Starting phenix.real_space_refine on Mon Jun 16 02:48:45 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6nav_0397/06_2025/6nav_0397.cif Found real_map, /net/cci-nas-00/data/ceres_data/6nav_0397/06_2025/6nav_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_0397/06_2025/6nav_0397.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6nav_0397/06_2025/6nav_0397.map" model { file = "/net/cci-nas-00/data/ceres_data/6nav_0397/06_2025/6nav_0397.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6nav_0397/06_2025/6nav_0397.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T Time building chain proxies: 5.80, per 1000 atoms: 0.31 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: 5.67 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 3.41 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: 7.02 Time building geometry restraints manager: 6.55 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: 0.20 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' } 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: 5.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.830 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 41.600 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.090 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 51.530 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 PHE 0.024 0.004 PHE E 29 TYR 0.021 0.005 TYR P 91 Details of bonding type rmsd hydrogen bonds : bond 0.11289 ( 1009) hydrogen bonds : angle 5.48383 ( 3027) covalent geometry : bond 0.00502 (18795) covalent geometry : angle 0.82301 (25704) *********************** 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 : 2.153 Fit side-chains revert: symmetry clash REVERT: A 35 GLN cc_start: 0.8673 (pp30) cc_final: 0.8123 (pp30) REVERT: A 81 GLN cc_start: 0.7381 (mp10) cc_final: 0.6621 (tp40) REVERT: B 81 GLN cc_start: 0.7138 (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: 0.8460 (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: 0.8666 (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: 0.8365 (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: 0.8464 (tt0) cc_final: 0.7931 (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: 0.8575 (t0) REVERT: J 81 GLN cc_start: 0.6674 (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: 0.7050 (tp-100) REVERT: L 29 PHE cc_start: 0.7751 (t80) cc_final: 0.7509 (t80) REVERT: L 59 ASN cc_start: 0.8679 (t0) cc_final: 0.8130 (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: 0.7632 (t80) cc_final: 0.7321 (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: 0.7955 (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: 0.2475 time to fit residues: 143.7456 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 : 2.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 230 optimal weight: 0.0170 chunk 206 optimal weight: 2.9990 chunk 114 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 139 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 213 optimal weight: 0.8980 chunk 82 optimal weight: 3.9990 chunk 130 optimal weight: 0.7980 chunk 159 optimal weight: 0.1980 chunk 247 optimal weight: 0.4980 overall best weight: 0.4418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN B 88 GLN D 121 GLN E 88 GLN E 121 GLN F 88 GLN F 121 GLN G 40 GLN G 88 GLN I 40 GLN I 88 GLN I 121 GLN K 40 GLN K 88 GLN L 88 GLN M 59 ASN ** M 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 121 GLN N 88 GLN O 88 GLN Q 40 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 40 GLN R 88 GLN S 88 GLN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3148 r_free = 0.3148 target = 0.081531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.072460 restraints weight = 44731.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.074414 restraints weight = 26783.