Starting phenix.real_space_refine on Wed Mar 4 20:01:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rib_4887/03_2026/6rib_4887_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rib_4887/03_2026/6rib_4887.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6rib_4887/03_2026/6rib_4887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rib_4887/03_2026/6rib_4887.map" model { file = "/net/cci-nas-00/data/ceres_data/6rib_4887/03_2026/6rib_4887_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rib_4887/03_2026/6rib_4887_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 22 5.16 5 C 10208 2.51 5 N 2926 2.21 5 O 3212 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 220 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 16368 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 744 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 2, 'TRANS': 98} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V Time building chain proxies: 1.10, per 1000 atoms: 0.07 Number of scatterers: 16368 At special positions: 0 Unit cell: (49.22, 78.11, 337.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 22 16.00 O 3212 8.00 N 2926 7.00 C 10208 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.16 Conformation dependent library (CDL) restraints added in 752.7 milliseconds 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3828 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 0 helices and 88 sheets defined 0.0% alpha, 23.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing sheet with id= A, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU A 36 " --> pdb=" O VAL A 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= A Processing sheet with id= B, first strand: chain 'A' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU A 42 " --> pdb=" O ALA A 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= B Processing sheet with id= C, first strand: chain 'A' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER A 64 " --> pdb=" O LEU A 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL A 49 " --> pdb=" O SER A 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU A 66 " --> pdb=" O VAL A 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS A 79 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE A 67 " --> pdb=" O LYS A 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL A 81 " --> pdb=" O ILE A 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA A 96 " --> pdb=" O VAL A 80 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU A 70 " --> pdb=" O VAL A 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= D Processing sheet with id= E, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU B 36 " --> pdb=" O VAL B 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= E Processing sheet with id= F, first strand: chain 'B' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU B 42 " --> pdb=" O ALA B 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= F Processing sheet with id= G, first strand: chain 'B' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER B 64 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL B 49 " --> pdb=" O SER B 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU B 66 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS B 79 " --> pdb=" O VAL B 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE B 67 " --> pdb=" O LYS B 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL B 81 " --> pdb=" O ILE B 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA B 96 " --> pdb=" O VAL B 80 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU B 70 " --> pdb=" O VAL B 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= H Processing sheet with id= I, first strand: chain 'C' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU C 36 " --> pdb=" O VAL C 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'C' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU C 42 " --> pdb=" O ALA C 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= J Processing sheet with id= K, first strand: chain 'C' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER C 64 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL C 49 " --> pdb=" O SER C 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU C 66 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS C 79 " --> pdb=" O VAL C 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE C 67 " --> pdb=" O LYS C 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL C 81 " --> pdb=" O ILE C 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA C 96 " --> pdb=" O VAL C 80 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU C 70 " --> pdb=" O VAL C 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= L Processing sheet with id= M, first strand: chain 'D' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU D 36 " --> pdb=" O VAL D 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= M Processing sheet with id= N, first strand: chain 'D' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU D 42 " --> pdb=" O ALA D 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= N Processing sheet with id= O, first strand: chain 'D' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER D 64 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL D 49 " --> pdb=" O SER D 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU D 66 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS D 79 " --> pdb=" O VAL D 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE D 67 " --> pdb=" O LYS D 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL D 81 " --> pdb=" O ILE D 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA D 96 " --> pdb=" O VAL D 80 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU D 70 " --> pdb=" O VAL D 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= P Processing sheet with id= Q, first strand: chain 'E' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU E 36 " --> pdb=" O VAL E 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Q Processing sheet with id= R, first strand: chain 'E' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU E 42 " --> pdb=" O ALA E 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= R Processing sheet with id= S, first strand: chain 'E' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER E 64 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL E 49 " --> pdb=" O SER E 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU E 66 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS E 79 " --> pdb=" O VAL E 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE E 67 " --> pdb=" O LYS E 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL E 81 " --> pdb=" O ILE E 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA E 96 " --> pdb=" O VAL E 80 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU E 70 " --> pdb=" O VAL E 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= T Processing sheet with id= U, first strand: chain 'F' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU F 36 " --> pdb=" O VAL F 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= U Processing sheet with id= V, first strand: chain 'F' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU F 42 " --> pdb=" O ALA F 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= V Processing sheet with id= W, first strand: chain 'F' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER F 64 " --> pdb=" O LEU F 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL F 49 " --> pdb=" O SER F 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU F 66 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS F 79 " --> pdb=" O VAL F 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE F 67 " --> pdb=" O LYS F 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL F 81 " --> pdb=" O ILE F 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA F 96 " --> pdb=" O VAL F 80 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU F 70 " --> pdb=" O VAL F 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= X Processing sheet with id= Y, first strand: chain 'G' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU G 36 " --> pdb=" O VAL G 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= Y Processing sheet with id= Z, first strand: chain 'G' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU G 42 " --> pdb=" O ALA G 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= Z Processing sheet with id= AA, first strand: chain 'G' and resid 31 through 33 removed outlier: 6.075A pdb=" N SER G 64 " --> pdb=" O LEU G 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL G 49 " --> pdb=" O SER G 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU G 66 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS G 79 " --> pdb=" O VAL G 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE G 67 " --> pdb=" O LYS G 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL G 81 " --> pdb=" O ILE G 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA G 96 " --> pdb=" O VAL G 80 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU G 70 " --> pdb=" O VAL G 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AB Processing sheet with id= AC, first strand: chain 'H' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU H 36 " --> pdb=" O VAL H 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AC Processing sheet with id= AD, first strand: chain 'H' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU H 42 " --> pdb=" O ALA H 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AD Processing sheet with id= AE, first strand: chain 'H' and resid 31 through 33 removed outlier: 6.078A pdb=" N SER H 64 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL H 49 " --> pdb=" O SER H 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU H 66 " --> pdb=" O VAL H 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS H 79 " --> pdb=" O VAL H 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE H 67 " --> pdb=" O LYS H 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL H 81 " --> pdb=" O ILE H 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA H 96 " --> pdb=" O VAL H 80 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU H 70 " --> pdb=" O VAL H 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AF Processing sheet with id= AG, first strand: chain 'I' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU I 36 " --> pdb=" O VAL I 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AG Processing sheet with id= AH, first strand: chain 'I' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU I 42 " --> pdb=" O ALA I 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AH Processing sheet with id= AI, first strand: chain 'I' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER I 64 " --> pdb=" O LEU I 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL I 49 " --> pdb=" O SER I 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU I 66 " --> pdb=" O VAL I 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS I 79 " --> pdb=" O VAL I 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE I 67 " --> pdb=" O LYS I 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 81 " --> pdb=" O ILE I 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA I 96 " --> pdb=" O VAL I 80 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU I 70 " --> pdb=" O VAL I 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AJ Processing sheet with id= AK, first strand: chain 'J' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU J 36 " --> pdb=" O VAL J 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AK Processing sheet with id= AL, first strand: chain 'J' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU J 42 " --> pdb=" O ALA J 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AL Processing sheet with id= AM, first strand: chain 'J' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER J 64 " --> pdb=" O LEU J 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL J 49 " --> pdb=" O SER J 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU J 66 " --> pdb=" O VAL J 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS J 79 " --> pdb=" O VAL J 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE J 67 " --> pdb=" O LYS J 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL J 81 " --> pdb=" O ILE J 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA J 96 " --> pdb=" O VAL J 80 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU J 70 " --> pdb=" O VAL J 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AN Processing sheet with id= AO, first strand: chain 'K' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU K 36 " --> pdb=" O VAL K 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AO Processing sheet with id= AP, first strand: chain 'K' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU K 42 " --> pdb=" O ALA K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AP Processing sheet with id= AQ, first strand: chain 'K' and resid 31 through 33 removed outlier: 6.075A pdb=" N SER K 64 " --> pdb=" O LEU K 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL K 49 " --> pdb=" O SER K 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU K 66 " --> pdb=" O VAL K 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS K 79 " --> pdb=" O VAL K 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE