Starting phenix.real_space_refine on Sat Sep 28 03:45:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/09_2024/6nav_0397.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/09_2024/6nav_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/09_2024/6nav_0397.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/09_2024/6nav_0397.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/09_2024/6nav_0397.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6nav_0397/09_2024/6nav_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-5461/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: 4.82, per 1000 atoms: 0.26 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: 4.34 Conformation dependent library (CDL) restraints added in 2.7 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: 3.98 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: 6.26 Time building geometry restraints manager: 5.09 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 9.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.440 Check model and map are aligned: 0.130 Set scattering table: 0.180 Process input model: 37.340 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.330 ------------------------------------------------------------------------------- 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= 0.337 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 346 time to evaluate : 2.170 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: 0.2405 time to fit residues: 139.6036 Evaluate side-chains 137 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 137 time to evaluate : 1.966 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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= 0.171 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 1.810 Fit side-chains REVERT: A 35 GLN cc_start: 0.8531 (pp30) cc_final: 0.7755 (pp30) REVERT: A 81 GLN cc_start: 0.7288 (mp10) cc_final: 0.6763 (mm-40) REVERT: C 81 GLN cc_start: 0.7426 (mp10) cc_final: 0.6954 (mp10) REVERT: C 121 GLN cc_start: 0.8674 (tt0) cc_final: 0.8416 (tt0) REVERT: D 35 GLN cc_start: 0.8870 (pp30) cc_final: 0.7993 (pp30) REVERT: D 59 ASN cc_start: 0.8725 (t0) cc_final: 0.8406 (t0) REVERT: D 60 THR cc_start: 0.8513 (p) cc_final: 0.8186 (t) REVERT: E 40 GLN cc_start: 0.8250 (tt0) cc_final: 0.7770 (tt0) REVERT: E 81 GLN cc_start: 0.7348 (mp10) cc_final: 0.7074 (mp10) REVERT: G 81 GLN cc_start: 0.7502 (mp10) cc_final: 0.6877 (mp10) REVERT: H 40 GLN cc_start: 0.8496 (tt0) cc_final: 0.8082 (tt0) REVERT: H 59 ASN cc_start: 0.8912 (t0) cc_final: 0.8587 (t0) REVERT: H 81 GLN cc_start: 0.6732 (mp10) cc_final: 0.6481 (mm-40) REVERT: I 81 GLN cc_start: 0.7408 (mp10) cc_final: 0.6920 (mm-40) REVERT: J 59 ASN cc_start: 0.8998 (t0) cc_final: 0.8607 (t0) REVERT: K 81 GLN cc_start: 0.7358 (mp10) cc_final: 0.7009 (mm-40) REVERT: L 40 GLN cc_start: 0.8775 (tt0) cc_final: 0.8239 (tt0) REVERT: L 59 ASN cc_start: 0.8694 (t0) cc_final: 0.8222 (t0) REVERT: L 71 ILE cc_start: 0.9052 (tt) cc_final: 0.8762 (pt) REVERT: M 81 GLN cc_start: 0.7712 (mp10) cc_final: 0.6878 (tp40) REVERT: M 91 TYR cc_start: 0.6861 (m-80) cc_final: 0.6618 (m-80) REVERT: O 81 GLN cc_start: 0.7979 (mp10) cc_final: 0.7530 (mm-40) REVERT: O 91 TYR cc_start: 0.6887 (m-80) cc_final: 0.6575 (m-80) REVERT: P 40 GLN cc_start: 0.8992 (tt0) cc_final: 0.8577 (tt0) REVERT: Q 81 GLN cc_start: 0.7647 (mp10) cc_final: 0.7395 (mm110) outliers start: 0 outliers final: 0 residues processed: 206 average time/residue: 0.2330 time to fit residues: 80.3319 Evaluate side-chains 113 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 137 optimal weight: 3.9990 chunk 76 optimal weight: 2.9990 chunk 206 optimal weight: 0.9980 chunk 168 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 248 optimal weight: 0.9980 chunk 268 optimal weight: 3.9990 chunk 221 optimal weight: 3.9990 chunk 246 optimal weight: 3.9990 chunk 84 optimal weight: 5.9990 chunk 199 optimal weight: 1.