLN cc_start: 0.8415 (tt0) cc_final: 0.7806 (tt0) REVERT: E 59 ASN cc_start: 0.8773 (t0) cc_final: 0.8364 (t0) REVERT: G 81 GLN cc_start: 0.7616 (mp10) cc_final: 0.6958 (mp10) REVERT: H 21 VAL cc_start: 0.9126 (t) cc_final: 0.8892 (p) REVERT: H 40 GLN cc_start: 0.8586 (tt0) cc_final: 0.8034 (tt0) REVERT: H 59 ASN cc_start: 0.8936 (t0) cc_final: 0.8691 (t0) REVERT: I 81 GLN cc_start: 0.7282 (mp10) cc_final: 0.6726 (mm-40) REVERT: K 81 GLN cc_start: 0.7711 (mp10) cc_final: 0.7186 (mm-40) REVERT: L 29 PHE cc_start: 0.7656 (t80) cc_final: 0.7337 (t80) REVERT: L 40 GLN cc_start: 0.8778 (tt0) cc_final: 0.8304 (tt0) REVERT: L 71 ILE cc_start: 0.9096 (tt) cc_final: 0.8674 (pt) REVERT: M 81 GLN cc_start: 0.7690 (mp10) cc_final: 0.6819 (tp40) REVERT: N 29 PHE cc_start: 0.7629 (t80) cc_final: 0.7325 (t80) REVERT: O 81 GLN cc_start: 0.8017 (mp10) cc_final: 0.7492 (mm110) REVERT: O 91 TYR cc_start: 0.7065 (m-80) cc_final: 0.6731 (m-80) REVERT: P 40 GLN cc_start: 0.9028 (tt0) cc_final: 0.8688 (tt0) REVERT: U 8 LEU cc_start: 0.8020 (tt) cc_final: 0.7682 (tt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1016 time to fit residues: 29.6800 Evaluate side-chains 104 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 104 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 268 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 121 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 204 optimal weight: 0.5980 chunk 236 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 269 optimal weight: 1.9990 chunk 209 optimal weight: 2.9990 chunk 116 optimal weight: 0.0060 chunk 188 optimal weight: 0.3980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN J 81 GLN K 40 GLN L 88 GLN M 121 GLN Q 121 GLN T 121 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.079924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.070685 restraints weight = 45887.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.072589 restraints weight = 27827.569| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.073955 restraints weight = 18875.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.074824 restraints weight = 13837.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.075607 restraints weight = 10912.848| |-----------------------------------------------------------------------------| r_work (final): 0.3034 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 18795 Z= 0.109 Angle : 0.487 8.344 25704 Z= 0.266 Chirality : 0.042 0.167 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.452 30.453 2772 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -0.86 (0.17), residues: 2709 helix: 2.85 (0.21), residues: 651 sheet: -1.94 (0.17), residues: 819 loop : -1.45 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR L 91 PHE 0.026 0.001 PHE A 29 Details of bonding type rmsd covalent geometry : bond 0.00234 (18795) covalent geometry : angle 0.48689 (25704) hydrogen bonds : bond 0.02387 ( 1009) hydrogen bonds : angle 3.77840 ( 3027) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 156 time to evaluate : 0.518 Fit side-chains REVERT: A 81 GLN cc_start: 0.7267 (mp10) cc_final: 0.6798 (mm-40) REVERT: C 81 GLN cc_start: 0.7465 (mp10) cc_final: 0.6964 (mm-40) REVERT: D 35 GLN cc_start: 0.8765 (pp30) cc_final: 0.7758 (pp30) REVERT: D 38 VAL cc_start: 0.9189 (t) cc_final: 0.8798 (t) REVERT: D 40 GLN cc_start: 0.8134 (tt0) cc_final: 0.7589 (tt0) REVERT: D 59 ASN cc_start: 0.8733 (t0) cc_final: 0.8221 (t0) REVERT: E 38 VAL cc_start: 0.9363 (t) cc_final: 0.9055 (t) REVERT: E 40 GLN cc_start: 0.8524 (tt0) cc_final: 0.7934 (tt0) REVERT: E 59 ASN cc_start: 0.8810 (t0) cc_final: 0.8429 (t0) REVERT: E 81 GLN cc_start: 0.7240 (mp10) cc_final: 0.6930 (mp10) REVERT: G 81 GLN cc_start: 0.7659 (mp10) cc_final: 0.6641 (mm-40) REVERT: H 21 VAL cc_start: 0.9107 (t) cc_final: 0.8875 (p) REVERT: H 40 GLN cc_start: 0.8573 (tt0) cc_final: 0.8035 (tt0) REVERT: H 59 ASN cc_start: 0.8898 (t0) cc_final: 0.8679 (t0) REVERT: I 81 GLN cc_start: 0.7266 (mp10) cc_final: 0.6700 (mm-40) REVERT: K 81 GLN cc_start: 0.7659 (mp10) cc_final: 0.7082 (mm-40) REVERT: L 40 GLN cc_start: 0.8902 (tt0) cc_final: 0.8514 (tt0) REVERT: L 71 ILE cc_start: 0.8984 (tt) cc_final: 0.8621 (pt) REVERT: M 81 GLN cc_start: 0.7599 (mp10) cc_final: 0.6798 (tp40) REVERT: O 81 GLN cc_start: 0.8001 (mp10) cc_final: 0.7453 (mm110) REVERT: O 91 TYR cc_start: 0.7028 (m-80) cc_final: 0.6713 (m-80) REVERT: P 40 GLN cc_start: 0.9034 (tt0) cc_final: 0.8455 (tt0) REVERT: R 125 VAL cc_start: 0.9080 (t) cc_final: 0.8637 (p) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.1068 time to fit residues: 28.4208 Evaluate side-chains 107 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 21 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 192 optimal weight: 4.9990 chunk 141 optimal weight: 0.4980 chunk 162 optimal weight: 1.9990 chunk 218 optimal weight: 0.0070 chunk 8 optimal weight: 0.7980 chunk 202 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 158 optimal weight: 0.9990 overall best weight: 0.6200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN ** D 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 40 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN J 81 GLN K 40 GLN Q 121 GLN U 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.079700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070420 restraints weight = 46083.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.072386 restraints weight = 28084.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2991 r_free = 0.2991 target = 0.073757 restraints weight = 18785.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.074725 restraints weight = 13799.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.075358 restraints weight = 10754.936| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8225 moved from start: 0.3015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 18795 Z= 0.115 Angle : 0.492 7.096 25704 Z= 0.268 Chirality : 0.042 0.156 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.307 29.163 2772 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % 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: -0.74 (0.17), residues: 2709 helix: 2.92 (0.21), residues: 651 sheet: -1.76 (0.18), residues: 819 loop : -1.44 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.016 0.003 TYR N 91 PHE 0.037 0.002 PHE L 29 Details of bonding type rmsd covalent geometry : bond 0.00252 (18795) covalent geometry : angle 0.49232 (25704) hydrogen bonds : bond 0.02478 ( 1009) hydrogen bonds : angle 3.75451 ( 3027) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 154 time to evaluate : 0.632 Fit side-chains REVERT: A 81 GLN cc_start: 0.7308 (mp10) cc_final: 0.6803 (mm-40) REVERT: C 8 LEU cc_start: 0.8117 (tt) cc_final: 0.7485 (tt) REVERT: C 81 GLN cc_start: 0.7467 (mp10) cc_final: 0.6890 (mm-40) REVERT: D 38 VAL cc_start: 0.9167 (t) cc_final: 0.8818 (t) REVERT: D 59 ASN cc_start: 0.8792 (t0) cc_final: 0.8228 (t0) REVERT: E 40 GLN cc_start: 0.8577 (tt0) cc_final: 0.7924 (tt0) REVERT: E 59 ASN cc_start: 0.8851 (t0) cc_final: 0.8457 (t0) REVERT: E 81 GLN cc_start: 0.7255 (mp10) cc_final: 0.6863 (mp10) REVERT: G 81 GLN cc_start: 0.7701 (mp10) cc_final: 0.6989 (mp10) REVERT: H 40 GLN cc_start: 0.8588 (tt0) cc_final: 0.8000 (tt0) REVERT: I 81 GLN cc_start: 0.7273 (mp10) cc_final: 0.6664 (mm-40) REVERT: K 81 GLN cc_start: 0.7655 (mp10) cc_final: 0.7068 (mm-40) REVERT: L 29 PHE cc_start: 0.7718 (t80) cc_final: 0.7513 (t80) REVERT: L 40 GLN cc_start: 0.8860 (tt0) cc_final: 0.8458 (tt0) REVERT: L 71 ILE cc_start: 0.9088 (tt) cc_final: 0.8672 (pt) REVERT: M 81 GLN cc_start: 0.7587 (mp10) cc_final: 0.6778 (tp40) REVERT: O 81 GLN cc_start: 0.7911 (mp10) cc_final: 0.7301 (mm110) REVERT: O 91 TYR cc_start: 0.7084 (m-80) cc_final: 0.6851 (m-80) REVERT: P 40 GLN cc_start: 0.9094 (tt0) cc_final: 0.8575 (tt0) outliers start: 0 outliers final: 0 residues processed: 154 average time/residue: 0.0987 time to fit residues: 25.8241 Evaluate side-chains 100 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.514 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 181 optimal weight: 2.9990 chunk 235 optimal weight: 1.9990 chunk 149 optimal weight: 0.8980 chunk 145 optimal weight: 0.5980 chunk 70 optimal weight: 4.9990 chunk 125 optimal weight: 2.9990 chunk 223 optimal weight: 0.8980 chunk 112 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 15 optimal weight: 0.3980 chunk 232 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN E 121 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.079219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.070059 restraints weight = 46548.