K 67 " --> pdb=" O LYS K 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL K 81 " --> pdb=" O ILE K 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA K 96 " --> pdb=" O VAL K 80 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU K 70 " --> pdb=" O VAL K 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AR Processing sheet with id= AS, first strand: chain 'L' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU L 36 " --> pdb=" O VAL L 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AS Processing sheet with id= AT, first strand: chain 'L' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU L 42 " --> pdb=" O ALA L 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AT Processing sheet with id= AU, first strand: chain 'L' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER L 64 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL L 49 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU L 66 " --> pdb=" O VAL L 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS L 79 " --> pdb=" O VAL L 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE L 67 " --> pdb=" O LYS L 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL L 81 " --> pdb=" O ILE L 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA L 96 " --> pdb=" O VAL L 80 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU L 70 " --> pdb=" O VAL L 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AV Processing sheet with id= AW, first strand: chain 'M' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU M 36 " --> pdb=" O VAL M 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= AW Processing sheet with id= AX, first strand: chain 'M' and resid 26 through 28 removed outlier: 6.281A pdb=" N LEU M 42 " --> pdb=" O ALA M 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= AX Processing sheet with id= AY, first strand: chain 'M' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER M 64 " --> pdb=" O LEU M 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL M 49 " --> pdb=" O SER M 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU M 66 " --> pdb=" O VAL M 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS M 79 " --> pdb=" O VAL M 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE M 67 " --> pdb=" O LYS M 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL M 81 " --> pdb=" O ILE M 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA M 96 " --> pdb=" O VAL M 80 " (cutoff:3.500A) Processing sheet with id= AZ, first strand: chain 'M' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU M 70 " --> pdb=" O VAL M 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= AZ Processing sheet with id= BA, first strand: chain 'N' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU N 36 " --> pdb=" O VAL N 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BA Processing sheet with id= BB, first strand: chain 'N' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU N 42 " --> pdb=" O ALA N 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BB Processing sheet with id= BC, first strand: chain 'N' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER N 64 " --> pdb=" O LEU N 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL N 49 " --> pdb=" O SER N 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU N 66 " --> pdb=" O VAL N 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS N 79 " --> pdb=" O VAL N 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE N 67 " --> pdb=" O LYS N 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL N 81 " --> pdb=" O ILE N 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA N 96 " --> pdb=" O VAL N 80 " (cutoff:3.500A) Processing sheet with id= BD, first strand: chain 'N' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU N 70 " --> pdb=" O VAL N 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BD Processing sheet with id= BE, first strand: chain 'O' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU O 36 " --> pdb=" O VAL O 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BE Processing sheet with id= BF, first strand: chain 'O' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU O 42 " --> pdb=" O ALA O 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BF Processing sheet with id= BG, first strand: chain 'O' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER O 64 " --> pdb=" O LEU O 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL O 49 " --> pdb=" O SER O 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU O 66 " --> pdb=" O VAL O 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS O 79 " --> pdb=" O VAL O 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE O 67 " --> pdb=" O LYS O 79 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL O 81 " --> pdb=" O ILE O 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA O 96 " --> pdb=" O VAL O 80 " (cutoff:3.500A) Processing sheet with id= BH, first strand: chain 'O' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU O 70 " --> pdb=" O VAL O 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BH Processing sheet with id= BI, first strand: chain 'P' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU P 36 " --> pdb=" O VAL P 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BI Processing sheet with id= BJ, first strand: chain 'P' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU P 42 " --> pdb=" O ALA P 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BJ Processing sheet with id= BK, first strand: chain 'P' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER P 64 " --> pdb=" O LEU P 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL P 49 " --> pdb=" O SER P 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU P 66 " --> pdb=" O VAL P 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS P 79 " --> pdb=" O VAL P 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE P 67 " --> pdb=" O LYS P 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL P 81 " --> pdb=" O ILE P 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA P 96 " --> pdb=" O VAL P 80 " (cutoff:3.500A) Processing sheet with id= BL, first strand: chain 'P' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU P 70 " --> pdb=" O VAL P 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BL Processing sheet with id= BM, first strand: chain 'Q' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU Q 36 " --> pdb=" O VAL Q 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BM Processing sheet with id= BN, first strand: chain 'Q' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU Q 42 " --> pdb=" O ALA Q 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BN Processing sheet with id= BO, first strand: chain 'Q' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER Q 64 " --> pdb=" O LEU Q 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL Q 49 " --> pdb=" O SER Q 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU Q 66 " --> pdb=" O VAL Q 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS Q 79 " --> pdb=" O VAL Q 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE Q 67 " --> pdb=" O LYS Q 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL Q 81 " --> pdb=" O ILE Q 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA Q 96 " --> pdb=" O VAL Q 80 " (cutoff:3.500A) Processing sheet with id= BP, first strand: chain 'Q' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU Q 70 " --> pdb=" O VAL Q 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BP Processing sheet with id= BQ, first strand: chain 'R' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU R 36 " --> pdb=" O VAL R 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BQ Processing sheet with id= BR, first strand: chain 'R' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU R 42 " --> pdb=" O ALA R 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BR Processing sheet with id= BS, first strand: chain 'R' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER R 64 " --> pdb=" O LEU R 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL R 49 " --> pdb=" O SER R 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU R 66 " --> pdb=" O VAL R 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS R 79 " --> pdb=" O VAL R 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE R 67 " --> pdb=" O LYS R 79 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N VAL R 81 " --> pdb=" O ILE R 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA R 96 " --> pdb=" O VAL R 80 " (cutoff:3.500A) Processing sheet with id= BT, first strand: chain 'R' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU R 70 " --> pdb=" O VAL R 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BT Processing sheet with id= BU, first strand: chain 'S' and resid 20 through 22 removed outlier: 6.854A pdb=" N LEU S 36 " --> pdb=" O VAL S 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BU Processing sheet with id= BV, first strand: chain 'S' and resid 26 through 28 removed outlier: 6.281A pdb=" N LEU S 42 " --> pdb=" O ALA S 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BV Processing sheet with id= BW, first strand: chain 'S' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER S 64 " --> pdb=" O LEU S 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL S 49 " --> pdb=" O SER S 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU S 66 " --> pdb=" O VAL S 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS S 79 " --> pdb=" O VAL S 65 " (cutoff:3.500A) removed outlier: 7.511A pdb=" N ILE S 67 " --> pdb=" O LYS S 79 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N VAL S 81 " --> pdb=" O ILE S 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA S 96 " --> pdb=" O VAL S 80 " (cutoff:3.500A) Processing sheet with id= BX, first strand: chain 'S' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU S 70 " --> pdb=" O VAL S 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= BX Processing sheet with id= BY, first strand: chain 'T' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU T 36 " --> pdb=" O VAL T 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= BY Processing sheet with id= BZ, first strand: chain 'T' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU T 42 " --> pdb=" O ALA T 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= BZ Processing sheet with id= CA, first strand: chain 'T' and resid 31 through 33 removed outlier: 6.077A pdb=" N SER T 64 " --> pdb=" O LEU T 47 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N VAL T 49 " --> pdb=" O SER T 64 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU T 66 " --> pdb=" O VAL T 49 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N LYS T 79 " --> pdb=" O VAL T 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE T 67 " --> pdb=" O LYS T 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL T 81 " --> pdb=" O ILE T 67 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ALA T 96 " --> pdb=" O VAL T 80 " (cutoff:3.500A) Processing sheet with id= CB, first strand: chain 'T' and resid 54 through 56 removed outlier: 7.484A pdb=" N GLU T 70 " --> pdb=" O VAL T 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CB Processing sheet with id= CC, first strand: chain 'U' and resid 20 through 22 removed outlier: 6.853A pdb=" N LEU U 36 " --> pdb=" O VAL U 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= CC Processing sheet with id= CD, first strand: chain 'U' and resid 26 through 28 removed outlier: 6.280A pdb=" N LEU U 42 " --> pdb=" O ALA U 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CD Processing sheet with id= CE, first strand: chain 'U' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER U 64 " --> pdb=" O LEU U 47 " (cutoff:3.500A) removed outlier: 7.600A pdb=" N VAL U 49 " --> pdb=" O SER U 64 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N LEU U 66 " --> pdb=" O VAL U 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS U 79 " --> pdb=" O VAL U 65 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N ILE U 67 " --> pdb=" O LYS U 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL U 81 " --> pdb=" O ILE U 67 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ALA U 96 " --> pdb=" O VAL U 80 " (cutoff:3.500A) Processing sheet with id= CF, first strand: chain 'U' and resid 54 through 56 removed outlier: 7.486A pdb=" N GLU U 70 " --> pdb=" O VAL U 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CF Processing sheet with id= CG, first strand: chain 'V' and resid 20 through 22 removed outlier: 6.855A pdb=" N LEU V 36 " --> pdb=" O VAL V 21 " (cutoff:3.500A) No H-bonds generated for sheet with id= CG Processing sheet with id= CH, first strand: chain 'V' and resid 26 through 28 removed outlier: 6.279A pdb=" N LEU V 42 " --> pdb=" O ALA V 27 " (cutoff:3.500A) No H-bonds generated for sheet with id= CH Processing sheet with id= CI, first strand: chain 'V' and resid 31 through 33 removed outlier: 6.076A pdb=" N SER V 64 " --> pdb=" O LEU V 47 " (cutoff:3.500A) removed outlier: 7.599A pdb=" N VAL V 49 " --> pdb=" O SER V 64 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N LEU V 66 " --> pdb=" O VAL V 49 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LYS V 79 " --> pdb=" O VAL V 65 " (cutoff:3.500A) removed outlier: 7.512A pdb=" N ILE V 67 " --> pdb=" O LYS V 79 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL V 81 " --> pdb=" O ILE V 67 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA V 96 " --> pdb=" O VAL V 80 " (cutoff:3.500A) Processing sheet with id= CJ, first strand: chain 'V' and resid 54 through 56 removed outlier: 7.485A pdb=" N GLU V 70 " --> pdb=" O VAL V 55 " (cutoff:3.500A) No H-bonds generated for sheet with id= CJ 66 hydrogen bonds defined for protein. 