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.075827 restraints weight = 17984.594| |-----------------------------------------------------------------------------| r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 18795 Z= 0.113 Angle : 0.515 8.443 25704 Z= 0.282 Chirality : 0.042 0.129 3696 Planarity : 0.002 0.014 3108 Dihedral : 5.127 39.756 2772 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.77 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.16), residues: 2709 helix: 1.35 (0.19), residues: 651 sheet: -2.24 (0.17), residues: 819 loop : -1.73 (0.17), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.028 0.001 PHE A 29 TYR 0.018 0.003 TYR M 91 Details of bonding type rmsd hydrogen bonds : bond 0.02473 ( 1009) hydrogen bonds : angle 4.09296 ( 3027) covalent geometry : bond 0.00250 (18795) covalent geometry : angle 0.51539 (25704) *********************** 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 206 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 206 time to evaluate : 1.900 Fit side-chains REVERT: A 35 GLN cc_start: 0.8430 (pp30) cc_final: 0.7757 (pp30) REVERT: A 81 GLN cc_start: 0.7320 (mp10) cc_final: 0.6859 (mm-40) REVERT: C 81 GLN cc_start: 0.7417 (mp10) cc_final: 0.7087 (mp10) REVERT: C 121 GLN cc_start: 0.8487 (tt0) cc_final: 0.8285 (tt0) REVERT: D 35 GLN cc_start: 0.8741 (pp30) cc_final: 0.7959 (pp30) REVERT: D 59 ASN cc_start: 0.8755 (t0) cc_final: 0.8353 (t0) REVERT: D 60 THR cc_start: 0.8205 (p) cc_final: 0.7915 (t) REVERT: E 40 GLN cc_start: 0.8278 (tt0) cc_final: 0.7840 (tt0) REVERT: G 81 GLN cc_start: 0.7488 (mp10) cc_final: 0.6967 (mp10) REVERT: H 40 GLN cc_start: 0.8507 (tt0) cc_final: 0.8125 (tt0) REVERT: H 59 ASN cc_start: 0.8873 (t0) cc_final: 0.8634 (t0) REVERT: I 59 ASN cc_start: 0.8746 (t0) cc_final: 0.8537 (t0) REVERT: I 81 GLN cc_start: 0.7431 (mp10) cc_final: 0.7015 (mm-40) REVERT: J 59 ASN cc_start: 0.9012 (t0) cc_final: 0.8669 (t0) REVERT: K 81 GLN cc_start: 0.7410 (mp10) cc_final: 0.7110 (mm-40) REVERT: L 40 GLN cc_start: 0.8799 (tt0) cc_final: 0.8283 (tt0) REVERT: L 59 ASN cc_start: 0.8686 (t0) cc_final: 0.8247 (t0) REVERT: L 71 ILE cc_start: 0.9094 (tt) cc_final: 0.8773 (pt) REVERT: M 81 GLN cc_start: 0.7787 (mp10) cc_final: 0.7037 (tp40) REVERT: M 91 TYR cc_start: 0.6934 (m-80) cc_final: 0.6695 (m-80) REVERT: O 81 GLN cc_start: 0.8006 (mp10) cc_final: 0.7652 (mm-40) REVERT: O 91 TYR cc_start: 0.6946 (m-80) cc_final: 0.6642 (m-80) REVERT: P 40 GLN cc_start: 0.9021 (tt0) cc_final: 0.8592 (tt0) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2363 time to fit residues: 81.4594 Evaluate side-chains 111 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 111 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 50 optimal weight: 0.7980 chunk 135 optimal weight: 0.8980 chunk 214 optimal weight: 1.9990 chunk 178 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 157 optimal weight: 5.9990 chunk 1 optimal weight: 0.5980 chunk 216 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 chunk 144 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN F 88 GLN G 40 GLN G 88 GLN H 121 GLN I 40 GLN J 81 GLN K 40 GLN M 88 GLN N 88 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 121 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078981 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.069889 restraints weight = 45973.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.071790 restraints weight = 27704.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.073051 restraints weight = 18759.716| |-----------------------------------------------------------------------------| r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2552 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= 0.137 Angle : 0.531 8.084 25704 Z= 0.289 Chirality : 0.042 0.135 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.738 34.241 2772 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.51 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.17), residues: 2709 helix: 2.58 (0.20), residues: 651 sheet: -2.11 (0.17), residues: 819 loop : -1.53 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE C 29 TYR 0.019 0.003 TYR S 91 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 1009) hydrogen bonds : angle 3.97165 ( 3027) covalent geometry : bond 0.00301 (18795) covalent geometry : angle 0.53131 (25704) *********************** 