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.071914 restraints weight = 28647.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.073277 restraints weight = 19534.595| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.074234 restraints weight = 14428.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.074938 restraints weight = 11276.518| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.3191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 18795 Z= 0.117 Angle : 0.488 7.047 25704 Z= 0.267 Chirality : 0.042 0.235 3696 Planarity : 0.002 0.014 3108 Dihedral : 4.268 28.858 2772 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 6.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % 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: -0.63 (0.17), residues: 2709 helix: 3.01 (0.21), residues: 651 sheet: -1.64 (0.18), residues: 819 loop : -1.42 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR G 91 PHE 0.030 0.002 PHE H 29 Details of bonding type rmsd covalent geometry : bond 0.00256 (18795) covalent geometry : angle 0.48806 (25704) hydrogen bonds : bond 0.02454 ( 1009) hydrogen bonds : angle 3.70598 ( 3027) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.629 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7324 (mp10) cc_final: 0.6807 (mm-40) REVERT: B 29 PHE cc_start: 0.8194 (t80) cc_final: 0.7988 (t80) REVERT: C 81 GLN cc_start: 0.7445 (mp10) cc_final: 0.6893 (mm-40) REVERT: D 35 GLN cc_start: 0.8526 (pp30) cc_final: 0.8244 (pp30) REVERT: E 38 VAL cc_start: 0.9361 (t) cc_final: 0.9060 (t) REVERT: E 59 ASN cc_start: 0.8886 (t0) cc_final: 0.8501 (t0) REVERT: G 81 GLN cc_start: 0.7620 (mp10) cc_final: 0.6879 (mp10) REVERT: H 40 GLN cc_start: 0.8615 (tt0) cc_final: 0.8113 (tt0) REVERT: I 81 GLN cc_start: 0.7276 (mp10) cc_final: 0.6660 (mm-40) REVERT: K 81 GLN cc_start: 0.7634 (mp10) cc_final: 0.7072 (mm-40) REVERT: L 40 GLN cc_start: 0.8903 (tt0) cc_final: 0.8458 (tt0) REVERT: L 71 ILE cc_start: 0.9093 (tt) cc_final: 0.8787 (pt) REVERT: M 81 GLN cc_start: 0.7587 (mp10) cc_final: 0.6775 (tp40) REVERT: O 81 GLN cc_start: 0.7896 (mp10) cc_final: 0.7274 (mm110) REVERT: P 40 GLN cc_start: 0.9120 (tt0) cc_final: 0.8607 (tt0) outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.1038 time to fit residues: 25.7139 Evaluate side-chains 100 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 240 optimal weight: 0.7980 chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 176 optimal weight: 2.9990 chunk 108 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 74 optimal weight: 0.4980 chunk 36 optimal weight: 2.9990 chunk 33 optimal weight: 5.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 59 ASN D 88 GLN D 121 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Q 121 GLN ** U 59 ASN ** 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 = 0.3055 r_free = 0.3055 target = 0.075599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.066155 restraints weight = 48736.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.068018 restraints weight = 29710.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.069353 restraints weight = 20283.253| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.070306 restraints weight = 15047.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.070906 restraints weight = 11907.382| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.3379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18795 Z= 0.187 Angle : 0.580 7.137 25704 Z= 0.315 Chirality : 0.044 0.219 3696 Planarity : 0.002 0.019 3108 Dihedral : 4.607 30.158 2772 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.50 % Favored : 94.39 % Rotamer: Outliers : 0.05 % Allowed : 1.90 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % 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: -0.78 (0.17), residues: 2709 helix: 2.87 (0.21), residues: 651 sheet: -1.76 (0.18), residues: 