Starting phenix.real_space_refine on Fri Sep 27 12:56:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/09_2024/6rib_4887_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/09_2024/6rib_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/09_2024/6rib_4887.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/09_2024/6rib_4887.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/09_2024/6rib_4887_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6rib_4887/09_2024/6rib_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-5461/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: 4.12, per 1000 atoms: 0.25 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: 3.76 Conformation dependent library (CDL) restraints added in 2.1 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: 3.57 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: 4.56 Time building geometry restraints manager: 4.41 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' 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: 1.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.160 Process input model: 31.670 Find NCS groups from input model: 0.730 Set up NCS constraints: 0.050 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.670 ------------------------------------------------------------------------------- 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= 0.511 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 *********************** 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 fitting. rotamer outliers: 154 poor density : 532 time to evaluate : 1.832 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: 0.4467 time to fit residues: 348.8207 Evaluate side-chains 374 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 318 time to evaluate : 1.860 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6452 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= 0.212 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 *********************** 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 fitting. rotamer outliers: 0 poor density : 392 time to evaluate : 1.959 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: 0.6466 (t70) cc_final: 0.6129 (t70) REVERT: A 72 LYS cc_start: 0.7965 (tmtt) cc_final: 0.7744 (tptp) REVERT: A 91 GLN cc_start: 0.7003 (mp10) cc_final: 0.6092 (tm-30) REVERT: B 72 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7857 (tptp) REVERT: B 91 GLN cc_start: 0.7272 (mp10) cc_final: 0.6405 (tm-30) REVERT: C 24 ASP cc_start: 0.7150 (m-30) cc_final: 0.6699 (t0) REVERT: C 38 ARG cc_start: 0.6549 (ttp80) cc_final: 0.6112 (ttp80) REVERT: C 40 SER cc_start: 0.7128 (p) cc_final: 0.6868 (t) REVERT: C 58 GLU cc_start: 0.4397 (pm20) cc_final: 0.4162 (pm20) REVERT: D 25 MET cc_start: 0.7509 (tmm) cc_final: 0.6900 (tmm) REVERT: D 36 LEU cc_start: 0.6901 (tt) cc_final: 0.6685 (mt) REVERT: D 93 LYS cc_start: 0.8170 (tttt) cc_final: 0.7790 (tptp) REVERT: E 25 MET cc_start: 0.7365 (ttm) cc_final: 0.6542 (tmm) REVERT: E 26 ARG cc_start: 0.7143 (mtt180) cc_final: 0.6843 (tpt-90) REVERT: E 72 LYS cc_start: 0.8759 (tttt) cc_final: 0.8437 (tmtt) REVERT: E 78 GLU cc_start: 0.8592 (tp30) cc_final: 0.7642 (tp30) REVERT: E 79 LYS cc_start: 0.8949 (mmtm) cc_final: 0.8740 (mmpt) REVERT: F 26 ARG cc_start: 0.7505 (mtt180) cc_final: 0.6672 (ttm110) REVERT: F 38 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7662 (tpt90) REVERT: F 44 GLU cc_start: 0.6489 (tm-30) cc_final: 0.6252 (tm-30) REVERT: F 59 ARG cc_start: 0.7817 (mmt-90) cc_final: 0.7382 (mmm-85) REVERT: F 70 GLU cc_start: 0.8073 (mt-10) cc_final: 0.7664 (mp0) REVERT: G 20 GLU cc_start: 0.8016 (mp0) cc_final: 0.7702 (mt-10) REVERT: G 38 ARG cc_start: 0.7920 (tpt90) cc_final: 0.7367 (tpt90) REVERT: H 18 ASP cc_start: 0.7419 (p0) cc_final: 0.7042 (p0) REVERT: H 24 ASP cc_start: 0.7011 (t0) cc_final: 0.6807 (t0) REVERT: H 95 GLN cc_start: 0.8580 (mm-40) cc_final: 0.8242 (mm-40) REVERT: H 100 GLU cc_start: 0.7447 (mm-30) cc_final: 0.7109 (mm-30) REVERT: I 25 MET cc_start: 0.6539 (ttm) cc_final: 0.5815 (tmm) REVERT: I 70 GLU cc_start: 0.8120 (mt-10) cc_final: 0.7389 (tm-30) REVERT: I 72 LYS cc_start: 0.8179 (tttt) cc_final: 0.7666 (tptp) REVERT: I 84 LYS cc_start: 0.8190 (tptp) cc_final: 0.7959 (tptp) REVERT: I 93 LYS cc_start: 0.7563 (tttt) cc_final: 0.6827 (mmtm) REVERT: J 20 GLU cc_start: 0.7980 (mp0) cc_final: 0.7710 (mp0) REVERT: J 38 ARG cc_start: 0.7980 (tpt90) cc_final: 0.7442 (tpt90) REVERT: J 72 LYS cc_start: 0.8382 (tttt) cc_final: 0.7604 (mppt) REVERT: J 93 LYS cc_start: 0.7562 (tttt) cc_final: 0.6607 (mmtm) REVERT: K 28 LYS cc_start: 0.7408 (mtpp) cc_final: 0.6826 (mtpp) REVERT: K 40 SER cc_start: 0.6966 (p) cc_final: 0.6223 (t) REVERT: K 58 GLU cc_start: 0.6736 (pt0) cc_final: 0.6170 (pt0) REVERT: K 72 LYS cc_start: 0.8107 (tttt) cc_final: 0.7759 (mmtm) REVERT: K 87 ARG cc_start: 0.7421 (ttm-80) cc_final: 0.7108 (mtp85) REVERT: K 93 LYS cc_start: 0.7426 (tttt) cc_final: 0.7207 (mtpt) REVERT: K 95 GLN cc_start: 0.8226 (mm-40) cc_final: 0.7985 (mm-40) REVERT: K 100 GLU cc_start: 0.7280 (mm-30) cc_final: 0.7078 (mm-30) REVERT: L 18 ASP cc_start: 0.7614 (p0) cc_final: 0.6842 (p0) REVERT: L 38 ARG cc_start: 0.7972 (tpt90) cc_final: 0.7569 (tpt90) REVERT: L 78 GLU cc_start: 0.8111 (mm-30) cc_final: 0.7522 (tp30) REVERT: L 93 LYS cc_start: 0.7586 (tttt) cc_final: 0.6633 (mmtm) REVERT: L 95 GLN cc_start: 0.8578 (mm-40) cc_final: 