132 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.29 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5764 1.34 - 1.45: 1804 1.45 - 1.57: 8866 1.57 - 1.68: 0 1.68 - 1.80: 44 Bond restraints: 16478 Sorted by residual: bond pdb=" CA GLU S 74 " pdb=" CB GLU S 74 " ideal model delta sigma weight residual 1.524 1.499 0.024 1.33e-02 5.65e+03 3.35e+00 bond pdb=" CA GLU Q 74 " pdb=" CB GLU Q 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.27e+00 bond pdb=" CA GLU C 74 " pdb=" CB GLU C 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.26e+00 bond pdb=" CA GLU A 74 " pdb=" CB GLU A 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.26e+00 bond pdb=" CA GLU K 74 " pdb=" CB GLU K 74 " ideal model delta sigma weight residual 1.524 1.500 0.024 1.33e-02 5.65e+03 3.25e+00 ... (remaining 16473 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.31: 18479 1.31 - 2.61: 3016 2.61 - 3.92: 417 3.92 - 5.22: 176 5.22 - 6.53: 110 Bond angle restraints: 22198 Sorted by residual: angle pdb=" CA ARG I 59 " pdb=" CB ARG I 59 " pdb=" CG ARG I 59 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.32e+00 angle pdb=" CA ARG U 59 " pdb=" CB ARG U 59 " pdb=" CG ARG U 59 " ideal model delta sigma weight residual 114.10 120.15 -6.05 2.00e+00 2.50e-01 9.15e+00 angle pdb=" CA ARG E 59 " pdb=" CB ARG E 59 " pdb=" CG ARG E 59 " ideal model delta sigma weight residual 114.10 120.14 -6.04 2.00e+00 2.50e-01 9.13e+00 angle pdb=" CA ARG M 59 " pdb=" CB ARG M 59 " pdb=" CG ARG M 59 " ideal model delta sigma weight residual 114.10 120.13 -6.03 2.00e+00 2.50e-01 9.11e+00 angle pdb=" CA ARG Q 59 " pdb=" CB ARG Q 59 " pdb=" CG ARG Q 59 " ideal model delta sigma weight residual 114.10 120.12 -6.02 2.00e+00 2.50e-01 9.05e+00 ... (remaining 22193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.17: 8680 17.17 - 34.33: 824 34.33 - 51.50: 242 51.50 - 68.66: 176 68.66 - 85.83: 44 Dihedral angle restraints: 9966 sinusoidal: 3916 harmonic: 6050 Sorted by residual: dihedral pdb=" CA ALA A 101 " pdb=" C ALA A 101 " pdb=" N GLY A 102 " pdb=" CA GLY A 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA H 101 " pdb=" C ALA H 101 " pdb=" N GLY H 102 " pdb=" CA GLY H 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.81e+01 dihedral pdb=" CA ALA D 101 " pdb=" C ALA D 101 " pdb=" N GLY D 102 " pdb=" CA GLY D 102 " ideal model delta harmonic sigma weight residual -180.00 -158.76 -21.24 0 5.00e+00 4.00e-02 1.80e+01 ... (remaining 9963 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 1368 0.032 - 0.065: 626 0.065 - 0.097: 367 0.097 - 0.130: 222 0.130 - 0.162: 101 Chirality restraints: 2684 Sorted by residual: chirality pdb=" CA VAL P 71 " pdb=" N VAL P 71 " pdb=" C VAL P 71 " pdb=" CB VAL P 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.58e-01 chirality pdb=" CA VAL T 71 " pdb=" N VAL T 71 " pdb=" C VAL T 71 " pdb=" CB VAL T 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA VAL A 71 " pdb=" N VAL A 71 " pdb=" C VAL A 71 " pdb=" CB VAL A 71 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.54e-01 ... (remaining 2681 not shown) Planarity restraints: 2904 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 18 " 0.009 2.00e-02 2.50e+03 1.73e-02 3.00e+00 pdb=" C ASP B 18 " -0.030 2.00e-02 2.50e+03 pdb=" O ASP B 18 " 0.011 2.00e-02 2.50e+03 pdb=" N THR B 19 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP T 18 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASP T 18 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP T 18 " -0.011 2.00e-02 2.50e+03 pdb=" N THR T 19 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP H 18 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C ASP H 18 " 0.030 2.00e-02 2.50e+03 pdb=" O ASP H 18 " -0.011 2.00e-02 2.50e+03 pdb=" N THR H 19 " -0.010 2.00e-02 2.50e+03 ... (remaining 2901 not shown) Histogram of nonbonded interaction distances: 0.56 - 1.43: 20 1.43 - 2.30: 40 2.30 - 3.17: 12178 3.17 - 4.03: 42757 4.03 - 4.90: 78621 Warning: very small nonbonded interaction distances. Nonbonded interactions: 133616 Sorted by model distance: nonbonded pdb=" OE1 GLU A 98 " pdb=" O GLU T 100 " model vdw 0.563 3.040 nonbonded pdb=" O GLU P 100 " pdb=" OE1 GLU S 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU L 100 " pdb=" OE1 GLU O 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU D 100 " pdb=" OE1 GLU G 98 " model vdw 0.563 3.040 nonbonded pdb=" O GLU H 100 " pdb=" OE1 GLU K 98 " model vdw 0.564 3.040 ... (remaining 133611 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: 0.05 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' selection = chain 'V' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 11.750 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.060 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6383 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 : 0.008 0.039 16478 Z= 0.394 Angle : 1.117 6.531 22198 Z= 0.630 Chirality : 0.058 0.162 2684 Planarity : 0.004 0.017 2904 Dihedral : 18.477 85.829 6138 Min Nonbonded Distance : 0.563 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.15 % Favored : 89.85 % Rotamer: Outliers : 9.09 % Allowed : 11.69 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.68 (0.13), residues: 2178 helix: None (None), residues: 0 sheet: -3.45 (0.12), residues: 1122 loop : -4.09 (0.13), residues: 1056 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 59 TYR 0.003 0.001 TYR O 14 PHE 0.008 0.003 PHE E 88 HIS 0.005 0.003 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00756 (16478) covalent geometry : angle 1.11657 (22198) hydrogen bonds : bond 0.12949 ( 66) hydrogen bonds : angle 8.64282 ( 132) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 686 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 154 poor density : 532 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 40 SER cc_start: 0.3394 (OUTLIER) cc_final: 0.3154 (t) REVERT: A 78 GLU cc_start: 0.8183 (OUTLIER) cc_final: 0.7724 (tt0) REVERT: A 79 LYS cc_start: 0.8169 (mmtm) cc_final: 0.7653 (tptt) REVERT: A 91 GLN cc_start: 0.6739 (mp10) cc_final: 0.5991 (tm-30) REVERT: B 40 SER cc_start: 0.3284 (OUTLIER) cc_final: 0.3023 (t) REVERT: B 78 GLU cc_start: 0.8187 (OUTLIER) cc_final: 0.7837 (tt0) REVERT: B 79 LYS cc_start: 0.8285 (mmtm) cc_final: 0.7811 (tptt) REVERT: B 91 GLN cc_start: 0.6945 (mp10) cc_final: 0.6494 (tm-30) REVERT: C 20 GLU cc_start: 0.7830 (mp0) cc_final: 0.7600 (mp0) REVERT: C 24 ASP cc_start: 0.6996 (m-30) cc_final: 0.6419 (t0) REVERT: C 40 SER cc_start: 0.6854 (OUTLIER) cc_final: 0.6179 (t) REVERT: C 44 GLU cc_start: 0.5766 (OUTLIER) cc_final: 0.5329 (mm-30) REVERT: D 36 LEU cc_start: 0.8182 (tt) cc_final: 0.7671 (mp) REVERT: D 79 LYS cc_start: 0.8521 (mmtm) cc_final: 0.8143 (mmmm) REVERT: D 93 LYS cc_start: 0.8366 (tttt) cc_final: 0.8005 (tptp) REVERT: E 25 MET cc_start: 0.7459 (ttm) cc_final: 0.6568 (tmm) REVERT: E 26 ARG cc_start: 0.7317 (mtt180) cc_final: 0.6926 (tpt-90) REVERT: E 56 GLU cc_start: 0.7956 (OUTLIER) cc_final: 0.7612 (mm-30) REVERT: E 63 ARG cc_start: 0.8297 (mmt180) cc_final: 0.7904 (mmt180) REVERT: E 72 LYS cc_start: 0.8707 (tttt) cc_final: 0.8438 (tptp) REVERT: F 19 THR cc_start: 0.7128 (OUTLIER) cc_final: 0.6823 (p) REVERT: F 20 GLU cc_start: 0.8034 (mp0) cc_final: 0.7765 (mp0) REVERT: F 26 ARG cc_start: 0.7518 (mtt180) cc_final: 0.6689 (ttm110) REVERT: F 38 ARG cc_start: 0.7939 (tpt90) cc_final: 0.7621 (tpt90) REVERT: F 48 GLU cc_start: 0.7225 (tt0) cc_final: 0.6508 (tm-30) REVERT: F 76 THR cc_start: 0.8215 (m) cc_final: 0.7859 (p) REVERT: F 78 GLU cc_start: 0.7766 (OUTLIER) cc_final: 0.6968 (mm-30) REVERT: G 19 THR cc_start: 0.7480 (OUTLIER) cc_final: 0.6732 (p) REVERT: G 20 GLU cc_start: 0.8083 (mp0) cc_final: 0.7862 (mt-10) REVERT: G 38 ARG cc_start: 0.7893 (tpt90) cc_final: 0.7447 (tpt90) REVERT: G 44 GLU cc_start: 0.6404 (OUTLIER) cc_final: 0.6109 (tm-30) REVERT: G 58 GLU cc_start: 0.7662 (pt0) cc_final: 0.7425 (pt0) REVERT: G 66 LEU cc_start: 0.8074 (mm) cc_final: 0.7807 (mp) REVERT: G 72 LYS cc_start: 0.8733 (tttt) cc_final: 0.8407 (mmtm) REVERT: H 48 GLU cc_start: 0.7248 (tt0) cc_final: 0.6953 (tm-30) REVERT: H 54 ARG cc_start: 0.8036 (ttm110) cc_final: 0.7805 (ttp-110) REVERT: H 70 GLU cc_start: 0.7726 (mt-10) cc_final: 0.7493 (tm-30) REVERT: H 72 LYS cc_start: 0.8753 (tttt) cc_final: 0.8474 (tptp) REVERT: H 78 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: H 79 LYS cc_start: 0.8229 (mmtm) cc_final: 0.7966 (mptt) REVERT: H 93 LYS cc_start: 0.8105 (tttt) cc_final: 0.7871 (tttp) REVERT: H 95 GLN cc_start: 0.8398 (mm-40) cc_final: 0.8033 (mm-40) REVERT: I 19 THR cc_start: 0.6740 (OUTLIER) cc_final: 0.6394 (p) REVERT: I 25 MET cc_start: 0.7028 (ttm) cc_final: 0.6210 (tmm) REVERT: I 44 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7085 (tp30) REVERT: I 70 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7560 (tm-30) REVERT: I 72 LYS cc_start: 0.8504 (tttt) cc_final: 0.7753 (tptp) REVERT: I 78 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.8085 (tp30) REVERT: I 93 LYS cc_start: 0.7814 (tttt) cc_final: 0.7110 (mmtm) REVERT: I 95 GLN cc_start: 0.8833 (mm-40) cc_final: 0.8331 (mm110) REVERT: J 20 GLU cc_start: 0.8029 (mp0) cc_final: 0.7703 (mp0) REVERT: J 38 ARG cc_start: 0.7646 (tpt90) cc_final: 0.7122 (tpt90) REVERT: J 44 GLU cc_start: 0.5607 (OUTLIER) cc_final: 0.5205 (tm-30) REVERT: J 46 GLU cc_start: 0.7757 (tm-30) cc_final: 0.7440 (tm-30) REVERT: J 72 LYS cc_start: 0.8472 (tttt) cc_final: 0.7704 (mppt) REVERT: J 93 LYS cc_start: 0.7493 (tttt) cc_final: 0.6544 (mmtm) REVERT: K 20 GLU cc_start: 0.7694 (mp0) cc_final: 0.7330 (mp0) REVERT: K 24 ASP cc_start: 0.7395 (m-30) cc_final: 0.7109 (t0) REVERT: K 28 LYS cc_start: 0.7178 (mtpp) cc_final: 0.6922 (mtpp) REVERT: K 38 ARG cc_start: 0.7696 (tpt90) cc_final: 0.7486 (tpt90) REVERT: K 59 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.6859 (mmt180) REVERT: K 72 LYS cc_start: 0.8274 (tttt) cc_final: 0.7872 (mmtm) REVERT: K 79 LYS cc_start: 0.8266 (mmtm) cc_final: 0.7910 (tptt) REVERT: K 87 ARG cc_start: 0.7571 (ttm-80) cc_final: 0.7333 (mtp85) REVERT: K 95 GLN cc_start: 0.8339 (mm-40) cc_final: 0.7647 (tp40) REVERT: L 18 ASP cc_start: 0.7436 (p0) cc_final: 0.6544 (p0) REVERT: L 19 THR cc_start: 0.6396 (OUTLIER) cc_final: 0.6189 (p) REVERT: L 20 GLU cc_start: 0.7514 (mp0) cc_final: 0.7176 (mp0) REVERT: L 30 GLN cc_start: 0.7961 (tt0) cc_final: 0.7700 (tm-30) REVERT: L 38 ARG cc_start: 0.7950 (tpt90) cc_final: 0.7520 (tpt90) REVERT: L 78 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7542 (tp30) REVERT: L 93 LYS cc_start: 0.7645 (tttt) cc_final: 0.7324 (tttp) REVERT: L 95 GLN cc_start: 0.8640 (mm-40) cc_final: 0.7928 (mm110) REVERT: M 18 ASP cc_start: 0.7618 (p0) cc_final: 0.7209 (p0) REVERT: M 19 THR cc_start: 0.6797 (OUTLIER) cc_final: 0.6438 (p) REVERT: M 20 GLU cc_start: 0.7586 (mp0) cc_final: 0.7354 (mp0) REVERT: M 30 GLN cc_start: 0.8080 (tt0) cc_final: 0.7838 (tm-30) REVERT: M 38 ARG cc_start: 0.7862 (tpt90) cc_final: 0.7462 (tpt90) REVERT: M 78 GLU cc_start: 0.8439 (OUTLIER) cc_final: 0.7673 (mm-30) REVERT: N 20 GLU cc_start: 0.7740 (mp0) cc_final: 0.7426 (mp0) REVERT: N 24 ASP cc_start: 0.7235 (m-30) cc_final: 0.6821 (t0) REVERT: N 59 ARG cc_start: 0.7662 (OUTLIER) cc_final: 0.7063 (mmm-85) REVERT: N 72 LYS cc_start: 0.8450 (tttt) cc_final: 0.8142 (mmtm) REVERT: N 79 LYS cc_start: 0.8486 (mmtm) cc_final: 0.8139 (tptt) REVERT: N 95 GLN cc_start: 0.8405 (mm-40) cc_final: 0.7764 (tp40) REVERT: O 20 GLU cc_start: 0.8126 (mp0) cc_final: 0.7755 (mp0) REVERT: O 38 ARG cc_start: 0.7685 (tpt90) cc_final: 0.7177 (tpt90) REVERT: O 40 SER cc_start: 0.8314 (OUTLIER) cc_final: 0.8081 (p) REVERT: O 44 GLU cc_start: 0.5761 (OUTLIER) cc_final: 0.5225 (tm-30) REVERT: O 46 GLU cc_start: 0.7655 (tm-30) cc_final: 0.7282 (tm-30) REVERT: O 72 LYS cc_start: 0.8341 (tttt) cc_final: 0.7527 (mppt) REVERT: O 93 LYS cc_start: 0.7317 (tttt) cc_final: 0.6452 (mmtm) REVERT: P 25 MET cc_start: 0.6945 (ttm) cc_final: 0.6166 (tmm) REVERT: P 44 GLU cc_start: 0.7819 (OUTLIER) cc_final: 0.7434 (tp30) REVERT: P 52 THR cc_start: 0.7542 (t) cc_final: 0.7323 (p) REVERT: P 70 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7555 (tm-30) REVERT: P 72 LYS cc_start: 0.8525 (tttt) cc_final: 0.7854 (tptp) REVERT: P 78 GLU cc_start: 0.8641 (OUTLIER) cc_final: 0.8148 (tp30) REVERT: P 93 LYS cc_start: 0.8039 (tttt) cc_final: 0.7282 (mmtm) REVERT: P 95 GLN cc_start: 0.8822 (mm-40) cc_final: 0.8419 (mm110) REVERT: Q 26 ARG cc_start: 0.7540 (mtt180) cc_final: 0.6307 (tpt-90) REVERT: Q 40 SER cc_start: 0.7973 (OUTLIER) cc_final: 0.7761 (t) REVERT: Q 48 GLU cc_start: 0.7392 (tt0) cc_final: 0.7153 (tm-30) REVERT: Q 72 LYS cc_start: 0.8746 (tttt) cc_final: 0.8447 (tptp) REVERT: Q 93 LYS cc_start: 0.8072 (tttt) cc_final: 0.7834 (tttp) REVERT: Q 95 GLN cc_start: 0.8473 (mm-40) cc_final: 0.8137 (mm-40) REVERT: R 19 THR cc_start: 0.7648 (OUTLIER) cc_final: 0.7002 (p) REVERT: R 38 ARG cc_start: 0.7805 (tpt90) cc_final: 0.7391 (tpt90) REVERT: R 44 GLU cc_start: 0.6241 (OUTLIER) cc_final: 0.5969 (tm-30) REVERT: R 58 GLU cc_start: 0.7554 (pt0) cc_final: 0.7161 (pt0) REVERT: S 19 THR cc_start: 0.6933 (OUTLIER) cc_final: 0.6525 (p) REVERT: S 26 ARG cc_start: 0.7307 (mtt180) cc_final: 0.6843 (ttm110) REVERT: S 38 ARG cc_start: 0.8060 (tpt90) cc_final: 0.7695 (tpt90) REVERT: S 40 SER cc_start: 0.8423 (OUTLIER) cc_final: 0.7904 (t) REVERT: S 48 GLU cc_start: 0.7521 (tt0) cc_final: 0.6903 (tm-30) REVERT: S 59 ARG cc_start: 0.8212 (OUTLIER) cc_final: 0.7660 (mmm-85) REVERT: S 66 LEU cc_start: 0.8271 (mm) cc_final: 0.7950 (mp) REVERT: S 72 LYS cc_start: 0.8670 (tttt) cc_final: 0.8443 (mppt) REVERT: S 76 THR cc_start: 0.8007 (m) cc_final: 0.7675 (p) REVERT: S 78 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.6845 (mm-30) REVERT: S 93 LYS cc_start: 0.7903 (tttt) cc_final: 0.7699 (tptp) REVERT: S 95 GLN cc_start: 0.8303 (mm-40) cc_final: 0.8074 (mt0) REVERT: S 108 GLN cc_start: 0.6493 (tt0) cc_final: 0.6249 (pm20) REVERT: T 25 MET cc_start: 0.7459 (ttm) cc_final: 0.6523 (tmm) REVERT: T 26 ARG cc_start: 0.7222 (mtt180) cc_final: 0.6849 (tpt-90) REVERT: T 56 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7595 (mm-30) REVERT: T 58 GLU cc_start: 0.6801 (pt0) cc_final: 0.6177 (pm20) REVERT: T 59 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7149 (tpp80) REVERT: T 92 LEU cc_start: 0.8388 (tt) cc_final: 0.8138 (tp) REVERT: U 25 MET cc_start: 0.7182 (ttm) cc_final: 0.6957 (tmm) REVERT: U 36 LEU cc_start: 0.7920 (tt) cc_final: 0.7631 (mp) REVERT: U 75 LEU cc_start: 0.7846 (tt) cc_final: 0.7628 (tt) REVERT: U 79 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8222 (mmmm) REVERT: U 93 LYS cc_start: 0.8431 (tttt) cc_final: 0.8106 (mptt) REVERT: V 20 GLU cc_start: 0.7842 (mp0) cc_final: 0.7626 (mp0) REVERT: V 24 ASP cc_start: 0.7013 (m-30) cc_final: 0.6600 (t0) REVERT: V 44 GLU cc_start: 0.5540 (OUTLIER) cc_final: 0.5100 (mm-30) outliers start: 154 outliers final: 20 residues processed: 608 average time/residue: 0.1959 time to fit residues: 153.7989 Evaluate side-chains 374 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 318 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 216 optimal weight: 6.9990 chunk 98 optimal weight: 2.9990 chunk 194 optimal weight: 5.9990 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 20.0000 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 6.9990 chunk 200 optimal weight: 9.9990 chunk 212 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN H 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 68 HIS ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4915 r_free = 0.4915 target = 0.114930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4393 r_free = 0.4393 target = 0.086599 restraints weight = 33534.816| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.087319 restraints weight = 21763.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.087237 restraints weight = 19878.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.087764 restraints weight = 17277.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.088290 restraints weight = 15457.066| |-----------------------------------------------------------------------------| r_work (final): 0.4397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7162 moved from start: 0.4307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 16478 Z= 0.325 Angle : 0.815 7.718 22198 Z= 0.430 Chirality : 0.053 0.150 2684 Planarity : 0.006 0.048 2904 Dihedral : 6.725 25.248 2376 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 17.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.58 % Favored : 87.42 % Rotamer: Outliers : 0.12 % Allowed : 7.02 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.51 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.73 (0.12), residues: 1320 loop : -3.10 (0.18), residues: 858 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG T 59 TYR 0.015 0.002 TYR J 14 PHE 0.023 0.003 PHE O 105 HIS 0.003 0.001 HIS F 68 Details of bonding type rmsd covalent geometry : bond 0.00640 (16478) covalent geometry : angle 0.81493 (22198) hydrogen bonds : bond 0.02209 ( 66) hydrogen bonds : angle 5.63862 ( 132) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 363 time to evaluate : 0.571 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.6808 (t70) cc_final: 0.6108 (t70) REVERT: A 72 LYS cc_start: 0.7680 (tmtt) cc_final: 0.7418 (tptp) REVERT: B 72 LYS cc_start: 0.7862 (tmtt) cc_final: 0.7480 (tptp) REVERT: C 24 ASP cc_start: 0.6834 (m-30) cc_final: 0.6539 (t0) REVERT: C 38 ARG cc_start: 0.6354 (ttp80) cc_final: 0.6011 (ttp80) REVERT: C 44 GLU cc_start: 0.5570 (tm-30) cc_final: 0.5347 (mm-30) REVERT: D 78 GLU cc_start: 0.7977 (tt0) cc_final: 0.7663 (tt0) REVERT: D 93 LYS cc_start: 0.8423 (tttt) cc_final: 0.8075 (tptp) REVERT: E 25 MET cc_start: 0.7531 (ttm) cc_final: 0.6605 (tmm) REVERT: E 54 ARG cc_start: 0.7735 (ttm110) cc_final: 0.7525 (mtp-110) REVERT: E 72 LYS cc_start: 0.8715 (tttt) cc_final: 0.8147 (tptp) REVERT: E 78 GLU cc_start: 0.8513 (tp30) cc_final: 0.7501 (tp30) REVERT: E 79 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8691 (mmpt) REVERT: F 26 ARG cc_start: 0.7657 (mtt180) cc_final: 0.6857 (ttm110) REVERT: F 38 ARG cc_start: 0.8191 (tpt90) cc_final: 0.7674 (tpt90) REVERT: F 59 ARG cc_start: 0.7489 (mmt-90) cc_final: 0.7167 (mmm-85) REVERT: G 20 GLU cc_start: 0.8172 (mp0) cc_final: 0.7647 (mt-10) REVERT: G 93 LYS cc_start: 0.8531 (tttt) cc_final: 0.8281 (tttp) REVERT: H 18 ASP cc_start: 0.7655 (p0) cc_final: 0.7013 (p0) REVERT: H 24 ASP cc_start: 0.7362 (t0) cc_final: 0.7162 (t0) REVERT: H 93 LYS cc_start: 0.8112 (tttt) cc_final: 0.7872 (tttm) REVERT: H 95 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7508 (mp10) REVERT: I 93 LYS cc_start: 0.8152 (tttt) cc_final: 0.7282 (mmtm) REVERT: J 72 LYS cc_start: 0.8752 (tttt) cc_final: 0.8104 (mtmm) REVERT: J 93 LYS cc_start: 0.8563 (tttt) cc_final: 0.7560 (mtmm) REVERT: K 59 ARG cc_start: 0.7646 (mmt-90) cc_final: 0.7226 (mmm-85) REVERT: K 72 LYS cc_start: 0.8714 (tttt) cc_final: 0.8310 (mtmm) REVERT: K 95 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7586 (tp40) REVERT: L 18 ASP cc_start: 0.7300 (p0) cc_final: 0.6834 (p0) REVERT: L 78 GLU cc_start: 0.7879 (mm-30) cc_final: 0.7456 (mm-30) REVERT: L 93 LYS cc_start: 0.8312 (tttt) cc_final: 0.7262 (mmtm) REVERT: L 95 GLN cc_start: 0.8337 (mm-40) cc_final: 0.7944 (mm-40) REVERT: M 25 MET cc_start: 0.7554 (ttt) cc_final: 0.7043 (mtp) REVERT: M 78 GLU cc_start: 0.7901 (mm-30) cc_final: 0.7662 (tp30) REVERT: M 93 LYS cc_start: 0.8381 (tttt) cc_final: 0.7729 (mtpp) REVERT: M 95 GLN cc_start: 0.8376 (mm-40) cc_final: 0.7546 (mp10) REVERT: N 59 ARG cc_start: 0.7516 (mmt-90) cc_final: 0.7257 (mmm-85) REVERT: N 72 LYS cc_start: 0.8759 (tttt) cc_final: 0.8406 (mtmm) REVERT: N 93 LYS cc_start: 0.8636 (tttt) cc_final: 0.8301 (mtpt) REVERT: N 95 GLN cc_start: 0.8468 (mm-40) cc_final: 0.7573 (tp40) REVERT: O 72 LYS cc_start: 0.8704 (tttt) cc_final: 0.8233 (mptt) REVERT: O 93 LYS cc_start: 0.8602 (tttt) cc_final: 0.7605 (mtmm) REVERT: P 17 PRO cc_start: 0.7808 (Cg_exo) cc_final: 0.7508 (Cg_endo) REVERT: P 25 MET cc_start: 0.7408 (ttm) cc_final: 0.7063 (tmm) REVERT: P 32 ARG cc_start: 0.8013 (ttt90) cc_final: 0.7164 (ttt-90) REVERT: P 93 LYS cc_start: 0.8168 (tttt) cc_final: 0.7790 (tttp) REVERT: Q 18 ASP cc_start: 0.7580 (p0) cc_final: 0.7277 (p0) REVERT: Q 93 LYS cc_start: 0.8052 (tttt) cc_final: 0.7845 (tttp) REVERT: Q 95 GLN cc_start: 0.8011 (mm-40) cc_final: 0.7742 (mp10) REVERT: R 38 ARG cc_start: 0.7858 (tpt90) cc_final: 0.7463 (tpt90) REVERT: R 93 LYS cc_start: 0.8439 (tttt) cc_final: 0.8183 (tttp) REVERT: S 26 ARG cc_start: 0.7611 (mtt180) cc_final: 0.6864 (ttm110) REVERT: S 30 GLN cc_start: 0.7761 (tm-30) cc_final: 0.7522 (tm-30) REVERT: S 38 ARG cc_start: 0.8220 (tpt90) cc_final: 0.7741 (tpt90) REVERT: S 59 ARG cc_start: 0.7800 (mmt-90) cc_final: 0.7206 (mmm-85) REVERT: S 78 GLU cc_start: 0.7773 (mm-30) cc_final: 0.7573 (mm-30) REVERT: S 93 LYS cc_start: 0.8400 (tttt) cc_final: 0.8086 (tptp) REVERT: T 25 MET cc_start: 0.7369 (ttm) cc_final: 0.6468 (tmm) REVERT: T 26 ARG cc_start: 0.7157 (mtt180) cc_final: 0.6882 (tpt-90) REVERT: T 59 ARG cc_start: 0.7861 (mmt-90) cc_final: 0.7359 (mmt-90) REVERT: T 72 LYS cc_start: 0.8486 (tmtt) cc_final: 0.7963 (tptp) REVERT: T 78 GLU cc_start: 0.8475 (tp30) cc_final: 0.7497 (tp30) REVERT: T 79 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8719 (mmpt) REVERT: T 84 LYS cc_start: 0.8504 (mmpt) cc_final: 0.8190 (tptp) REVERT: U 18 ASP cc_start: 0.7341 (p0) cc_final: 0.6816 (p0) REVERT: U 24 ASP cc_start: 0.7138 (t70) cc_final: 0.6688 (t0) REVERT: U 59 ARG cc_start: 0.7675 (mmt-90) cc_final: 0.7247 (mmt-90) REVERT: U 93 LYS cc_start: 0.8406 (tttt) cc_final: 0.7963 (mptt) REVERT: V 24 ASP cc_start: 0.7278 (m-30) cc_final: 0.6571 (t0) REVERT: V 38 ARG cc_start: 0.6280 (ttp80) cc_final: 0.5850 (ttp80) REVERT: V 68 HIS cc_start: 0.4254 (m-70) cc_final: 0.3975 (m90) outliers start: 2 outliers final: 0 residues processed: 365 average time/residue: 0.2109 time to fit residues: 98.2271 Evaluate side-chains 276 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 276 time to evaluate : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 190 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 58 optimal weight: 6.9990 chunk 165 optimal weight: 8.9990 chunk 125 optimal weight: 6.9990 chunk 7 optimal weight: 9.9990 chunk 115 optimal weight: 7.9990 chunk 42 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 64 optimal weight: 3.9990 chunk 197 optimal weight: 0.9980 overall best weight: 3.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS J 68 HIS L 108 GLN O 68 HIS P 68 HIS S 68 HIS ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4903 r_free = 0.4903 target = 0.114091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.082555 restraints weight = 34168.309| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.084312 restraints weight = 24810.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.085584 restraints weight = 19346.282| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.086751 restraints weight = 15860.295| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.087612 restraints weight = 13491.094| |-----------------------------------------------------------------------------| r_work (final): 0.4379 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.5068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 16478 Z= 0.288 Angle : 0.763 8.177 22198 Z= 0.400 Chirality : 0.052 0.183 2684 Planarity : 0.005 0.084 2904 Dihedral : 6.514 25.013 2376 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.88 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.75 (0.11), residues: 1452 loop : -3.59 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG P 32 TYR 0.014 0.002 TYR B 14 PHE 0.017 0.002 PHE N 105 HIS 0.005 0.001 HIS L 68 Details of bonding type rmsd covalent geometry : bond 0.00571 (16478) covalent geometry : angle 0.76330 (22198) hydrogen bonds : bond 0.01845 ( 66) hydrogen bonds : angle 5.56123 ( 132) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 338 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8050 (tmtt) cc_final: 0.7642 (tptp) REVERT: B 61 GLU cc_start: 0.5104 (mp0) cc_final: 0.4235 (tm-30) REVERT: B 72 LYS cc_start: 0.8023 (tmtt) cc_final: 0.7609 (tmtt) REVERT: C 24 ASP cc_start: 0.6980 (m-30) cc_final: 0.6393 (t0) REVERT: C 38 ARG cc_start: 0.6388 (ttp80) cc_final: 0.6093 (ttp80) REVERT: D 24 ASP cc_start: 0.6913 (t0) cc_final: 0.6554 (t0) REVERT: D 93 LYS cc_start: 0.8515 (tttt) cc_final: 0.8060 (tptp) REVERT: E 25 MET cc_start: 0.7869 (ttm) cc_final: 0.6843 (tmm) REVERT: E 59 ARG cc_start: 0.7762 (mmp80) cc_final: 0.7405 (mmp80) REVERT: E 72 LYS cc_start: 0.8671 (tttt) cc_final: 0.8202 (tptp) REVERT: E 78 GLU cc_start: 0.8378 (tp30) cc_final: 0.8114 (tp30) REVERT: E 79 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8831 (mmmt) REVERT: F 20 GLU cc_start: 0.8286 (mp0) cc_final: 0.8032 (mp0) REVERT: F 26 ARG cc_start: 0.7777 (mtt180) cc_final: 0.7101 (ttm110) REVERT: F 38 ARG cc_start: 0.8240 (tpt90) cc_final: 0.7709 (tpt90) REVERT: F 59 ARG cc_start: 0.7498 (mmt-90) cc_final: 0.7237 (mmm-85) REVERT: G 66 LEU cc_start: 0.8157 (mm) cc_final: 0.7819 (mp) REVERT: G 93 LYS cc_start: 0.8464 (tttt) cc_final: 0.8148 (tttp) REVERT: H 18 ASP cc_start: 0.7890 (p0) cc_final: 0.7371 (p0) REVERT: H 93 LYS cc_start: 0.8100 (tttt) cc_final: 0.7888 (tttp) REVERT: H 95 GLN cc_start: 0.8116 (mm-40) cc_final: 0.7896 (mp10) REVERT: I 79 LYS cc_start: 0.8480 (mmtt) cc_final: 0.8142 (mmmt) REVERT: I 93 LYS cc_start: 0.8016 (tttt) cc_final: 0.7270 (mmtm) REVERT: J 25 MET cc_start: 0.7987 (ttm) cc_final: 0.7779 (ttt) REVERT: J 93 LYS cc_start: 0.8430 (tttt) cc_final: 0.7653 (mtpp) REVERT: K 20 GLU cc_start: 0.8254 (mp0) cc_final: 0.7042 (mp0) REVERT: K 59 ARG cc_start: 0.7736 (mmt-90) cc_final: 0.7298 (mmt180) REVERT: K 72 LYS cc_start: 0.8709 (tttt) cc_final: 0.8374 (mtmm) REVERT: K 95 GLN cc_start: 0.8515 (mm-40) cc_final: 0.7556 (tp40) REVERT: L 18 ASP cc_start: 0.7153 (p0) cc_final: 0.6566 (p0) REVERT: M 18 ASP cc_start: 0.7297 (p0) cc_final: 0.6927 (p0) REVERT: M 25 