840 loop : -1.46 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.020 0.003 TYR S 91 PHE 0.043 0.002 PHE L 29 Details of bonding type rmsd covalent geometry : bond 0.00420 (18795) covalent geometry : angle 0.58020 (25704) hydrogen bonds : bond 0.03068 ( 1009) hydrogen bonds : angle 3.96504 ( 3027) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 140 time to evaluate : 0.622 Fit side-chains REVERT: A 81 GLN cc_start: 0.7443 (mp10) cc_final: 0.6494 (tp-100) REVERT: C 81 GLN cc_start: 0.7569 (mp10) cc_final: 0.6963 (mm-40) REVERT: D 35 GLN cc_start: 0.8690 (pp30) cc_final: 0.8296 (pp30) REVERT: D 38 VAL cc_start: 0.9233 (t) cc_final: 0.9020 (t) REVERT: D 59 ASN cc_start: 0.8929 (OUTLIER) cc_final: 0.8451 (t0) REVERT: E 40 GLN cc_start: 0.8578 (tt0) cc_final: 0.8131 (tt0) REVERT: E 81 GLN cc_start: 0.7302 (mp10) cc_final: 0.7101 (mp10) REVERT: G 81 GLN cc_start: 0.7628 (mp10) cc_final: 0.6819 (mp10) REVERT: H 40 GLN cc_start: 0.8672 (tt0) cc_final: 0.8122 (tt0) REVERT: I 81 GLN cc_start: 0.7534 (mp10) cc_final: 0.6707 (mm-40) REVERT: K 81 GLN cc_start: 0.7636 (mp10) cc_final: 0.7083 (mm-40) REVERT: L 29 PHE cc_start: 0.7669 (t80) cc_final: 0.7459 (t80) REVERT: L 71 ILE cc_start: 0.9092 (tt) cc_final: 0.8773 (pt) REVERT: M 81 GLN cc_start: 0.7705 (mp10) cc_final: 0.6799 (tp40) REVERT: O 81 GLN cc_start: 0.7748 (mp10) cc_final: 0.7100 (mm110) REVERT: P 40 GLN cc_start: 0.9173 (tt0) cc_final: 0.8663 (tt0) outliers start: 1 outliers final: 0 residues processed: 141 average time/residue: 0.0949 time to fit residues: 23.0555 Evaluate side-chains 97 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 96 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 142 optimal weight: 3.9990 chunk 201 optimal weight: 0.8980 chunk 177 optimal weight: 0.9990 chunk 154 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 61 optimal weight: 0.0040 chunk 105 optimal weight: 0.8980 chunk 265 optimal weight: 0.8980 chunk 89 optimal weight: 0.6980 chunk 183 optimal weight: 0.9990 overall best weight: 0.6792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN C 88 GLN D 88 GLN E 121 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.077418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.068083 restraints weight = 47603.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.070018 restraints weight = 28648.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.071407 restraints weight = 19320.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2985 r_free = 0.2985 target = 0.072387 restraints weight = 14128.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.073084 restraints weight = 11028.377| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3472 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 18795 Z= 0.122 Angle : 0.512 11.168 25704 Z= 0.280 Chirality : 0.043 0.213 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.339 28.905 2772 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.62 (0.17), residues: 2709 helix: 2.86 (0.21), residues: 651 sheet: -1.27 (0.19), residues: 777 loop : -1.61 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.015 0.003 TYR G 91 PHE 0.025 0.002 PHE F 29 Details of bonding type rmsd covalent geometry : bond 0.00268 (18795) covalent geometry : angle 0.51159 (25704) hydrogen bonds : bond 0.02693 ( 1009) hydrogen bonds : angle 3.86723 ( 3027) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 143 time to evaluate : 0.615 Fit side-chains REVERT: A 81 GLN cc_start: 0.7359 (mp10) cc_final: 0.6820 (mm-40) REVERT: C 81 GLN cc_start: 0.7498 (mp10) cc_final: 0.6884 (mm-40) REVERT: D 35 GLN cc_start: 0.8602 (pp30) cc_final: 0.8225 (pp30) REVERT: E 40 GLN cc_start: 0.8570 (tt0) cc_final: 0.8048 (tt0) REVERT: E 81 GLN cc_start: 0.7245 (mp10) cc_final: 0.6445 (mm110) REVERT: G 81 GLN cc_start: 0.7615 (mp10) cc_final: 0.6845 (mp10) REVERT: H 40 GLN cc_start: 0.8610 (tt0) cc_final: 0.8097 (tt0) REVERT: I 81 GLN cc_start: 0.7474 (mp10) cc_final: 0.6661 (mm-40) REVERT: K 81 GLN cc_start: 0.7633 (mp10) cc_final: 0.7104 (mm-40) REVERT: L 40 GLN cc_start: 0.8947 (tt0) cc_final: 0.8450 (tt0) REVERT: L 71 ILE cc_start: 0.9062 (tt) cc_final: 0.8728 (pt) REVERT: M 81 GLN cc_start: 