0.8102 (mm110) REVERT: M 18 ASP cc_start: 0.7635 (p0) cc_final: 0.7263 (p0) REVERT: M 25 MET cc_start: 0.6477 (ttt) cc_final: 0.6094 (mtp) REVERT: M 44 GLU cc_start: 0.6497 (tm-30) cc_final: 0.6188 (tm-30) REVERT: M 78 GLU cc_start: 0.8030 (mm-30) cc_final: 0.7299 (tp30) REVERT: M 93 LYS cc_start: 0.7390 (tttt) cc_final: 0.6490 (mmtm) REVERT: M 95 GLN cc_start: 0.8578 (mm-40) cc_final: 0.7978 (mm110) REVERT: N 59 ARG cc_start: 0.7556 (mmt-90) cc_final: 0.7000 (mmm-85) REVERT: N 72 LYS cc_start: 0.8269 (tttt) cc_final: 0.7944 (mmtm) REVERT: N 93 LYS cc_start: 0.7680 (tttt) cc_final: 0.7423 (mtpt) REVERT: N 95 GLN cc_start: 0.8381 (mm-40) cc_final: 0.8135 (mm-40) REVERT: O 26 ARG cc_start: 0.6966 (mtt180) cc_final: 0.6652 (mtt-85) REVERT: O 38 ARG cc_start: 0.7892 (tpt90) cc_final: 0.7442 (tpt90) REVERT: O 72 LYS cc_start: 0.8248 (tttt) cc_final: 0.7514 (mppt) REVERT: O 93 LYS cc_start: 0.7308 (tttt) cc_final: 0.6428 (mmtm) REVERT: P 25 MET cc_start: 0.6757 (ttm) cc_final: 0.6116 (tmm) REVERT: P 52 THR cc_start: 0.7602 (t) cc_final: 0.7251 (p) REVERT: P 70 GLU cc_start: 0.8116 (mt-10) cc_final: 0.7379 (tm-30) REVERT: P 72 LYS cc_start: 0.8174 (tttt) cc_final: 0.7767 (tptp) REVERT: P 93 LYS cc_start: 0.7850 (tttt) cc_final: 0.7082 (mmtm) REVERT: Q 25 MET cc_start: 0.7860 (tmm) cc_final: 0.7198 (tmm) REVERT: Q 72 LYS cc_start: 0.8812 (tttt) cc_final: 0.8507 (tptp) REVERT: Q 100 GLU cc_start: 0.7244 (mm-30) cc_final: 0.6945 (mm-30) REVERT: R 38 ARG cc_start: 0.7735 (tpt90) cc_final: 0.7283 (tpt90) REVERT: R 93 LYS cc_start: 0.8466 (tttt) cc_final: 0.8262 (tttp) REVERT: S 26 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6709 (ttm110) REVERT: S 38 ARG cc_start: 0.8208 (tpt90) cc_final: 0.7675 (tpt90) REVERT: S 59 ARG cc_start: 0.7979 (mmt-90) cc_final: 0.7279 (mmm-85) REVERT: S 93 LYS cc_start: 0.7854 (tttt) cc_final: 0.7477 (tptp) REVERT: S 95 GLN cc_start: 0.8488 (mm-40) cc_final: 0.8143 (mm110) REVERT: T 25 MET cc_start: 0.7150 (ttm) cc_final: 0.6338 (tmm) REVERT: T 26 ARG cc_start: 0.7162 (mtt180) cc_final: 0.6768 (tpt-90) REVERT: T 59 ARG cc_start: 0.7832 (mmt-90) cc_final: 0.7391 (tpp80) REVERT: T 72 LYS cc_start: 0.8435 (tmtt) cc_final: 0.7965 (tptp) REVERT: T 78 GLU cc_start: 0.8324 (tp30) cc_final: 0.7433 (tp30) REVERT: T 79 LYS cc_start: 0.9013 (mmtm) cc_final: 0.8803 (mmpt) REVERT: T 84 LYS cc_start: 0.8287 (mmpt) cc_final: 0.8050 (tptp) REVERT: U 18 ASP cc_start: 0.7142 (p0) cc_final: 0.6805 (p0) REVERT: U 25 MET cc_start: 0.7073 (ttm) cc_final: 0.6753 (tmm) REVERT: U 36 LEU cc_start: 0.6907 (tt) cc_final: 0.6663 (mt) REVERT: U 74 GLU cc_start: 0.7487 (mt-10) cc_final: 0.7264 (mt-10) REVERT: U 93 LYS cc_start: 0.8151 (tttt) cc_final: 0.7798 (mptt) REVERT: V 24 ASP cc_start: 0.7537 (m-30) cc_final: 0.6666 (t0) outliers start: 0 outliers final: 0 residues processed: 392 average time/residue: 0.4563 time to fit residues: 229.8510 Evaluate side-chains 286 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 286 time to evaluate : 1.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 111 optimal weight: 7.9990 chunk 62 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 136 optimal weight: 2.9990 chunk 55 optimal weight: 10.0000 chunk 200 optimal weight: 10.0000 chunk 216 optimal weight: 10.0000 chunk 178 optimal weight: 2.9990 chunk 198 optimal weight: 10.0000 chunk 68 optimal weight: 9.9990 chunk 160 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 16478 Z= 0.489 Angle : 0.844 8.234 22198 Z= 0.448 Chirality : 0.054 0.218 2684 Planarity : 0.006 0.047 2904 Dihedral : 6.815 24.947 2376 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.38 % Favored : 84.62 % Rotamer: Outliers : 0.06 % Allowed : 6.49 % Favored : 93.45 % 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: -5.52 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -3.42 (0.13), residues: 1188 loop : -3.84 (0.15), 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 0.019 0.003 TYR C 14 ARG 0.015 0.001 ARG C 32 *********************** 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 335 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 334 time to evaluate : 2.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 72 LYS cc_start: 0.8064 (tmtt) cc_final: 0.7686 (tptp) REVERT: B 61 GLU cc_start: 0.5558 (mp0) cc_final: 0.4414 (tm-30) REVERT: B 72 LYS cc_start: 0.8226 (tmtt) cc_final: 0.7783 (tmtt) REVERT: C 24 ASP cc_start: 0.7450 (m-30) cc_final: 0.6775 (t0) REVERT: C 38 ARG cc_start: 0.6297 (ttp80) cc_final: 0.5985 (ttp80) REVERT: D 24 ASP cc_start: 0.6929 (t0) cc_final: 0.6618 (t0) REVERT: D 78 GLU cc_start: 0.8137 (tt0) cc_final: 0.7888 (tm-30) REVERT: D 93 LYS cc_start: 0.8466 (tttt) cc_final: 0.7928 (mptt) REVERT: D 100 GLU cc_start: 0.8450 (mp0) cc_final: 0.8068 (mp0) REVERT: E 25 MET cc_start: 0.7790 (ttm) cc_final: 0.6685 (tmm) REVERT: E 38 ARG cc_start: 0.8035 (tpm170) cc_final: 0.7817 (tpm170) REVERT: E 55 VAL cc_start: 0.9107 (t) cc_final: 0.8877 (p) REVERT: E 72 LYS cc_start: 0.8804 (tttt) cc_final: 0.8241 (tptp) REVERT: E 79 LYS cc_start: 0.9099 (mmtm) cc_final: 0.8811 (mmpt) REVERT: F 18 ASP cc_start: 0.7288 (p0) cc_final: 0.6903 (p0) REVERT: F 26 ARG cc_start: 0.7590 (mtt180) cc_final: 0.6882 (ttm110) REVERT: F 30 GLN cc_start: 0.7502 (tm-30) cc_final: 0.7215 (tm-30) REVERT: F 38 ARG cc_start: 0.8315 (tpt90) cc_final: 0.7813 (tpt90) REVERT: F 59 ARG cc_start: 0.7584 (mmt-90) cc_final: 0.7136 (mmm-85) REVERT: F 63 ARG cc_start: 0.7604 (mmt180) cc_final: 0.7145 (mpt180) REVERT: G 20 GLU cc_start: 0.8293 (mp0) cc_final: 0.7839 (mt-10) REVERT: G 26 ARG cc_start: 0.6012 (mtt90) cc_final: 0.5729 (mtt90) REVERT: G 38 ARG cc_start: 0.8198 (tpt90) cc_final: 0.7656 (tpt90) REVERT: G 93 LYS cc_start: 0.8207 (tttt) cc_final: 0.7914 (tttp) REVERT: H 18 ASP cc_start: 0.7960 (p0) cc_final: 0.7445 (p0) REVERT: H 24 ASP cc_start: 0.7046 (t0) cc_final: 0.6819 (t0) REVERT: H 25 MET cc_start: 0.8087 (tmm) cc_final: 0.7323 (tmm) REVERT: H 95 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8097 (mp10) REVERT: I 79 LYS cc_start: 0.8256 (mmtt) cc_final: 0.7819 (mmmt) REVERT: I 84 LYS cc_start: 0.8198 (tptp) cc_final: 0.7952 (tptp) REVERT: I 93 LYS cc_start: 0.7580 (tttt) cc_final: 0.6777 (mmtm) REVERT: J 20 GLU cc_start: 0.8163 (mp0) cc_final: 0.7845 (mp0) REVERT: J 38 ARG cc_start: 0.8189 (tpt90) cc_final: 0.7570 (tpt90) REVERT: J 72 LYS cc_start: 0.8505 (tttt) cc_final: 0.8140 (ttmm) REVERT: J 78 GLU cc_start: 0.7925 (mt-10) cc_final: 0.7414 (tm-30) REVERT: J 93 LYS cc_start: 0.7825 (tttt) cc_final: 0.6779 (mtmm) REVERT: K 59 ARG cc_start: 0.7517 (mmt-90) cc_final: 0.7080 (mmt90) REVERT: K 72 LYS cc_start: 0.8525 (tttt) cc_final: 0.7751 (mtmm) REVERT: K 78 GLU cc_start: 0.7630 (tp30) cc_final: 0.6628 (tm-30) REVERT: K 93 LYS cc_start: 0.7627 (tttt) cc_final: 0.7302 (mtpt) REVERT: K 95 GLN cc_start: 0.8193 (mm-40) cc_final: 0.7307 (tp40) REVERT: K 100 GLU cc_start: 0.7396 (mm-30) cc_final: 0.7032 (mm-30) REVERT: L 18 ASP cc_start: 0.7248 (p0) cc_final: 0.6636 (p0) REVERT: L 20 GLU cc_start: 0.7734 (mp0) cc_final: 0.7523 (mp0) REVERT: L 93 LYS cc_start: 0.7986 (tttt) cc_final: 0.6955 (mmtm) REVERT: L 95 GLN cc_start: 0.8636 (mm-40) cc_final: 0.8283 (mm-40) REVERT: M 18 ASP cc_start: 0.7427 (p0) cc_final: 0.6788 (p0) REVERT: M 25 MET cc_start: 0.6810 (ttt) cc_final: 0.6045 (mtp) REVERT: M 72 LYS cc_start: 0.8424 (mppt) cc_final: 0.8220 (mmtp) REVERT: M 93 LYS cc_start: 0.7767 (tttt) cc_final: 0.6767 (mmtm) REVERT: M 95 GLN cc_start: 0.8584 (mm-40) cc_final: 0.8230 (mm-40) REVERT: N 59 ARG cc_start: 0.7591 (mmt-90) cc_final: 0.7071 (mmm-85) REVERT: N 72 LYS cc_start: 0.8665 (tttt) cc_final: 0.7867 (mtmm) REVERT: N 78 GLU cc_start: 0.7726 (tp30) cc_final: 0.7082 (tm-30) REVERT: N 93 LYS cc_start: 0.7813 (tttt) cc_final: 0.7460 (mtpt) REVERT: N 95 GLN cc_start: 0.8375 (mm-40) cc_final: 0.7560 (tp40) REVERT: O 20 GLU cc_start: 0.8312 (mp0) cc_final: 0.7915 (mp0) REVERT: O 38 ARG cc_start: 0.8205 (tpt90) cc_final: 0.7658 (tpt90) REVERT: O 72 LYS cc_start: 0.8353 (tttt) cc_final: 0.7506 (mptt) REVERT: O 78 GLU cc_start: 0.7637 (mt-10) cc_final: 0.7232 (tm-30) REVERT: O 93 LYS cc_start: 0.7522 (tttt) cc_final: 0.6502 (mtmm) REVERT: P 79 LYS cc_start: 0.8514 (mmtt) cc_final: 0.7995 (mmmt) REVERT: P 84 LYS cc_start: 0.8156 (tptp) cc_final: 0.7937 (tptp) REVERT: P 93 LYS cc_start: 0.7853 (tttt) cc_final: 0.7482 (tttp) REVERT: Q 18 ASP cc_start: 0.7875 (p0) cc_final: 0.7541 (p0) REVERT: Q 25 MET cc_start: 0.7986 (tmm) cc_final: 0.7268 (tmm) REVERT: Q 72 LYS cc_start: 0.8749 (tttt) cc_final: 0.8548 (tmtt) REVERT: Q 95 GLN cc_start: 0.8166 (mm110) cc_final: 0.7926 (mm110) REVERT: R 38 ARG cc_start: 0.8093 (tpt90) cc_final: 0.7513 (tpt90) REVERT: R 93 LYS cc_start: 0.8333 (tttt) cc_final: 0.8014 (tttp) REVERT: S 26 ARG cc_start: 0.7373 (mtt180) cc_final: 0.6820 (ttm110) REVERT: S 38 ARG cc_start: 0.8368 (tpt90) cc_final: 0.7917 (tpt90) REVERT: S 59 ARG cc_start: 0.7649 (mmt-90) cc_final: 0.7232 (mmm-85) REVERT: S 63 ARG cc_start: 0.7688 (mmt180) cc_final: 0.7392 (mpt180) REVERT: S 93 LYS cc_start: 0.8153 (tttt) cc_final: 0.7675 (tptp) REVERT: S 95 GLN cc_start: 0.8634 (mm-40) cc_final: 0.8204 (mm110) REVERT: T 25 MET cc_start: 0.7723 (ttm) cc_final: 0.6550 (tmm) REVERT: T 72 LYS cc_start: 0.8691 (tmtt) cc_final: 0.7983 (tptp) REVERT: T 79 LYS cc_start: 0.9143 (mmtm) cc_final: 0.8823 (mmpt) REVERT: T 84 LYS cc_start: 0.8415 (mmpt) cc_final: 0.8070 (tptp) REVERT: U 18 ASP cc_start: 0.7272 (p0) cc_final: 0.6645 (p0) REVERT: U 25 MET cc_start: 0.6772 (ttm) cc_final: 0.6497 (tmm) REVERT: U 78 GLU cc_start: 0.8261 (tt0) cc_final: 0.7941 (tm-30) REVERT: U 93 LYS cc_start: 0.8376 (tttt) cc_final: 0.7915 (mptt) REVERT: V 20 GLU cc_start: 0.7917 (mp0) cc_final: 0.7671 (mp0) REVERT: V 24 ASP cc_start: 0.7660 (m-30) cc_final: 0.6863 (t0) REVERT: V 38 ARG cc_start: 0.6935 (mtm110) cc_final: 0.6356 (ttp80) outliers start: 1 outliers final: 0 residues processed: 335 average time/residue: 0.5108 time to fit residues: 220.6966 Evaluate side-chains 266 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 266 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 197 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 103 optimal weight: 1.9990 chunk 22 optimal weight: 8.9990 chunk 95 optimal weight: 0.6980 chunk 134 optimal weight: 1.9990 chunk 200 optimal weight: 10.0000 chunk 212 optimal weight: 4.9990 chunk 104 optimal weight: 3.9990 chunk 190 optimal weight: 5.9990 chunk 57 optimal weight: 1.