Starting phenix.real_space_refine on Sat Jun 14 10:30:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6rib_4887/06_2025/6rib_4887_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/6rib_4887/06_2025/6rib_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_4887/06_2025/6rib_4887.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6rib_4887/06_2025/6rib_4887.map" model { file = "/net/cci-nas-00/data/ceres_data/6rib_4887/06_2025/6rib_4887_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6rib_4887/06_2025/6rib_4887_neut.cif" } resolution = 4.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, U, T, V Time building chain proxies: 4.43, per 1000 atoms: 0.27 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: 3.71 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 4.09 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: 4.73 Time building geometry restraints manager: 4.42 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' selection = chain 'U' selection = chain 'T' 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: 20.870 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: 0.630 Check model and map are aligned: 0.120 Set scattering table: 0.150 Process input model: 33.850 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.660 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.005 0.003 HIS J 68 PHE 0.008 0.003 PHE E 88 TYR 0.003 0.001 TYR O 14 ARG 0.006 0.001 ARG H 59 Details of bonding type rmsd hydrogen bonds : bond 0.12949 ( 66) hydrogen bonds : angle 8.64282 ( 132) covalent geometry : bond 0.00756 (16478) covalent geometry : angle 1.11657 (22198) *********************** 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 : 1.697 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: 0.3285 (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: 0.8296 (mmt180) cc_final: 0.7904 (mmt180) REVERT: E 72 LYS cc_start: 0.8708 (tttt) cc_final: 0.8438 (tptp) REVERT: F 19 THR cc_start: 0.7129 (OUTLIER) cc_final: 0.6823 (p) REVERT: F 20 GLU cc_start: 0.8034 (mp0) cc_final: 0.7766 (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: 0.8214 (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: 0.6731 (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: 0.7084 (tp30) REVERT: I 70 GLU cc_start: 0.8138 (mt-10) cc_final: 0.7560 (tm-30) REVERT: I 72 LYS cc_start: 0.8505 (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: 0.7487 (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: 0.7435 (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: 0.7175 (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: 0.7323 (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: 0.7837 (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: 0.7741 (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: 0.8140 (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: 0.7318 (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: 0.8149 (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: 0.8448 (tptp) REVERT: Q 93 LYS cc_start: 0.8072 (tttt) cc_final: 0.7834 (tttp) REVERT: Q 95 GLN cc_start: 0.8472 (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: 0.7308 (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: 0.8073 (mt0) REVERT: S 108 GLN cc_start: 0.6493 (tt0) cc_final: 0.6249 (pm20) REVERT: T 25 MET cc_start: 0.7458 (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: 0.6800 (pt0) cc_final: 0.6177 (pm20) REVERT: T 59 ARG cc_start: 0.7820 (OUTLIER) cc_final: 0.7148 (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: 0.7629 (tt) REVERT: U 79 LYS cc_start: 0.8607 (mmtm) cc_final: 0.8223 (mmmm) REVERT: U 93 LYS cc_start: 0.8431 (tttt) cc_final: 0.8107 (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: 0.4416 time to fit residues: 347.4356 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 : 3.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 4.9990 chunk 166 optimal weight: 5.9990 chunk 92 optimal weight: 0.2980 chunk 56 optimal weight: 7.9990 chunk 112 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 172 optimal weight: 6.9990 chunk 66 optimal weight: 3.9990 chunk 104 optimal weight: 5.9990 chunk 128 optimal weight: 2.9990 chunk 199 optimal weight: 0.0170 overall best weight: 1.6222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 91 GLN ** 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: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5007 r_free = 0.5007 target = 0.121416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.088275 restraints weight = 31773.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4454 r_free = 0.4454 target = 0.090465 restraints weight = 22510.920| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.092139 restraints weight = 17103.489| |-----------------------------------------------------------------------------| r_work (final): 0.4452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7065 moved from start: 0.3554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 16478 Z= 0.156 Angle : 0.651 6.872 22198 Z= 0.328 Chirality : 0.050 0.142 2684 Planarity : 0.003 0.050 2904 Dihedral : 5.189 19.159 2376 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.35 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.14 (0.12), residues: 1342 loop : -3.97 (0.14), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS V 68 PHE 0.008 0.001 PHE R 88 TYR 0.007 0.001 TYR U 14 ARG 0.007 0.001 ARG E 54 Details of bonding type rmsd hydrogen bonds : bond 0.01608 ( 66) hydrogen bonds : angle 5.32988 ( 132) covalent geometry : bond 0.00316 (16478) covalent geometry : angle 0.65084 (22198) *********************** 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 392 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 392 time to evaluate : 2.070 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 34 ASP cc_start: 0.6659 (t70) cc_final: 0.6156 (t70) REVERT: A 72 LYS cc_start: 0.7840 (tmtt) cc_final: 0.7631 (tptp) REVERT: A 91 GLN cc_start: 0.7021 (mp10) cc_final: 0.6159 (tm-30) REVERT: B 72 LYS cc_start: 0.8076 (tmtt) cc_final: 0.7685 (tptp) REVERT: B 91 GLN cc_start: 0.7140 (mp10) cc_final: 0.6279 (tm-30) REVERT: C 24 ASP cc_start: 0.6925 (m-30) cc_final: 0.6531 (t0) REVERT: C 38 ARG cc_start: 0.6474 (ttp80) cc_final: 0.6022 (ttp80) REVERT: C 40 SER cc_start: 0.6729 (p) cc_final: 0.6310 (t) REVERT: C 58 GLU cc_start: 0.4141 (pm20) cc_final: 0.3922 (pm20) REVERT: D 25 MET cc_start: 0.7457 (tmm) cc_final: 0.6860 (tmm) REVERT: D 36 LEU cc_start: 0.6923 (tt) cc_final: 0.6710 (mt) REVERT: D 93 LYS cc_start: 0.8313 (tttt) cc_final: 0.7939 (tptp) REVERT: E 25 MET cc_start: 0.7581 (ttm) cc_final: 0.6869 (tmm) REVERT: E 26 ARG cc_start: 0.7256 (mtt180) cc_final: 0.7006 (tpt-90) REVERT: E 78 GLU cc_start: 0.8240 (tp30) cc_final: 0.7322 (tp30) REVERT: F 26 ARG cc_start: 0.7606 (mtt180) cc_final: 0.6868 (ttm110) REVERT: F 38 ARG cc_start: 0.8063 (tpt90) cc_final: 0.7640 (tpt90) REVERT: F 44 GLU cc_start: 0.6428 (tm-30) cc_final: 0.6200 (tm-30) REVERT: F 59 ARG cc_start: 0.7677 (mmt-90) cc_final: 0.7399 (mmm-85) REVERT: G 20 GLU cc_start: 0.7885 (mp0) cc_final: 0.7551 (mt-10) REVERT: H 18 ASP cc_start: 0.7159 (p0) cc_final: 0.6929 (p0) REVERT: I 25 MET cc_start: 0.7413 (ttm) cc_final: 0.6996 (tmm) REVERT: I 70 GLU cc_start: 0.8355 (mt-10) cc_final: 0.8093 (tm-30) REVERT: I 93 LYS cc_start: 0.8135 (tttt) cc_final: 0.7415 (mmtm) REVERT: I 100 GLU cc_start: 0.6886 (mm-30) cc_final: 0.6653 (mm-30) REVERT: J 72 LYS cc_start: 0.8638 (tttt) cc_final: 0.8237 (mppt) REVERT: J 93 LYS cc_start: 0.8400 (tttt) cc_final: 0.7452 (mmtm) REVERT: K 28 LYS cc_start: 0.7868 (mtpp) cc_final: 0.7223 (mtpp) REVERT: K 40 SER cc_start: 0.7921 (p) cc_final: 0.7653 (t) REVERT: K 93 LYS cc_start: 0.8497 (tttt) cc_final: 0.8212 (mtpt) REVERT: L 18 ASP cc_start: 0.7241 (p0) cc_final: 0.6627 (p0) REVERT: L 93 LYS cc_start: 0.8134 (tttt) cc_final: 0.7147 (mmtm) REVERT: L 95 GLN cc_start: 0.8178 (mm-40) cc_final: 0.7858 (mm110) REVERT: M 25 MET cc_start: 0.7436 (ttt) cc_final: 0.7215 (mtp) REVERT: M 34 ASP cc_start: 0.6603 (t0) cc_final: 0.6320 (m-30) REVERT: M 44 GLU cc_start: 0.6472 (tm-30) cc_final: 0.6122 (tm-30) REVERT: M 93 LYS cc_start: 0.8136 (tttt) cc_final: 0.7141 (mmtm) REVERT: M 95 GLN cc_start: 0.8251 (mm-40) cc_final: 0.7813 (mm110) REVERT: N 93 LYS cc_start: 0.8505 (tttt) cc_final: 0.8226 (mtpt) REVERT: O 26 ARG cc_start: 0.7932 (mtt180) cc_final: 0.7731 (mtt-85) REVERT: O 72 LYS cc_start: 0.8587 (tttt) cc_final: 0.8297 (mppt) REVERT: O 93 LYS cc_start: 0.8398 (tttt) cc_final: 0.7472 (mmtm) REVERT: P 25 MET cc_start: 0.7430 (ttm) cc_final: 0.7134 (tmm) REVERT: P 70 GLU cc_start: 0.8327 (mt-10) cc_final: 0.7916 (tm-30) REVERT: P 93 LYS cc_start: 0.8162 (tttt) cc_final: 0.7399 (mmtm) REVERT: P 100 GLU cc_start: 0.6891 (mm-30) cc_final: 0.6691 (mm-30) REVERT: Q 25 MET cc_start: 0.8433 (tmm) cc_final: 0.7884 (tmm) REVERT: S 26 ARG cc_start: 0.7532 (mtt180) cc_final: 0.7011 (ttm110) REVERT: S 38 ARG cc_start: 0.8061 (tpt90) cc_final: 0.7699 (tpt90) REVERT: S 59 ARG cc_start: 0.7820 (mmt-90) cc_final: 0.7305 (mmm-85) REVERT: S 93 LYS cc_start: 0.8218 (tttt) cc_final: 0.7999 (tptp) REVERT: T 25 MET cc_start: 0.7266 (ttm) cc_final: 0.6582 (tmm) REVERT: T 26 ARG cc_start: 0.7233 (mtt180) cc_final: 0.6918 (tpt-90) REVERT: T 59 ARG cc_start: 0.7718 (mmt-90) cc_final: 0.7356 (tpp80) REVERT: T 72 LYS cc_start: 0.8452 (tmtt) cc_final: 0.7970 (tptp) REVERT: T 78 GLU cc_start: 0.8191 (tp30) cc_final: 0.7375 (tp30) REVERT: T 79 LYS cc_start: 0.8961 (mmtm) cc_final: 0.8760 (mmpt) REVERT: T 84 LYS cc_start: 0.8221 (mmpt) cc_final: 0.8000 (tptp) REVERT: U 18 ASP cc_start: 0.7102 (p0) cc_final: 0.6720 (p0) REVERT: U 25 MET cc_start: 0.7122 (ttm) cc_final: 0.6922 (tmm) REVERT: U 36 LEU cc_start: 0.7028 (tt) cc_final: 0.6782 (mt) REVERT: U 74 GLU cc_start: 0.7465 (mt-10) cc_final: 0.7249 (mt-10) REVERT: U 93 LYS cc_start: 0.8323 (tttt) cc_final: 0.7963 (mptt) REVERT: V 24 ASP cc_start: 0.7280 (m-30) cc_final: 0.6472 (t0) REVERT: V 70 GLU cc_start: 0.5867 (mt-10) cc_final: 0.5446 (tm-30) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.5354 time to fit residues: 270.3697 Evaluate side-chains 278 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 278 time to evaluate : 1.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 36 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 105 optimal weight: 5.9990 chunk 47 optimal weight: 6.9990 chunk 165 optimal weight: 9.9990 chunk 204 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 chunk 132 optimal weight: 8.9990 chunk 1 optimal weight: 0.8980 chunk 201 optimal weight: 10.0000 overall best weight: 4.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN F 68 HIS G 95 GLN H 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 68 HIS O 68 HIS P 68 HIS Q 68 HIS R 95 GLN S 68 HIS V 68 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4890 r_free = 0.4890 target = 0.112518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.4268 r_free = 0.4268 target = 0.081561 restraints weight = 34228.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.083126 restraints weight = 25731.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.084358 restraints weight = 20530.276| |-----------------------------------------------------------------------------| r_work (final): 0.4321 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.5028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 16478 Z= 0.357 Angle : 0.839 8.433 22198 Z= 0.445 Chirality : 0.054 0.199 2684 Planarity : 0.006 0.047 2904 Dihedral : 6.729 25.064 2376 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.11 % Favored : 84.89 % Rotamer: Outliers : 0.06 % Allowed : 6.55 % Favored : 93.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.39 (0.13), residues: 1188 loop : -3.85 (0.14), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS L 68 PHE 0.028 0.003 PHE O 105 TYR 0.016 0.002 TYR B 14 ARG 0.008 0.001 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.02054 ( 66) hydrogen bonds : angle 5.10582 ( 132) covalent geometry : bond 0.00702 (16478) covalent geometry : angle 0.83936 (22198) *********************** 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 331 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 330 time to evaluate : 1.895 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 34 ASP cc_start: 0.6896 (t70) cc_final: 0.6583 (t70) REVERT: A 72 LYS cc_start: 0.7929 (tmtt) cc_final: 0.7558 (tptp) REVERT: B 61 GLU cc_start: 0.5323 (mp0) cc_final: 0.4198 (tm-30) REVERT: B 72 LYS cc_start: 0.8034 (tmtt) cc_final: 0.7572 (tmtt) REVERT: C 24 ASP cc_start: 0.7075 (m-30) cc_final: 0.6455 (t0) REVERT: C 38 ARG cc_start: 0.6210 (ttp80) cc_final: 0.5876 (ttp80) REVERT: C 44 GLU cc_start: 0.5676 (tm-30) cc_final: 0.5382 (mm-30) REVERT: D 24 ASP cc_start: 0.6808 (t0) cc_final: 0.6510 (t0) REVERT: D 93 LYS cc_start: 0.8559 (tttt) cc_final: 0.7994 (mptt) REVERT: D 100 GLU cc_start: 0.8504 (mp0) cc_final: 0.8185 (mp0) REVERT: E 25 MET cc_start: 0.7927 (ttm) cc_final: 0.6901 (tmm) REVERT: E 55 VAL cc_start: 0.9119 (t) cc_final: 0.8906 (p) REVERT: E 72 LYS cc_start: 0.8472 (tptp) cc_final: 0.7997 (tptp) REVERT: E 78 GLU cc_start: 0.8313 (tp30) cc_final: 0.8096 (tp30) REVERT: F 26 ARG cc_start: 0.7755 (mtt180) cc_final: 0.7068 (ttm110) REVERT: F 30 GLN cc_start: 0.7599 (tm-30) cc_final: 0.7318 (tm-30) REVERT: F 38 ARG cc_start: 0.8252 (tpt90) cc_final: 0.7723 (tpt90) REVERT: F 59 ARG cc_start: 0.7486 (mmt-90) cc_final: 0.7166 (mmm-85) REVERT: F 63 ARG cc_start: 0.7500 (mmt180) cc_final: 0.7177 (mpt180) REVERT: G 20 GLU cc_start: 0.8237 (mp0) cc_final: 0.7772 (mt-10) REVERT: G 26 ARG cc_start: 0.6475 (mtt90) cc_final: 0.6247 (mtt90) REVERT: G 93 LYS cc_start: 0.8468 (tttt) cc_final: 0.8167 (tttp) REVERT: H 18 ASP cc_start: 0.7927 (p0) cc_final: 0.7486 (p0) REVERT: H 25 MET cc_start: 0.8491 (tmm) cc_final: 0.7695 (tmm) REVERT: H 95 GLN cc_start: 0.8071 (mm-40) cc_final: 0.7779 (mp10) REVERT: I 79 LYS cc_start: 0.8610 (mmtt) cc_final: 0.8118 (mmmt) REVERT: I 93 LYS cc_start: 0.8106 (tttt) cc_final: 0.7263 (mmtm) REVERT: J 78 GLU cc_start: 0.8131 (mt-10) cc_final: 0.7902 (tm-30) REVERT: J 93 LYS cc_start: 0.8578 (tttt) cc_final: 0.7618 (mtmm) REVERT: K 59 ARG cc_start: 0.7644 (mmt-90) cc_final: 0.7439 (mmt90) REVERT: K 78 GLU cc_start: 0.7867 (tp30) cc_final: 0.7525 (tm-30) REVERT: K 93 LYS cc_start: 0.8623 (tttt) cc_final: 0.8227 (mtpt) REVERT: K 95 GLN cc_start: 0.8290 (mm-40) cc_final: 0.7478 (tp-100) REVERT: L 18 ASP cc_start: 0.7153 (p0) cc_final: 0.6728 (p0) REVERT: L 78 GLU cc_start: 0.7886 (tp30) cc_final: 0.7438 (tm-30) REVERT: L 93 LYS cc_start: 0.8477 (tttt) cc_final: 0.7450 (mmtm) REVERT: M 18 ASP cc_start: 0.7235 (p0) cc_final: 0.6947 (p0) REVERT: M 25 MET cc_start: 0.7640 (ttt) cc_final: 0.7027 (mtp) REVERT: M 78 GLU cc_start: 0.7758 (tp30) cc_final: 0.7273 (tm-30) REVERT: M 93 LYS cc_start: 0.8446 (tttt) cc_final: 0.7373 (mmtm) REVERT: N 78 GLU cc_start: 0.7851 (tp30) cc_final: 0.7524 (tm-30) REVERT: N 93 LYS cc_start: 0.8581 (tttt) cc_final: 0.8167 (mtpt) REVERT: N 95 GLN cc_start: 0.8364 (mm-40) cc_final: 0.7615 (tp-100) REVERT: O 20 GLU cc_start: 0.8698 (mp0) cc_final: 0.8324 (mp0) REVERT: O 72 LYS cc_start: 0.8785 (tttt) cc_final: 0.8257 (mtmm) REVERT: O 93 LYS cc_start: 0.8561 (tttt) cc_final: 0.7551 (mtmm) REVERT: P 17 PRO cc_start: 0.7777 (Cg_exo) cc_final: 0.7562 (Cg_endo) REVERT: P 25 MET cc_start: 0.7812 (ttm) cc_final: 0.7101 (tmm) REVERT: P 79 LYS cc_start: 0.8709 (mmtt) cc_final: 0.8187 (mmmt) REVERT: P 93 LYS cc_start: 0.8167 (tttt) cc_final: 0.7777 (tttp) REVERT: P 95 GLN cc_start: 0.8594 (mm110) cc_final: 0.8164 (mm-40) REVERT: Q 18 ASP cc_start: 0.7767 (p0) cc_final: 0.7549 (p0) REVERT: Q 25 MET cc_start: 0.8583 (tmm) cc_final: 0.7887 (tmm) REVERT: S 26 ARG cc_start: 0.7635 (mtt180) cc_final: 0.7046 (ttm110) REVERT: S 38 ARG cc_start: 0.8272 (tpt90) cc_final: 0.7885 (tpt90) REVERT: S 59 ARG cc_start: 0.7472 (mmt-90) cc_final: 0.7239 (mmm-85) REVERT: S 93 LYS cc_start: 0.8513 (tttt) cc_final: 0.8195 (tptp) REVERT: S 95 GLN cc_start: 0.8266 (mm110) cc_final: 0.7971 (mm-40) REVERT: T 25 MET cc_start: 0.7774 (ttm) cc_final: 0.6689 (tmm) REVERT: T 72 LYS cc_start: 0.8704 (tmtt) cc_final: 0.7998 (tptp) REVERT: T 79 LYS cc_start: 0.9105 (mmtm) cc_final: 0.8794 (mmpt) REVERT: T 84 LYS cc_start: 0.8319 (mmpt) cc_final: 0.8004 (tptp) REVERT: U 18 ASP cc_start: 0.7215 (p0) cc_final: 0.6565 (p0) REVERT: U 93 LYS cc_start: 0.8523 (tttt) cc_final: 0.8010 (mptt) REVERT: V 20 GLU cc_start: 0.7643 (mp0) cc_final: 0.7303 (mp0) REVERT: V 24 ASP cc_start: 0.7290 (m-30) cc_final: 0.6548 (t0) REVERT: V 38 ARG cc_start: 0.6850 (mtm110) cc_final: 0.6169 (ttp80) REVERT: V 70 GLU cc_start: 0.5732 (mt-10) cc_final: 0.5495 (tm-30) outliers start: 1 outliers final: 0 residues processed: 331 average time/residue: 0.4739 time to fit residues: 201.6248 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 : 1.