0.7482 (mp10) cc_final: 0.6587 (tp40) REVERT: O 81 GLN cc_start: 0.7831 (mp10) cc_final: 0.7039 (mm110) REVERT: P 40 GLN cc_start: 0.9083 (tt0) cc_final: 0.8437 (tt0) outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.1003 time to fit residues: 24.5986 Evaluate side-chains 100 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 100 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 204 optimal weight: 0.6980 chunk 148 optimal weight: 0.9990 chunk 55 optimal weight: 3.9990 chunk 170 optimal weight: 2.9990 chunk 107 optimal weight: 2.9990 chunk 240 optimal weight: 0.9990 chunk 266 optimal weight: 0.9980 chunk 74 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 147 optimal weight: 0.9990 chunk 269 optimal weight: 4.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN F 88 GLN G 40 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Q 121 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.076347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.067291 restraints weight = 48180.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.069089 restraints weight = 29641.011| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.070291 restraints weight = 20434.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.071249 restraints weight = 15405.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.071836 restraints weight = 12190.791| |-----------------------------------------------------------------------------| r_work (final): 0.2979 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.3548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 18795 Z= 0.150 Angle : 0.537 10.998 25704 Z= 0.293 Chirality : 0.043 0.200 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.355 29.669 2772 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -0.61 (0.17), residues: 2709 helix: 2.86 (0.21), residues: 651 sheet: -1.24 (0.19), residues: 777 loop : -1.62 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR M 91 PHE 0.038 0.002 PHE H 29 Details of bonding type rmsd covalent geometry : bond 0.00337 (18795) covalent geometry : angle 0.53706 (25704) hydrogen bonds : bond 0.02814 ( 1009) hydrogen bonds : angle 3.90074 ( 3027) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.671 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7411 (mp10) cc_final: 0.6595 (tp-100) REVERT: C 8 LEU cc_start: 0.8169 (tt) cc_final: 0.7664 (tt) REVERT: C 81 GLN cc_start: 0.7542 (mp10) cc_final: 0.6975 (mm-40) REVERT: D 35 GLN cc_start: 0.8612 (pp30) cc_final: 0.8186 (pp30) REVERT: D 59 ASN cc_start: 0.8966 (t0) cc_final: 0.8453 (t0) REVERT: E 40 GLN cc_start: 0.8603 (tt0) cc_final: 0.8225 (tt0) REVERT: E 81 GLN cc_start: 0.7275 (mp10) cc_final: 0.6482 (mm110) REVERT: G 81 GLN cc_start: 0.7616 (mp10) cc_final: 0.6825 (mp10) REVERT: H 40 GLN cc_start: 0.8629 (tt0) cc_final: 0.8095 (tt0) REVERT: I 81 GLN cc_start: 0.7492 (mp10) cc_final: 0.6701 (mm-40) REVERT: K 81 GLN cc_start: 0.7587 (mp10) cc_final: 0.7077 (mm-40) REVERT: K 91 TYR cc_start: 0.7701 (m-80) cc_final: 0.7494 (m-10) REVERT: L 40 GLN cc_start: 0.8949 (tt0) cc_final: 0.8452 (tt0) REVERT: L 71 ILE cc_start: 0.9089 (tt) cc_final: 0.8728 (pt) REVERT: M 81 GLN cc_start: 0.7524 (mp10) cc_final: 0.6649 (tp40) REVERT: O 81 GLN cc_start: 0.7749 (mp10) cc_final: 0.7098 (mm110) REVERT: P 40 GLN cc_start: 0.9103 (tt0) cc_final: 0.8417 (tt0) REVERT: P 71 ILE cc_start: 0.9205 (tt) cc_final: 0.8837 (pt) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.1064 time to fit residues: 23.7708 Evaluate side-chains 99 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 196 optimal weight: 0.5980 chunk 16 optimal weight: 2.9990 chunk 120 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 84 optimal weight: 5.9990 chunk 205 optimal weight: 0.9990 chunk 141 optimal weight: 2.9990 chunk 145 optimal weight: 0.5980 chunk 92 optimal weight: 2.9990 chunk 133 optimal weight: 0.4980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 88 GLN C 88 GLN D 121 GLN E 121 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN ** J 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Q 121 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.076053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.066884 restraints weight = 48004.