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.5250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 16478 Z= 0.239 Angle : 0.670 6.572 22198 Z= 0.339 Chirality : 0.051 0.153 2684 Planarity : 0.004 0.037 2904 Dihedral : 5.720 26.549 2376 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.44 % Favored : 92.56 % Rotamer: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % 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: -5.28 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.43 (0.14), residues: 1232 loop : -3.38 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 68 PHE 0.011 0.001 PHE N 105 TYR 0.010 0.001 TYR O 14 ARG 0.007 0.001 ARG H 54 *********************** 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 336 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 336 time to evaluate : 1.839 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 25 MET cc_start: 0.1019 (ttt) cc_final: 0.0522 (mtp) REVERT: A 72 LYS cc_start: 0.8021 (tmtt) cc_final: 0.7612 (tptp) REVERT: A 91 GLN cc_start: 0.6993 (mp10) cc_final: 0.5862 (tm-30) REVERT: B 61 GLU cc_start: 0.5445 (mp0) cc_final: 0.4516 (tm-30) REVERT: B 72 LYS cc_start: 0.8267 (tmtt) cc_final: 0.7866 (tmtt) REVERT: B 91 GLN cc_start: 0.7234 (mp10) cc_final: 0.6060 (tm-30) REVERT: C 24 ASP cc_start: 0.7300 (m-30) cc_final: 0.6607 (t0) REVERT: C 38 ARG cc_start: 0.6526 (ttp80) cc_final: 0.6226 (ttp80) REVERT: C 58 GLU cc_start: 0.4475 (pm20) cc_final: 0.4027 (pm20) REVERT: C 78 GLU cc_start: 0.4727 (pt0) cc_final: 0.4168 (mm-30) REVERT: D 24 ASP cc_start: 0.6969 (t0) cc_final: 0.6680 (t0) REVERT: D 59 ARG cc_start: 0.7474 (mmp80) cc_final: 0.7126 (mmp80) REVERT: D 78 GLU cc_start: 0.8151 (tt0) cc_final: 0.7930 (tm-30) REVERT: D 93 LYS cc_start: 0.8284 (tttt) cc_final: 0.7848 (tptp) REVERT: D 100 GLU cc_start: 0.8440 (mp0) cc_final: 0.8142 (mp0) REVERT: E 25 MET cc_start: 0.7377 (ttm) cc_final: 0.6546 (tmm) REVERT: E 55 VAL cc_start: 0.9066 (t) cc_final: 0.8829 (p) REVERT: E 72 LYS cc_start: 0.8841 (tttt) cc_final: 0.8376 (tptp) REVERT: E 79 LYS cc_start: 0.9071 (mmtm) cc_final: 0.8791 (mmpt) REVERT: F 26 ARG cc_start: 0.7727 (mtt180) cc_final: 0.6852 (ttm110) REVERT: F 30 GLN cc_start: 0.7444 (tm-30) cc_final: 0.7230 (tm-30) REVERT: F 38 ARG cc_start: 0.8177 (tpt90) cc_final: 0.7607 (tpt90) REVERT: F 63 ARG cc_start: 0.7589 (mmt180) cc_final: 0.7007 (mpt180) REVERT: G 20 GLU cc_start: 0.8326 (mp0) cc_final: 0.8058 (mt-10) REVERT: G 38 ARG cc_start: 0.8053 (tpt90) cc_final: 0.7384 (tpt90) REVERT: G 93 LYS cc_start: 0.8472 (tttt) cc_final: 0.8115 (tttp) REVERT: H 18 ASP cc_start: 0.7893 (p0) cc_final: 0.7403 (p0) REVERT: H 24 ASP cc_start: 0.7016 (t0) cc_final: 0.6788 (t0) REVERT: H 95 GLN cc_start: 0.8404 (mm-40) cc_final: 0.8186 (mp10) REVERT: I 25 MET cc_start: 0.6703 (ttm) cc_final: 0.5728 (tmm) REVERT: I 79 LYS cc_start: 0.8274 (mmtt) cc_final: 0.7807 (mmmt) REVERT: I 93 LYS cc_start: 0.7614 (tttt) cc_final: 0.6915 (mmtm) REVERT: I 95 GLN cc_start: 0.8703 (mm110) cc_final: 0.8230 (mm110) REVERT: J 38 ARG cc_start: 0.7995 (tpt90) cc_final: 0.7608 (tpt90) REVERT: J 59 ARG cc_start: 0.7558 (mmm-85) cc_final: 0.7055 (ptm160) REVERT: J 72 LYS cc_start: 0.8365 (tttt) cc_final: 0.8044 (ttmm) REVERT: J 93 LYS cc_start: 0.7682 (tttt) cc_final: 0.6923 (mtpp) REVERT: K 20 GLU cc_start: 0.7891 (mp0) cc_final: 0.7635 (mp0) REVERT: K 24 ASP cc_start: 0.8006 (t0) cc_final: 0.7689 (m-30) REVERT: K 36 LEU cc_start: 0.7126 (tt) cc_final: 0.6388 (mp) REVERT: K 59 ARG cc_start: 0.7439 (mmt-90) cc_final: 0.6935 (mmm-85) REVERT: K 72 LYS cc_start: 0.8306 (tttt) cc_final: 0.7626 (mtmm) REVERT: K 74 GLU cc_start: 0.6697 (mt-10) cc_final: 0.6339 (mp0) REVERT: K 93 LYS cc_start: 0.7492 (tttt) cc_final: 0.7274 (mtpt) REVERT: K 95 GLN cc_start: 0.8041 (mm-40) cc_final: 0.7060 (tp40) REVERT: L 18 ASP cc_start: 0.7174 (p0) cc_final: 0.6500 (p0) REVERT: L 20 GLU cc_start: 0.7338 (mp0) cc_final: 0.6728 (mp0) REVERT: L 72 LYS cc_start: 0.8356 (mppt) cc_final: 0.8020 (mmtp) REVERT: L 100 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7675 (mm-30) REVERT: M 18 ASP cc_start: 0.7432 (p0) cc_final: 0.6982 (p0) REVERT: M 20 GLU cc_start: 0.7869 (mp0) cc_final: 0.7572 (mp0) REVERT: M 25 MET cc_start: 0.6677 (ttt) cc_final: 0.6000 (mtp) REVERT: M 38 ARG cc_start: 0.7997 (tpt90) cc_final: 0.7458 (tpt90) REVERT: M 72 LYS cc_start: 0.8095 (mppt) cc_final: 0.7655 (mmtp) REVERT: N 59 ARG cc_start: 0.7480 (mmt-90) cc_final: 0.7102 (mmm-85) REVERT: N 72 LYS cc_start: 0.8484 (tttt) cc_final: 0.7827 (mtmm) REVERT: N 93 LYS cc_start: 0.7936 (tttt) cc_final: 0.7664 (mtpt) REVERT: N 95 GLN cc_start: 0.8269 (mm-40) cc_final: 0.7231 (tp40) REVERT: O 25 MET cc_start: 0.7089 (ttt) cc_final: 0.6588 (ttt) REVERT: O 38 ARG cc_start: 0.7945 (tpt90) cc_final: 0.7520 (tpt90) REVERT: O 72 LYS cc_start: 0.8214 (tttt) cc_final: 0.7522 (mptt) REVERT: O 93 LYS cc_start: 0.7457 (tttt) cc_final: 0.6758 (mtpp) REVERT: P 25 MET cc_start: 0.7081 (ttm) cc_final: 0.6040 (tmm) REVERT: P 79 LYS cc_start: 0.8411 (mmtt) cc_final: 0.7870 (mmmt) REVERT: P 93 LYS cc_start: 0.7747 (tttt) cc_final: 0.6995 (mmtm) REVERT: Q 18 ASP cc_start: 0.7791 (p0) cc_final: 0.7487 (p0) REVERT: Q 95 GLN cc_start: 0.8163 (mm110) cc_final: 0.7897 (mp10) REVERT: Q 100 GLU cc_start: 0.7611 (mm-30) cc_final: 0.7199 (mm-30) REVERT: R 38 ARG cc_start: 0.7867 (tpt90) cc_final: 0.7443 (tpt90) REVERT: R 93 LYS cc_start: 0.8508 (tttt) cc_final: 0.8179 (tttp) REVERT: S 32 ARG cc_start: 0.7561 (tpt-90) cc_final: 0.7259 (tpt-90) REVERT: S 38 ARG cc_start: 0.8337 (tpt90) cc_final: 0.7768 (tpt90) REVERT: S 59 ARG cc_start: 0.7683 (mmt-90) cc_final: 0.7286 (mmm-85) REVERT: S 63 ARG cc_start: 0.7719 (mmt180) cc_final: 0.7416 (mpt180) REVERT: S 72 LYS cc_start: 0.8455 (tptt) cc_final: 0.7812 (tppt) REVERT: S 93 LYS cc_start: 0.8039 (tttt) cc_final: 0.7568 (tptp) REVERT: S 95 GLN cc_start: 0.8671 (mm-40) cc_final: 0.8397 (mm110) REVERT: S 108 GLN cc_start: 0.7415 (mt0) cc_final: 0.6958 (mp10) REVERT: T 25 MET cc_start: 0.7731 (ttm) cc_final: 0.6775 (tmm) REVERT: T 72 LYS cc_start: 0.8677 (tmtt) cc_final: 0.7990 (tptp) REVERT: T 79 LYS cc_start: 0.9097 (mmtm) cc_final: 0.8760 (mmpt) REVERT: T 93 LYS cc_start: 0.7743 (mmtt) cc_final: 0.7532 (mmtt) REVERT: U 18 ASP cc_start: 0.7252 (p0) cc_final: 0.6719 (p0) REVERT: U 78 GLU cc_start: 0.8194 (tt0) cc_final: 0.7905 (tm-30) REVERT: U 93 LYS cc_start: 0.8204 (tttt) cc_final: 0.7735 (tptp) REVERT: V 24 ASP cc_start: 0.7607 (m-30) cc_final: 0.6779 (t0) REVERT: V 32 ARG cc_start: 0.7089 (tmt-80) cc_final: 0.6733 (tmt-80) REVERT: V 38 ARG cc_start: 0.6885 (mtm110) cc_final: 0.6198 (ttp80) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.4782 time to fit residues: 204.9773 Evaluate side-chains 269 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 177 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 3 optimal weight: 6.9990 chunk 158 optimal weight: 9.9990 chunk 87 optimal weight: 6.9990 chunk 181 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 0 optimal weight: 30.0000 chunk 108 optimal weight: 7.9990 chunk 190 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.5914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 16478 Z= 0.437 Angle : 0.795 8.288 22198 Z= 0.419 Chirality : 0.053 0.160 2684 Planarity : 0.005 0.047 2904 Dihedral : 6.697 23.993 2376 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.54 % Favored : 82.46 % Rotamer: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % 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: -3.72 (0.13), residues: 1232 loop : -3.42 (0.17), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS O 68 PHE 0.018 0.002 PHE H 105 TYR 0.019 0.002 TYR O 14 ARG 0.006 0.001 ARG K 26 *********************** 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 316 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 316 time to evaluate : 1.707 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: 0.8093 (tmtt) cc_final: 0.7685 (tmtt) REVERT: B 72 LYS cc_start: 0.8184 (tmtt) cc_final: 0.7733 (tmtt) REVERT: C 24 ASP cc_start: 0.7220 (m-30) cc_final: 0.6567 (t0) REVERT: C 38 ARG cc_start: 0.6346 (ttp80) cc_final: 0.6095 (ttp80) REVERT: C 78 GLU cc_start: 0.4749 (pt0) cc_final: 0.4117 (mm-30) REVERT: D 24 ASP cc_start: 0.7105 (t0) cc_final: 0.6822 (t0) REVERT: D 32 ARG cc_start: 0.7821 (tmt170) cc_final: 0.7304 (ttt90) REVERT: D 78 GLU cc_start: 0.8133 (tt0) cc_final: 0.7753 (tm-30) REVERT: D 93 LYS cc_start: 0.8512 (tttt) cc_final: 0.8052 (tptp) REVERT: D 100 GLU cc_start: 0.8556 (mp0) cc_final: 0.8277 (mp0) REVERT: E 25 MET cc_start: 0.7756 (ttm) cc_final: 0.6743 (tmm) REVERT: E 72 LYS cc_start: 0.8787 (tttt) cc_final: 0.8229 (tptp) REVERT: E 78 GLU cc_start: 0.8521 (tp30) cc_final: 0.7497 (tp30) REVERT: E 79 LYS cc_start: 0.9122 (mmtm) cc_final: 0.8655 (mmpt) REVERT: E 93 LYS cc_start: 0.7712 (mmtt) cc_final: 0.7435 (mmtt) REVERT: F 18 ASP cc_start: 0.7776 (p0) cc_final: 0.7417 (p0) REVERT: F 26 ARG cc_start: 0.7665 (mtt180) cc_final: 0.6792 (ttm110) REVERT: F 38 ARG cc_start: 0.8240 (tpt90) cc_final: 0.7743 (tpt90) REVERT: F 59 ARG cc_start: 0.7890 (mpt180) cc_final: 0.7509 (mmm-85) REVERT: G 20 GLU cc_start: 0.8321 (mp0) cc_final: 0.8062 (mt-10) REVERT: G 26 ARG cc_start: 0.6072 (mtt90) cc_final: 0.5854 (mtt90) REVERT: G 38 ARG cc_start: 0.8295 (tpt90) cc_final: 0.7678 (tpt90) REVERT: G 93 LYS cc_start: 0.8291 (tttt) cc_final: 0.7939 (tttp) REVERT: H 18 ASP cc_start: 0.8179 (p0) cc_final: 0.7487 (p0) REVERT: H 24 ASP cc_start: 0.7259 (t0) cc_final: 0.6973 (t0) REVERT: H 95 GLN cc_start: 0.8490 (mm-40) cc_final: 0.8122 (mp10) REVERT: I 25 MET cc_start: 0.7065 (ttm) cc_final: 0.5978 (tmm) REVERT: I 61 GLU cc_start: 0.7083 (mp0) cc_final: 0.6870 (mp0) REVERT: I 79 LYS cc_start: 0.8514 (mmtt) cc_final: 0.8016 (mmmt) REVERT: I 93 LYS cc_start: 0.7486 (tttt) cc_final: 0.6794 (mmtm) REVERT: I 95 GLN cc_start: 0.8774 (mm110) cc_final: 0.8306 (mm110) REVERT: I 109 SER cc_start: 0.8830 (t) cc_final: 0.8369 (t) REVERT: J 25 MET cc_start: 0.7647 (ttm) cc_final: 0.6958 (tmm) REVERT: J 38 ARG cc_start: 0.8148 (tpt90) cc_final: 0.7636 (tpt90) REVERT: J 44 GLU cc_start: 0.5779 (tm-30) cc_final: 0.5542 (tm-30) REVERT: J 63 ARG cc_start: 0.7193 (mmt-90) cc_final: 0.6866 (mpt180) REVERT: J 72 LYS cc_start: 0.8459 (tttt) cc_final: 0.8050 (ttmm) REVERT: J 93 LYS cc_start: 0.7727 (tttt) cc_final: 0.6698 (mtmm) REVERT: K 20 GLU cc_start: 0.8145 (mp0) cc_final: 0.7736 (mp0) REVERT: K 59 ARG cc_start: 0.7393 (mmt-90) cc_final: 0.6861 (mmt180) REVERT: K 72 LYS cc_start: 0.8481 (tttt) cc_final: 0.7877 (tmtt) REVERT: K 78 GLU cc_start: 0.7564 (tp30) cc_final: 0.6732 (tm-30) REVERT: K 93 LYS cc_start: 0.7625 (tttt) cc_final: 0.7363 (mtpt) REVERT: K 95 GLN cc_start: 0.7945 (mm-40) cc_final: 0.7378 (tp-100) REVERT: L 18 ASP cc_start: 0.7213 (p0) cc_final: 0.6552 (p0) REVERT: L 20 GLU cc_start: 0.7828 (mp0) cc_final: 0.7591 (mp0) REVERT: L 79 LYS cc_start: 0.8094 (mppt) cc_final: 0.7737 (mmtm) REVERT: L 93 LYS cc_start: 0.7957 (tttt) cc_final: 0.7573 (tttp) REVERT: M 18 ASP cc_start: 0.7236 (p0) cc_final: 0.6668 (p0) REVERT: M 20 GLU cc_start: 0.8074 (mp0) cc_final: 0.7813 (mp0) REVERT: M 25 MET