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 68 optimal weight: 4.9990 chunk 47 optimal weight: 4.9990 chunk 27 optimal weight: 20.0000 chunk 167 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 181 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 151 optimal weight: 3.9990 chunk 212 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 overall best weight: 2.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.116421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.084534 restraints weight = 32894.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4384 r_free = 0.4384 target = 0.086292 restraints weight = 23931.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.087696 restraints weight = 18597.125| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7132 moved from start: 0.5369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 16478 Z= 0.183 Angle : 0.681 6.302 22198 Z= 0.346 Chirality : 0.051 0.154 2684 Planarity : 0.004 0.036 2904 Dihedral : 5.785 26.266 2376 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.29 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.43 (0.14), residues: 1232 loop : -3.40 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 68 PHE 0.012 0.001 PHE K 105 TYR 0.011 0.001 TYR O 14 ARG 0.007 0.001 ARG H 54 Details of bonding type rmsd hydrogen bonds : bond 0.01444 ( 66) hydrogen bonds : angle 4.65814 ( 132) covalent geometry : bond 0.00373 (16478) covalent geometry : angle 0.68117 (22198) *********************** 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 333 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 333 time to evaluate : 2.227 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: 0.6786 (t70) cc_final: 0.6475 (t70) REVERT: A 72 LYS cc_start: 0.7852 (tmtt) cc_final: 0.7425 (tptp) REVERT: A 91 GLN cc_start: 0.6882 (mp10) cc_final: 0.5799 (tm-30) REVERT: B 61 GLU cc_start: 0.5163 (mp0) cc_final: 0.4246 (tm-30) REVERT: B 72 LYS cc_start: 0.8112 (tmtt) cc_final: 0.7674 (tmtt) REVERT: B 91 GLN cc_start: 0.6967 (mp10) cc_final: 0.5867 (tm-30) REVERT: C 24 ASP cc_start: 0.6979 (m-30) cc_final: 0.6363 (t0) REVERT: C 38 ARG cc_start: 0.6504 (ttp80) cc_final: 0.6158 (ttp80) REVERT: C 44 GLU cc_start: 0.5749 (tm-30) cc_final: 0.5446 (mm-30) REVERT: D 24 ASP cc_start: 0.6799 (t0) cc_final: 0.6569 (t0) REVERT: D 59 ARG cc_start: 0.7500 (mmp80) cc_final: 0.7129 (mmp80) REVERT: D 93 LYS cc_start: 0.8397 (tttt) cc_final: 0.7933 (tptp) REVERT: D 100 GLU cc_start: 0.8394 (mp0) cc_final: 0.8160 (mp0) REVERT: E 25 MET cc_start: 0.7528 (ttm) cc_final: 0.6814 (tmm) REVERT: E 55 VAL cc_start: 0.8970 (t) cc_final: 0.8730 (p) REVERT: E 72 LYS cc_start: 0.8381 (tptp) cc_final: 0.7938 (tptp) REVERT: E 79 LYS cc_start: 0.9049 (mmtm) cc_final: 0.8783 (mmpt) REVERT: F 26 ARG cc_start: 0.7823 (mtt180) cc_final: 0.6873 (ttm110) REVERT: F 38 ARG cc_start: 0.8109 (tpt90) cc_final: 0.7592 (tpt90) REVERT: F 63 ARG cc_start: 0.7578 (mmt180) cc_final: 0.7191 (mpt180) REVERT: G 20 GLU cc_start: 0.8333 (mp0) cc_final: 0.8110 (mt-10) REVERT: G 26 ARG cc_start: 0.6416 (mtt90) cc_final: 0.6066 (mtt90) REVERT: G 93 LYS cc_start: 0.8613 (tttt) cc_final: 0.8315 (tttp) REVERT: H 18 ASP cc_start: 0.7839 (p0) cc_final: 0.7391 (p0) REVERT: H 95 GLN cc_start: 0.7841 (mm-40) cc_final: 0.7615 (mp10) REVERT: I 25 MET cc_start: 0.7565 (ttm) cc_final: 0.6876 (tmm) REVERT: I 79 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8255 (mmmt) REVERT: I 93 LYS cc_start: 0.7975 (tttt) cc_final: 0.7314 (mmtm) REVERT: I 95 GLN cc_start: 0.8615 (mm110) cc_final: 0.8236 (mm110) REVERT: J 93 LYS cc_start: 0.8369 (tttt) cc_final: 0.7654 (mtpp) REVERT: K 24 ASP cc_start: 0.8640 (t0) cc_final: 0.8079 (m-30) REVERT: K 36 LEU cc_start: 0.8176 (tt) cc_final: 0.7228 (mp) REVERT: K 59 ARG cc_start: 0.7611 (mmt-90) cc_final: 0.7370 (mmm-85) REVERT: K 93 LYS cc_start: 0.8464 (tttt) cc_final: 0.8217 (mtpt) REVERT: K 95 GLN cc_start: 0.8249 (mm-40) cc_final: 0.7233 (tp40) REVERT: L 18 ASP cc_start: 0.7187 (p0) cc_final: 0.6604 (p0) REVERT: L 72 LYS cc_start: 0.8639 (mppt) cc_final: 0.8438 (mmtp) REVERT: M 18 ASP cc_start: 0.7357 (p0) cc_final: 0.7062 (p0) REVERT: M 20 GLU cc_start: 0.8246 (mp0) cc_final: 0.7966 (mp0) REVERT: M 25 MET cc_start: 0.7575 (ttt) cc_final: 0.7048 (mtp) REVERT: M 38 ARG cc_start: 0.8151 (tpt90) cc_final: 0.7864 (tpt90) REVERT: M 93 LYS cc_start: 0.8277 (tttt) cc_final: 0.7381 (mmtm) REVERT: N 28 LYS cc_start: 0.7788 (mtpp) cc_final: 0.7503 (mtpp) REVERT: N 93 LYS cc_start: 0.8498 (tttt) cc_final: 0.8253 (mtpt) REVERT: N 95 GLN cc_start: 0.8234 (mm-40) cc_final: 0.7360 (tp40) REVERT: O 25 MET cc_start: 0.8065 (ttt) cc_final: 0.7668 (ttt) REVERT: O 72 LYS cc_start: 0.8644 (tttt) cc_final: 0.8259 (mptt) REVERT: O 93 LYS cc_start: 0.8403 (tttt) cc_final: 0.7687 (mtpp) REVERT: P 79 LYS cc_start: 0.8508 (mmtt) cc_final: 0.8001 (mmmt) REVERT: P 93 LYS cc_start: 0.8001 (tttt) cc_final: 0.7277 (mmtm) REVERT: Q 18 ASP cc_start: 0.7692 (p0) cc_final: 0.7485 (p0) REVERT: S 26 ARG cc_start: 0.7622 (mtt180) cc_final: 0.7303 (ttm110) REVERT: S 32 ARG cc_start: 0.7764 (tpt-90) cc_final: 0.7495 (tpt-90) REVERT: S 38 ARG cc_start: 0.8229 (tpt90) cc_final: 0.7772 (tpt90) REVERT: S 72 LYS cc_start: 0.8751 (tptt) cc_final: 0.8147 (tppt) REVERT: S 79 LYS cc_start: 0.8645 (mmtm) cc_final: 0.8353 (mmtm) REVERT: S 93 LYS cc_start: 0.8440 (tttt) cc_final: 0.8072 (tptp) REVERT: S 108 GLN cc_start: 0.7924 (mt0) cc_final: 0.7566 (mp10) REVERT: T 25 MET cc_start: 0.7829 (ttm) cc_final: 0.6875 (tmm) REVERT: T 56 GLU cc_start: 0.7460 (mm-30) cc_final: 0.6892 (mm-30) REVERT: T 72 LYS cc_start: 0.8696 (tmtt) cc_final: 0.7946 (tptp) REVERT: T 79 LYS cc_start: 0.9067 (mmtm) cc_final: 0.8731 (mmpt) REVERT: T 93 LYS cc_start: 0.7740 (mmtt) cc_final: 0.7530 (mmtt) REVERT: U 18 ASP cc_start: 0.7210 (p0) cc_final: 0.6651 (p0) REVERT: U 93 LYS cc_start: 0.8395 (tttt) cc_final: 0.8027 (tptp) REVERT: V 20 GLU cc_start: 0.7659 (mp0) cc_final: 0.7392 (mp0) REVERT: V 24 ASP cc_start: 0.7237 (m-30) cc_final: 0.6473 (t0) REVERT: V 32 ARG cc_start: 0.6173 (tmt-80) cc_final: 0.5878 (tmt-80) REVERT: V 38 ARG cc_start: 0.6920 (mtm110) cc_final: 0.6078 (ttp80) outliers start: 0 outliers final: 0 residues processed: 333 average time/residue: 0.6131 time to fit residues: 262.2329 Evaluate side-chains 262 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 262 time to evaluate : 2.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 50 optimal weight: 10.0000 chunk 1 optimal weight: 20.0000 chunk 179 optimal weight: 9.9990 chunk 209 optimal weight: 9.9990 chunk 113 optimal weight: 6.9990 chunk 57 optimal weight: 5.9990 chunk 142 optimal weight: 3.9990 chunk 86 optimal weight: 6.9990 chunk 51 optimal weight: 0.9990 chunk 93 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 68 HIS ** 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 = 0.4834 r_free = 0.4834 target = 0.108760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.080325 restraints weight = 32842.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4281 r_free = 0.4281 target = 0.081493 restraints weight = 24941.