MET cc_start: 0.7593 (ttt) cc_final: 0.7053 (mtp) REVERT: M 93 LYS cc_start: 0.8437 (tttt) cc_final: 0.7392 (mmtm) REVERT: N 59 ARG cc_start: 0.7661 (mmt-90) cc_final: 0.7242 (mmt180) REVERT: N 72 LYS cc_start: 0.8759 (tttt) cc_final: 0.8425 (mtmm) REVERT: N 78 GLU cc_start: 0.7816 (tp30) cc_final: 0.7119 (tm-30) REVERT: N 93 LYS cc_start: 0.8527 (tttt) cc_final: 0.8182 (mtpt) REVERT: N 95 GLN cc_start: 0.8462 (mm-40) cc_final: 0.7517 (tp40) REVERT: O 93 LYS cc_start: 0.8454 (tttt) cc_final: 0.7679 (mtpp) REVERT: P 25 MET cc_start: 0.7688 (ttm) cc_final: 0.6981 (tmm) REVERT: P 32 ARG cc_start: 0.7792 (ttt90) cc_final: 0.7428 (ttt-90) REVERT: P 79 LYS cc_start: 0.8504 (mmtt) cc_final: 0.8148 (mmmt) REVERT: P 93 LYS cc_start: 0.8014 (tttt) cc_final: 0.7268 (mmtm) REVERT: Q 18 ASP cc_start: 0.7645 (p0) cc_final: 0.7404 (p0) REVERT: Q 25 MET cc_start: 0.8474 (tmm) cc_final: 0.7903 (tmm) REVERT: Q 93 LYS cc_start: 0.8114 (tttt) cc_final: 0.7883 (tttp) REVERT: Q 95 GLN cc_start: 0.8056 (mm-40) cc_final: 0.7789 (mp10) REVERT: R 38 ARG cc_start: 0.7990 (tpt90) cc_final: 0.7670 (tpt90) REVERT: R 93 LYS cc_start: 0.8461 (tttt) cc_final: 0.8119 (tttp) REVERT: S 26 ARG cc_start: 0.7736 (mtt180) cc_final: 0.7260 (ttm110) REVERT: S 30 GLN cc_start: 0.7839 (tm-30) cc_final: 0.7440 (tm-30) REVERT: S 38 ARG cc_start: 0.8243 (tpt90) cc_final: 0.7892 (tpt90) REVERT: S 46 GLU cc_start: 0.8258 (tm-30) cc_final: 0.7957 (tm-30) REVERT: S 58 GLU cc_start: 0.7593 (pt0) cc_final: 0.7291 (pm20) REVERT: S 59 ARG cc_start: 0.7806 (mmt-90) cc_final: 0.7469 (mmm-85) REVERT: S 63 ARG cc_start: 0.7802 (mmt180) cc_final: 0.7589 (mpt180) REVERT: S 72 LYS cc_start: 0.8720 (tttt) cc_final: 0.8442 (tptm) REVERT: S 79 LYS cc_start: 0.8541 (mppt) cc_final: 0.8104 (mmtm) REVERT: S 93 LYS cc_start: 0.8498 (tttt) cc_final: 0.8154 (tptp) REVERT: T 25 MET cc_start: 0.7722 (ttm) cc_final: 0.6783 (tmm) REVERT: T 72 LYS cc_start: 0.8684 (tmtt) cc_final: 0.7955 (tptp) REVERT: T 78 GLU cc_start: 0.8326 (tp30) cc_final: 0.7423 (tp30) REVERT: T 79 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8772 (mmpt) REVERT: T 84 LYS cc_start: 0.8373 (mmpt) cc_final: 0.8054 (tptp) REVERT: U 18 ASP cc_start: 0.7183 (p0) cc_final: 0.6560 (p0) REVERT: U 24 ASP cc_start: 0.6571 (t70) cc_final: 0.6354 (t0) REVERT: U 54 ARG cc_start: 0.7817 (tmm-80) cc_final: 0.6215 (tmm-80) REVERT: U 93 LYS cc_start: 0.8538 (tttt) cc_final: 0.8044 (mptt) REVERT: V 24 ASP cc_start: 0.7248 (m-30) cc_final: 0.6369 (t0) REVERT: V 38 ARG cc_start: 0.6672 (tmm160) cc_final: 0.6016 (ttp80) REVERT: V 68 HIS cc_start: 0.3992 (m-70) cc_final: 0.3749 (m90) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.2162 time to fit residues: 92.9284 Evaluate side-chains 257 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 257 time to evaluate : 0.558 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 4.9990 chunk 53 optimal weight: 7.9990 chunk 6 optimal weight: 6.9990 chunk 164 optimal weight: 6.9990 chunk 183 optimal weight: 9.9990 chunk 94 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 202 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 117 optimal weight: 3.9990 chunk 156 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4914 r_free = 0.4914 target = 0.114742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.083072 restraints weight = 34145.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.084879 restraints weight = 24752.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.086270 restraints weight = 19226.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.4401 r_free = 0.4401 target = 0.087392 restraints weight = 15706.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.088139 restraints weight = 13292.489| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7138 moved from start: 0.5548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 16478 Z= 0.230 Angle : 0.722 7.243 22198 Z= 0.373 Chirality : 0.052 0.146 2684 Planarity : 0.004 0.050 2904 Dihedral : 6.183 24.194 2376 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.84 % Favored : 89.16 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.54 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.65 (0.13), residues: 1232 loop : -3.47 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG P 32 TYR 0.011 0.002 TYR O 14 PHE 0.011 0.002 PHE H 105 HIS 0.006 0.002 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00465 (16478) covalent geometry : angle 0.72234 (22198) hydrogen bonds : bond 0.01484 ( 66) hydrogen bonds : angle 5.06070 ( 132) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 0.508 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.6690 (t70) cc_final: 0.6296 (t70) REVERT: A 72 LYS cc_start: 0.7981 (tmtt) cc_final: 0.7546 (tmtt) REVERT: B 72 LYS cc_start: 0.8011 (tmtt) cc_final: 0.7570 (tmtt) REVERT: C 14 TYR cc_start: 0.7126 (t80) cc_final: 0.6597 (t80) REVERT: C 20 GLU cc_start: 0.7080 (mp0) cc_final: 0.6627 (tm-30) REVERT: C 24 ASP cc_start: 0.6763 (m-30) cc_final: 0.6301 (t0) REVERT: C 32 ARG cc_start: 0.6672 (tpt90) cc_final: 0.5469 (ttp80) REVERT: C 38 ARG cc_start: 0.6509 (tmm160) cc_final: 0.5860 (ttp80) REVERT: C 78 GLU cc_start: 0.5219 (pt0) cc_final: 0.4439 (mm-30) REVERT: D 24 ASP cc_start: 0.6817 (t0) cc_final: 0.6426 (t0) REVERT: D 59 ARG cc_start: 0.7684 (mmp80) cc_final: 0.7390 (mmp80) REVERT: D 93 LYS cc_start: 0.8520 (tttt) cc_final: 0.8125 (tptp) REVERT: E 25 MET cc_start: 0.7487 (ttm) cc_final: 0.6847 (tmm) REVERT: E 72 LYS cc_start: 0.8657 (tttt) cc_final: 0.8171 (tptp) REVERT: E 78 GLU cc_start: 0.8350 (tp30) cc_final: 0.8138 (tp30) REVERT: E 79 LYS cc_start: 0.9087 (mmtm) cc_final: 0.8874 (mmmt) REVERT: F 26 ARG cc_start: 0.7641 (mtt180) cc_final: 0.6963 (ttm110) REVERT: F 38 ARG cc_start: 0.8137 (tpt90) cc_final: 0.7654 (tpt90) REVERT: F 79 LYS cc_start: 0.8570 (mmtm) cc_final: 0.8341 (mmtm) REVERT: G 26 ARG cc_start: 0.6388 (mtt90) cc_final: 0.6028 (mtt90) REVERT: G 66 LEU cc_start: 0.8192 (mm) cc_final: 0.7772 (mp) REVERT: G 93 LYS cc_start: 0.8505 (tttt) cc_final: 0.8132 (tttp) REVERT: H 18 ASP cc_start: 0.8083 (p0) cc_final: 0.7684 (p0) REVERT: I 25 MET cc_start: 0.7664 (ttm) cc_final: 0.6941 (tmm) REVERT: I 79 LYS cc_start: 0.8457 (mmtt) cc_final: 0.8021 (mmmt) REVERT: I 93 LYS cc_start: 0.8028 (tttt) cc_final: 0.7207 (mmtm) REVERT: I 95 GLN cc_start: 0.8552 (mm110) cc_final: 0.8186 (mm110) REVERT: J 93 LYS cc_start: 0.8330 (tttt) cc_final: 0.7553 (mtpp) REVERT: K 59 ARG cc_start: 0.7767 (mmt-90) cc_final: 0.7366 (mmm-85) REVERT: K 72 LYS cc_start: 0.8667 (tttt) cc_final: 0.8294 (mtmm) REVERT: K 95 GLN cc_start: 0.8424 (mm-40) cc_final: 0.7355 (tp40) REVERT: L 18 ASP cc_start: 0.7338 (p0) cc_final: 0.6655 (p0) REVERT: L 93 LYS cc_start: 0.8342 (tttt) cc_final: 0.7993 (tttp) REVERT: M 18 ASP cc_start: 0.7417 (p0) cc_final: 0.6774 (p0) REVERT: M 25 MET cc_start: 0.7684 (ttt) cc_final: 0.7074 (mtp) REVERT: M 93 LYS cc_start: 0.8366 (tttt) cc_final: 0.8003 (tttp) REVERT: M 95 GLN cc_start: 0.8102 (mm110) cc_final: 0.7896 (mm110) REVERT: N 59 ARG cc_start: 0.7746 (mmt-90) cc_final: 0.7247 (mmm-85) REVERT: N 72 LYS cc_start: 0.8737 (tttt) cc_final: 0.8389 (mtmm) REVERT: N 78 GLU cc_start: 0.7919 (tp30) cc_final: 0.7109 (tm-30) REVERT: N 93 LYS cc_start: 0.8548 (tttt) cc_final: 0.8229 (mtpt) REVERT: N 95 GLN cc_start: 0.8389 (mm-40) cc_final: 0.7463 (tp40) REVERT: O 72 LYS cc_start: 0.8743 (ttmm) cc_final: 0.7967 (mptt) REVERT: O 93 LYS cc_start: 0.8326 (tttt) cc_final: 0.7587 (mtpp) REVERT: P 32 ARG cc_start: 0.7783 (ttt90) cc_final: 0.7451 (ttt-90) REVERT: P 79 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8370 (mmmt) REVERT: P 93 LYS cc_start: 0.8067 (tttt) cc_final: 0.7716 (tttp) REVERT: P 95 GLN cc_start: 0.8530 (mm110) cc_final: 0.8140 (mm110) REVERT: Q 18 ASP cc_start: 0.7812 (p0) cc_final: 0.7549 (p0) REVERT: Q 93 LYS cc_start: 0.8089 (tttt) cc_final: 0.7870 (tttp) REVERT: R 38 ARG cc_start: 0.7966 (tpt90) cc_final: 0.7638 (tpt90) REVERT: R 66 LEU cc_start: 0.8303 (mm) cc_final: 0.8039 (mp) REVERT: R 84 LYS cc_start: 0.8342 (tptp) cc_final: 0.8009 (pptt) REVERT: R 93 LYS cc_start: 0.8493 (tttt) cc_final: 0.8120 (tttp) REVERT: S 26 ARG cc_start: 0.7600 (mtt180) cc_final: 0.7074 (ttm110) REVERT: S 38 ARG cc_start: 0.8153 (tpt90) cc_final: 0.7739 (tpt90) REVERT: S 59 ARG cc_start: 0.7843 (mmt-90) cc_final: 0.7418 (mmm-85) REVERT: S 66 LEU cc_start: 0.8597 (mm) cc_final: 0.8394 (mm) REVERT: S 72 LYS cc_start: 0.8763 (tttt) cc_final: 0.8526 (tptm) REVERT: S 79 LYS cc_start: 0.8597 (mppt) cc_final: 0.8235 (mmtm) REVERT: S 93 LYS cc_start: 0.8512 (tttt) cc_final: 0.8120 (tptp) REVERT: T 25 MET cc_start: 0.7631 (ttm) cc_final: 0.6923 (tmm) REVERT: T 59 ARG cc_start: 0.8112 (mmt-90) cc_final: 0.7818 (tpp-160) REVERT: T 72 LYS cc_start: 0.8603 (tmtt) cc_final: 0.7942 (tptp) REVERT: T 78 GLU cc_start: 0.8296 (tp30) cc_final: 0.7387 (tp30) REVERT: T 79 LYS cc_start: 0.9091 (mmtm) cc_final: 0.8764 (mmpt) REVERT: T 84 LYS cc_start: 0.8516 (mmpt) cc_final: 0.8306 (tptp) REVERT: U 18 ASP cc_start: 0.7288 (p0) cc_final: 0.6643 (p0) REVERT: U 24 ASP cc_start: 0.6630 (t70) cc_final: 0.6405 (t0) REVERT: U 59 ARG cc_start: 0.7912 (mpt180) cc_final: 0.7542 (mmt-90) REVERT: U 78 GLU cc_start: 0.7845 (tt0) cc_final: 0.7501 (tt0) REVERT: U 93 LYS cc_start: 0.8546 (tttt) cc_final: 0.8118 (tptp) REVERT: U 100 GLU cc_start: 0.8379 (mp0) cc_final: 0.8087 (mp0) REVERT: V 24 ASP cc_start: 0.7280 (m-30) cc_final: 0.6384 (t0) REVERT: V 38 ARG cc_start: 0.6622 (tmm160) cc_final: 0.5935 (ttp80) outliers start: 0 outliers final: 0 residues processed: 322 average time/residue: 0.2231 time to fit residues: 90.9883 Evaluate side-chains 263 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 218 optimal weight: 30.0000 chunk 114 optimal weight: 8.9990 chunk 88 optimal weight: 8.9990 chunk 178 optimal weight: 1.9990 chunk 149 optimal weight: 3.9990 chunk 155 optimal weight: 10.0000 chunk 66 optimal weight: 10.0000 chunk 32 optimal weight: 0.9980 chunk 151 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 45 optimal weight: 6.9990 overall best weight: 2.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4913 r_free = 0.4913 target = 0.115117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.083257 restraints weight = 33532.278| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.085023 restraints weight = 24445.664| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.086407 restraints weight = 19086.084| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4396 r_free = 0.4396 target = 0.087398 restraints weight = 15658.582| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 55)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.088277 restraints weight = 13364.696| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16478 Z= 0.219 Angle : 0.718 7.569 22198 Z= 0.368 Chirality : 0.052 0.150 2684 Planarity : 0.004 0.036 2904 Dihedral : 6.035 24.384 2376 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 17.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.85 % Favored : 88.15 % Rotamer: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.70 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.66 (0.13), residues: 1342 loop : -3.58 (0.17), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 32 TYR 0.013 0.002 TYR O 14 PHE 0.013 0.002 PHE H 105 HIS 0.006 0.001 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00444 (16478) covalent geometry : angle 0.71812 (22198) hydrogen bonds : bond 0.01501 ( 66) hydrogen bonds : angle 5.01576 ( 132) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 320 time to evaluate : 0.446 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.7938 (tmtt) cc_final: 0.7516 (tmtt) REVERT: A 91 GLN cc_start: 0.6957 (mp10) cc_final: 0.5888 (tm-30) REVERT: A 95 GLN cc_start: 0.7963 (mm-40) cc_final: 0.7494 (mm-40) REVERT: B 72 LYS cc_start: 0.7992 (tmtt) cc_final: 0.7517 (tmtt) REVERT: B 91 GLN cc_start: 0.7005 (mp10) cc_final: 0.5892 (tm-30) REVERT: C 20 GLU cc_start: 0.7138 (mp0) cc_final: 0.6669 (tm-30) REVERT: C 24 ASP cc_start: 0.6836 (m-30) cc_final: 0.6356 (t0) REVERT: C 38 ARG cc_start: 0.6274 (tmm160) cc_final: 0.5740 (tmm160) REVERT: C 78 GLU cc_start: 0.5630 (pt0) cc_final: 0.4934 (mm-30) REVERT: D 24 ASP cc_start: 0.6980 (t0) cc_final: 0.6639 (t0) REVERT: D 91 GLN cc_start: 0.7625 (tm-30) cc_final: 0.7235 (tm-30) REVERT: D 93 LYS cc_start: 0.8634 (tttt) cc_final: 0.8180 (tptp) REVERT: E 25 MET cc_start: 0.7614 (ttm) cc_final: 0.6687 (tmm) REVERT: E 55 VAL cc_start: 0.9232 (t) cc_final: 0.8930 (p) REVERT: E 72 LYS cc_start: 0.8652 (tttt) cc_final: 0.8088 (tptp) REVERT: E 79 LYS cc_start: 0.9109 (mmtm) cc_final: 0.8821 (mmmt) REVERT: F 21 VAL cc_start: 0.8985 (m) cc_final: 0.8773 (p) REVERT: F 26 ARG cc_start: 0.7779 (mtt180) cc_final: 0.6911 (ttm110) REVERT: F 38 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7588 (tpt90) REVERT: F 59 ARG cc_start: 0.8043 (mmt180) cc_final: 0.7413 (mmm-85) REVERT: F 79 LYS cc_start: 0.8642 (mmtm) cc_final: 0.8371 (mmtm) REVERT: G 26 ARG cc_start: 0.6392 (mtt90) cc_final: 0.6058 (mtt90) REVERT: G 66 LEU cc_start: 0.8395 (mm) cc_final: 0.7895 (tp) REVERT: G 84 LYS cc_start: 0.8320 (tptp) cc_final: 0.8021 (pptt) REVERT: G 93 LYS cc_start: 0.8635 (tttt) cc_final: 0.8224 (tttp) REVERT: H 18 ASP cc_start: 