cc_start: 0.6869 (ttt) cc_final: 0.6141 (mtp) REVERT: M 38 ARG cc_start: 0.8174 (tpt90) cc_final: 0.7607 (tpt90) REVERT: M 79 LYS cc_start: 0.7881 (mppt) cc_final: 0.7492 (mmtm) REVERT: M 93 LYS cc_start: 0.7690 (tttt) cc_final: 0.6707 (mmtm) REVERT: N 59 ARG cc_start: 0.7662 (mmt-90) cc_final: 0.7084 (mmm-85) REVERT: N 72 LYS cc_start: 0.8670 (tttt) cc_final: 0.8111 (tmtt) REVERT: N 78 GLU cc_start: 0.7691 (tp30) cc_final: 0.6856 (tm-30) REVERT: N 93 LYS cc_start: 0.7891 (tttt) cc_final: 0.7576 (mtpt) REVERT: N 95 GLN cc_start: 0.8229 (mm-40) cc_final: 0.7623 (tp-100) REVERT: O 38 ARG cc_start: 0.8172 (tpt90) cc_final: 0.7740 (tpt90) REVERT: O 59 ARG cc_start: 0.7378 (mmm-85) cc_final: 0.6958 (ptm160) REVERT: O 63 ARG cc_start: 0.7042 (mmt-90) cc_final: 0.6708 (mpt180) REVERT: O 72 LYS cc_start: 0.8252 (tttt) cc_final: 0.7858 (ttmm) REVERT: O 93 LYS cc_start: 0.7456 (tttt) cc_final: 0.6498 (mtmm) REVERT: P 25 MET cc_start: 0.7234 (ttm) cc_final: 0.6135 (tmm) REVERT: P 79 LYS cc_start: 0.8556 (mmtt) cc_final: 0.7996 (mmmt) REVERT: P 93 LYS cc_start: 0.7669 (tttt) cc_final: 0.7448 (tttp) REVERT: P 95 GLN cc_start: 0.8756 (mm110) cc_final: 0.8348 (mm110) REVERT: Q 18 ASP cc_start: 0.8017 (p0) cc_final: 0.7578 (p0) REVERT: Q 95 GLN cc_start: 0.8234 (mm110) cc_final: 0.7973 (mm110) REVERT: Q 100 GLU cc_start: 0.7781 (mm-30) cc_final: 0.7382 (mm-30) REVERT: R 38 ARG cc_start: 0.8118 (tpt90) cc_final: 0.7641 (tpt90) REVERT: R 93 LYS cc_start: 0.8260 (tttt) cc_final: 0.7929 (tttp) REVERT: S 26 ARG cc_start: 0.7346 (mtt180) cc_final: 0.6843 (ttm110) REVERT: S 38 ARG cc_start: 0.8326 (tpt90) cc_final: 0.7793 (tpt90) REVERT: S 59 ARG cc_start: 0.7576 (mmt-90) cc_final: 0.7260 (mmm-85) REVERT: S 66 LEU cc_start: 0.8395 (mm) cc_final: 0.8179 (mm) REVERT: S 72 LYS cc_start: 0.8492 (tptt) cc_final: 0.7857 (tppt) REVERT: S 93 LYS cc_start: 0.8104 (tttt) cc_final: 0.7617 (tptp) REVERT: T 25 MET cc_start: 0.7867 (ttm) cc_final: 0.6887 (tmm) REVERT: T 59 ARG cc_start: 0.8435 (tpp-160) cc_final: 0.7629 (tpp80) REVERT: T 72 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8001 (tptp) REVERT: T 78 GLU cc_start: 0.8317 (tp30) cc_final: 0.7298 (tp30) REVERT: T 79 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8605 (mmpt) REVERT: T 93 LYS cc_start: 0.7792 (mmtt) cc_final: 0.7481 (mmtt) REVERT: U 18 ASP cc_start: 0.7391 (p0) cc_final: 0.6854 (p0) REVERT: U 59 ARG cc_start: 0.7888 (mpt180) cc_final: 0.7660 (mmt-90) REVERT: U 78 GLU cc_start: 0.8242 (tt0) cc_final: 0.7914 (tm-30) REVERT: U 93 LYS cc_start: 0.8428 (tttt) cc_final: 0.7953 (tptp) REVERT: V 24 ASP cc_start: 0.7731 (m-30) cc_final: 0.6805 (t0) REVERT: V 38 ARG cc_start: 0.6746 (mtm110) cc_final: 0.6255 (ttp80) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.4755 time to fit residues: 192.2625 Evaluate side-chains 268 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 268 time to evaluate : 1.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 71 optimal weight: 9.9990 chunk 191 optimal weight: 9.9990 chunk 42 optimal weight: 10.0000 chunk 124 optimal weight: 0.0980 chunk 52 optimal weight: 10.0000 chunk 212 optimal weight: 0.7980 chunk 176 optimal weight: 8.9990 chunk 98 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 70 optimal weight: 5.9990 chunk 111 optimal weight: 8.9990 overall best weight: 3.3786 ------------------------------------------------------------------------------- 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** E 68 HIS ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6608 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 : 0.005 0.040 16478 Z= 0.342 Angle : 0.755 7.576 22198 Z= 0.390 Chirality : 0.052 0.175 2684 Planarity : 0.004 0.061 2904 Dihedral : 6.385 23.944 2376 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 19.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.65 % Favored : 89.35 % Rotamer: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.60 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.77 (0.12), residues: 1342 loop : -3.17 (0.18), residues: 836 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS J 68 PHE 0.012 0.002 PHE Q 105 TYR 0.014 0.002 TYR J 14 ARG 0.006 0.001 ARG C 32 *********************** 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 329 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 1.690 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: A 72 LYS cc_start: 0.8109 (tmtt) cc_final: 0.7719 (tmtt) REVERT: B 72 LYS cc_start: 0.8156 (tmtt) cc_final: 0.7715 (tmtt) REVERT: C 24 ASP cc_start: 0.7332 (m-30) cc_final: 0.6571 (t0) REVERT: C 38 ARG cc_start: 0.6395 (tmm160) cc_final: 0.5914 (ttp80) REVERT: C 78 GLU cc_start: 0.5214 (pt0) cc_final: 0.4679 (mm-30) REVERT: D 18 ASP cc_start: 0.7753 (p0) cc_final: 0.7298 (p0) REVERT: D 24 ASP cc_start: 0.7072 (t0) cc_final: 0.6779 (t0) REVERT: D 25 MET cc_start: 0.8108 (tmm) cc_final: 0.7436 (tmm) REVERT: D 78 GLU cc_start: 0.8047 (tt0) cc_final: 0.7776 (tm-30) REVERT: D 93 LYS cc_start: 0.8493 (tttt) cc_final: 0.8023 (tptp) REVERT: D 100 GLU cc_start: 0.8494 (mp0) cc_final: 0.8131 (mp0) REVERT: E 25 MET cc_start: 0.7494 (ttm) cc_final: 0.6717 (tmm) REVERT: E 72 LYS cc_start: 0.8739 (tttt) cc_final: 0.8146 (tptp) REVERT: E 78 GLU cc_start: 0.8456 (tp30) cc_final: 0.7456 (tp30) REVERT: E 79 LYS cc_start: 0.9115 (mmtm) cc_final: 0.8635 (mmpt) REVERT: E 93 LYS cc_start: 0.7547 (mmtt) cc_final: 0.7214 (mmtt) REVERT: F 20 GLU cc_start: 0.8113 (mp0) cc_final: 0.7886 (mp0) REVERT: F 26 ARG cc_start: 0.7400 (mtt180) cc_final: 0.6835 (ttm110) REVERT: F 38 ARG cc_start: 0.8220 (tpt90) cc_final: 0.7700 (tpt90) REVERT: F 59 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7450 (mmm-85) REVERT: F 70 GLU cc_start: 0.7942 (mt-10) cc_final: 0.7377 (mp0) REVERT: G 20 GLU cc_start: 0.8133 (mp0) cc_final: 0.7911 (mt-10) REVERT: G 38 ARG cc_start: 0.8201 (tpt90) cc_final: 0.7603 (tpt90) REVERT: G 93 LYS cc_start: 0.8325 (tttt) cc_final: 0.7935 (tttp) REVERT: H 18 ASP cc_start: 0.8274 (p0) cc_final: 0.7732 (p0) REVERT: H 24 ASP cc_start: 0.7144 (t0) cc_final: 0.6883 (t0) REVERT: H 95 GLN cc_start: 0.8451 (mm-40) cc_final: 0.8124 (mp10) REVERT: I 25 MET cc_start: 0.7089 (ttm) cc_final: 0.6026 (tmm) REVERT: I 79 LYS cc_start: 0.8519 (mmtt) cc_final: 0.8180 (mmmt) REVERT: I 93 LYS cc_start: 0.7742 (tttt) cc_final: 0.6959 (mmtm) REVERT: I 95 GLN cc_start: 0.8716 (mm110) cc_final: 0.8249 (mm110) REVERT: J 25 MET cc_start: 0.7637 (ttm) cc_final: 0.6930 (tmm) REVERT: J 38 ARG cc_start: 0.8075 (tpt90) cc_final: 0.7675 (tpt90) REVERT: J 63 ARG cc_start: 0.7217 (mmt-90) cc_final: 0.6866 (mpt180) REVERT: J 72 LYS cc_start: 0.8523 (tttt) cc_final: 0.8095 (ttmm) REVERT: J 93 LYS cc_start: 0.7678 (tttt) cc_final: 0.6881 (mtpp) REVERT: K 59 ARG cc_start: 0.7475 (mmt-90) cc_final: 0.7010 (mmt180) REVERT: K 72 LYS cc_start: 0.8486 (tttt) cc_final: 0.7771 (mtmm) REVERT: K 74 GLU cc_start: 0.6922 (mt-10) cc_final: 0.6471 (mp0) REVERT: K 93 LYS cc_start: 0.7475 (tttt) cc_final: 0.7213 (mtpt) REVERT: K 95 GLN cc_start: 0.8003 (mm-40) cc_final: 0.7152 (tp40) REVERT: L 18 ASP cc_start: 0.7149 (p0) cc_final: 0.6483 (p0) REVERT: L 20 GLU cc_start: 0.7756 (mp0) cc_final: 0.7531 (mp0) REVERT: L 79 LYS cc_start: 0.8070 (mppt) cc_final: 0.7647 (mmtt) REVERT: L 93 LYS cc_start: 0.7988 (tttt) cc_final: 0.7348 (mtpp) REVERT: M 18 ASP cc_start: 0.7377 (p0) cc_final: 0.6936 (p0) REVERT: M 20 GLU cc_start: 0.8066 (mp0) cc_final: 0.7820 (mp0) REVERT: M 25 MET cc_start: 0.6776 (ttt) cc_final: 0.6087 (mtp) REVERT: M 93 LYS cc_start: 0.7784 (tttt) cc_final: 0.7220 (mtpp) REVERT: N 59 ARG cc_start: 0.7608 (mmt-90) cc_final: 0.7034 (mmm-85) REVERT: N 72 LYS cc_start: 0.8650 (tttt) cc_final: 0.7998 (mtmm) REVERT: N 74 GLU cc_start: 0.7001 (mt-10) cc_final: 0.6676 (mp0) REVERT: N 93 LYS cc_start: 0.7839 (tttt) cc_final: 0.7530 (mtpt) REVERT: N 95 GLN cc_start: 0.8181 (mm-40) cc_final: 0.7292 (tp40) REVERT: O 38 ARG cc_start: 0.8092 (tpt90) cc_final: 0.7652 (tpt90) REVERT: O 59 ARG cc_start: 0.7403 (mmm-85) cc_final: 0.6969 (ptm160) REVERT: O 63 ARG cc_start: 0.7203 (mmt-90) cc_final: 0.6995 (mpt180) REVERT: O 66 LEU cc_start: 0.7815 (mm) cc_final: 0.7609 (mm) REVERT: O 72 LYS cc_start: 0.8307 (tttt) cc_final: 0.7906 (ttmm) REVERT: O 78 GLU cc_start: 0.7846 (mt-10) cc_final: 0.7098 (tm-30) REVERT: O 93 LYS cc_start: 0.7505 (tttt) cc_final: 0.6767 (mtpp) REVERT: P 25 MET cc_start: 0.7265 (ttm) cc_final: 0.6154 (tmm) REVERT: P 79 LYS cc_start: 0.8629 (mmtt) cc_final: 0.8321 (mmmt) REVERT: P 93 LYS cc_start: 0.7807 (tttt) cc_final: 0.7514 (tttp) REVERT: P 95 GLN cc_start: 0.8771 (mm110) cc_final: 0.8364 (mm110) REVERT: Q 18 ASP cc_start: 0.8188 (p0) cc_final: 0.7767 (p0) REVERT: Q 95 GLN cc_start: 0.8214 (mm110) cc_final: 0.7899 (mp10) REVERT: R 38 ARG cc_start: 0.8069 (tpt90) cc_final: 0.7633 (tpt90) REVERT: R 66 LEU cc_start: 0.8452 (mm) cc_final: 0.8237 (mm) REVERT: R 79 LYS cc_start: 0.8797 (pptt) cc_final: 0.8587 (ptmm) REVERT: R 84 LYS cc_start: 0.8130 (tptp) cc_final: 0.7519 (pptt) REVERT: R 93 LYS cc_start: 0.8446 (tttt) cc_final: 0.8029 (tttp) REVERT: S 18 ASP cc_start: 0.7430 (p0) cc_final: 0.6940 (p0) REVERT: S 21 VAL cc_start: 0.8928 (m) cc_final: 0.8706 (p) REVERT: S 26 ARG cc_start: 0.7524 (mtt180) cc_final: 0.7001 (ttm110) REVERT: S 38 ARG cc_start: 0.8324 (tpt90) cc_final: 0.7792 (tpt90) REVERT: S 59 ARG cc_start: 0.7593 (mmt-90) cc_final: 0.7343 (mmm-85) REVERT: S 72 LYS cc_start: 0.8505 (tptt) cc_final: 0.7898 (tppt) REVERT: S 93 LYS cc_start: 0.8054 (tttt) cc_final: 0.7550 (tptp) REVERT: T 25 MET cc_start: 0.7553 (ttm) cc_final: 0.6693 (tmm) REVERT: T 28 LYS cc_start: 0.7942 (tptp) cc_final: 0.7562 (ttpt) REVERT: T 56 GLU cc_start: 0.7863 (mm-30) cc_final: 0.7534 (mm-30) REVERT: T 59 ARG cc_start: 0.8126 (tpp-160) cc_final: 0.7405 (tpp80) REVERT: T 72 LYS cc_start: 0.8626 (tmtt) cc_final: 0.7992 (tptp) REVERT: T 78 GLU cc_start: 0.8290 (tp30) cc_final: 0.7938 (tp30) REVERT: T 79 LYS cc_start: 0.9083 (mmtm) cc_final: 0.8716 (mmmt) REVERT: T 93 LYS cc_start: 0.7824 (mmtt) cc_final: 0.7467 (mmtm) REVERT: U 18 ASP cc_start: 0.7241 (p0) cc_final: 0.6661 (p0) REVERT: U 25 MET cc_start: 0.7799 (tmm) cc_final: 0.7049 (tmm) REVERT: U 78 GLU cc_start: 0.8125 (tt0) cc_final: 0.7875 (tm-30) REVERT: U 93 LYS cc_start: 0.8401 (tttt) cc_final: 0.7925 (tptp) REVERT: U 100 GLU cc_start: 0.8049 (mp0) cc_final: 0.7746 (mp0) REVERT: V 24 ASP cc_start: 0.7767 (m-30) cc_final: 0.6792 (t0) REVERT: V 28 LYS cc_start: 0.6441 (mmmm) cc_final: 0.5829 (mmmm) REVERT: V 32 ARG cc_start: 0.7440 (tmt-80) cc_final: 0.6878 (tpt90) REVERT: V 88 PHE cc_start: 0.4500 (t80) cc_final: 0.4225 (t80) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.4709 time to fit residues: 200.2431 Evaluate side-chains 275 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 205 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 121 optimal weight: 4.9990 chunk 155 optimal weight: 0.8980 chunk 120 optimal weight: 7.9990 chunk 179 optimal weight: 0.0980 chunk 118 optimal weight: 8.9990 chunk 212 optimal weight: 9.9990 chunk 132 optimal weight: 5.9990 chunk 129 optimal weight: 4.9990 chunk 97 optimal weight: 0.8980 overall best weight: 2.