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 88 GLN H 88 GLN H 121 GLN I 40 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 81 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** M 88 GLN N 88 GLN O 88 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 121 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8332 moved from start: 0.2924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 18795 Z= 0.453 Angle : 0.741 8.208 25704 Z= 0.394 Chirality : 0.047 0.169 3696 Planarity : 0.003 0.019 3108 Dihedral : 5.541 38.990 2772 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.89 % Allowed : 5.94 % Favored : 93.17 % Rotamer: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.73 % 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: -1.17 (0.16), residues: 2709 helix: 2.52 (0.21), residues: 651 sheet: -1.97 (0.18), residues: 777 loop : -1.76 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.003 PHE C 29 TYR 0.037 0.004 TYR S 91 *********************** 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 140 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 2.061 Fit side-chains REVERT: A 81 GLN cc_start: 0.7536 (mp10) cc_final: 0.6566 (tp40) REVERT: A 121 GLN cc_start: 0.8438 (tt0) cc_final: 0.8158 (tt0) REVERT: C 81 GLN cc_start: 0.7521 (mp10) cc_final: 0.6969 (mm-40) REVERT: C 121 GLN cc_start: 0.8729 (tt0) cc_final: 0.8525 (tt0) REVERT: E 81 GLN cc_start: 0.7469 (mp10) cc_final: 0.7133 (mp10) REVERT: G 81 GLN cc_start: 0.7827 (mp10) cc_final: 0.6876 (mp10) REVERT: H 21 VAL cc_start: 0.9091 (t) cc_final: 0.8835 (p) REVERT: H 40 GLN cc_start: 0.8553 (tt0) cc_final: 0.7881 (tt0) REVERT: H 81 GLN cc_start: 0.7249 (mp10) cc_final: 0.6927 (mm-40) REVERT: I 81 GLN cc_start: 0.7515 (mp10) cc_final: 0.6867 (mm-40) REVERT: K 81 GLN cc_start: 0.7722 (mp10) cc_final: 0.7135 (mm-40) REVERT: M 81 GLN cc_start: 0.7712 (mp10) cc_final: 0.6777 (tp40) REVERT: N 29 PHE cc_start: 0.7929 (t80) cc_final: 0.7528 (t80) REVERT: O 81 GLN cc_start: 0.7978 (mp10) cc_final: 0.7124 (mm110) REVERT: O 91 TYR cc_start: 0.7229 (m-80) cc_final: 0.6910 (m-80) REVERT: Q 81 GLN cc_start: 0.7742 (mp10) cc_final: 0.7416 (mm110) REVERT: Q 104 GLN cc_start: 0.8748 (mm-40) cc_final: 0.8524 (mm-40) REVERT: S 121 GLN cc_start: 0.8143 (tp-100) cc_final: 0.7918 (tp-100) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2452 time to fit residues: 57.5325 Evaluate side-chains 93 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 2.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 245 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 128 optimal weight: 0.6980 chunk 27 optimal weight: 0.5980 chunk 118 optimal weight: 0.5980 chunk 166 optimal weight: 1.9990 chunk 249 optimal weight: 0.5980 chunk 263 optimal weight: 2.9990 chunk 130 optimal weight: 0.8980 chunk 236 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 121 GLN F 88 GLN G 40 GLN G 88 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 18795 Z= 0.182 Angle : 0.537 9.199 25704 Z= 0.291 Chirality : 0.043 0.147 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.852 34.045 2772 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.51 % Favored : 96.42 % 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: -0.89 (0.17), residues: 2709 helix: 2.75 (0.21), residues: 651 sheet: -1.88 (0.18), residues: 777 loop : -1.51 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.033 0.001 PHE A 29 TYR 0.015 0.003 TYR H 91 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5418 Ramachandran restraints generated. 