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 170 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 170 time to evaluate : 2.118 Fit side-chains REVERT: A 38 VAL cc_start: 0.9305 (t) cc_final: 0.9017 (t) REVERT: A 81 GLN cc_start: 0.7363 (mp10) cc_final: 0.6868 (mm-40) REVERT: C 81 GLN cc_start: 0.7506 (mp10) cc_final: 0.6990 (mm-40) REVERT: D 35 GLN cc_start: 0.8727 (pp30) cc_final: 0.7724 (pp30) REVERT: D 59 ASN cc_start: 0.8726 (t0) cc_final: 0.8238 (t0) REVERT: E 40 GLN cc_start: 0.8461 (tt0) cc_final: 0.7820 (tt0) REVERT: G 81 GLN cc_start: 0.7598 (mp10) cc_final: 0.6986 (mp10) REVERT: H 21 VAL cc_start: 0.9122 (t) cc_final: 0.8903 (p) REVERT: H 40 GLN cc_start: 0.8603 (tt0) cc_final: 0.8095 (tt0) REVERT: H 59 ASN cc_start: 0.8941 (t0) cc_final: 0.8705 (t0) REVERT: I 81 GLN cc_start: 0.7379 (mp10) cc_final: 0.6683 (mm-40) REVERT: K 81 GLN cc_start: 0.7671 (mp10) cc_final: 0.7188 (mm-40) REVERT: L 29 PHE cc_start: 0.7660 (t80) cc_final: 0.7447 (t80) REVERT: L 71 ILE cc_start: 0.9087 (tt) cc_final: 0.8682 (pt) REVERT: M 29 PHE cc_start: 0.7524 (t80) cc_final: 0.7309 (t80) REVERT: M 81 GLN cc_start: 0.7757 (mp10) cc_final: 0.6845 (tp40) REVERT: N 29 PHE cc_start: 0.7645 (t80) cc_final: 0.7324 (t80) REVERT: O 81 GLN cc_start: 0.8087 (mp10) cc_final: 0.7527 (mm110) REVERT: O 91 TYR cc_start: 0.7150 (m-80) cc_final: 0.6780 (m-80) REVERT: P 40 GLN cc_start: 0.9030 (tt0) cc_final: 0.8713 (tt0) outliers start: 0 outliers final: 0 residues processed: 170 average time/residue: 0.2411 time to fit residues: 69.2342 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 : 2.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 206 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 143 optimal weight: 0.9990 chunk 190 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 243 optimal weight: 3.9990 chunk 15 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 57 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN D 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 81 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN R 121 GLN T 121 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.077863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.068554 restraints weight = 46578.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.070478 restraints weight = 28641.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.071777 restraints weight = 19341.619| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.2895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 18795 Z= 0.159 Angle : 0.550 7.616 25704 Z= 0.298 Chirality : 0.043 0.152 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.758 32.627 2772 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.04 % Allowed : 4.36 % Favored : 95.61 % 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 : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.17), residues: 2709 helix: 2.81 (0.21), residues: 651 sheet: -2.01 (0.17), residues: 819 loop : -1.46 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.002 PHE A 29 TYR 0.018 0.003 TYR M 91 Details of bonding type rmsd hydrogen bonds : bond 0.02766 ( 1009) hydrogen bonds : angle 3.93914 ( 3027) covalent geometry : bond 0.00355 (18795) covalent geometry : angle 0.54995 (25704) *********************** 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 142 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 142 time to evaluate : 2.132 Fit side-chains revert: symmetry clash REVERT: A 29 PHE cc_start: 0.8000 (t80) cc_final: 0.7748 (t80) REVERT: A 81 GLN cc_start: 0.7461 (mp10) cc_final: 0.6918 (mm-40) REVERT: C 81 GLN cc_start: 0.7554 (mp10) cc_final: 0.7000 (mm-40) REVERT: D 35 GLN cc_start: 0.8828 (pp30) cc_final: 0.8196 (pp30) REVERT: D 38 VAL cc_start: 0.9289 (t) cc_final: 0.8995 (t) REVERT: D 59 ASN cc_start: 0.8782 (t0) cc_final: 0.8216 (t0) REVERT: E 38 VAL cc_start: 0.9432 (t) cc_final: 0.9127 (t) REVERT: E 40 GLN cc_start: 0.8487 (tt0) cc_final: 0.7843 (tt0) REVERT: E 59 ASN cc_start: 0.8928 (t0) cc_final: 0.8465 (t0) REVERT: G 81 GLN cc_start: 0.7713 (mp10) cc_final: 0.6937 (mp10) REVERT: H 40 GLN cc_start: 0.8619 (tt0) cc_final: 0.8037 (tt0) REVERT: I 81 GLN cc_start: 0.7337 (mp10) cc_final: 0.6751 (mm-40) REVERT: K 81 GLN cc_start: 0.7770 (mp10) cc_final: 0.7172 (mm-40) REVERT: L 71 ILE cc_start: 0.8941 (tt) cc_final: 0.8482 (pt) REVERT: M 81 GLN cc_start: 0.7698 (mp10) cc_final: 0.6870 (tp40) REVERT: O 81 GLN cc_start: 0.7963 (mp10) cc_final: 0.7373 (mm110) REVERT: O 91 TYR cc_start: 0.7108 (m-80) cc_final: 0.6821 (m-80) REVERT: P 40 GLN cc_start: 0.9093 (tt0) cc_final: 0.8736 (tt0) REVERT: R 125 VAL cc_start: 0.9136 (t) cc_final: 0.8791 (p) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.3073 time to fit residues: 76.2534 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 : 3.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 55 optimal weight: 2.9990 chunk 224 optimal weight: 0.5980 chunk 212 optimal weight: 0.9990 chunk 179 optimal weight: 3.9990 chunk 109 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 221 optimal weight: 4.9990 chunk 204 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 262 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 88 GLN C 72 ASN D 88 GLN F 88 GLN G 88 GLN H 88 GLN I 40 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3056 r_free = 0.3056 target = 0.076618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.067358 restraints weight = 47280.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.069164 restraints weight = 29190.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.070468 restraints weight = 20052.953| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 18795 Z= 0.188 Angle : 0.577 7.333 25704 Z= 0.313 Chirality : 0.044 0.169 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.807 32.718 2772 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.28 % Favored : 94.65 % 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 : 0.26 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.90 (0.17), residues: 2709 helix: 2.85 (0.21), residues: 651 sheet: -1.96 (0.17), residues: 819 loop : -1.50 (0.18), residues: 1239 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.002 PHE E 29 TYR 0.020 0.003 TYR S 91 Details of bonding type rmsd hydrogen bonds : bond 0.02983 ( 1009) hydrogen bonds : angle 4.00799 ( 3027) covalent geometry : bond 0.00423 (18795) covalent geometry : angle 0.57746 (25704) *********************** 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 149 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 149 time to evaluate : 1.939 Fit side-chains REVERT: A 81 GLN cc_start: 0.7490 (mp10) cc_final: 0.6954 (mm-40) REVERT: C 81 GLN cc_start: 0.7657 (mp10) cc_final: 0.7062 (mm-40) REVERT: D 35 GLN cc_start: 0.8879 (pp30) cc_final: 0.8364 (pp30) REVERT: D 38 VAL cc_start: 0.9331 (t) cc_final: 0.8986 (t) REVERT: D 59 ASN cc_start: 0.8847 (t0) cc_final: 0.8215 (t0) REVERT: E 40 GLN cc_start: 0.8551 (tt0) cc_final: 0.8312 (tt0) REVERT: F 29 PHE cc_start: 0.7723 (t80) cc_final: 0.7380 (t80) REVERT: G 81 GLN cc_start: 0.7722 (mp10) cc_final: 0.6915 (mp10) REVERT: H 40 GLN cc_start: 0.8623 (tt0) cc_final: 0.7920 (tt0) REVERT: H 124 THR cc_start: 0.8915 (p) cc_final: 0.8701 (p) REVERT: I 81 GLN cc_start: 0.7568 (mp10) cc_final: 0.6780 (mm-40) REVERT: I 114 THR cc_start: 0.9260 (m) cc_final: 0.9035 (p) REVERT: K 81 GLN cc_start: 0.7710 (mp10) cc_final: 0.7172 (mm-40) REVERT: L 71 ILE cc_start: 0.8986 (tt) cc_final: 0.8556 (pt) REVERT: M 81 GLN cc_start: 0.7756 (mp10) cc_final: 0.6875 (tp40) REVERT: O 81 GLN cc_start: 0.8037 (mp10) cc_final: 0.7220 (mm110) REVERT: P 40 GLN cc_start: 0.9086 (tt0) cc_final: 0.8764 (tt0) REVERT: R 125 VAL cc_start: 0.9163 (t) cc_final: 0.8853 (p) REVERT: U 114 THR cc_start: 0.8947 (m) cc_final: 0.8675 (p) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.2398 time to fit residues: 60.3093 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 : 2.