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4306 r_free = 0.4306 target = 0.082408 restraints weight = 20107.871| |-----------------------------------------------------------------------------| r_work (final): 0.4323 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7343 moved from start: 0.6166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.047 16478 Z= 0.361 Angle : 0.841 8.920 22198 Z= 0.447 Chirality : 0.054 0.218 2684 Planarity : 0.006 0.054 2904 Dihedral : 6.962 24.371 2376 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 21.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 19.01 % Favored : 80.99 % Rotamer: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.67 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.79 (0.13), residues: 1232 loop : -3.46 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS O 68 PHE 0.022 0.003 PHE H 105 TYR 0.020 0.002 TYR J 14 ARG 0.005 0.001 ARG C 32 Details of bonding type rmsd hydrogen bonds : bond 0.02033 ( 66) hydrogen bonds : angle 5.78514 ( 132) covalent geometry : bond 0.00721 (16478) covalent geometry : angle 0.84084 (22198) *********************** 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 319 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.772 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: 0.8127 (tmtt) cc_final: 0.7699 (tmtt) REVERT: B 72 LYS cc_start: 0.8170 (tmtt) cc_final: 0.7699 (tmtt) REVERT: C 24 ASP cc_start: 0.7219 (m-30) cc_final: 0.6619 (t0) REVERT: C 38 ARG cc_start: 0.6308 (ttp80) cc_final: 0.6063 (ttp80) REVERT: C 78 GLU cc_start: 0.5180 (pt0) cc_final: 0.4347 (mm-30) REVERT: D 24 ASP cc_start: 0.7178 (t0) cc_final: 0.6908 (t0) REVERT: D 32 ARG cc_start: 0.7825 (tmt170) cc_final: 0.7272 (ttt90) REVERT: D 59 ARG cc_start: 0.7514 (mmp80) cc_final: 0.7311 (mmp80) REVERT: D 93 LYS cc_start: 0.8707 (tttt) cc_final: 0.8328 (tptp) REVERT: E 25 MET cc_start: 0.7944 (ttm) cc_final: 0.7261 (tmm) REVERT: E 72 LYS cc_start: 0.8431 (tptp) cc_final: 0.7830 (tptp) REVERT: E 78 GLU cc_start: 0.8069 (tp30) cc_final: 0.7215 (tp30) REVERT: E 79 LYS cc_start: 0.9064 (mmtm) cc_final: 0.8734 (mmpt) REVERT: E 93 LYS cc_start: 0.7809 (mmtt) cc_final: 0.7572 (mmtt) REVERT: F 18 ASP cc_start: 0.7339 (p0) cc_final: 0.7118 (p0) REVERT: F 26 ARG cc_start: 0.8011 (mtt180) cc_final: 0.7093 (ttm110) REVERT: F 30 GLN cc_start: 0.7686 (tm-30) cc_final: 0.7454 (tm-30) REVERT: F 38 ARG cc_start: 0.8017 (tpt90) cc_final: 0.7691 (tpt90) REVERT: G 26 ARG cc_start: 0.6708 (mtt90) cc_final: 0.6397 (mtt90) REVERT: G 93 LYS cc_start: 0.8565 (tttt) cc_final: 0.8239 (tttp) REVERT: H 18 ASP cc_start: 0.8350 (p0) cc_final: 0.7889 (p0) REVERT: H 95 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7689 (mp10) REVERT: I 25 MET cc_start: 0.7870 (ttm) cc_final: 0.7348 (tmm) REVERT: I 61 GLU cc_start: 0.7680 (mp0) cc_final: 0.7384 (mp0) REVERT: I 79 LYS cc_start: 0.8799 (mmtt) cc_final: 0.8358 (mmmt) REVERT: I 93 LYS cc_start: 0.8153 (tttt) cc_final: 0.7470 (mmtm) REVERT: I 95 GLN cc_start: 0.8555 (mm110) cc_final: 0.8160 (mm-40) REVERT: I 109 SER cc_start: 0.9127 (t) cc_final: 0.8586 (t) REVERT: J 25 MET cc_start: 0.8294 (ttm) cc_final: 0.8014 (tmm) REVERT: J 78 GLU cc_start: 0.8152 (mt-10) cc_final: 0.7808 (tm-30) REVERT: J 93 LYS cc_start: 0.8477 (tttt) cc_final: 0.7623 (mtmm) REVERT: K 59 ARG cc_start: 0.7699 (mmt-90) cc_final: 0.7410 (mmt180) REVERT: K 78 GLU cc_start: 0.7869 (tp30) cc_final: 0.7256 (tm-30) REVERT: K 93 LYS cc_start: 0.8614 (tttt) cc_final: 0.8392 (mtpt) REVERT: L 18 ASP cc_start: 0.7246 (p0) cc_final: 0.6704 (p0) REVERT: L 20 GLU cc_start: 0.8263 (mp0) cc_final: 0.8007 (mp0) REVERT: L 38 ARG cc_start: 0.8141 (tmt-80) cc_final: 0.7688 (tpt90) REVERT: L 93 LYS cc_start: 0.8626 (tttt) cc_final: 0.8294 (tttp) REVERT: M 18 ASP cc_start: 0.7417 (p0) cc_final: 0.7104 (p0) REVERT: M 25 MET cc_start: 0.7887 (ttt) cc_final: 0.7389 (mtp) REVERT: M 38 ARG cc_start: 0.8188 (tpt90) cc_final: 0.7972 (tpt90) REVERT: M 93 LYS cc_start: 0.8531 (tttt) cc_final: 0.7632 (mmtm) REVERT: N 78 GLU cc_start: 0.7846 (tp30) cc_final: 0.7201 (tm-30) REVERT: N 93 LYS cc_start: 0.8680 (tttt) cc_final: 0.8361 (mtpt) REVERT: O 20 GLU cc_start: 0.8800 (mp0) cc_final: 0.8576 (mp0) REVERT: O 93 LYS cc_start: 0.8541 (tttt) cc_final: 0.7683 (mtmm) REVERT: P 79 LYS cc_start: 0.8783 (mmtt) cc_final: 0.8338 (mmmt) REVERT: P 93 LYS cc_start: 0.8229 (tttt) cc_final: 0.7967 (tttp) REVERT: P 95 GLN cc_start: 0.8537 (mm110) cc_final: 0.8150 (mm-40) REVERT: Q 18 ASP cc_start: 0.7938 (p0) cc_final: 0.7561 (p0) REVERT: S 26 ARG cc_start: 0.7691 (mtt180) cc_final: 0.7163 (ttm110) REVERT: S 38 ARG cc_start: 0.8076 (tpt90) cc_final: 0.7736 (tpt90) REVERT: S 72 LYS cc_start: 0.9035 (tptt) cc_final: 0.8480 (tppt) REVERT: S 79 LYS cc_start: 0.8836 (mmtm) cc_final: 0.8603 (mmtm) REVERT: S 93 LYS cc_start: 0.8545 (tttt) cc_final: 0.8182 (tptp) REVERT: T 25 MET cc_start: 0.8103 (ttm) cc_final: 0.7276 (tmm) REVERT: T 59 ARG cc_start: 0.8296 (tpp-160) cc_final: 0.7662 (tpp80) REVERT: T 72 LYS cc_start: 0.8537 (tmtt) cc_final: 0.8060 (tptp) REVERT: T 78 GLU cc_start: 0.8090 (tp30) cc_final: 0.7801 (tp30) REVERT: T 79 LYS cc_start: 0.9074 (mmtm) cc_final: 0.8725 (mmmt) REVERT: T 93 LYS cc_start: 0.7855 (mmtt) cc_final: 0.7575 (mmtt) REVERT: U 18 ASP cc_start: 0.7179 (p0) cc_final: 0.6547 (p0) REVERT: U 93 LYS cc_start: 0.8643 (tttt) cc_final: 0.8322 (tptt) REVERT: V 24 ASP cc_start: 0.7710 (m-30) cc_final: 0.6907 (t0) REVERT: V 44 GLU cc_start: 0.5315 (tm-30) cc_final: 0.5063 (mm-30) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.4704 time to fit residues: 192.0966 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 : 1.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 90 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 155 optimal weight: 6.9990 chunk 97 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 150 optimal weight: 0.9980 chunk 112 optimal weight: 0.9990 chunk 45 optimal weight: 9.9990 chunk 162 optimal weight: 0.1980 chunk 218 optimal weight: 30.0000 chunk 63 optimal weight: 9.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN ** D 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.113888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.085786 restraints weight = 30377.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.087006 restraints weight = 20563.714| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4429 r_free = 0.4429 target = 0.087672 restraints weight = 15601.472| |-----------------------------------------------------------------------------| r_work (final): 0.4429 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7110 moved from start: 0.6132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 16478 Z= 0.134 Angle : 0.691 7.898 22198 Z= 0.344 Chirality : 0.051 0.159 2684 Planarity : 0.003 0.041 2904 Dihedral : 5.533 22.538 2376 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.50 (0.14), residues: 1232 loop : -3.29 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 68 PHE 0.010 0.001 PHE B 88 TYR 0.006 0.001 TYR B 14 ARG 0.007 0.000 ARG E 38 Details of bonding type rmsd hydrogen bonds : bond 0.01167 ( 66) hydrogen bonds : angle 4.82745 ( 132) covalent geometry : bond 0.00289 (16478) covalent geometry : angle 0.69112 (22198) *********************** 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 334 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 334 time to evaluate : 2.288 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: 0.7932 (tmtt) cc_final: 0.7540 (tmtt) REVERT: A 91 GLN cc_start: 0.7015 (mp10) cc_final: 0.5989 (tm-30) REVERT: B 72 LYS cc_start: 0.8110 (tmtt) cc_final: 0.7691 (tmtt) REVERT: B 91 GLN cc_start: 0.6991 (mp10) cc_final: 0.5961 (tm-30) REVERT: C 20 GLU cc_start: 0.7170 (mp0) cc_final: 0.6928 (tm-30) REVERT: C 24 ASP cc_start: 0.7130 (m-30) cc_final: 0.6478 (t0) REVERT: C 32 ARG cc_start: 0.7083 (tpt90) cc_final: 0.6843 (tpt90) REVERT: C 38 ARG cc_start: 0.6370 (tmm160) cc_final: 0.5807 (ttp80) REVERT: C 78 GLU cc_start: 0.5530 (pt0) cc_final: 0.4801 (mm-30) REVERT: D 24 ASP cc_start: 0.6771 (t0) cc_final: 0.6512 (t0) REVERT: D 93 LYS cc_start: 0.8546 (tttt) cc_final: 0.8128 (tptp) REVERT: E 25 MET cc_start: 0.7445 (ttm) cc_final: 0.6889 (tmm) REVERT: E 72 LYS cc_start: 0.8393 (tptp) cc_final: 0.7812 (tptp) REVERT: E 78 GLU cc_start: 0.8197 (tp30) cc_final: 0.7805 (tp30) REVERT: E 79 LYS cc_start: 0.9096 (mmtm) cc_final: 0.8808 (mmmt) REVERT: F 26 ARG cc_start: 0.7618 (mtt180) cc_final: 0.7008 (ttm110) REVERT: F 38 ARG cc_start: 0.7890 (tpt90) cc_final: 0.7504 (tpt90) REVERT: F 74 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7771 (mt-10) REVERT: G 66 LEU cc_start: 0.8301 (mm) cc_final: 0.7673 (tp) REVERT: G 84 LYS cc_start: 0.7911 (tptp) cc_final: 0.7487 (pptt) REVERT: G 93 LYS cc_start: 0.8746 (tttt) cc_final: 0.7985 (mmtm) REVERT: H 18 ASP cc_start: 0.8035 (p0) cc_final: 0.7494 (p0) REVERT: I 25 MET cc_start: 0.7685 (ttm) cc_final: 0.7116 (tmm) REVERT: I 79 LYS cc_start: 0.8641 (mmtt) cc_final: 0.8165 (mmmt) REVERT: I 93 LYS cc_start: 0.8145 (tttt) cc_final: 0.7891 (tttp) REVERT: I 95 GLN cc_start: 0.8572 (mm110) cc_final: 0.8169 (mm-40) REVERT: J 78 GLU cc_start: 0.8119 (mt-10) cc_final: 0.7722 (tm-30) REVERT: J 93 LYS cc_start: 0.8293 (tttt) cc_final: 0.7568 (mtpp) REVERT: K 93 LYS cc_start: 0.8530 (tttt) cc_final: 0.8317 (mtpt) REVERT: K 95 GLN cc_start: 0.8219 (mm-40) cc_final: 0.7163 (tp40) REVERT: L 18 ASP cc_start: 0.7123 (p0) cc_final: 0.6534 (p0) REVERT: L 20 GLU cc_start: 0.7625 (mp0) cc_final: 0.6716 (pm20) REVERT: L 38 ARG cc_start: 0.7795 (tmt-80) cc_final: 0.7511 (tpt90) REVERT: M 18 ASP cc_start: 0.7303 (p0) cc_final: 0.6901 (p0) REVERT: M 20 GLU cc_start: 0.8135 (mp0) cc_final: 0.7931 (mp0) REVERT: M 21 VAL cc_start: 0.9070 (m) cc_final: 0.8744 (m) REVERT: M 79 LYS cc_start: 0.8781 (mmtm) cc_final: 0.8469 (mmmm) REVERT: N 93 LYS cc_start: 0.8593 (tttt) cc_final: 0.8347 (mtpt) REVERT: N 95 GLN cc_start: 0.8174 (mm-40) cc_final: 0.7186 (tp40) REVERT: O 93 LYS cc_start: 0.8323 (tttt) cc_final: 0.7555 (mtpp) REVERT: P 25 MET cc_start: 0.7709 (ttm) cc_final: 0.7104 (tmm) REVERT: P 52 THR cc_start: 0.7056 (p) cc_final: 0.6825 (p) REVERT: P 79 LYS cc_start: 0.8603 (mmtt) cc_final: 0.8072 (mmmt) REVERT: P 93 LYS cc_start: 0.8188 (tttt) cc_final: 0.7862 (tttp) REVERT: P 95 GLN cc_start: 0.8485 (mm110) cc_final: 0.8151 (mm-40) REVERT: Q 18 ASP cc_start: 0.7877 (p0) cc_final: 0.7466 (p0) REVERT: Q 25 MET cc_start: 0.8373 (tmm) cc_final: 0.7974 (tmm) REVERT: R 66 LEU cc_start: 0.8387 (mm) cc_final: 0.7766 (tp) REVERT: R 84 LYS cc_start: 0.8119 (tptp) cc_final: 0.7583 (pptt) REVERT: S 21 VAL cc_start: 0.9084 (m) cc_final: 0.8876 (p) REVERT: S 26 ARG cc_start: 0.7810 (mtt180) cc_final: 0.7315 (ttm110) REVERT: S 38 ARG cc_start: 0.7991 (tpt90) cc_final: 0.7676 (tpt90) REVERT: S 72 LYS cc_start: 0.8954 (tptt) cc_final: 0.8359 (tppt) REVERT: S 79 LYS cc_start: 0.8771 (mmtm) cc_final: 0.8474 (mmtm) REVERT: S 93 LYS cc_start: 0.8453 (tttt) cc_final: 0.8128 (tptp) REVERT: T 25 MET cc_start: 0.7612 (ttm) cc_final: 0.7040 (tmm) REVERT: T 56 GLU cc_start: 0.7878 (mm-30) cc_final: 0.7329 (mm-30) REVERT: T 59 ARG cc_start: 0.7858 (tpp-160) cc_final: 0.7421 (tpp80) REVERT: T 72 LYS cc_start: 0.8582 (tmtt) cc_final: 0.7943 (tptp) REVERT: T 78 GLU cc_start: 0.8164 (tp30) cc_final: 0.7841 (tp30) REVERT: T 79 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8778 (mmmt) REVERT: U 18 ASP cc_start: 0.7237 (p0) cc_final: 0.6769 (p0) REVERT: U 93 LYS cc_start: 0.8533 (tttt) cc_final: 0.8141 (tptp) REVERT: V 20 GLU cc_start: 0.7477 (mp0) cc_final: 0.7193 (tm-30) REVERT: V 24 ASP cc_start: 0.7534 (m-30) cc_final: 0.6697 (t0) REVERT: V 28 LYS cc_start: 0.6686 (mmmm) cc_final: 0.6354 (mmmm) REVERT: V 32 ARG cc_start: 0.7161 (tmt-80) cc_final: 0.6703 (tpt90) REVERT: V 38 ARG cc_start: 0.6074 (ttp80) cc_final: 0.5873 (tmm160) outliers start: 0 outliers final: 0 residues processed: 334 average time/residue: 0.6646 time to fit residues: 287.6497 Evaluate side-chains 268 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 268 time to evaluate : 2.568 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 9 optimal weight: 4.9990 chunk 183 optimal weight: 5.9990 chunk 219 optimal weight: 30.0000 chunk 163 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 116 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 171 optimal weight: 9.9990 chunk 112 optimal weight: 7.9990 chunk 10 optimal weight: 30.0000 chunk 56 optimal weight: 10.0000 overall best weight: 4.9788 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4869 r_free = 0.4869 target = 0.111073 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.081773 restraints weight = 35478.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.083408 restraints weight = 27107.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4328 r_free = 0.4328 target = 0.083674 restraints weight = 20623.195| |-----------------------------------------------------------------------------| r_work (final): 0.4314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.050 16478 Z= 0.355 Angle : 0.853 7.868 22198 Z= 0.452 Chirality : 0.055 0.187 2684 Planarity : 0.006 0.064 2904 Dihedral : 6.915 25.351 2376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 22.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.84 % Favored : 79.16 % Rotamer: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.53 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.78 (0.13), residues: 1188 loop : -3.30 (0.16), residues: 990 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.002 HIS J 68 PHE 0.025 0.003 PHE H 105 TYR 0.022 0.002 TYR O 14 ARG 0.009 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.02100 ( 66) hydrogen bonds : angle 6.02464 ( 132) covalent geometry : bond 0.00716 (16478) covalent geometry : angle 0.85334 (22198) *********************** 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 308 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 308 time to evaluate : 1.753 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: 0.7986 (tmtt) cc_final: 0.7513 (tmtt) REVERT: B 72 LYS cc_start: 0.7935 (tmtt) cc_final: 0.7464 (tmtt) REVERT: C 24 ASP cc_start: 0.7167 (m-30) cc_final: 0.6593 (t0) REVERT: C 38 ARG cc_start: 0.6274 (tmm160) cc_final: 0.5686 (ttp80) REVERT: C 78 GLU cc_start: 0.5610 (pt0) cc_final: 0.4908 (mm-30) REVERT: D 24 ASP cc_start: 0.7068 (t0) cc_final: 0.6743 (t0) REVERT: D 93 LYS cc_start: 0.8642 (tttt) cc_final: 0.8128 (tptp) REVERT: E 25 MET cc_start: 0.7868 (ttm) cc_final: 0.6987 (tmm) REVERT: E 78 GLU cc_start: 0.8283 (tp30) cc_final: 0.8041 (tp30) REVERT: E 79 LYS cc_start: 0.9142 (mmtm) cc_final: 0.8794 (mmmt) REVERT: F 18 ASP cc_start: 0.7517 (p0) cc_final: 0.7197 (p0) REVERT: F 26 ARG cc_start: 0.7632 (mtt180) cc_final: 0.7030 (ttm110) REVERT: F 38 ARG cc_start: 0.8131 (tpt90) cc_final: 0.7621 (tpt90) REVERT: F 59 ARG cc_start: 0.7744 (mmt90) cc_final: 0.7453 (mmm-85) REVERT: G 84 LYS cc_start: 0.8047 (tptp) cc_final: 0.7666 (tptp) REVERT: G 93 LYS cc_start: 0.8625 (tttt) cc_final: 0.8254 (tttp) REVERT: H 18 ASP cc_start: 0.8503 (p0) cc_final: 0.8200 (p0) REVERT: H 25 MET cc_start: 0.8699 (tmm) cc_final: 0.8392 (tmm) REVERT: H 95 GLN cc_start: 0.7705 (mp10) cc_final: 0.7170 (mp10) REVERT: I 61 GLU cc_start: 0.7639 (mp0) cc_final: 0.7326 (mp0) REVERT: I 79 LYS cc_start: 0.8822 (mmtt) cc_final: 0.8344 (mmmt) REVERT: I 93 LYS cc_start: 0.8119 (tttt) cc_final: 0.7799 (tttp) REVERT: I 95 GLN cc_start: 0.8658 (mm110) cc_final: 0.8267 (mm110) REVERT: J 44 GLU cc_start: 0.8316 (mt-10) cc_final: 0.8050 (mt-10) REVERT: J 78 GLU cc_start: 0.8092 (mt-10) cc_final: 0.7622 (tm-30) REVERT: J 93 LYS cc_start: 0.8514 (tttt) cc_final: 0.7716 (mtpp) REVERT: K 78 GLU cc_start: 0.7627 (tp30) cc_final: 0.6990 (tm-30) REVERT: K 93 LYS cc_start: 0.8531 (tttt) cc_final: 0.8184 (mtpt) REVERT: L 18 ASP cc_start: 0.7149 (p0) cc_final: 0.6619 (p0) REVERT: L 38 ARG cc_start: 0.8121 (tmt-80) cc_final: 0.7457 (tpt90) REVERT: L 93 LYS cc_start: 0.8570 (tttt) cc_final: 0.7520 (mmtm) REVERT: M 25 MET cc_start: 0.7838 (ttt) cc_final: 0.7262 (mtp) REVERT: M 38 ARG cc_start: 0.8181 (tpt90) cc_final: 0.7822 (tpt90) REVERT: M 79 LYS cc_start: 0.8779 (mmtm) cc_final: 0.8569 (mmtm) REVERT: M 93 LYS cc_start: 0.8520 (tttt) cc_final: 