2709 Oldfield, 0 Emsley, 2709 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 156 time to evaluate : 1.969 Fit side-chains REVERT: A 59 ASN cc_start: 0.8835 (t0) cc_final: 0.8572 (t0) REVERT: A 81 GLN cc_start: 0.7343 (mp10) cc_final: 0.6816 (mm-40) REVERT: A 121 GLN cc_start: 0.8364 (tt0) cc_final: 0.8113 (tt0) REVERT: C 81 GLN cc_start: 0.7570 (mp10) cc_final: 0.6886 (mm-40) REVERT: D 35 GLN cc_start: 0.8987 (pp30) cc_final: 0.8369 (pp30) REVERT: D 59 ASN cc_start: 0.8933 (t0) cc_final: 0.8316 (t0) REVERT: E 40 GLN cc_start: 0.8563 (tt0) cc_final: 0.8021 (tt0) REVERT: E 81 GLN cc_start: 0.7382 (mp10) cc_final: 0.7049 (mp10) REVERT: G 81 GLN cc_start: 0.7642 (mp10) cc_final: 0.6774 (mp10) REVERT: H 40 GLN cc_start: 0.8567 (tt0) cc_final: 0.7991 (tt0) REVERT: H 59 ASN cc_start: 0.8923 (t0) cc_final: 0.8682 (t0) REVERT: H 71 ILE cc_start: 0.8925 (tt) cc_final: 0.8670 (pt) REVERT: H 81 GLN cc_start: 0.7170 (mp10) cc_final: 0.6964 (mm-40) REVERT: H 124 THR cc_start: 0.8813 (p) cc_final: 0.8440 (p) REVERT: I 81 GLN cc_start: 0.7544 (mp10) cc_final: 0.6708 (mm-40) REVERT: K 81 GLN cc_start: 0.7587 (mp10) cc_final: 0.7019 (mm-40) REVERT: M 81 GLN cc_start: 0.7494 (mp10) cc_final: 0.6671 (tp40) REVERT: O 81 GLN cc_start: 0.7882 (mp10) cc_final: 0.7160 (mm110) REVERT: O 91 TYR cc_start: 0.6855 (m-80) cc_final: 0.6567 (m-80) REVERT: Q 81 GLN cc_start: 0.7663 (mp10) cc_final: 0.7350 (mm110) REVERT: S 121 GLN cc_start: 0.7914 (tp-100) cc_final: 0.7690 (tp-100) outliers start: 0 outliers final: 0 residues processed: 156 average time/residue: 0.2349 time to fit residues: 61.8630 Evaluate side-chains 104 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 219 optimal weight: 0.4980 chunk 149 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 196 optimal weight: 1.9990 chunk 108 optimal weight: 0.5980 chunk 225 optimal weight: 2.9990 chunk 182 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 134 optimal weight: 1.9990 chunk 236 optimal weight: 0.9990 chunk 66 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: D 88 GLN D 121 GLN G 88 GLN ** I 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** 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: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8268 moved from start: 0.3194 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= 0.235 Angle : 0.546 8.372 25704 Z= 0.297 Chirality : 0.043 0.151 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.717 33.447 2772 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.51 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.06 % Favored : 94.87 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % 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: -0.80 (0.17), residues: 2709 helix: 2.86 (0.21), residues: 651 sheet: -1.79 (0.18), residues: 777 loop : -1.51 (0.17), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.030 0.002 PHE B 29 TYR 0.016 0.003 TYR P 91 *********************** 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 140 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.987 Fit side-chains REVERT: A 38 VAL cc_start: 0.9357 (t) cc_final: 0.9086 (t) REVERT: A 59 ASN cc_start: 0.8861 (t0) cc_final: 0.8506 (t0) REVERT: A 81 GLN cc_start: 0.7381 (mp10) cc_final: 0.6845 (mm-40) REVERT: A 121 GLN cc_start: 0.8392 (tt0) cc_final: 0.8125 (tt0) REVERT: C 81 GLN cc_start: 0.7590 (mp10) cc_final: 0.6986 (mm-40) REVERT: D 35 GLN cc_start: 0.9049 (pp30) cc_final: 0.8414 (pp30) REVERT: E 40 GLN cc_start: 0.8690 (tt0) cc_final: 0.8160 (tt0) REVERT: E 81 GLN cc_start: 0.7292 (mp10) cc_final: 0.7040 (mp10) REVERT: F 29 PHE cc_start: 0.7828 (t80) cc_final: 0.7567 (t80) REVERT: G 81 GLN cc_start: 0.7628 (mp10) cc_final: 0.6725 (mp10) REVERT: H 40 GLN cc_start: 0.8595 (tt0) cc_final: 0.8237 (tt0) REVERT: H 59 ASN cc_start: 0.8979 (t0) cc_final: 0.8776 (t0) REVERT: H 81 GLN cc_start: 0.7158 (mp10) cc_final: 0.6896 (mm-40) REVERT: I 81 GLN cc_start: 0.7563 (mp10) cc_final: 0.6727 (mm-40) REVERT: K 81 GLN cc_start: 0.7574 (mp10) cc_final: 0.7031 (mm-40) REVERT: L 71 ILE cc_start: 0.8923 (tt) cc_final: 0.8513 (pt) REVERT: M 81 GLN cc_start: 0.7439 (mp10) cc_final: 0.6582 (tp40) REVERT: O 81 GLN cc_start: 0.7935 (mp10) cc_final: 0.7055 (mm110) REVERT: Q 81 GLN cc_start: 0.7616 (mp10) cc_final: 0.7316 (mm110) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2499 time to fit residues: 59.0321 Evaluate side-chains 101 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 1.794 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 88 optimal weight: 5.9990 chunk 237 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 154 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 264 optimal weight: 1.9990 chunk 219 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 87 optimal weight: 0.7980 chunk 138 optimal weight: 5.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN T 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 18795 Z= 0.210 Angle : 0.526 9.677 25704 Z= 0.288 Chirality : 0.042 0.160 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.618 32.537 2772 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.11 % Allowed : 4.17 % Favored : 95.72 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.64 (0.17), residues: 2709 helix: 2.88 (0.21), residues: 651 sheet: -1.40 (0.19), residues: 735 loop : -1.58 (0.17), residues: 1323 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE E 29 TYR 0.020 0.003 TYR B 91 *********************** 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 138 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.949 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7352 (mp10) cc_final: 0.6524 (tp-100) REVERT: A 121 GLN cc_start: 0.8382 (tt0) cc_final: 0.8168 (tt0) REVERT: C 81 GLN cc_start: 0.7536 (mp10) cc_final: 0.6785 (mm-40) REVERT: D 35 GLN cc_start: 0.9012 (pp30) cc_final: 0.8321 (pp30) REVERT: D 59 ASN cc_start: 0.8881 (t0) cc_final: 0.8115 (t0) REVERT: E 40 GLN cc_start: 0.8670 (tt0) cc_final: 0.8142 (tt0) REVERT: E 81 GLN cc_start: 0.7357 (mp10) cc_final: 0.7070 (mp10) REVERT: G 81 GLN cc_start: 0.7630 (mp10) cc_final: 0.6721 (mp10) REVERT: H 40 GLN cc_start: 0.8600 (tt0) cc_final: 0.7909 (tt0) REVERT: H 81 GLN cc_start: 0.7188 (mp10) cc_final: 0.6909 (mm-40) REVERT: I 81 GLN cc_start: 0.7546 (mp10) cc_final: 0.6732 (mm-40) REVERT: I 114 THR cc_start: 0.9358 (m) cc_final: 0.9006 (p) REVERT: K 81 GLN cc_start: 0.7536 (mp10) cc_final: 0.6997 (mm-40) REVERT: L 71 ILE cc_start: 0.8958 (tt) cc_final: 0.8563 (pt) REVERT: M 81 GLN cc_start: 0.7407 (mp10) cc_final: 0.6568 (tp40) REVERT: O 81 GLN cc_start: 0.7844 (mp10) cc_final: 0.7040 (mm110) REVERT: Q 81 GLN cc_start: 0.7604 (mp10) cc_final: 0.7305 (mm110) REVERT: R 29 PHE cc_start: 0.7743 (t80) cc_final: 0.7494 (t80) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.2451 time to fit residues: 57.0354 Evaluate side-chains 98 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 254 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 150 optimal weight: 0.9990 chunk 192 optimal weight: 0.7980 chunk 149 optimal weight: 1.9990 chunk 222 optimal weight: 0.8980 chunk 147 optimal weight: 5.9990 chunk 263 optimal weight: 0.5980 chunk 164 optimal weight: 0.5980 chunk 160 optimal weight: 0.8980 chunk 121 optimal weight: 3.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 88 GLN D 121 GLN F 88 GLN G 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.3448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18795 Z= 0.193 Angle : 0.516 6.702 25704 Z= 0.284 Chirality : 0.043 0.162 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.466 32.699 2772 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.86 (0.17), residues: 2709 helix: 2.86 (0.21), residues: 651 sheet: -1.88 (0.18), residues: 840 loop : -1.48 (0.18), residues: 1218 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.037 