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068787 restraints weight = 28893.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.070078 restraints weight = 19521.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.071039 restraints weight = 14431.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.071678 restraints weight = 11268.903| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 18795 Z= 0.129 Angle : 0.511 7.555 25704 Z= 0.282 Chirality : 0.043 0.199 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.262 28.719 2772 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.56 (0.17), residues: 2709 helix: 2.86 (0.21), residues: 651 sheet: -1.17 (0.19), residues: 777 loop : -1.60 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR G 91 PHE 0.033 0.002 PHE H 29 Details of bonding type rmsd covalent geometry : bond 0.00287 (18795) covalent geometry : angle 0.51068 (25704) hydrogen bonds : bond 0.02768 ( 1009) hydrogen bonds : angle 3.88697 ( 3027) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 133 time to evaluate : 0.613 Fit side-chains REVERT: A 81 GLN cc_start: 0.7379 (mp10) cc_final: 0.6631 (tp-100) REVERT: C 81 GLN cc_start: 0.7522 (mp10) cc_final: 0.6905 (mm-40) REVERT: D 33 THR cc_start: 0.9051 (m) cc_final: 0.8493 (p) REVERT: D 35 GLN cc_start: 0.8598 (pp30) cc_final: 0.8139 (pp30) REVERT: D 59 ASN cc_start: 0.8998 (t0) cc_final: 0.8496 (t0) REVERT: E 40 GLN cc_start: 0.8592 (tt0) cc_final: 0.8181 (tt0) REVERT: E 81 GLN cc_start: 0.7281 (mp10) cc_final: 0.6450 (mm110) REVERT: G 81 GLN cc_start: 0.7587 (mp10) cc_final: 0.6779 (mp10) REVERT: H 40 GLN cc_start: 0.8615 (tt0) cc_final: 0.8200 (tt0) REVERT: I 81 GLN cc_start: 0.7470 (mp10) cc_final: 0.6655 (mm-40) REVERT: K 81 GLN cc_start: 0.7606 (mp10) cc_final: 0.7119 (mm-40) REVERT: K 91 TYR cc_start: 0.7681 (m-80) cc_final: 0.7477 (m-10) REVERT: L 40 GLN cc_start: 0.8935 (tt0) cc_final: 0.8452 (tt0) REVERT: L 71 ILE cc_start: 0.9069 (tt) cc_final: 0.8723 (pt) REVERT: M 81 GLN cc_start: 0.7500 (mp10) cc_final: 0.6623 (tp40) REVERT: O 81 GLN cc_start: 0.7709 (mp10) cc_final: 0.7027 (mm110) REVERT: P 40 GLN cc_start: 0.9092 (tt0) cc_final: 0.8370 (tt0) REVERT: P 71 ILE cc_start: 0.9188 (tt) cc_final: 0.8826 (pt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1006 time to fit residues: 22.9920 Evaluate side-chains 102 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 102 time to evaluate : 0.646 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 0.0980 chunk 202 optimal weight: 1.9990 chunk 210 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 118 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 211 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 49 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 88 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 40 GLN K 40 GLN Q 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.066057 restraints weight = 48460.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.067931 restraints weight = 29184.831| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.069158 restraints weight = 19776.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.070165 restraints weight = 14702.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.070810 restraints weight = 11515.419| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 18795 Z= 0.145 Angle : 0.527 7.815 25704 Z= 0.289 Chirality : 0.043 0.188 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.294 29.265 2772 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.58 (0.17), residues: 2709 helix: 2.84 (0.21), residues: 651 sheet: -1.16 (0.19), residues: 777 loop : -1.62 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.014 0.003 TYR M 91 PHE 0.034 0.002 PHE A 29 Details of bonding type rmsd covalent geometry : bond 0.00324 (18795) covalent geometry : angle 0.52707 (25704) hydrogen bonds : bond 0.02790 ( 1009) hydrogen bonds : angle 3.89932 ( 3027) =============================================================================== Job complete usr+sys time: 2054.41 seconds wall clock time: 37 minutes 8.33 seconds (2228.33 seconds total)