0.8164 (p0) cc_final: 0.7786 (p0) REVERT: H 25 MET cc_start: 0.8545 (tmm) cc_final: 0.8344 (tmm) REVERT: I 25 MET cc_start: 0.7818 (ttm) cc_final: 0.7074 (tmm) REVERT: I 79 LYS cc_start: 0.8648 (mmtt) cc_final: 0.8193 (mmmt) REVERT: I 93 LYS cc_start: 0.8198 (tttt) cc_final: 0.7357 (mmtm) REVERT: I 95 GLN cc_start: 0.8556 (mm110) cc_final: 0.8227 (mm110) REVERT: I 109 SER cc_start: 0.9008 (t) cc_final: 0.8291 (t) REVERT: J 25 MET cc_start: 0.8103 (ttt) cc_final: 0.7624 (tmm) REVERT: J 63 ARG cc_start: 0.7438 (mmt-90) cc_final: 0.7169 (mpt180) REVERT: J 93 LYS cc_start: 0.8315 (tttt) cc_final: 0.7537 (mtpp) REVERT: K 36 LEU cc_start: 0.8179 (tt) cc_final: 0.7301 (mp) REVERT: K 59 ARG cc_start: 0.7757 (mmt-90) cc_final: 0.7348 (mmm-85) REVERT: K 72 LYS cc_start: 0.8707 (tttt) cc_final: 0.8385 (mtmm) REVERT: K 95 GLN cc_start: 0.8408 (mm-40) cc_final: 0.7430 (tp40) REVERT: L 18 ASP cc_start: 0.7322 (p0) cc_final: 0.6610 (p0) REVERT: L 79 LYS cc_start: 0.8373 (mppt) cc_final: 0.8003 (mmtt) REVERT: L 93 LYS cc_start: 0.8368 (tttt) cc_final: 0.7902 (mtpp) REVERT: M 25 MET cc_start: 0.7667 (ttt) cc_final: 0.7045 (mtp) REVERT: M 93 LYS cc_start: 0.8345 (tttt) cc_final: 0.7297 (mmtm) REVERT: N 36 LEU cc_start: 0.8521 (tt) cc_final: 0.7444 (mp) REVERT: N 59 ARG cc_start: 0.7826 (mmt-90) cc_final: 0.7267 (mmm-85) REVERT: N 72 LYS cc_start: 0.8761 (tttt) cc_final: 0.8408 (mtmm) REVERT: N 78 GLU cc_start: 0.7835 (tp30) cc_final: 0.7090 (tm-30) REVERT: N 93 LYS cc_start: 0.8484 (tttt) cc_final: 0.8165 (mtpt) REVERT: N 95 GLN cc_start: 0.8322 (mm-40) cc_final: 0.7445 (tp40) REVERT: O 63 ARG cc_start: 0.7458 (mmt-90) cc_final: 0.7202 (mpt180) REVERT: O 72 LYS cc_start: 0.8775 (ttmm) cc_final: 0.8011 (mptt) REVERT: O 93 LYS cc_start: 0.8345 (tttt) cc_final: 0.7617 (mtpp) REVERT: P 25 MET cc_start: 0.7800 (ttm) cc_final: 0.7011 (tmm) REVERT: P 32 ARG cc_start: 0.7701 (ttt90) cc_final: 0.7388 (ttt-90) REVERT: P 79 LYS cc_start: 0.8703 (mmtt) cc_final: 0.8407 (mmmt) REVERT: P 93 LYS cc_start: 0.8144 (tttt) cc_final: 0.7813 (tttp) REVERT: P 95 GLN cc_start: 0.8599 (mm110) cc_final: 0.8222 (mm110) REVERT: R 38 ARG cc_start: 0.7992 (tpt90) cc_final: 0.7619 (tpt90) REVERT: R 84 LYS cc_start: 0.8332 (tptp) cc_final: 0.8004 (pptt) REVERT: R 93 LYS cc_start: 0.8584 (tttt) cc_final: 0.8178 (tttp) REVERT: S 21 VAL cc_start: 0.8980 (m) cc_final: 0.8774 (p) REVERT: S 26 ARG cc_start: 0.7760 (mtt180) cc_final: 0.7189 (ttm110) REVERT: S 38 ARG cc_start: 0.8180 (tpt90) cc_final: 0.7759 (tpt90) REVERT: S 59 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7382 (mmm-85) REVERT: S 72 LYS cc_start: 0.8792 (tttt) cc_final: 0.8505 (tptm) REVERT: S 79 LYS cc_start: 0.8419 (mppt) cc_final: 0.8096 (mmtm) REVERT: S 93 LYS cc_start: 0.8495 (tttt) cc_final: 0.8111 (tptp) REVERT: T 25 MET cc_start: 0.7699 (ttm) cc_final: 0.6828 (tmm) REVERT: T 72 LYS cc_start: 0.8568 (tmtt) cc_final: 0.7978 (tptp) REVERT: T 79 LYS cc_start: 0.9094 (mmtm) cc_final: 0.8699 (mmpt) REVERT: U 18 ASP cc_start: 0.7374 (p0) cc_final: 0.6813 (p0) REVERT: U 24 ASP cc_start: 0.6786 (t70) cc_final: 0.6431 (t0) REVERT: U 93 LYS cc_start: 0.8578 (tttt) cc_final: 0.8122 (tptp) REVERT: U 100 GLU cc_start: 0.8403 (mp0) cc_final: 0.8192 (mp0) REVERT: V 20 GLU cc_start: 0.7389 (mp0) cc_final: 0.6925 (tm-30) REVERT: V 24 ASP cc_start: 0.7240 (m-30) cc_final: 0.6320 (t0) REVERT: V 38 ARG cc_start: 0.6487 (tmm160) cc_final: 0.5844 (ttp80) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.2149 time to fit residues: 88.0102 Evaluate side-chains 265 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 265 time to evaluate : 0.580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 95 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 202 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 161 optimal weight: 10.0000 chunk 41 optimal weight: 9.9990 chunk 188 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 chunk 216 optimal weight: 20.0000 chunk 140 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4821 r_free = 0.4821 target = 0.109240 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4204 r_free = 0.4204 target = 0.079494 restraints weight = 35993.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.080927 restraints weight = 27239.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.082012 restraints weight = 21773.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.082799 restraints weight = 18287.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.083512 restraints weight = 15896.154| |-----------------------------------------------------------------------------| r_work (final): 0.4301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7317 moved from start: 0.6784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.065 16478 Z= 0.461 Angle : 0.966 8.731 22198 Z= 0.522 Chirality : 0.058 0.220 2684 Planarity : 0.007 0.072 2904 Dihedral : 7.821 28.063 2376 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 27.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.85 % Favored : 78.15 % Rotamer: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.28 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.90 (0.15), residues: 858 loop : -3.31 (0.14), residues: 1320 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 87 TYR 0.025 0.003 TYR O 14 PHE 0.027 0.003 PHE Q 105 HIS 0.016 0.003 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00924 (16478) covalent geometry : angle 0.96646 (22198) hydrogen bonds : bond 0.02880 ( 66) hydrogen bonds : angle 6.44097 ( 132) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 34 ASP cc_start: 0.6160 (t70) cc_final: 0.5906 (t70) REVERT: A 72 LYS cc_start: 0.8000 (tmtt) cc_final: 0.7541 (tmtt) REVERT: A 79 LYS cc_start: 0.8334 (mmtm) cc_final: 0.8105 (mmmt) REVERT: B 72 LYS cc_start: 0.7990 (tmtt) cc_final: 0.7509 (tmtt) REVERT: C 24 ASP cc_start: 0.7145 (m-30) cc_final: 0.6499 (t0) REVERT: C 38 ARG cc_start: 0.6251 (tmm160) cc_final: 0.5690 (tmm160) REVERT: C 78 GLU cc_start: 0.5554 (pt0) cc_final: 0.5083 (mm-30) REVERT: D 24 ASP cc_start: 0.7050 (t0) cc_final: 0.6760 (t0) REVERT: D 78 GLU cc_start: 0.7757 (tt0) cc_final: 0.7478 (tp30) REVERT: D 79 LYS cc_start: 0.8804 (mmtm) cc_final: 0.7843 (mmmm) REVERT: D 91 GLN cc_start: 0.7902 (tm-30) cc_final: 0.7491 (tm-30) REVERT: D 93 LYS cc_start: 0.8752 (tttt) cc_final: 0.8278 (tptp) REVERT: E 25 MET cc_start: 0.7840 (ttm) cc_final: 0.7065 (tmm) REVERT: E 26 ARG cc_start: 0.7239 (tpt-90) cc_final: 0.6692 (ptp90) REVERT: E 55 VAL cc_start: 0.9389 (t) cc_final: 0.9128 (p) REVERT: E 72 LYS cc_start: 0.8712 (tttt) cc_final: 0.8067 (tptp) REVERT: E 78 GLU cc_start: 0.8337 (tp30) cc_final: 0.7664 (tp30) REVERT: E 79 LYS cc_start: 0.9176 (mmtm) cc_final: 0.8641 (mmpt) REVERT: E 93 LYS cc_start: 0.7782 (mptt) cc_final: 0.7536 (mmtm) REVERT: F 18 ASP cc_start: 0.7555 (p0) cc_final: 0.7110 (p0) REVERT: F 21 VAL cc_start: 0.8965 (m) cc_final: 0.8722 (p) REVERT: F 26 ARG cc_start: 0.7563 (mtt180) cc_final: 0.7066 (ttm110) REVERT: F 28 LYS cc_start: 0.7585 (mptt) cc_final: 0.7265 (mmtm) REVERT: F 38 ARG cc_start: 0.8195 (tpt90) cc_final: 0.7795 (tpt90) REVERT: F 59 ARG cc_start: 0.8073 (mmt180) cc_final: 0.7495 (mmm-85) REVERT: G 26 ARG cc_start: 0.6694 (mtt90) cc_final: 0.6432 (mtt90) REVERT: G 84 LYS cc_start: 0.8419 (tptp) cc_final: 0.8194 (tmmt) REVERT: G 93 LYS cc_start: 0.8487 (tttt) cc_final: 0.8159 (tttp) REVERT: H 18 ASP cc_start: 0.8518 (p0) cc_final: 0.8157 (p0) REVERT: H 20 GLU cc_start: 0.8434 (mp0) cc_final: 0.8209 (mp0) REVERT: I 61 GLU cc_start: 0.7917 (mp0) cc_final: 0.7413 (mp0) REVERT: I 79 LYS cc_start: 0.8854 (mmtt) cc_final: 0.8402 (mmmt) REVERT: I 95 GLN cc_start: 0.8615 (mm110) cc_final: 0.8252 (mm-40) REVERT: J 25 MET cc_start: 0.8352 (ttt) cc_final: 0.7883 (tmm) REVERT: J 78 GLU cc_start: 0.8167 (mt-10) cc_final: 0.7734 (tm-30) REVERT: J 93 LYS cc_start: 0.8482 (tttt) cc_final: 0.7461 (mtmm) REVERT: K 58 GLU cc_start: 0.6113 (pt0) cc_final: 0.5386 (pm20) REVERT: K 59 ARG cc_start: 0.7955 (mmt-90) cc_final: 0.7299 (mmt180) REVERT: K 78 GLU cc_start: 0.7691 (tp30) cc_final: 0.7006 (tm-30) REVERT: K 95 GLN cc_start: 0.8449 (mm-40) cc_final: 0.7781 (tp-100) REVERT: L 18 ASP cc_start: 0.7289 (p0) cc_final: 0.6470 (p0) REVERT: L 38 ARG cc_start: 0.8163 (tpt90) cc_final: 0.7601 (tpt90) REVERT: L 79 LYS cc_start: 0.8488 (mppt) cc_final: 0.7944 (mmtm) REVERT: L 93 LYS cc_start: 0.8618 (tttt) cc_final: 0.7993 (mtpp) REVERT: M 25 MET cc_start: 0.7777 (ttt) cc_final: 0.7238 (mtp) REVERT: M 79 LYS cc_start: 0.8543 (mppt) cc_final: 0.8009 (mmtm) REVERT: M 93 LYS cc_start: 0.8583 (tttt) cc_final: 0.7935 (mtpp) REVERT: N 59 ARG cc_start: 0.7926 (mmt-90) cc_final: 0.7404 (mmt180) REVERT: N 72 LYS cc_start: 0.8930 (tttt) cc_final: 0.8726 (tmtt) REVERT: N 78 GLU cc_start: 0.7670 (tp30) cc_final: 0.6979 (tm-30) REVERT: N 93 LYS cc_start: 0.8530 (tttt) cc_final: 0.8249 (mtpp) REVERT: N 95 GLN cc_start: 0.8298 (mm-40) cc_final: 0.7716 (tp-100) REVERT: O 25 MET cc_start: 0.8139 (ttt) cc_final: 0.7748 (tmm) REVERT: O 78 GLU cc_start: 0.8335 (mt-10) cc_final: 0.7817 (tm-30) REVERT: O 93 LYS cc_start: 0.8526 (tttt) cc_final: 0.7511 (mtmm) REVERT: P 61 GLU cc_start: 0.7678 (mp0) cc_final: 0.7289 (mp0) REVERT: P 79 LYS cc_start: 0.8892 (mmtt) cc_final: 0.8449 (mmmt) REVERT: P 93 LYS cc_start: 0.8189 (tttt) cc_final: 0.7941 (tttp) REVERT: P 95 GLN cc_start: 0.8631 (mm110) cc_final: 0.8217 (mm-40) REVERT: P 108 GLN cc_start: 0.7158 (tt0) cc_final: 0.6882 (tm-30) REVERT: P 109 SER cc_start: 0.9108 (t) cc_final: 0.8552 (t) REVERT: R 38 ARG cc_start: 0.8189 (tpt90) cc_final: 0.7735 (tpt90) REVERT: R 84 LYS cc_start: 0.8389 (tptp) cc_final: 0.8109 (tmmt) REVERT: R 93 LYS cc_start: 0.8515 (tttt) cc_final: 0.8164 (tttp) REVERT: S 26 ARG cc_start: 0.7642 (mtt180) cc_final: 0.7232 (ttm110) REVERT: S 28 LYS cc_start: 0.7507 (mptt) cc_final: 0.7240 (mmtm) REVERT: S 38 ARG cc_start: 0.8224 (tpt90) cc_final: 0.7836 (tpt90) REVERT: S 59 ARG cc_start: 0.7770 (mmt-90) cc_final: 0.7310 (mmm-85) REVERT: S 72 LYS cc_start: 0.8876 (tttt) cc_final: 0.8584 (tptm) REVERT: S 93 LYS cc_start: 0.8623 (tttt) cc_final: 0.8230 (tptp) REVERT: T 25 MET cc_start: 0.7878 (ttm) cc_final: 0.7032 (tmm) REVERT: T 28 LYS cc_start: 0.8476 (tmtt) cc_final: 0.8141 (ttpt) REVERT: T 59 ARG cc_start: 0.8304 (tpp-160) cc_final: 0.7794 (tpp80) REVERT: T 63 ARG cc_start: 0.7898 (mmt-90) cc_final: 0.7633 (ptt90) REVERT: T 72 LYS cc_start: 0.8646 (tmtt) cc_final: 0.8226 (tptp) REVERT: T 78 GLU cc_start: 0.8316 (tp30) cc_final: 0.7609 (tp30) REVERT: T 79 LYS cc_start: 0.9061 (mmtm) cc_final: 0.8393 (mmpt) REVERT: U 18 ASP cc_start: 0.7438 (p0) cc_final: 0.6800 (p0) REVERT: U 24 ASP cc_start: 0.6995 (t70) cc_final: 0.6719 (t0) REVERT: U 72 LYS cc_start: 0.8897 (tptt) cc_final: 0.8490 (tppt) REVERT: U 93 LYS cc_start: 0.8746 (tttt) cc_final: 0.8250 (tptp) REVERT: V 38 ARG cc_start: 0.6342 (tmm160) cc_final: 0.5782 (ttp80) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.2041 time to fit residues: 78.6621 Evaluate side-chains 254 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 254 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 166 optimal weight: 2.9990 chunk 70 optimal weight: 5.9990 chunk 78 optimal weight: 0.7980 chunk 143 optimal weight: 0.6980 chunk 192 optimal weight: 2.9990 chunk 170 optimal weight: 7.9990 chunk 59 optimal weight: 0.5980 chunk 169 optimal weight: 0.7980 chunk 94 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 171 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** D 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4932 r_free = 0.4932 target = 0.114433 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.086275 restraints weight = 30444.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.087301 restraints weight = 21565.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4420 r_free = 0.4420 target = 0.087690 restraints weight = 17701.