0.002 PHE H 29 TYR 0.015 0.003 TYR K 91 *********************** 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 150 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.988 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7357 (mp10) cc_final: 0.6464 (tp-100) REVERT: A 121 GLN cc_start: 0.8379 (tt0) cc_final: 0.8153 (tt0) REVERT: C 81 GLN cc_start: 0.7541 (mp10) cc_final: 0.6781 (mm-40) REVERT: D 38 VAL cc_start: 0.9262 (t) cc_final: 0.9004 (t) REVERT: D 59 ASN cc_start: 0.8896 (t0) cc_final: 0.8149 (t0) REVERT: E 40 GLN cc_start: 0.8612 (tt0) cc_final: 0.8193 (tt0) REVERT: G 81 GLN cc_start: 0.7600 (mp10) cc_final: 0.6713 (mp10) REVERT: H 40 GLN cc_start: 0.8593 (tt0) cc_final: 0.8132 (tt0) REVERT: H 71 ILE cc_start: 0.8891 (tt) cc_final: 0.8585 (pt) REVERT: H 81 GLN cc_start: 0.7220 (mp10) cc_final: 0.6916 (mm-40) REVERT: I 81 GLN cc_start: 0.7539 (mp10) cc_final: 0.6693 (mm-40) REVERT: I 114 THR cc_start: 0.9349 (m) cc_final: 0.9034 (p) REVERT: J 71 ILE cc_start: 0.8892 (tt) cc_final: 0.8682 (pt) REVERT: K 81 GLN cc_start: 0.7560 (mp10) cc_final: 0.6962 (mm-40) REVERT: L 71 ILE cc_start: 0.8906 (tt) cc_final: 0.8487 (pt) REVERT: M 81 GLN cc_start: 0.7401 (mp10) cc_final: 0.6543 (tp40) REVERT: O 81 GLN cc_start: 0.7801 (mp10) cc_final: 0.7118 (mm110) REVERT: Q 81 GLN cc_start: 0.7600 (mp10) cc_final: 0.7305 (mm110) REVERT: R 29 PHE cc_start: 0.7800 (t80) cc_final: 0.7512 (t80) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2458 time to fit residues: 62.4840 Evaluate side-chains 105 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 1.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 162 optimal weight: 0.9990 chunk 105 optimal weight: 0.5980 chunk 157 optimal weight: 0.9980 chunk 79 optimal weight: 0.6980 chunk 51 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 167 optimal weight: 0.9980 chunk 179 optimal weight: 2.9990 chunk 130 optimal weight: 0.4980 chunk 24 optimal weight: 0.0060 chunk 206 optimal weight: 0.7980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 88 GLN C 88 GLN E 121 GLN F 88 GLN G 88 GLN ** H 88 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Q 121 GLN U 40 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.3543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 18795 Z= 0.142 Angle : 0.474 7.111 25704 Z= 0.263 Chirality : 0.042 0.153 3696 Planarity : 0.002 0.016 3108 Dihedral : 4.207 28.647 2772 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.57 (0.17), residues: 2709 helix: 2.73 (0.21), residues: 672 sheet: -1.36 (0.19), residues: 777 loop : -1.47 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.038 0.002 PHE E 29 TYR 0.013 0.002 TYR P 91 *********************** 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 152 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 2.095 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7334 (mp10) cc_final: 0.6784 (mm-40) REVERT: A 121 GLN cc_start: 0.8343 (tt0) cc_final: 0.8106 (tt0) REVERT: C 81 GLN cc_start: 0.7498 (mp10) cc_final: 0.6708 (mm-40) REVERT: C 121 GLN cc_start: 0.8694 (tt0) cc_final: 0.8480 (tt0) REVERT: D 35 GLN cc_start: 0.8659 (pp30) cc_final: 0.8275 (pp30) REVERT: D 59 ASN cc_start: 0.8866 (t0) cc_final: 0.8211 (t0) REVERT: E 40 GLN cc_start: 0.8552 (tt0) cc_final: 0.8117 (tt0) REVERT: E 81 GLN cc_start: 0.7320 (mp10) cc_final: 0.6508 (mm110) REVERT: G 81 GLN cc_start: 0.7566 (mp10) cc_final: 0.6677 (mp10) REVERT: H 40 GLN cc_start: 0.8558 (tt0) cc_final: 0.7907 (tt0) REVERT: H 71 ILE cc_start: 0.8904 (tt) cc_final: 0.8582 (pt) REVERT: H 81 GLN cc_start: 0.7217 (mp10) cc_final: 0.6891 (mm-40) REVERT: I 81 GLN cc_start: 0.7463 (mp10) cc_final: 0.6605 (mm-40) REVERT: K 81 GLN cc_start: 0.7509 (mp10) cc_final: 0.6914 (mm-40) REVERT: L 40 GLN cc_start: 0.8847 (tt0) cc_final: 0.8440 (tt0) REVERT: L 71 ILE cc_start: 0.8910 (tt) cc_final: 0.8485 (pt) REVERT: M 81 GLN cc_start: 0.7362 (mp10) cc_final: 0.6506 (tp40) REVERT: O 81 GLN cc_start: 0.7902 (mp10) cc_final: 0.7278 (mm110) REVERT: Q 81 GLN cc_start: 0.7567 (mp10) cc_final: 0.7282 (mm110) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.2476 time to fit residues: 63.1627 Evaluate side-chains 108 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 1.