0.7465 (mmtm) REVERT: N 78 GLU cc_start: 0.7602 (tp30) cc_final: 0.7007 (tm-30) REVERT: N 93 LYS cc_start: 0.8558 (tttt) cc_final: 0.8252 (mtpt) REVERT: O 44 GLU cc_start: 0.8331 (mt-10) cc_final: 0.8078 (mt-10) REVERT: O 93 LYS cc_start: 0.8497 (tttt) cc_final: 0.7457 (mtmm) REVERT: P 32 ARG cc_start: 0.8039 (ttt90) cc_final: 0.7492 (ttm-80) REVERT: P 79 LYS cc_start: 0.8753 (mmtt) cc_final: 0.8228 (mmmt) REVERT: P 93 LYS cc_start: 0.8217 (tttt) cc_final: 0.7811 (tttp) REVERT: P 95 GLN cc_start: 0.8655 (mm110) cc_final: 0.8299 (mm110) REVERT: Q 18 ASP cc_start: 0.8413 (p0) cc_final: 0.7803 (p0) REVERT: R 26 ARG cc_start: 0.6998 (mtt90) cc_final: 0.6791 (mtt90) REVERT: S 21 VAL cc_start: 0.9069 (m) cc_final: 0.8860 (p) REVERT: S 26 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7110 (ttm110) REVERT: S 28 LYS cc_start: 0.7541 (mptt) cc_final: 0.7220 (mmtm) REVERT: S 38 ARG cc_start: 0.8159 (tpt90) cc_final: 0.7765 (tpt90) REVERT: S 72 LYS cc_start: 0.8874 (tptt) cc_final: 0.8197 (tppt) REVERT: S 79 LYS cc_start: 0.8646 (mmtm) cc_final: 0.8438 (mmtm) REVERT: S 93 LYS cc_start: 0.8563 (tttt) cc_final: 0.8145 (tptp) REVERT: T 25 MET cc_start: 0.7933 (ttm) cc_final: 0.6968 (tmm) REVERT: T 56 GLU cc_start: 0.8356 (mm-30) cc_final: 0.8049 (mm-30) REVERT: T 59 ARG cc_start: 0.8199 (tpp-160) cc_final: 0.7641 (tpp80) REVERT: T 72 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8089 (tptp) REVERT: T 78 GLU cc_start: 0.8376 (tp30) cc_final: 0.8149 (tp30) REVERT: T 79 LYS cc_start: 0.9056 (mmtm) cc_final: 0.8622 (mmmt) REVERT: U 18 ASP cc_start: 0.7120 (p0) cc_final: 0.6492 (p0) REVERT: U 32 ARG cc_start: 0.7654 (ttt90) cc_final: 0.7390 (ttt90) REVERT: U 59 ARG cc_start: 0.7773 (mpt180) cc_final: 0.7130 (mmt-90) REVERT: U 93 LYS cc_start: 0.8638 (tttt) cc_final: 0.8194 (tptp) REVERT: U 100 GLU cc_start: 0.8083 (mp0) cc_final: 0.7871 (mp0) REVERT: V 24 ASP cc_start: 0.7470 (m-30) cc_final: 0.6540 (t0) REVERT: V 30 GLN cc_start: 0.7781 (tt0) cc_final: 0.7476 (tm-30) REVERT: V 32 ARG cc_start: 0.6906 (tmt-80) cc_final: 0.6566 (tpt90) REVERT: V 38 ARG cc_start: 0.6161 (ttp80) cc_final: 0.5907 (tmm160) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.4924 time to fit residues: 194.5050 Evaluate side-chains 253 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 142 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 166 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 22 optimal weight: 7.9990 chunk 60 optimal weight: 10.0000 chunk 58 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 165 optimal weight: 0.9980 chunk 206 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 95 GLN ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4910 r_free = 0.4910 target = 0.112966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4321 r_free = 0.4321 target = 0.083337 restraints weight = 34387.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4362 r_free = 0.4362 target = 0.085052 restraints weight = 25775.887| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.085578 restraints weight = 18804.793| |-----------------------------------------------------------------------------| r_work (final): 0.4362 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7206 moved from start: 0.6848 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= 0.251 Angle : 0.799 8.440 22198 Z= 0.408 Chirality : 0.053 0.160 2684 Planarity : 0.005 0.046 2904 Dihedral : 6.423 24.282 2376 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -6.02 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.96 (0.11), residues: 1452 loop : -3.38 (0.19), residues: 726 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS U 68 PHE 0.016 0.002 PHE Q 105 TYR 0.014 0.002 TYR O 14 ARG 0.008 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.01570 ( 66) hydrogen bonds : angle 5.75767 ( 132) covalent geometry : bond 0.00515 (16478) covalent geometry : angle 0.79891 (22198) *********************** 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 300 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 300 time to evaluate : 2.693 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: A 72 LYS cc_start: 0.7953 (tmtt) cc_final: 0.7489 (tmtt) REVERT: B 72 LYS cc_start: 0.7846 (tmtt) cc_final: 0.7382 (tmtt) REVERT: C 24 ASP cc_start: 0.7327 (m-30) cc_final: 0.6577 (t0) REVERT: C 38 ARG cc_start: 0.6431 (tmm160) cc_final: 0.5860 (ttp80) REVERT: C 78 GLU cc_start: 0.5812 (pt0) cc_final: 0.5046 (mm-30) REVERT: D 24 ASP cc_start: 0.6935 (t0) cc_final: 0.6600 (t0) REVERT: D 78 GLU cc_start: 0.7940 (tm-30) cc_final: 0.7701 (tt0) REVERT: D 93 LYS cc_start: 0.8589 (tttt) cc_final: 0.8127 (tptp) REVERT: E 25 MET cc_start: 0.7546 (ttm) cc_final: 0.6904 (tmm) REVERT: E 72 LYS cc_start: 0.8398 (tptp) cc_final: 0.7688 (tptp) REVERT: E 79 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8891 (mmmt) REVERT: E 93 LYS cc_start: 0.7778 (mptt) cc_final: 0.7520 (mmtm) REVERT: F 26 ARG cc_start: 0.7902 (mtt180) cc_final: 0.7079 (ttm110) REVERT: F 28 LYS cc_start: 0.7487 (mptt) cc_final: 0.7209 (mmtm) REVERT: F 38 ARG cc_start: 0.8060 (tpt90) cc_final: 0.7537 (tpt90) REVERT: F 59 ARG cc_start: 0.7766 (mmt90) cc_final: 0.7542 (mmm-85) REVERT: G 79 LYS cc_start: 0.9019 (tmmt) cc_final: 0.8613 (tmmt) REVERT: G 93 LYS cc_start: 0.8573 (tttt) cc_final: 0.8154 (tttp) REVERT: H 18 ASP cc_start: 0.8420 (p0) cc_final: 0.8080 (p0) REVERT: H 95 GLN cc_start: 0.7635 (mp10) cc_final: 0.7125 (mp-120) REVERT: I 25 MET cc_start: 0.7874 (ttm) cc_final: 0.7169 (tmm) REVERT: I 79 LYS cc_start: 0.8733 (mmtt) cc_final: 0.8173 (mmmt) REVERT: I 93 LYS cc_start: 0.8197 (tttt) cc_final: 0.7849 (tttp) REVERT: I 95 GLN cc_start: 0.8626 (mm110) cc_final: 0.8266 (mm110) REVERT: J 25 MET cc_start: 0.8169 (ttt) cc_final: 0.7799 (tmm) REVERT: J 44 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7660 (mt-10) REVERT: J 78 GLU cc_start: 0.8015 (mt-10) cc_final: 0.7574 (tm-30) REVERT: J 93 LYS cc_start: 0.8432 (tttt) cc_final: 0.7670 (mtpp) REVERT: K 55 VAL cc_start: 0.8927 (t) cc_final: 0.8635 (t) REVERT: K 93 LYS cc_start: 0.8483 (tttt) cc_final: 0.8121 (mtpt) REVERT: L 18 ASP cc_start: 0.7315 (p0) cc_final: 0.6609 (p0) REVERT: L 93 LYS cc_start: 0.8534 (tttt) cc_final: 0.8061 (mtpp) REVERT: M 25 MET cc_start: 0.7801 (ttt) cc_final: 0.7232 (mtp) REVERT: M 79 LYS cc_start: 0.8765 (mmtm) cc_final: 0.8526 (mmtm) REVERT: N 78 GLU cc_start: 0.7618 (tp30) cc_final: 0.6836 (tm-30) REVERT: N 93 LYS cc_start: 0.8490 (tttt) cc_final: 0.8141 (mtpt) REVERT: O 93 LYS cc_start: 0.8466 (tttt) cc_final: 0.7769 (mtpp) REVERT: P 25 MET cc_start: 0.7826 (ttm) cc_final: 0.6998 (tmm) REVERT: P 32 ARG cc_start: 0.7993 (ttt90) cc_final: 0.7460 (ttm-80) REVERT: P 52 THR cc_start: 0.7318 (p) cc_final: 0.7082 (p) REVERT: P 79 LYS cc_start: 0.8617 (mmtt) cc_final: 0.8063 (mmmt) REVERT: P 93 LYS cc_start: 0.8139 (tttt) cc_final: 0.7754 (tttp) REVERT: P 95 GLN cc_start: 0.8609 (mm110) cc_final: 0.8284 (mm110) REVERT: Q 18 ASP cc_start: 0.8264 (p0) cc_final: 0.7750 (p0) REVERT: R 84 LYS cc_start: 0.8182 (tptp) cc_final: 0.7621 (pptt) REVERT: S 18 ASP cc_start: 0.7154 (p0) cc_final: 0.6661 (p0) REVERT: S 21 VAL cc_start: 0.8926 (m) cc_final: 0.8701 (p) REVERT: S 26 ARG cc_start: 0.7711 (mtt180) cc_final: 0.7170 (ttm110) REVERT: S 38 ARG cc_start: 0.8099 (tpt90) cc_final: 0.7723 (tpt90) REVERT: S 72 LYS cc_start: 0.8803 (tptt) cc_final: 0.8139 (tppt) REVERT: S 79 LYS cc_start: 0.8612 (mmtm) cc_final: 0.8374 (mmtm) REVERT: S 93 LYS cc_start: 0.8541 (tttt) cc_final: 0.8118 (tptp) REVERT: T 25 MET cc_start: 0.7825 (ttm) cc_final: 0.6900 (tmm) REVERT: T 72 LYS cc_start: 0.8655 (tmtt) cc_final: 0.8175 (tptp) REVERT: T 78 GLU cc_start: 0.8367 (tp30) cc_final: 0.8108 (tp30) REVERT: T 79 LYS cc_start: 0.9027 (mmtm) cc_final: 0.8550 (mmmt) REVERT: U 18 ASP cc_start: 0.7226 (p0) cc_final: 0.6619 (p0) REVERT: U 32 ARG cc_start: 0.7565 (ttt90) cc_final: 0.7294 (ttt90) REVERT: U 93 LYS cc_start: 0.8598 (tttt) cc_final: 0.8077 (tptp) REVERT: V 24 ASP cc_start: 0.7412 (m-30) cc_final: 0.6478 (t0) REVERT: V 30 GLN cc_start: 0.7671 (tt0) cc_final: 0.7131 (tm-30) REVERT: V 38 ARG cc_start: 0.6076 (ttp80) cc_final: 0.5823 (tmm160) outliers start: 0 outliers final: 0 residues processed: 300 average time/residue: 0.5200 time to fit residues: 201.2142 Evaluate side-chains 260 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 260 time to evaluate : 2.092 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 200 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 154 optimal weight: 0.3980 chunk 35 optimal weight: 0.7980 chunk 2 optimal weight: 20.0000 chunk 89 optimal weight: 1.9990 chunk 166 optimal weight: 4.9990 chunk 179 optimal weight: 0.5980 chunk 28 optimal weight: 20.0000 chunk 120 optimal weight: 8.9990 chunk 52 optimal weight: 6.