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.088140 restraints weight = 15210.506| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.088444 restraints weight = 13493.406| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7064 moved from start: 0.6561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 16478 Z= 0.119 Angle : 0.716 8.654 22198 Z= 0.351 Chirality : 0.052 0.178 2684 Planarity : 0.003 0.038 2904 Dihedral : 5.514 25.515 2376 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.63 (0.14), residues: 2178 helix: None (None), residues: 0 sheet: -3.88 (0.13), residues: 1034 loop : -3.55 (0.14), residues: 1144 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 87 TYR 0.015 0.001 TYR B 14 PHE 0.011 0.002 PHE N 88 HIS 0.004 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00265 (16478) covalent geometry : angle 0.71623 (22198) hydrogen bonds : bond 0.01228 ( 66) hydrogen bonds : angle 5.05710 ( 132) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 328 time to evaluate : 0.621 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 61 GLU cc_start: 0.6643 (pm20) cc_final: 0.5256 (pp20) REVERT: A 72 LYS cc_start: 0.7979 (tmtt) cc_final: 0.7524 (tmtt) REVERT: A 95 GLN cc_start: 0.7947 (mm-40) cc_final: 0.7458 (mm-40) REVERT: B 72 LYS cc_start: 0.8046 (tmtt) cc_final: 0.7572 (tmtt) REVERT: C 24 ASP cc_start: 0.7239 (m-30) cc_final: 0.6720 (t0) REVERT: C 32 ARG cc_start: 0.7015 (tpt90) cc_final: 0.6606 (tpt90) REVERT: C 38 ARG cc_start: 0.6396 (tmm160) cc_final: 0.5748 (ttp80) REVERT: C 78 GLU cc_start: 0.5701 (pt0) cc_final: 0.5027 (mm-30) REVERT: D 24 ASP cc_start: 0.6800 (t0) cc_final: 0.6556 (t0) REVERT: D 91 GLN cc_start: 0.7755 (tm-30) cc_final: 0.7153 (tm-30) REVERT: D 93 LYS cc_start: 0.8612 (tttt) cc_final: 0.8234 (tptp) REVERT: E 25 MET cc_start: 0.7166 (ttm) cc_final: 0.6669 (tmm) REVERT: E 38 ARG cc_start: 0.8229 (tpm170) cc_final: 0.7896 (tpm170) REVERT: E 55 VAL cc_start: 0.9269 (t) cc_final: 0.9063 (p) REVERT: E 72 LYS cc_start: 0.8656 (tttt) cc_final: 0.8163 (tptp) REVERT: E 79 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8812 (mmmt) REVERT: F 26 ARG cc_start: 0.7520 (mtt180) cc_final: 0.7070 (ttm110) REVERT: F 38 ARG cc_start: 0.8014 (tpt90) cc_final: 0.7596 (tpt90) REVERT: F 46 GLU cc_start: 0.8430 (tm-30) cc_final: 0.7693 (tm-30) REVERT: F 59 ARG cc_start: 0.8149 (mmt180) cc_final: 0.7593 (mmm-85) REVERT: G 42 LEU cc_start: 0.8741 (mt) cc_final: 0.8501 (mt) REVERT: G 66 LEU cc_start: 0.8200 (mm) cc_final: 0.7751 (mp) REVERT: G 84 LYS cc_start: 0.8296 (tptp) cc_final: 0.8046 (tmmt) REVERT: G 93 LYS cc_start: 0.8570 (tttt) cc_final: 0.8159 (tttp) REVERT: H 18 ASP cc_start: 0.8276 (p0) cc_final: 0.8024 (p0) REVERT: I 25 MET cc_start: 0.7635 (ttm) cc_final: 0.7046 (tmm) REVERT: I 79 LYS cc_start: 0.8560 (mmtt) cc_final: 0.8167 (mmmt) REVERT: J 25 MET cc_start: 0.8024 (ttt) cc_final: 0.7708 (tmm) REVERT: J 66 LEU cc_start: 0.8169 (mm) cc_final: 0.7881 (mm) REVERT: J 78 GLU cc_start: 0.8032 (mt-10) cc_final: 0.7425 (tm-30) REVERT: J 93 LYS cc_start: 0.8213 (tttt) cc_final: 0.7320 (mmtm) REVERT: K 20 GLU cc_start: 0.7717 (mp0) cc_final: 0.7404 (mp0) REVERT: K 59 ARG cc_start: 0.7733 (mmt-90) cc_final: 0.7420 (mmm-85) REVERT: K 78 GLU cc_start: 0.7679 (tp30) cc_final: 0.6729 (tm-30) REVERT: K 95 GLN cc_start: 0.8138 (mm-40) cc_final: 0.7081 (tp40) REVERT: L 18 ASP cc_start: 0.7178 (p0) cc_final: 0.6491 (p0) REVERT: L 20 GLU cc_start: 0.7919 (mp0) cc_final: 0.6955 (pm20) REVERT: M 20 GLU cc_start: 0.7908 (mp0) cc_final: 0.7540 (mp0) REVERT: N 59 ARG cc_start: 0.7828 (mmt-90) cc_final: 0.7445 (mmt180) REVERT: N 93 LYS cc_start: 0.8348 (tttt) cc_final: 0.8064 (mtpt) REVERT: N 95 GLN cc_start: 0.8102 (mm-40) cc_final: 0.7065 (tp40) REVERT: O 66 LEU cc_start: 0.8218 (mm) cc_final: 0.7972 (mm) REVERT: O 72 LYS cc_start: 0.8721 (ttmm) cc_final: 0.7952 (mptt) REVERT: O 78 GLU cc_start: 0.8088 (mt-10) cc_final: 0.7573 (tm-30) REVERT: O 93 LYS cc_start: 0.8317 (tttt) cc_final: 0.7348 (mmtm) REVERT: P 25 MET cc_start: 0.7671 (ttm) cc_final: 0.6959 (tmm) REVERT: P 79 LYS cc_start: 0.8632 (mmtt) cc_final: 0.8220 (mmmt) REVERT: P 93 LYS cc_start: 0.8287 (tttt) cc_final: 0.7939 (tttp) REVERT: P 95 GLN cc_start: 0.8454 (mm110) cc_final: 0.8181 (mm-40) REVERT: Q 25 MET cc_start: 0.8389 (tmm) cc_final: 0.7971 (tmm) REVERT: R 38 ARG cc_start: 0.7855 (tpt90) cc_final: 0.7584 (tpt90) REVERT: R 84 LYS cc_start: 0.8232 (tptp) cc_final: 0.7929 (tmmt) REVERT: R 93 LYS cc_start: 0.8545 (tttt) cc_final: 0.8127 (tttp) REVERT: S 26 ARG cc_start: 0.7847 (mtt180) cc_final: 0.7239 (ttm110) REVERT: S 38 ARG cc_start: 0.8091 (tpt90) cc_final: 0.7703 (tpt90) REVERT: S 59 ARG cc_start: 0.7705 (mmt-90) cc_final: 0.7398 (mmm-85) REVERT: S 66 LEU cc_start: 0.8384 (mm) cc_final: 0.8173 (mm) REVERT: S 72 LYS cc_start: 0.8867 (tttt) cc_final: 0.8566 (tptm) REVERT: S 79 LYS cc_start: 0.8596 (mmtm) cc_final: 0.8312 (mmtm) REVERT: S 93 LYS cc_start: 0.8466 (tttt) cc_final: 0.8074 (tptp) REVERT: S 95 GLN cc_start: 0.8437 (mm110) cc_final: 0.8132 (mm110) REVERT: T 25 MET cc_start: 0.7862 (ttm) cc_final: 0.6745 (tmm) REVERT: T 28 LYS cc_start: 0.8578 (tmtt) cc_final: 0.8277 (tmmt) REVERT: T 72 LYS cc_start: 0.8561 (tmtt) cc_final: 0.8020 (tptp) REVERT: T 78 GLU cc_start: 0.8236 (tp30) cc_final: 0.7979 (tp30) REVERT: T 79 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8522 (mmmt) REVERT: T 93 LYS cc_start: 0.7850 (mptt) cc_final: 0.7644 (mmtm) REVERT: U 18 ASP cc_start: 0.7274 (p0) cc_final: 0.6753 (p0) REVERT: U 24 ASP cc_start: 0.6934 (t70) cc_final: 0.6620 (t0) REVERT: U 93 LYS cc_start: 0.8532 (tttt) cc_final: 0.8092 (tptp) REVERT: V 24 ASP cc_start: 0.7567 (m-30) cc_final: 0.6608 (t0) REVERT: V 38 ARG cc_start: 0.6361 (tmm160) cc_final: 0.5802 (ttp80) outliers start: 0 outliers final: 0 residues processed: 328 average time/residue: 0.2117 time to fit residues: 88.4915 Evaluate side-chains 263 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 263 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 37 optimal weight: 8.9990 chunk 103 optimal weight: 9.9990 chunk 131 optimal weight: 10.0000 chunk 71 optimal weight: 3.9990 chunk 219 optimal weight: 9.9990 chunk 121 optimal weight: 3.9990 chunk 159 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 145 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 14 optimal weight: 20.0000 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.108005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.079615 restraints weight = 33637.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.080888 restraints weight = 25017.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.081865 restraints weight = 19874.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.082599 restraints weight = 16554.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4310 r_free = 0.4310 target = 0.083212 restraints weight = 14349.164| |-----------------------------------------------------------------------------| r_work (final): 0.4329 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.7124 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 16478 Z= 0.366 Angle : 0.894 8.043 22198 Z= 0.473 Chirality : 0.056 0.178 2684 Planarity : 0.006 0.060 2904 Dihedral : 7.080 25.646 2376 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 25.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.03 % Favored : 78.97 % Rotamer: Outliers : 0.00 % Allowed : 1.30 % Favored : 98.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.84 (0.14), residues: 2178 helix: None (None), residues: 0 sheet: -4.09 (0.14), residues: 924 loop : -3.78 (0.13), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG M 38 TYR 0.023 0.002 TYR O 14 PHE 0.023 0.003 PHE O 105 HIS 0.011 0.002 HIS J 68 Details of bonding type rmsd covalent geometry : bond 0.00741 (16478) covalent geometry : angle 0.89411 (22198) hydrogen bonds : bond 0.02848 ( 66) hydrogen bonds : angle 6.24923 ( 132) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 281 time to evaluate : 0.601 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8030 (tmtt) cc_final: 0.7558 (tmtt) REVERT: B 72 LYS cc_start: 0.8111 (tmtt) cc_final: 0.7593 (tmtt) REVERT: C 24 ASP cc_start: 0.7383 (m-30) cc_final: 0.6566 (t0) REVERT: C 38 ARG cc_start: 0.6276 (tmm160) cc_final: 0.5955 (tmm160) REVERT: C 78 GLU cc_start: 0.5554 (pt0) cc_final: 0.4935 (mm-30) REVERT: C 88 PHE cc_start: 0.4390 (t80) cc_final: 0.4121 (t80) REVERT: D 24 ASP cc_start: 0.6913 (t0) cc_final: 0.6649 (t0) REVERT: D 91 GLN cc_start: 0.7884 (tm-30) cc_final: 0.7357 (tm-30) REVERT: D 93 LYS cc_start: 0.8641 (tttt) cc_final: 0.8183 (tptp) REVERT: E 25 MET cc_start: 0.7945 (ttm) cc_final: 0.6834 (tmm) REVERT: E 26 ARG cc_start: 0.7301 (tpt-90) cc_final: 0.6653 (ptp90) REVERT: E 55 VAL cc_start: 0.9455 (t) cc_final: 0.9167 (p) REVERT: E 72 LYS cc_start: 0.8704 (tttt) cc_final: 0.8157 (tptp) REVERT: E 79 LYS cc_start: 0.9182 (mmtm) cc_final: 0.8719 (mmpt) REVERT: E 93 LYS cc_start: 0.7817 (mptt) cc_final: 0.7552 (mmtm) REVERT: F 20 GLU cc_start: 0.8190 (mp0) cc_final: 0.7664 (mp0) REVERT: F 26 ARG cc_start: 0.7519 (mtt180) cc_final: 0.7004 (ttm110) REVERT: F 28 LYS cc_start: 0.7528 (mptt) cc_final: 0.7201 (mmtm) REVERT: F 38 ARG cc_start: 0.8129 (tpt90) cc_final: 0.7714 (tpt90) REVERT: F 59 ARG cc_start: 0.8011 (mmt180) cc_final: 0.7629 (mmm-85) REVERT: G 84 LYS cc_start: 0.8336 (tptp) cc_final: 0.8122 (tmmt) REVERT: G 93 LYS cc_start: 0.8531 (tttt) cc_final: 0.8137 (tttp) REVERT: H 18 ASP cc_start: 0.8502 (p0) cc_final: 0.8177 (p0) REVERT: I 61 GLU cc_start: 0.7866 (mp0) cc_final: 0.7432 (mp0) REVERT: I 79 LYS cc_start: 0.8710 (mmtt) cc_final: 0.8176 (mmmt) REVERT: J 25 MET cc_start: 0.8280 (ttt) cc_final: 0.7825 (tmm) REVERT: J 78 GLU cc_start: 0.8198 (mt-10) cc_final: 0.7632 (tm-30) REVERT: J 93 LYS cc_start: 0.8540 (tttt) cc_final: 0.7567 (mtmm) REVERT: K 59 ARG cc_start: 0.7941 (mmt-90) cc_final: 0.7441 (mmt180) REVERT: K 78 GLU cc_start: 0.7513 (tp30) cc_final: 0.6758 (tm-30) REVERT: K 95 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7723 (tp-100) REVERT: L 18 ASP cc_start: 0.7430 (p0) cc_final: 0.6801 (p0) REVERT: L 93 LYS cc_start: 0.8585 (tttt) cc_final: 0.7985 (mtpp) REVERT: M 25 MET cc_start: 0.7827 (ttt) cc_final: 0.7304 (mtp) REVERT: M 79 LYS cc_start: 0.8509 (mppt) cc_final: 0.8113 (mmtp) REVERT: M 93 LYS cc_start: 0.8587 (tttt) cc_final: 0.7993 (mtpp) REVERT: N 59 ARG cc_start: 0.7934 (mmt-90) cc_final: 0.7507 (mmt180) REVERT: N 93 LYS cc_start: 0.8526 (tttt) cc_final: 0.8126 (mtpt) REVERT: N 95 GLN cc_start: 0.8165 (mm-40) cc_final: 0.7254 (tp-100) REVERT: O 78 GLU cc_start: 0.8137 (mt-10) cc_final: 0.7756 (tm-30) REVERT: O 93 LYS cc_start: 0.8565 (tttt) cc_final: 0.7576 (mtmm) REVERT: P 25 MET cc_start: 0.7904 (ttm) cc_final: 0.7169 (tmm) REVERT: P 79 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8211 (mmmt) REVERT: P 93 LYS cc_start: 0.8215 (tttt) cc_final: 0.7948 (tttp) REVERT: Q 61 GLU cc_start: 0.7331 (mp0) cc_final: 0.6739 (mp0) REVERT: R 26 ARG cc_start: 0.7087 (mtt90) cc_final: 0.6786 (mtt90) REVERT: R 38 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7682 (tpt90) REVERT: R 84 LYS cc_start: 0.8282 (tptp) cc_final: 0.8070 (tmmt) REVERT: R 93 LYS cc_start: 0.8481 (tttt) cc_final: 0.8107 (tttp) REVERT: S 26 ARG cc_start: 0.7595 (mtt180) cc_final: 0.6927 (ttm110) REVERT: S 38 ARG cc_start: 0.8167 (tpt90) cc_final: 0.7803 (tpt90) REVERT: S 59 ARG cc_start: 0.7725 (mmt-90) cc_final: 0.7296 (mmm-85) REVERT: S 72 LYS cc_start: 0.8813 (tttt) cc_final: 0.8497 (tptm) REVERT: S 93 LYS cc_start: 0.8528 (tttt) cc_final: 0.8059 (tptp) REVERT: T 25 MET cc_start: 0.8137 (ttm) cc_final: 0.6771 (tmm) REVERT: T 26 ARG cc_start: 0.7285 (tpt-90) cc_final: 0.6633 (ptp90) REVERT: T 55 VAL cc_start: 0.9495 (t) cc_final: 0.9176 (p) REVERT: T 72 LYS cc_start: 0.8593 (tmtt) cc_final: 0.8154 (tptp) REVERT: T 78 GLU cc_start: 0.8286 (tp30) cc_final: 0.7480 (tp30) REVERT: T 79 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8311 (mmpt) REVERT: U 18 ASP cc_start: 0.7252 (p0) cc_final: 0.6909 (p0) REVERT: U 24 ASP cc_start: 0.7023 (t70) cc_final: 0.6753 (t0) REVERT: U 78 GLU cc_start: 0.7755 (tm-30) cc_final: 0.7496 (tm-30) REVERT: U 93 LYS cc_start: 0.8671 (tttt) cc_final: 0.8045 (mptt) REVERT: V 24 ASP cc_start: 0.7349 (m-30) cc_final: 0.6457 (t0) REVERT: V 38 ARG cc_start: 0.6270 (tmm160) cc_final: 0.5668 (ttp80) outliers start: 0 outliers final: 0 residues processed: 281 average time/residue: 0.2143 time to fit residues: 76.7212 Evaluate side-chains 240 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 240 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 103 optimal weight: 0.9980 chunk 122 optimal weight: 0.8980 chunk 114 optimal weight: 5.9990 chunk 207 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 178 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 187 optimal weight: 3.9990 chunk 181 optimal weight: 10.0000 chunk 63 optimal weight: 5.9990 chunk 153 optimal weight: 6.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4907 r_free = 0.4907 target = 0.112231 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.082798 restraints weight = 31628.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.084271 restraints weight = 22971.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.085405 restraints weight = 17906.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.086284 restraints weight = 14670.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.086978 restraints weight = 12500.929| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7104 moved from start: 0.7032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 16478 Z= 0.178 Angle : 0.774 9.971 22198 Z= 0.387 Chirality : 0.053 0.169 2684 Planarity : 0.004 0.037 2904 Dihedral : 5.975 24.473 2376 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 18.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 0.71 % Favored : 99.