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 239 optimal weight: 3.9990 chunk 252 optimal weight: 0.9990 chunk 229 optimal weight: 5.9990 chunk 245 optimal weight: 1.9990 chunk 147 optimal weight: 4.9990 chunk 106 optimal weight: 0.9990 chunk 192 optimal weight: 4.9990 chunk 75 optimal weight: 0.9990 chunk 221 optimal weight: 0.0170 chunk 231 optimal weight: 4.9990 chunk 244 optimal weight: 3.9990 overall best weight: 1.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 121 GLN F 88 GLN G 40 GLN G 88 GLN H 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8262 moved from start: 0.3634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 18795 Z= 0.240 Angle : 0.551 6.185 25704 Z= 0.301 Chirality : 0.044 0.185 3696 Planarity : 0.002 0.015 3108 Dihedral : 4.439 30.306 2772 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.50 % Favored : 94.50 % Rotamer: Outliers : 0.00 % Allowed : 0.76 % Favored : 99.24 % 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: -0.63 (0.17), residues: 2709 helix: 2.63 (0.21), residues: 672 sheet: -1.33 (0.19), residues: 777 loop : -1.52 (0.18), residues: 1260 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.035 0.002 PHE B 29 TYR 0.016 0.003 TYR M 91 *********************** 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 135 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 1.958 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7458 (mp10) cc_final: 0.6644 (tp-100) REVERT: A 121 GLN cc_start: 0.8400 (tt0) cc_final: 0.8175 (tt0) REVERT: B 88 GLN cc_start: 0.7997 (mt0) cc_final: 0.7743 (mt0) REVERT: B 114 THR cc_start: 0.9488 (m) cc_final: 0.8942 (p) REVERT: C 81 GLN cc_start: 0.7502 (mp10) cc_final: 0.6817 (mm-40) REVERT: C 91 TYR cc_start: 0.7516 (m-80) cc_final: 0.7241 (m-80) REVERT: D 35 GLN cc_start: 0.8738 (pp30) cc_final: 0.8262 (pp30) REVERT: D 38 VAL cc_start: 0.9238 (t) cc_final: 0.8974 (t) REVERT: D 59 ASN cc_start: 0.8977 (t0) cc_final: 0.8271 (t0) REVERT: E 40 GLN cc_start: 0.8638 (tt0) cc_final: 0.8167 (tt0) REVERT: E 81 GLN cc_start: 0.7352 (mp10) cc_final: 0.6500 (mm110) REVERT: G 81 GLN cc_start: 0.7619 (mp10) cc_final: 0.6723 (mp10) REVERT: H 40 GLN cc_start: 0.8554 (tt0) cc_final: 0.8042 (tt0) REVERT: H 71 ILE cc_start: 0.8931 (tt) cc_final: 0.8601 (pt) REVERT: H 81 GLN cc_start: 0.7435 (mp10) cc_final: 0.7000 (mm-40) REVERT: I 81 GLN cc_start: 0.7528 (mp10) cc_final: 0.6678 (mm-40) REVERT: K 81 GLN cc_start: 0.7546 (mp10) cc_final: 0.6948 (mm-40) REVERT: L 71 ILE cc_start: 0.8906 (tt) cc_final: 0.8503 (pt) REVERT: M 81 GLN cc_start: 0.7445 (mp10) cc_final: 0.6553 (tp40) REVERT: O 81 GLN cc_start: 0.7783 (mp10) cc_final: 0.7094 (mm110) REVERT: Q 81 GLN cc_start: 0.7608 (mp10) cc_final: 0.7310 (mm110) REVERT: T 88 GLN cc_start: 0.7147 (pm20) cc_final: 0.6930 (pt0) outliers start: 0 outliers final: 0 residues processed: 135 average time/residue: 0.2527 time to fit residues: 57.6709 Evaluate side-chains 104 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 1.