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 156 optimal weight: 0.9980 chunk 168 optimal weight: 0.8980 chunk 116 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 191 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 61 optimal weight: 0.2980 chunk 142 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 177 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 ** I 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Q 104 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 = 0.3074 r_free = 0.3074 target = 0.076622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.067210 restraints weight = 48069.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.069097 restraints weight = 29021.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.070476 restraints weight = 19606.521| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 18795 Z= 0.137 Angle : 0.521 10.244 25704 Z= 0.283 Chirality : 0.043 0.256 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.586 30.661 2772 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.73 (0.17), residues: 2709 helix: 2.99 (0.21), residues: 651 sheet: -1.59 (0.18), residues: 777 loop : -1.63 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.038 0.002 PHE A 29 TYR 0.017 0.003 TYR B 91 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 1009) hydrogen bonds : angle 3.86864 ( 3027) covalent geometry : bond 0.00304 (18795) covalent geometry : angle 0.52138 (25704) *********************** 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 140 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 140 time to evaluate : 2.024 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7454 (mp10) cc_final: 0.6930 (mm-40) REVERT: B 8 LEU cc_start: 0.8469 (tt) cc_final: 0.6358 (tt) REVERT: C 81 GLN cc_start: 0.7625 (mp10) cc_final: 0.7028 (mm-40) REVERT: D 35 GLN cc_start: 0.8862 (pp30) cc_final: 0.8301 (pp30) REVERT: D 59 ASN cc_start: 0.8845 (t0) cc_final: 0.8244 (t0) REVERT: E 40 GLN cc_start: 0.8562 (tt0) cc_final: 0.8325 (tt0) REVERT: G 81 GLN cc_start: 0.7675 (mp10) cc_final: 0.6864 (mp10) REVERT: H 40 GLN cc_start: 0.8651 (tt0) cc_final: 0.7989 (tt0) REVERT: I 81 GLN cc_start: 0.7559 (mp10) cc_final: 0.6771 (mm-40) REVERT: K 81 GLN cc_start: 0.7656 (mp10) cc_final: 0.7113 (mm-40) REVERT: L 71 ILE cc_start: 0.8988 (tt) cc_final: 0.8578 (pt) REVERT: M 81 GLN cc_start: 0.7541 (mp10) cc_final: 0.6722 (tp40) REVERT: O 81 GLN cc_start: 0.7899 (mp10) cc_final: 0.7152 (mm110) REVERT: P 40 GLN cc_start: 0.9099 (tt0) cc_final: 0.8456 (tt0) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2381 time to fit residues: 56.7406 Evaluate side-chains 97 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 52 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 147 optimal weight: 5.9990 chunk 252 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 164 optimal weight: 2.9990 chunk 179 optimal weight: 2.9990 chunk 236 optimal weight: 1.9990 chunk 240 optimal weight: 0.8980 overall best weight: 1.5386 ------------------------------------------------------------------------------- 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 88 GLN D 121 GLN F 88 GLN G 40 GLN G 88 GLN Q 121 GLN U 40 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.072994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.063766 restraints weight = 49084.221| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.065529 restraints weight = 29874.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.066781 restraints weight = 20576.032| |-----------------------------------------------------------------------------| r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.3539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 18795 Z= 0.232 Angle : 0.648 7.210 25704 Z= 0.348 Chirality : 0.046 0.217 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.965 33.764 2772 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.39 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.22 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2709 helix: 2.76 (0.21), residues: 651 sheet: -1.40 (0.19), residues: 735 loop : -1.70 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE E 29 TYR 0.020 0.004 TYR M 91 Details of bonding type rmsd hydrogen bonds : bond 0.03409 ( 1009) hydrogen bonds : angle 