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4962 r_free = 0.4962 target = 0.115818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.086935 restraints weight = 33258.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.088109 restraints weight = 22136.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.088828 restraints weight = 17194.476| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.6849 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 16478 Z= 0.153 Angle : 0.743 8.066 22198 Z= 0.366 Chirality : 0.052 0.161 2684 Planarity : 0.003 0.039 2904 Dihedral : 5.553 22.761 2376 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 17.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.32 % Favored : 90.68 % Rotamer: Outliers : 0.00 % Allowed : 0.89 % Favored : 99.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.50 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.69 (0.13), residues: 1232 loop : -3.33 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS U 68 PHE 0.007 0.001 PHE K 88 TYR 0.009 0.001 TYR J 14 ARG 0.008 0.001 ARG A 87 Details of bonding type rmsd hydrogen bonds : bond 0.01327 ( 66) hydrogen bonds : angle 5.17204 ( 132) covalent geometry : bond 0.00331 (16478) covalent geometry : angle 0.74274 (22198) *********************** 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 318 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 318 time to evaluate : 2.327 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: 0.7923 (tmtt) cc_final: 0.7490 (tmtt) REVERT: B 72 LYS cc_start: 0.7884 (tmtt) cc_final: 0.7421 (tmtt) REVERT: B 91 GLN cc_start: 0.6976 (mp10) cc_final: 0.6020 (tm-30) REVERT: C 20 GLU cc_start: 0.7257 (mp0) cc_final: 0.7024 (tm-30) REVERT: C 24 ASP cc_start: 0.7329 (m-30) cc_final: 0.6437 (t0) REVERT: C 30 GLN cc_start: 0.7793 (tt0) cc_final: 0.7283 (tm-30) REVERT: C 38 ARG cc_start: 0.6295 (tmm160) cc_final: 0.5730 (ttp80) REVERT: C 78 GLU cc_start: 0.5717 (pt0) cc_final: 0.5054 (mm-30) REVERT: C 88 PHE cc_start: 0.4104 (t80) cc_final: 0.3882 (t80) REVERT: D 24 ASP cc_start: 0.6735 (t0) cc_final: 0.6424 (t0) REVERT: D 93 LYS cc_start: 0.8441 (tttt) cc_final: 0.7990 (tptp) REVERT: E 25 MET cc_start: 0.7373 (ttm) cc_final: 0.6648 (tmm) REVERT: E 38 ARG cc_start: 0.7986 (tpm170) cc_final: 0.7442 (tpt90) REVERT: E 72 LYS cc_start: 0.8349 (tptp) cc_final: 0.7975 (tppt) REVERT: E 93 LYS cc_start: 0.7903 (mptt) cc_final: 0.7560 (mmtm) REVERT: F 21 VAL cc_start: 0.8740 (m) cc_final: 0.8504 (p) REVERT: F 26 ARG cc_start: 0.7501 (mtt180) cc_final: 0.7075 (ttm110) REVERT: F 38 ARG cc_start: 0.7992 (tpt90) cc_final: 0.7456 (tpt90) REVERT: F 59 ARG cc_start: 0.7819 (mmt90) cc_final: 0.7542 (mmm-85) REVERT: F 74 GLU cc_start: 0.8124 (mt-10) cc_final: 0.7732 (mt-10) REVERT: G 79 LYS cc_start: 0.8979 (tmmt) cc_final: 0.8591 (tmmt) REVERT: G 84 LYS cc_start: 0.8054 (tptp) cc_final: 0.7674 (pptt) REVERT: G 93 LYS cc_start: 0.8563 (tttt) cc_final: 0.8241 (tttp) REVERT: H 18 ASP cc_start: 0.8358 (p0) cc_final: 0.7810 (p0) REVERT: H 20 GLU cc_start: 0.8307 (mp0) cc_final: 0.8065 (mp0) REVERT: I 25 MET cc_start: 0.7770 (ttm) cc_final: 0.7066 (tmm) REVERT: I 79 LYS cc_start: 0.8620 (mmtt) cc_final: 0.8028 (mmmt) REVERT: I 93 LYS cc_start: 0.8110 (tttt) cc_final: 0.7335 (mmtm) REVERT: I 95 GLN cc_start: 0.8518 (mm110) cc_final: 0.8225 (mm-40) REVERT: J 25 MET cc_start: 0.8004 (ttt) cc_final: 0.7720 (tmm) REVERT: J 78 GLU cc_start: 0.7955 (mt-10) cc_final: 0.7559 (tm-30) REVERT: J 93 LYS cc_start: 0.8351 (tttt) cc_final: 0.7664 (mtpp) REVERT: K 93 LYS cc_start: 0.8406 (tttt) cc_final: 0.8085 (mtpt) REVERT: K 95 GLN cc_start: 0.8002 (mm-40) cc_final: 0.6873 (tp40) REVERT: L 18 ASP cc_start: 0.7340 (p0) cc_final: 0.6656 (p0) REVERT: L 20 GLU cc_start: 0.8048 (mp0) cc_final: 0.7688 (mp0) REVERT: L 38 ARG cc_start: 0.7719 (tpt90) cc_final: 0.7057 (tpt90) REVERT: M 25 MET cc_start: 0.7845 (ttt) cc_final: 0.7334 (mtp) REVERT: M 78 GLU cc_start: 0.7954 (tp30) cc_final: 0.7466 (tm-30) REVERT: M 79 LYS cc_start: 0.8676 (mmtm) cc_final: 0.8253 (mmmm) REVERT: N 78 GLU cc_start: 0.7573 (tp30) cc_final: 0.6759 (tm-30) REVERT: N 93 LYS cc_start: 0.8393 (tttt) cc_final: 0.8087 (mtpt) REVERT: N 95 GLN cc_start: 0.7949 (mm-40) cc_final: 0.7051 (tp-100) REVERT: O 25 MET cc_start: 0.8057 (ttt) cc_final: 0.7760 (tmm) REVERT: O 93 LYS cc_start: 0.8341 (tttt) cc_final: 0.7581 (mtpp) REVERT: P 25 MET cc_start: 0.7673 (ttm) cc_final: 0.6995 (tmm) REVERT: P 32 ARG cc_start: 0.8010 (ttt90) cc_final: 0.7551 (ttt90) REVERT: P 79 LYS cc_start: 0.8580 (mmtt) cc_final: 0.8026 (mmmt) REVERT: P 93 LYS cc_start: 0.8084 (tttt) cc_final: 0.7756 (tttp) REVERT: P 95 GLN cc_start: 0.8603 (mm110) cc_final: 0.8291 (mm110) REVERT: Q 18 ASP cc_start: 0.7996 (p0) cc_final: 0.7515 (p0) REVERT: R 79 LYS cc_start: 0.8908 (tmmt) cc_final: 0.8634 (tmmt) REVERT: R 84 LYS cc_start: 0.8088 (tptp) cc_final: 0.7579 (pptt) REVERT: S 21 VAL cc_start: 0.8891 (m) cc_final: 0.8662 (p) REVERT: S 26 ARG cc_start: 0.7411 (mtt180) cc_final: 0.7096 (ttm110) REVERT: S 28 LYS cc_start: 0.7379 (mptt) cc_final: 0.7159 (mmtm) REVERT: S 38 ARG cc_start: 0.8002 (tpt90) cc_final: 0.7564 (tpt90) REVERT: S 72 LYS cc_start: 0.8840 (tptt) cc_final: 0.8561 (tptm) REVERT: S 79 LYS cc_start: 0.8589 (mmtm) cc_final: 0.8330 (mmtm) REVERT: S 93 LYS cc_start: 0.8469 (tttt) cc_final: 0.8049 (tptp) REVERT: T 25 MET cc_start: 0.7434 (ttm) cc_final: 0.6716 (tmm) REVERT: T 72 LYS cc_start: 0.8571 (tmtt) cc_final: 0.8084 (tptp) REVERT: T 78 GLU cc_start: 0.8417 (tp30) cc_final: 0.8169 (tp30) REVERT: T 79 LYS cc_start: 0.8953 (mmtm) cc_final: 0.8500 (mmmt) REVERT: T 100 GLU cc_start: 0.8256 (mm-30) cc_final: 0.7917 (mt-10) REVERT: U 18 ASP cc_start: 0.7185 (p0) cc_final: 0.6553 (p0) REVERT: U 20 GLU cc_start: 0.7901 (mp0) cc_final: 0.7560 (mp0) REVERT: U 54 ARG cc_start: 0.7799 (tmm-80) cc_final: 0.7138 (ttp80) REVERT: U 93 LYS cc_start: 0.8521 (tttt) cc_final: 0.8030 (tptp) REVERT: V 24 ASP cc_start: 0.7384 (m-30) cc_final: 0.6469 (t0) REVERT: V 30 GLN cc_start: 0.7597 (tt0) cc_final: 0.7068 (tm-30) REVERT: V 38 ARG cc_start: 0.6110 (ttp80) cc_final: 0.5805 (tmm160) REVERT: V 42 LEU cc_start: 0.5182 (mt) cc_final: 0.4942 (mm) outliers start: 0 outliers final: 0 residues processed: 318 average time/residue: 0.5123 time to fit residues: 210.0651 Evaluate side-chains 269 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 192 optimal weight: 0.0570 chunk 114 optimal weight: 3.9990 chunk 85 optimal weight: 2.9990 chunk 193 optimal weight: 4.9990 chunk 188 optimal weight: 4.9990 chunk 10 optimal weight: 30.0000 chunk 41 optimal weight: 8.9990 chunk 51 optimal weight: 0.9980 chunk 23 optimal weight: 8.9990 chunk 116 optimal weight: 0.9990 chunk 200 optimal weight: 10.0000 overall best weight: 1.8104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN B 68 HIS B 95 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 95 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4966 r_free = 0.4966 target = 0.116161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4424 r_free = 0.4424 target = 0.087385 restraints weight = 33483.995| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.088389 restraints weight = 22369.