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 161 optimal weight: 5.9990 chunk 259 optimal weight: 0.7980 chunk 158 optimal weight: 0.5980 chunk 123 optimal weight: 3.9990 chunk 180 optimal weight: 0.6980 chunk 271 optimal weight: 0.7980 chunk 250 optimal weight: 0.7980 chunk 216 optimal weight: 3.9990 chunk 22 optimal weight: 3.9990 chunk 167 optimal weight: 3.9990 chunk 132 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 F 88 GLN G 88 GLN H 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 18795 Z= 0.188 Angle : 0.507 5.937 25704 Z= 0.280 Chirality : 0.043 0.157 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.309 30.025 2772 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % 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: -0.59 (0.17), residues: 2709 helix: 2.90 (0.21), residues: 651 sheet: -1.26 (0.19), residues: 777 loop : -1.60 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.040 0.002 PHE E 29 TYR 0.016 0.003 TYR G 91 ********************** 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 141 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 1.851 Fit side-chains revert: symmetry clash REVERT: A 81 GLN cc_start: 0.7432 (mp10) cc_final: 0.6631 (tp-100) REVERT: A 121 GLN cc_start: 0.8376 (tt0) cc_final: 0.8144 (tt0) REVERT: C 81 GLN cc_start: 0.7558 (mp10) cc_final: 0.6763 (mm-40) REVERT: D 38 VAL cc_start: 0.9241 (t) cc_final: 0.9020 (t) REVERT: D 59 ASN cc_start: 0.8903 (t0) cc_final: 0.8228 (t0) REVERT: E 40 GLN cc_start: 0.8587 (tt0) cc_final: 0.8129 (tt0) REVERT: E 81 GLN cc_start: 0.7337 (mp10) cc_final: 0.6482 (mm110) REVERT: G 81 GLN cc_start: 0.7590 (mp10) cc_final: 0.6704 (mp10) REVERT: H 40 GLN cc_start: 0.8599 (tt0) cc_final: 0.8106 (tt0) REVERT: H 71 ILE cc_start: 0.8912 (tt) cc_final: 0.8605 (pt) REVERT: H 81 GLN cc_start: 0.7506 (mp10) cc_final: 0.6932 (mm-40) REVERT: I 81 GLN cc_start: 0.7483 (mp10) cc_final: 0.6620 (mm-40) REVERT: K 81 GLN cc_start: 0.7460 (mp10) cc_final: 0.6862 (mm-40) REVERT: L 40 GLN cc_start: 0.8875 (tt0) cc_final: 0.8406 (tt0) REVERT: L 71 ILE cc_start: 0.8893 (tt) cc_final: 0.8473 (pt) REVERT: M 81 GLN cc_start: 0.7386 (mp10) cc_final: 0.6537 (tp40) REVERT: O 81 GLN cc_start: 0.7872 (mp10) cc_final: 0.7237 (mm110) REVERT: Q 81 GLN cc_start: 0.7592 (mp10) cc_final: 0.7294 (mm110) REVERT: S 74 ASN cc_start: 0.7546 (m-40) cc_final: 0.6717 (p0) outliers start: 0 outliers final: 0 residues processed: 141 average time/residue: 0.2668 time to fit residues: 63.3605 Evaluate side-chains 107 residues out of total 2100 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 1.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 273 random chunks: chunk 172 optimal weight: 1.9990 chunk 230 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 199 optimal weight: 0.7980 chunk 31 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 216 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 222 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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** F 88 GLN G 88 GLN ** K 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 121 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.075499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.066223 restraints weight = 48370.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2900 r_free = 0.2900 target = 0.068106 restraints weight = 29037.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.069375 restraints weight = 19622.688| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.3763 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= 0.199 Angle : 0.515 5.861 25704 Z= 0.284 Chirality : 0.043 0.166 3696 Planarity : 0.002 0.017 3108 Dihedral : 4.269 29.888 2772 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.09 % Favored : 94.91 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.60 (0.17), residues: 2709 helix: 2.88 (0.21), residues: 651 sheet: -1.22 (0.19), residues: 777 loop : -1.63 (0.18), residues: 1281 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.039 0.002 PHE E 29 TYR 0.015 0.003 TYR G 91 =============================================================================== Job complete usr+sys time: 2871.65 seconds wall clock time: 54 minutes 18.68 seconds (3258.68 seconds total)