4.19971 ( 3027) covalent geometry : bond 0.00526 (18795) covalent geometry : angle 0.64759 (25704) *********************** 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 139 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 2.335 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7551 (mp10) cc_final: 0.6781 (tp40) REVERT: B 8 LEU cc_start: 0.8796 (tt) cc_final: 0.7558 (tt) REVERT: C 81 GLN cc_start: 0.7574 (mp10) cc_final: 0.6945 (mm-40) REVERT: D 35 GLN cc_start: 0.8913 (pp30) cc_final: 0.8346 (pp30) REVERT: E 40 GLN cc_start: 0.8657 (tt0) cc_final: 0.8426 (tt0) REVERT: G 81 GLN cc_start: 0.7706 (mp10) cc_final: 0.6880 (mp10) REVERT: H 40 GLN cc_start: 0.8582 (tt0) cc_final: 0.8026 (tt0) REVERT: I 81 GLN cc_start: 0.7628 (mp10) cc_final: 0.6846 (mm-40) REVERT: K 81 GLN cc_start: 0.7718 (mp10) cc_final: 0.7145 (mm-40) REVERT: K 91 TYR cc_start: 0.7640 (m-80) cc_final: 0.7417 (m-10) REVERT: L 71 ILE cc_start: 0.9023 (tt) cc_final: 0.8637 (pt) REVERT: M 81 GLN cc_start: 0.7659 (mp10) cc_final: 0.6819 (tp40) REVERT: O 81 GLN cc_start: 0.7832 (mp10) cc_final: 0.6940 (tp40) REVERT: P 29 PHE cc_start: 0.8221 (m-10) cc_final: 0.7948 (m-80) REVERT: P 40 GLN cc_start: 0.9109 (tt0) cc_final: 0.8560 (tt0) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2536 time to fit residues: 59.4854 Evaluate side-chains 92 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 92 time to evaluate : 1.914 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 203 optimal weight: 1.9990 chunk 208 optimal weight: 0.8980 chunk 59 optimal weight: 0.0370 chunk 148 optimal weight: 0.8980 chunk 156 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 92 optimal weight: 1.9990 chunk 256 optimal weight: 3.9990 chunk 231 optimal weight: 3.9990 chunk 217 optimal weight: 2.9990 overall best weight: 0.7060 ------------------------------------------------------------------------------- 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** C 88 GLN E 121 GLN G 88 GLN Q 121 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.075727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.066652 restraints weight = 47929.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.068525 restraints weight = 28554.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.069831 restraints weight = 19183.929| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 18795 Z= 0.127 Angle : 0.519 6.709 25704 Z= 0.285 Chirality : 0.043 0.192 3696 Planarity : 0.002 0.019 3108 Dihedral : 4.496 31.657 2772 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.17), residues: 2709 helix: 2.88 (0.21), residues: 651 sheet: -1.53 (0.18), residues: 777 loop : -1.65 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.043 0.002 PHE A 29 TYR 0.016 0.003 TYR G 91 Details of bonding type rmsd hydrogen bonds : bond 0.02681 ( 1009) hydrogen bonds : angle 3.92737 ( 3027) covalent geometry : bond 0.00280 (18795) covalent geometry : angle 0.51922 (25704) *********************** 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 131 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 131 time to evaluate : 1.869 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7421 (mp10) cc_final: 0.6653 (tp-100) REVERT: B 8 LEU cc_start: 0.8787 (tt) cc_final: 0.7355 (tt) REVERT: C 81 GLN cc_start: 0.7554 (mp10) cc_final: 0.6867 (mm-40) REVERT: D 35 GLN cc_start: 0.8823 (pp30) cc_final: 0.8313 (pp30) REVERT: D 59 ASN cc_start: 0.8976 (t0) cc_final: 0.8358 (t0) REVERT: E 40 GLN cc_start: 0.8543 (tt0) cc_final: 0.7790 (tt0) REVERT: G 81 GLN cc_start: 0.7848 (mp10) cc_final: 0.6985 (mp10) REVERT: H 40 GLN cc_start: 0.8626 (tt0) cc_final: 0.8115 (tt0) REVERT: I 81 GLN cc_start: 0.7534 (mp10) cc_final: 0.6722 (mm-40) REVERT: K 81 GLN cc_start: 0.7663 (mp10) cc_final: 0.7142 (mm-40) REVERT: K 91 TYR cc_start: 0.7555 (m-80) cc_final: 0.7348 (m-10) REVERT: L 71 ILE cc_start: 0.8940 (tt) cc_final: 0.8503 (pt) REVERT: M 81 GLN cc_start: 0.7533 (mp10) cc_final: 0.6720 (tp40) REVERT: O 81 GLN cc_start: 0.7743 (mp10) cc_final: 0.7123 (mm110) REVERT: P 40 GLN cc_start: 0.9081 (tt0) cc_final: 0.8413 (tt0) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.2417 time to fit residues: 53.7477 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 : 2.