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.85 (0.14), residues: 2178 helix: None (None), residues: 0 sheet: -4.09 (0.13), residues: 1078 loop : -3.58 (0.14), residues: 1100 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 59 TYR 0.010 0.001 TYR O 14 PHE 0.014 0.002 PHE O 105 HIS 0.005 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00377 (16478) covalent geometry : angle 0.77422 (22198) hydrogen bonds : bond 0.01706 ( 66) hydrogen bonds : angle 5.49979 ( 132) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.528 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8001 (tmtt) cc_final: 0.7546 (tmtt) REVERT: B 72 LYS cc_start: 0.8020 (tmtt) cc_final: 0.7561 (tmtt) REVERT: C 24 ASP cc_start: 0.7288 (m-30) cc_final: 0.6426 (t0) REVERT: C 38 ARG cc_start: 0.6398 (tmm160) cc_final: 0.6073 (tmm160) REVERT: C 78 GLU cc_start: 0.5494 (pt0) cc_final: 0.4884 (mm-30) REVERT: C 88 PHE cc_start: 0.4252 (t80) cc_final: 0.3947 (t80) REVERT: D 24 ASP cc_start: 0.6841 (t0) cc_final: 0.6572 (t0) REVERT: D 93 LYS cc_start: 0.8600 (tttt) cc_final: 0.8171 (tptp) REVERT: E 25 MET cc_start: 0.7943 (ttm) cc_final: 0.6643 (tmm) REVERT: E 26 ARG cc_start: 0.7202 (tpt-90) cc_final: 0.6666 (ptp90) REVERT: E 38 ARG cc_start: 0.8106 (tpm170) cc_final: 0.7827 (tpm170) REVERT: E 55 VAL cc_start: 0.9297 (t) cc_final: 0.9043 (p) REVERT: E 72 LYS cc_start: 0.8612 (tttt) cc_final: 0.8099 (tptp) REVERT: E 79 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8665 (mmpt) REVERT: E 93 LYS cc_start: 0.7781 (mptt) cc_final: 0.7471 (mmtm) REVERT: F 20 GLU cc_start: 0.8079 (mp0) cc_final: 0.7796 (mp0) REVERT: F 26 ARG cc_start: 0.7805 (mtt180) cc_final: 0.7053 (ttm110) REVERT: F 38 ARG cc_start: 0.8073 (tpt90) cc_final: 0.7629 (tpt90) REVERT: F 46 GLU cc_start: 0.8365 (tm-30) cc_final: 0.7686 (tm-30) REVERT: F 59 ARG cc_start: 0.8049 (mmt180) cc_final: 0.7568 (mmm-85) REVERT: F 95 GLN cc_start: 0.8619 (mt0) cc_final: 0.8369 (mt0) REVERT: G 93 LYS cc_start: 0.8559 (tttt) cc_final: 0.8115 (tttp) REVERT: H 18 ASP cc_start: 0.8399 (p0) cc_final: 0.8068 (p0) REVERT: I 25 MET cc_start: 0.7677 (ttm) cc_final: 0.6968 (tmm) REVERT: I 79 LYS cc_start: 0.8528 (mmtt) cc_final: 0.8007 (mmmt) REVERT: J 25 MET cc_start: 0.8067 (ttt) cc_final: 0.7609 (tmm) REVERT: J 66 LEU cc_start: 0.8266 (mm) cc_final: 0.8052 (mm) REVERT: J 78 GLU cc_start: 0.8042 (mt-10) cc_final: 0.7565 (tm-30) REVERT: J 93 LYS cc_start: 0.8432 (tttt) cc_final: 0.7683 (mtpp) REVERT: K 59 ARG cc_start: 0.7925 (mmt-90) cc_final: 0.7492 (mmt180) REVERT: K 78 GLU cc_start: 0.7495 (tp30) cc_final: 0.6620 (tm-30) REVERT: K 95 GLN cc_start: 0.8002 (mm-40) cc_final: 0.7189 (tp-100) REVERT: L 18 ASP cc_start: 0.7313 (p0) cc_final: 0.6559 (p0) REVERT: L 93 LYS cc_start: 0.8437 (tttt) cc_final: 0.7856 (mtpp) REVERT: M 20 GLU cc_start: 0.8248 (mp0) cc_final: 0.7730 (mp0) REVERT: M 78 GLU cc_start: 0.7794 (mm-30) cc_final: 0.7513 (mm-30) REVERT: M 79 LYS cc_start: 0.8546 (mppt) cc_final: 0.7965 (mmtm) REVERT: M 93 LYS cc_start: 0.8430 (tttt) cc_final: 0.7842 (mtpp) REVERT: N 28 LYS cc_start: 0.7903 (mtpp) cc_final: 0.7367 (mtpp) REVERT: N 59 ARG cc_start: 0.7865 (mmt-90) cc_final: 0.7545 (mmt180) REVERT: N 78 GLU cc_start: 0.7437 (tp30) cc_final: 0.7089 (tp30) REVERT: N 93 LYS cc_start: 0.8404 (tttt) cc_final: 0.8099 (mtpt) REVERT: N 95 GLN cc_start: 0.7837 (mm-40) cc_final: 0.6668 (tp-100) REVERT: O 78 GLU cc_start: 0.8041 (mt-10) cc_final: 0.7569 (tm-30) REVERT: O 93 LYS cc_start: 0.8448 (tttt) cc_final: 0.7668 (mtpp) REVERT: P 25 MET cc_start: 0.7851 (ttm) cc_final: 0.6980 (tmm) REVERT: P 79 LYS cc_start: 0.8616 (mmtt) cc_final: 0.8038 (mmmt) REVERT: P 93 LYS cc_start: 0.8182 (tttt) cc_final: 0.7855 (tttp) REVERT: P 95 GLN cc_start: 0.8501 (mm110) cc_final: 0.8280 (mm110) REVERT: R 26 ARG cc_start: 0.7132 (mtt90) cc_final: 0.6786 (mtt90) REVERT: R 38 ARG cc_start: 0.8039 (tpt90) cc_final: 0.7553 (tpt90) REVERT: R 93 LYS cc_start: 0.8462 (tttt) cc_final: 0.8031 (tttp) REVERT: S 26 ARG cc_start: 0.7817 (mtt180) cc_final: 0.7165 (ttm110) REVERT: S 38 ARG cc_start: 0.8142 (tpt90) cc_final: 0.7747 (tpt90) REVERT: S 59 ARG cc_start: 0.7670 (mmt-90) cc_final: 0.7331 (mmm-85) REVERT: S 72 LYS cc_start: 0.8775 (tttt) cc_final: 0.8451 (tptm) REVERT: S 79 LYS cc_start: 0.8433 (mmtm) cc_final: 0.8223 (mmtm) REVERT: S 93 LYS cc_start: 0.8442 (tttt) cc_final: 0.8008 (tptp) REVERT: S 95 GLN cc_start: 0.8479 (mm110) cc_final: 0.8199 (mm110) REVERT: T 25 MET cc_start: 0.7996 (ttm) cc_final: 0.6760 (tmm) REVERT: T 55 VAL cc_start: 0.9463 (t) cc_final: 0.9169 (p) REVERT: T 72 LYS cc_start: 0.8556 (tmtt) cc_final: 0.8082 (tptp) REVERT: T 78 GLU cc_start: 0.8204 (tp30) cc_final: 0.7912 (tp30) REVERT: T 79 LYS cc_start: 0.9018 (mmtm) cc_final: 0.8562 (mmmt) REVERT: T 93 LYS cc_start: 0.7792 (mptt) cc_final: 0.7558 (mmtm) REVERT: U 18 ASP cc_start: 0.7442 (p0) cc_final: 0.7185 (p0) REVERT: U 24 ASP cc_start: 0.6937 (t70) cc_final: 0.6720 (t0) REVERT: U 93 LYS cc_start: 0.8556 (tttt) cc_final: 0.8098 (tptp) REVERT: V 24 ASP cc_start: 0.7367 (m-30) cc_final: 0.6384 (t0) REVERT: V 38 ARG cc_start: 0.6290 (tmm160) cc_final: 0.5740 (ttp80) REVERT: V 78 GLU cc_start: 0.5661 (pt0) cc_final: 0.4647 (mm-30) outliers start: 0 outliers final: 0 residues processed: 285 average time/residue: 0.2185 time to fit residues: 79.6781 Evaluate side-chains 255 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 255 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 188 optimal weight: 0.4980 chunk 86 optimal weight: 4.9990 chunk 135 optimal weight: 4.9990 chunk 137 optimal weight: 2.9990 chunk 78 optimal weight: 9.9990 chunk 155 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 150 optimal weight: 0.4980 chunk 72 optimal weight: 5.9990 chunk 211 optimal weight: 8.9990 chunk 172 optimal weight: 6.9990 overall best weight: 2.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4898 r_free = 0.4898 target = 0.111315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.082189 restraints weight = 31926.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.083578 restraints weight = 23348.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.084578 restraints weight = 18306.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.085435 restraints weight = 15141.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.086042 restraints weight = 12999.701| |-----------------------------------------------------------------------------| r_work (final): 0.4403 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7167 moved from start: 0.7206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 16478 Z= 0.217 Angle : 0.793 8.560 22198 Z= 0.403 Chirality : 0.053 0.170 2684 Planarity : 0.004 0.045 2904 Dihedral : 6.093 24.563 2376 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.25 (0.14), residues: 2178 helix: None (None), residues: 0 sheet: -4.27 (0.15), residues: 704 loop : -3.24 (0.13), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 59 TYR 0.016 0.002 TYR O 14 PHE 0.022 0.002 PHE V 88 HIS 0.006 0.001 HIS D 68 Details of bonding type rmsd covalent geometry : bond 0.00454 (16478) covalent geometry : angle 0.79316 (22198) hydrogen bonds : bond 0.01952 ( 66) hydrogen bonds : angle 5.48232 ( 132) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4356 Ramachandran restraints generated. 2178 Oldfield, 0 Emsley, 2178 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 280 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8012 (tmtt) cc_final: 0.7561 (tmtt) REVERT: B 72 LYS cc_start: 0.8059 (tmtt) cc_final: 0.7597 (tmtt) REVERT: C 24 ASP cc_start: 0.7455 (m-30) cc_final: 0.6489 (t0) REVERT: C 38 ARG cc_start: 0.6373 (tmm160) cc_final: 0.6036 (tmm160) REVERT: C 78 GLU cc_start: 0.5425 (pt0) cc_final: 0.4889 (mm-30) REVERT: C 88 PHE cc_start: 0.4124 (t80) cc_final: 0.3812 (t80) REVERT: D 24 ASP cc_start: 0.7013 (t0) cc_final: 0.6703 (t0) REVERT: D 93 LYS cc_start: 0.8666 (tttt) cc_final: 0.8272 (tptt) REVERT: E 25 MET cc_start: 0.7831 (ttm) cc_final: 0.6690 (tmm) REVERT: E 26 ARG cc_start: 0.7285 (tpt-90) cc_final: 0.6662 (ptp90) REVERT: E 72 LYS cc_start: 0.8632 (tttt) cc_final: 0.8127 (tptp) REVERT: E 79 LYS cc_start: 0.9132 (mmtm) cc_final: 0.8837 (mmmt) REVERT: E 93 LYS cc_start: 0.7809 (mptt) cc_final: 0.7486 (mmtm) REVERT: F 20 GLU cc_start: 0.8046 (mp0) cc_final: 0.7536 (mp0) REVERT: F 26 ARG cc_start: 0.7503 (mtt180) cc_final: 0.7050 (ttm110) REVERT: F 28 LYS cc_start: 0.7388 (mptt) cc_final: 0.7136 (mmtm) REVERT: F 38 ARG cc_start: 0.8063 (tpt90) cc_final: 0.7630 (tpt90) REVERT: F 46 GLU cc_start: 0.8339 (tm-30) cc_final: 0.7684 (tm-30) REVERT: F 59 ARG cc_start: 0.8077 (mmt180) cc_final: 0.7639 (mmm-85) REVERT: G 93 LYS cc_start: 0.8581 (tttt) cc_final: 0.8147 (tttp) REVERT: H 18 ASP cc_start: 0.8367 (p0) cc_final: 0.8037 (p0) REVERT: I 25 MET cc_start: 0.7754 (ttm) cc_final: 0.7082 (tmm) REVERT: I 79 LYS cc_start: 0.8579 (mmtt) cc_final: 0.8119 (mmmt) REVERT: J 25 MET cc_start: 0.8144 (ttt) cc_final: 0.7700 (tmm) REVERT: J 78 GLU cc_start: 0.8127 (mt-10) cc_final: 0.7623 (tm-30) REVERT: J 93 LYS cc_start: 0.8428 (tttt) cc_final: 0.7678 (mtpp) REVERT: K 59 ARG cc_start: 0.7839 (mmt-90) cc_final: 0.7319 (mmt90) REVERT: K 78 GLU cc_start: 0.7511 (tp30) cc_final: 0.6704 (tm-30) REVERT: L 18 ASP cc_start: 0.7408 (p0) cc_final: 0.6671 (p0) REVERT: L 93 LYS cc_start: 0.8529 (tttt) cc_final: 0.7941 (mtpp) REVERT: M 93 LYS cc_start: 0.8465 (tttt) cc_final: 0.7903 (mtpp) REVERT: N 58 GLU cc_start: 0.6152 (pt0) cc_final: 0.5649 (pm20) REVERT: N 59 ARG cc_start: 0.7849 (mmt-90) cc_final: 0.7466 (mmt180) REVERT: N 78 GLU cc_start: 0.7499 (tp30) cc_final: 0.7153 (tp30) REVERT: N 93 LYS cc_start: 0.8499 (tttt) cc_final: 0.8144 (mtpt) REVERT: O 78 GLU cc_start: 0.8030 (mt-10) cc_final: 0.7584 (tm-30) REVERT: O 93 LYS cc_start: 0.8427 (tttt) cc_final: 0.7640 (mtpp) REVERT: P 25 MET cc_start: 0.7989 (ttm) cc_final: 0.7111 (tmm) REVERT: P 79 LYS cc_start: 0.8685 (mmtt) cc_final: 0.8167 (mmmt) REVERT: P 93 LYS cc_start: 0.8230 (tttt) cc_final: 0.7927 (tttp) REVERT: P 95 GLN cc_start: 0.8434 (mm110) cc_final: 0.8208 (mm110) REVERT: Q 61 GLU cc_start: 0.7365 (mp0) cc_final: 0.6742 (mp0) REVERT: Q 78 GLU cc_start: 0.8072 (tp30) cc_final: 0.7459 (tp30) REVERT: R 26 ARG cc_start: 0.7089 (mtt90) cc_final: 0.6745 (mtt90) REVERT: R 38 ARG cc_start: 0.8118 (tpt90) cc_final: 0.7639 (tpt90) REVERT: R 93 LYS cc_start: 0.8523 (tttt) cc_final: 0.8126 (tttp) REVERT: S 26 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7069 (ttm110) REVERT: S 38 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7694 (tpt90) REVERT: S 59 ARG cc_start: 0.7623 (mmt-90) cc_final: 0.7328 (mmm-85) REVERT: S 72 LYS cc_start: 0.8771 (tttt) cc_final: 0.8443 (tptm) REVERT: S 79 LYS cc_start: 0.8535 (mmtm) cc_final: 0.8334 (mmtm) REVERT: S 93 LYS cc_start: 0.8450 (tttt) cc_final: 0.7989 (tptp) REVERT: T 25 MET cc_start: 0.8109 (ttm) cc_final: 0.6747 (tmm) REVERT: T 26 ARG cc_start: 0.7279 (tpt-90) cc_final: 0.6645 (ptp90) REVERT: T 55 VAL cc_start: 0.9479 (t) cc_final: 0.9221 (p) REVERT: T 66 LEU cc_start: 0.8881 (tp) cc_final: 0.8677 (tp) REVERT: T 72 LYS cc_start: 0.8494 (tmtt) cc_final: 0.8030 (tptp) REVERT: T 78 GLU cc_start: 0.8183 (tp30) cc_final: 0.7967 (tp30) REVERT: T 79 LYS cc_start: 0.8975 (mmtm) cc_final: 0.8506 (mmmt) REVERT: T 93 LYS cc_start: 0.7653 (mptt) cc_final: 0.7436 (mmtm) REVERT: U 18 ASP cc_start: 0.7205 (p0) cc_final: 0.6864 (p0) REVERT: U 24 ASP cc_start: 0.7005 (t70) cc_final: 0.6799 (t0) REVERT: U 59 ARG cc_start: 0.7669 (mmt-90) cc_final: 0.7406 (mmt-90) REVERT: U 78 GLU cc_start: 0.7869 (tt0) cc_final: 0.7572 (tt0) REVERT: U 93 LYS cc_start: 0.8611 (tttt) cc_final: 0.8043 (mptt) REVERT: V 24 ASP cc_start: 0.7451 (m-30) cc_final: 0.6486 (t0) REVERT: V 38 ARG cc_start: 0.6286 (tmm160) cc_final: 0.5720 (ttp80) outliers start: 0 outliers final: 0 residues processed: 280 average time/residue: 0.2132 time to fit residues: 76.1683 Evaluate side-chains 249 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 249 time to evaluate : 0.606 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 63 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 185 optimal weight: 9.9990 chunk 182 optimal weight: 7.9990 chunk 3 optimal weight: 6.9990 chunk 104 optimal weight: 8.9990 chunk 7 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 9.9990 chunk 118 optimal weight: 3.9990 chunk 193 optimal weight: 8.9990 overall best weight: 3.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 95 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4875 r_free = 0.4875 target = 0.110029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.4259 r_free = 0.4259 target = 0.081184 restraints weight = 32617.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4298 r_free = 0.4298 target = 0.082532 restraints weight = 23988.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.083541 restraints weight = 18846.470| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.084270 restraints weight = 15613.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.084955 restraints weight = 13438.096| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7291 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 16478 Z= 0.272 Angle : 0.840 8.428 22198 Z= 0.432 Chirality : 0.054 0.161 2684 Planarity : 0.005 0.044 2904 Dihedral : 6.537 24.539 2376 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 21.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -5.34 (0.14), residues: 2178 helix: None (None), residues: 0 sheet: -4.37 (0.15), residues: 704 loop : -3.28 (0.13), residues: 1474 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 87 TYR 0.018 0.002 TYR O 14 PHE 0.020 0.002 PHE O 105 HIS 0.007 0.002 HIS O 68 Details of bonding type rmsd covalent geometry : bond 0.00558 (16478) covalent geometry : angle 0.84017 (22198) hydrogen bonds : bond 0.02135 ( 66) hydrogen bonds : angle 5.71472 ( 132) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2734.58 seconds wall clock time: 47 minutes 56.13 seconds (2876.13 seconds total)