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.088682 restraints weight = 18514.485| |-----------------------------------------------------------------------------| r_work (final): 0.4430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7116 moved from start: 0.6939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 16478 Z= 0.159 Angle : 0.747 8.484 22198 Z= 0.368 Chirality : 0.052 0.164 2684 Planarity : 0.004 0.034 2904 Dihedral : 5.433 21.759 2376 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.45 % Favored : 91.55 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.40 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.61 (0.13), residues: 1232 loop : -3.30 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 68 PHE 0.008 0.001 PHE E 105 TYR 0.011 0.001 TYR J 14 ARG 0.010 0.001 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.01420 ( 66) hydrogen bonds : angle 5.02865 ( 132) covalent geometry : bond 0.00343 (16478) covalent geometry : angle 0.74746 (22198) ********************** 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 315 residues out of total 1694 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 315 time to evaluate : 1.958 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 72 LYS cc_start: 0.7914 (tmtt) cc_final: 0.7468 (tmtt) REVERT: A 91 GLN cc_start: 0.6917 (mp10) cc_final: 0.6223 (tm-30) REVERT: B 72 LYS cc_start: 0.7847 (tmtt) cc_final: 0.7413 (tmtt) REVERT: B 91 GLN cc_start: 0.6957 (mp10) cc_final: 0.5997 (tm-30) REVERT: C 24 ASP cc_start: 0.7322 (m-30) cc_final: 0.6447 (t0) REVERT: C 38 ARG cc_start: 0.6283 (tmm160) cc_final: 0.5728 (ttp80) REVERT: C 78 GLU cc_start: 0.5672 (pt0) cc_final: 0.4951 (mm-30) REVERT: C 88 PHE cc_start: 0.4157 (t80) cc_final: 0.3813 (t80) REVERT: D 59 ARG cc_start: 0.7526 (mmp80) cc_final: 0.6914 (mmp80) REVERT: D 78 GLU cc_start: 0.7839 (tm-30) cc_final: 0.7512 (tt0) REVERT: D 93 LYS cc_start: 0.8411 (tttt) cc_final: 0.7896 (mptt) REVERT: E 25 MET cc_start: 0.7151 (ttm) cc_final: 0.6623 (tmm) REVERT: E 72 LYS cc_start: 0.8305 (tptp) cc_final: 0.7896 (tppt) REVERT: E 79 LYS cc_start: 0.8848 (mmpt) cc_final: 0.8618 (mmmt) REVERT: E 93 LYS cc_start: 0.7646 (mptt) cc_final: 0.7368 (mmtm) REVERT: F 26 ARG cc_start: 0.7491 (mtt180) cc_final: 0.7114 (ttm110) REVERT: F 38 ARG cc_start: 0.7916 (tpt90) cc_final: 0.7424 (tpt90) REVERT: G 84 LYS cc_start: 0.7932 (tptp) cc_final: 0.7668 (pptt) REVERT: G 93 LYS cc_start: 0.8533 (tttt) cc_final: 0.8225 (tttp) REVERT: H 18 ASP cc_start: 0.8372 (p0) cc_final: 0.7810 (p0) REVERT: H 20 GLU cc_start: 0.8214 (mp0) cc_final: 0.7989 (mp0) REVERT: I 25 MET cc_start: 0.7729 (ttm) cc_final: 0.7036 (tmm) REVERT: I 79 LYS cc_start: 0.8636 (mmtt) cc_final: 0.8105 (mmmt) REVERT: I 93 LYS cc_start: 0.8089 (tttt) cc_final: 0.7309 (mmtm) REVERT: I 95 GLN cc_start: 0.8489 (mm110) cc_final: 0.8241 (mm-40) REVERT: J 25 MET cc_start: 0.8189 (ttt) cc_final: 0.7735 (tmm) REVERT: J 66 LEU cc_start: 0.8290 (mm) cc_final: 0.8079 (mm) REVERT: J 78 GLU cc_start: 0.7973 (mt-10) cc_final: 0.7551 (tm-30) REVERT: J 93 LYS cc_start: 0.8277 (tttt) cc_final: 0.7499 (mtpp) REVERT: K 18 ASP cc_start: 0.7691 (t70) cc_final: 0.7428 (t70) REVERT: K 20 GLU cc_start: 0.7865 (mp0) cc_final: 0.7561 (mp0) REVERT: K 93 LYS cc_start: 0.8381 (tttt) cc_final: 0.8049 (mtpt) REVERT: K 95 GLN cc_start: 0.7978 (mm-40) cc_final: 0.6856 (tp40) REVERT: L 18 ASP cc_start: 0.7243 (p0) cc_final: 0.6614 (p0) REVERT: L 20 GLU cc_start: 0.7880 (mp0) cc_final: 0.7498 (mp0) REVERT: L 38 ARG cc_start: 0.7645 (tpt90) cc_final: 0.7035 (tpt90) REVERT: L 79 LYS cc_start: 0.8382 (mtpt) cc_final: 0.8098 (ttmm) REVERT: M 25 MET cc_start: 0.7834 (ttt) cc_final: 0.7298 (mtp) REVERT: M 78 GLU cc_start: 0.7984 (tp30) cc_final: 0.7444 (tm-30) REVERT: M 79 LYS cc_start: 0.8681 (mmtm) cc_final: 0.8276 (mmmm) REVERT: N 28 LYS cc_start: 0.8010 (mtpp) cc_final: 0.7781 (mtpp) REVERT: N 78 GLU cc_start: 0.7584 (tp30) cc_final: 0.6825 (tm-30) REVERT: N 93 LYS cc_start: 0.8351 (tttt) cc_final: 0.8080 (mtpt) REVERT: N 95 GLN cc_start: 0.7889 (mm-40) cc_final: 0.6966 (tp-100) REVERT: O 25 MET cc_start: 0.8177 (ttt) cc_final: 0.7728 (tmm) REVERT: O 93 LYS cc_start: 0.8328 (tttt) cc_final: 0.7526 (mtpp) REVERT: P 25 MET cc_start: 0.7697 (ttm) cc_final: 0.7024 (tmm) REVERT: P 32 ARG cc_start: 0.8025 (ttt90) cc_final: 0.7590 (ttt90) REVERT: P 52 THR cc_start: 0.7178 (p) cc_final: 0.6716 (p) REVERT: P 79 LYS cc_start: 0.8589 (mmtt) cc_final: 0.8087 (mmmt) REVERT: P 93 LYS cc_start: 0.8084 (tttt) cc_final: 0.7758 (tttp) REVERT: P 95 GLN cc_start: 0.8614 (mm110) cc_final: 0.8304 (mm110) REVERT: Q 18 ASP cc_start: 0.8000 (p0) cc_final: 0.7512 (p0) REVERT: R 79 LYS cc_start: 0.8958 (tmmt) cc_final: 0.8613 (tmmt) REVERT: R 84 LYS cc_start: 0.8049 (tptp) cc_final: 0.7582 (pptt) REVERT: S 26 ARG cc_start: 0.7536 (mtt180) cc_final: 0.7184 (ttm110) REVERT: S 38 ARG cc_start: 0.8022 (tpt90) cc_final: 0.7553 (tpt90) REVERT: S 63 ARG cc_start: 0.7799 (mmt-90) cc_final: 0.7479 (mpt180) REVERT: S 72 LYS cc_start: 0.8847 (tptt) cc_final: 0.8581 (tptm) REVERT: S 79 LYS cc_start: 0.8689 (mmtm) cc_final: 0.8400 (mmtm) REVERT: S 93 LYS cc_start: 0.8455 (tttt) cc_final: 0.8051 (tptp) REVERT: T 25 MET cc_start: 0.7050 (ttm) cc_final: 0.6590 (tmm) REVERT: T 54 ARG cc_start: 0.8097 (ttt180) cc_final: 0.7695 (mtp-110) REVERT: T 72 LYS cc_start: 0.8627 (tmtt) cc_final: 0.8093 (tptp) REVERT: T 79 LYS cc_start: 0.8934 (mmtm) cc_final: 0.8530 (mmmt) REVERT: U 18 ASP cc_start: 0.7265 (p0) cc_final: 0.6666 (p0) REVERT: U 24 ASP cc_start: 0.6744 (m-30) cc_final: 0.5817 (t0) REVERT: U 54 ARG cc_start: 0.7845 (tmm-80) cc_final: 0.7223 (ttp80) REVERT: U 78 GLU cc_start: 0.8137 (tt0) cc_final: 0.7904 (tt0) REVERT: U 93 LYS cc_start: 0.8470 (tttt) cc_final: 0.7896 (mptt) REVERT: U 100 GLU cc_start: 0.8007 (mp0) cc_final: 0.7787 (mp0) REVERT: V 24 ASP cc_start: 0.7399 (m-30) cc_final: 0.6458 (t0) REVERT: V 30 GLN cc_start: 0.7615 (tt0) cc_final: 0.7028 (tm-30) REVERT: V 38 ARG cc_start: 0.6099 (ttp80) cc_final: 0.5821 (tmm160) REVERT: V 42 LEU cc_start: 0.4972 (mt) cc_final: 0.4769 (mm) outliers start: 0 outliers final: 0 residues processed: 315 average time/residue: 0.4856 time to fit residues: 195.5860 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 : 1.728 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 132 optimal weight: 0.6980 chunk 32 optimal weight: 10.0000 chunk 78 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 77 optimal weight: 5.9990 chunk 97 optimal weight: 5.9990 chunk 122 optimal weight: 3.9990 chunk 127 optimal weight: 4.9990 chunk 199 optimal weight: 6.9990 chunk 10 optimal weight: 30.0000 chunk 67 optimal weight: 2.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 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 = 0.4931 r_free = 0.4931 target = 0.113709 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.082879 restraints weight = 34375.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.084479 restraints weight = 25204.047| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.085643 restraints weight = 19768.492| |-----------------------------------------------------------------------------| r_work (final): 0.4361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.7142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 16478 Z= 0.238 Angle : 0.799 8.970 22198 Z= 0.404 Chirality : 0.053 0.168 2684 Planarity : 0.004 0.047 2904 Dihedral : 6.055 22.316 2376 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 19.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.05 % Favored : 85.95 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.58 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.78 (0.12), residues: 1342 loop : -3.12 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 68 PHE 0.015 0.002 PHE H 105 TYR 0.017 0.002 TYR O 14 ARG 0.009 0.001 ARG E 59 Details of bonding type rmsd hydrogen bonds : bond 0.01689 ( 66) hydrogen bonds : angle 5.55392 ( 132) covalent geometry : bond 0.00491 (16478) covalent geometry : angle 0.79906 (22198) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6304.42 seconds wall clock time: 114 minutes 2.97 seconds (6842.97 seconds total)