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 170 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 206 optimal weight: 2.9990 chunk 147 optimal weight: 5.9990 chunk 76 optimal weight: 0.7980 chunk 225 optimal weight: 0.0670 chunk 154 optimal weight: 0.9990 chunk 268 optimal weight: 0.0370 chunk 224 optimal weight: 2.9990 chunk 247 optimal weight: 3.9990 overall best weight: 0.4996 ------------------------------------------------------------------------------- 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** C 88 GLN D 88 GLN D 121 GLN F 88 GLN G 88 GLN I 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 = 0.3076 r_free = 0.3076 target = 0.076847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2887 r_free = 0.2887 target = 0.067766 restraints weight = 48030.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069633 restraints weight = 28477.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.070978 restraints weight = 19013.123| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 18795 Z= 0.108 Angle : 0.497 7.795 25704 Z= 0.275 Chirality : 0.043 0.182 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.239 29.328 2772 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 0.00 % Allowed : 0.48 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.17), residues: 2709 helix: 2.90 (0.21), residues: 651 sheet: -1.36 (0.19), residues: 777 loop : -1.61 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.034 0.001 PHE E 29 TYR 0.014 0.003 TYR G 91 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 1009) hydrogen bonds : angle 3.82032 ( 3027) covalent geometry : bond 0.00233 (18795) covalent geometry : angle 0.49717 (25704) *********************** 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 139 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.926 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7421 (mp10) cc_final: 0.6909 (mm-40) REVERT: B 8 LEU cc_start: 0.8876 (tt) cc_final: 0.7638 (tt) REVERT: C 81 GLN cc_start: 0.7526 (mp10) cc_final: 0.6850 (mm-40) REVERT: D 33 THR cc_start: 0.8988 (m) cc_final: 0.8413 (p) REVERT: D 35 GLN cc_start: 0.8840 (pp30) cc_final: 0.8344 (pp30) REVERT: D 38 VAL cc_start: 0.9246 (t) cc_final: 0.8941 (t) REVERT: D 59 ASN cc_start: 0.8871 (t0) cc_final: 0.8502 (t0) REVERT: E 40 GLN cc_start: 0.8513 (tt0) cc_final: 0.7843 (tt0) REVERT: G 81 GLN cc_start: 0.7670 (mp10) cc_final: 0.6852 (mp10) REVERT: H 40 GLN cc_start: 0.8503 (tt0) cc_final: 0.7728 (tt0) REVERT: I 81 GLN cc_start: 0.7524 (mp10) cc_final: 0.6689 (mm-40) REVERT: K 81 GLN cc_start: 0.7634 (mp10) cc_final: 0.7128 (mm-40) REVERT: L 40 GLN cc_start: 0.8895 (tt0) cc_final: 0.8445 (tt0) REVERT: L 71 ILE cc_start: 0.8922 (tt) cc_final: 0.8492 (pt) REVERT: M 81 GLN cc_start: 0.7535 (mp10) cc_final: 0.6672 (tp40) REVERT: O 81 GLN cc_start: 0.7829 (mp10) cc_final: 0.7274 (mm110) REVERT: P 40 GLN cc_start: 0.9087 (tt0) cc_final: 0.8316 (tt0) REVERT: P 71 ILE cc_start: 0.9134 (tt) cc_final: 0.8768 (pt) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2348 time to fit residues: 55.4319 Evaluate side-chains 106 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 1.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 264 optimal weight: 2.9990 chunk 200 optimal weight: 3.9990 chunk 258 optimal weight: 0.9980 chunk 129 optimal weight: 0.9980 chunk 124 optimal weight: 4.9990 chunk 100 optimal weight: 0.7980 chunk 271 optimal weight: 0.9980 chunk 79 optimal weight: 0.5980 chunk 112 optimal weight: 1.9990 chunk 107 optimal weight: 1.9990 chunk 209 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 116 GLN E 121 GLN F 88 GLN G 40 GLN G 88 GLN I 40 GLN M 121 GLN Q 121 GLN S 40 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.075325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.066221 restraints weight = 48412.207| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.068033 restraints weight = 29097.402| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.069334 restraints weight = 19675.747| |-----------------------------------------------------------------------------| r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.3764 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 18795 Z= 0.144 Angle : 0.534 12.513 25704 Z= 0.291 Chirality : 0.044 0.452 3696 Planarity : 0.002 0.018 3108 Dihedral : 4.364 30.514 2772 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.17), residues: 2709 helix: 2.84 (0.21), residues: 651 sheet: -1.31 (0.19), residues: 777 loop : -1.60 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.042 0.002 PHE A 29 TYR 0.014 0.003 TYR G 91 Details of bonding type rmsd hydrogen bonds : bond 0.02769 ( 1009) hydrogen bonds : angle 3.87251 ( 3027) covalent geometry : bond 0.00323 (18795) covalent geometry : angle 0.53440 (25704) ********************** 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 120 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 120 time to evaluate : 1.924 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7471 (mp10) cc_final: 0.6712 (tp-100) REVERT: B 8 LEU cc_start: 0.8889 (tt) cc_final: 0.7698 (tt) REVERT: C 81 GLN cc_start: 0.7570 (mp10) cc_final: 0.6888 (mm-40) REVERT: D 35 GLN cc_start: 0.8832 (pp30) cc_final: 0.8249 (pp30) REVERT: D 59 ASN cc_start: 0.8929 (t0) cc_final: 0.8093 (t0) REVERT: E 40 GLN cc_start: 0.8570 (tt0) cc_final: 0.7814 (tt0) REVERT: G 81 GLN cc_start: 0.7687 (mp10) cc_final: 0.6872 (mp10) REVERT: H 40 GLN cc_start: 0.8569 (tt0) cc_final: 0.7973 (tt0) REVERT: I 81 GLN cc_start: 0.7554 (mp10) cc_final: 0.6733 (mm-40) REVERT: K 81 GLN cc_start: 0.7623 (mp10) cc_final: 0.7050 (mm-40) REVERT: L 71 ILE cc_start: 0.8938 (tt) cc_final: 0.8493 (pt) REVERT: M 81 GLN cc_start: 0.7516 (mp10) cc_final: 0.6716 (tp40) REVERT: O 81 GLN cc_start: 0.7711 (mp10) cc_final: 0.7106 (mm110) REVERT: P 40 GLN cc_start: 0.9103 (tt0) cc_final: 0.8283 (tt0) REVERT: P 71 ILE cc_start: 0.9167 (tt) cc_final: 0.8815 (pt) outliers start: 0 outliers final: 0 residues processed: 120 average time/residue: 0.2358 time to fit residues: 48.3310 Evaluate side-chains 97 residues out of total 2100 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 97 time to evaluate : 1.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 189 optimal weight: 0.9990 chunk 242 optimal weight: 2.9990 chunk 129 optimal weight: 1.9990 chunk 266 optimal weight: 4.9990 chunk 223 optimal weight: 0.5980 chunk 214 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 158 optimal weight: 0.7980 chunk 268 optimal weight: 2.9990 chunk 212 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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** C 88 GLN D 121 GLN F 88 GLN G 88 GLN Q 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.075903 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2869 r_free = 0.2869 target = 0.066729 restraints weight = 48326.936| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068588 restraints weight = 29092.043| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.069896 restraints weight = 19622.361| |-----------------------------------------------------------------------------| r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.3826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 18795 Z= 0.129 Angle : 0.513 9.493 25704 Z= 0.283 Chirality : 0.043 0.170 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.259 30.854 2772 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.17), residues: 2709 helix: 2.89 (0.21), residues: 651 sheet: -1.25 (0.19), residues: 777 loop : -1.59 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE P 29 TYR 0.015 0.003 TYR G 91 Details of bonding type rmsd hydrogen bonds : bond 0.02671 ( 1009) hydrogen bonds : angle 3.82190 ( 3027) covalent geometry : bond 0.00288 (18795) covalent geometry : angle 0.51341 (25704) =============================================================================== Job complete usr+sys time: 4912.94 seconds wall clock time: 89 minutes 20.55 seconds (5360.55 seconds total)