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.6303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 16478 Z= 0.260 Angle : 0.716 7.616 22198 Z= 0.360 Chirality : 0.051 0.157 2684 Planarity : 0.004 0.040 2904 Dihedral : 5.772 22.119 2376 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.16 % Favored : 88.84 % Rotamer: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.47 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.64 (0.13), residues: 1232 loop : -3.36 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS U 68 PHE 0.009 0.002 PHE H 105 TYR 0.012 0.001 TYR O 14 ARG 0.007 0.001 ARG C 32 *********************** 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 329 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 329 time to evaluate : 2.261 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 61 GLU cc_start: 0.4967 (mp0) cc_final: 0.3810 (tm-30) REVERT: A 72 LYS cc_start: 0.8116 (tmtt) cc_final: 0.7708 (tmtt) REVERT: B 72 LYS cc_start: 0.8139 (tmtt) cc_final: 0.7691 (tmtt) REVERT: B 91 GLN cc_start: 0.7213 (mp10) cc_final: 0.6391 (tm-30) REVERT: C 20 GLU cc_start: 0.7579 (mp0) cc_final: 0.7122 (tm-30) REVERT: C 24 ASP cc_start: 0.7384 (m-30) cc_final: 0.6821 (t0) REVERT: C 32 ARG cc_start: 0.7216 (tpt90) cc_final: 0.6907 (tpt90) REVERT: C 38 ARG cc_start: 0.6427 (tmm160) cc_final: 0.5969 (ttp80) REVERT: C 78 GLU cc_start: 0.5293 (pt0) cc_final: 0.4739 (mm-30) REVERT: D 24 ASP cc_start: 0.7026 (t0) cc_final: 0.6655 (t0) REVERT: D 25 MET cc_start: 0.8084 (tmm) cc_final: 0.7373 (tmm) REVERT: D 78 GLU cc_start: 0.7971 (tt0) cc_final: 0.7663 (tm-30) REVERT: D 93 LYS cc_start: 0.8435 (tttt) cc_final: 0.7939 (tptp) REVERT: D 100 GLU cc_start: 0.8414 (mp0) cc_final: 0.8140 (mp0) REVERT: E 25 MET cc_start: 0.7495 (ttm) cc_final: 0.6466 (tmm) REVERT: E 72 LYS cc_start: 0.8700 (tttt) cc_final: 0.8149 (tptp) REVERT: E 78 GLU cc_start: 0.8366 (tp30) cc_final: 0.7413 (tp30) REVERT: E 79 LYS cc_start: 0.9114 (mmtm) cc_final: 0.8624 (mmpt) REVERT: F 26 ARG cc_start: 0.7605 (mtt180) cc_final: 0.6731 (ttm110) REVERT: F 32 ARG cc_start: 0.7542 (tpt-90) cc_final: 0.7329 (tpt-90) REVERT: F 38 ARG cc_start: 0.8186 (tpt90) cc_final: 0.7667 (tpt90) REVERT: G 38 ARG cc_start: 0.8164 (tpt90) cc_final: 0.7549 (tpt90) REVERT: G 79 LYS cc_start: 0.8602 (tttp) cc_final: 0.8370 (tmmt) REVERT: G 84 LYS cc_start: 0.8111 (tptp) cc_final: 0.7639 (pptt) REVERT: G 93 LYS cc_start: 0.8286 (tttt) cc_final: 0.7897 (tttp) REVERT: H 18 ASP cc_start: 0.8273 (p0) cc_final: 0.7789 (p0) REVERT: H 20 GLU cc_start: 0.8198 (mp0) cc_final: 0.7899 (mp0) REVERT: H 24 ASP cc_start: 0.7160 (t0) cc_final: 0.6895 (t0) REVERT: H 95 GLN cc_start: 0.8460 (mm-40) cc_final: 0.8251 (mm110) REVERT: I 25 MET cc_start: 0.7080 (ttm) cc_final: 0.5997 (tmm) REVERT: I 79 LYS cc_start: 0.8401 (mmtt) cc_final: 0.7892 (mmmt) REVERT: I 93 LYS cc_start: 0.7680 (tttt) cc_final: 0.6978 (mmtm) REVERT: I 95 GLN cc_start: 0.8730 (mm110) cc_final: 0.8357 (mm110) REVERT: J 25 MET cc_start: 0.7568 (ttm) cc_final: 0.6877 (tmm) REVERT: J 38 ARG cc_start: 0.8045 (tpt90) cc_final: 0.7614 (tpt90) REVERT: J 63 ARG cc_start: 0.7240 (mmt-90) cc_final: 0.6865 (mpt180) REVERT: J 72 LYS cc_start: 0.8477 (tttt) cc_final: 0.8043 (ttpp) REVERT: J 93 LYS cc_start: 0.7649 (tttt) cc_final: 0.6807 (mtpp) REVERT: K 59 ARG cc_start: 0.7559 (mmt-90) cc_final: 0.7165 (mmt180) REVERT: K 72 LYS cc_start: 0.8435 (tttt) cc_final: 0.7812 (mptt) REVERT: K 74 GLU cc_start: 0.6881 (mt-10) cc_final: 0.6563 (mp0) REVERT: K 93 LYS cc_start: 0.7540 (tttt) cc_final: 0.7285 (mtpt) REVERT: K 95 GLN cc_start: 0.8077 (mm-40) cc_final: 0.7135 (tp40) REVERT: L 18 ASP cc_start: 0.7141 (p0) cc_final: 0.6505 (p0) REVERT: L 20 GLU cc_start: 0.7577 (mp0) cc_final: 0.7003 (mm-30) REVERT: M 18 ASP cc_start: 0.7462 (p0) cc_final: 0.7223 (p0) REVERT: M 20 GLU cc_start: 0.7916 (mp0) cc_final: 0.7694 (mp0) REVERT: M 93 LYS cc_start: 0.7736 (tttt) cc_final: 0.7152 (mtpp) REVERT: N 59 ARG cc_start: 0.7612 (mmt-90) cc_final: 0.7167 (mmm-85) REVERT: N 72 LYS cc_start: 0.8614 (tttt) cc_final: 0.8027 (mptt) REVERT: N 93 LYS cc_start: 0.7784 (tttt) cc_final: 0.7511 (mtpt) REVERT: N 95 GLN cc_start: 0.8262 (mm-40) cc_final: 0.7274 (tp40) REVERT: O 38 ARG cc_start: 0.8059 (tpt90) cc_final: 0.7596 (tpt90) REVERT: O 44 GLU cc_start: 0.7996 (mt-10) cc_final: 0.7731 (mt-10) REVERT: O 59 ARG cc_start: 0.7346 (mmm-85) cc_final: 0.6934 (ptm160) REVERT: O 63 ARG cc_start: 0.7243 (mmt-90) cc_final: 0.6983 (mpt180) REVERT: O 66 LEU cc_start: 0.7696 (mm) cc_final: 0.7495 (mm) REVERT: O 72 LYS cc_start: 0.8273 (tttt) cc_final: 0.7862 (ttpp) REVERT: O 78 GLU cc_start: 0.7729 (mt-10) cc_final: 0.6999 (tm-30) REVERT: O 93 LYS cc_start: 0.7476 (tttt) cc_final: 0.6766 (mtpp) REVERT: P 25 MET cc_start: 0.7254 (ttm) cc_final: 0.6159 (tmm) REVERT: P 32 ARG cc_start: 0.7710 (ttt90) cc_final: 0.7182 (ttm-80) REVERT: P 79 LYS cc_start: 0.8581 (mmtt) cc_final: 0.8063 (mmmt) REVERT: P 93 LYS cc_start: 0.7865 (tttt) cc_final: 0.7573 (tttp) REVERT: P 95 GLN cc_start: 0.8719 (mm110) cc_final: 0.8380 (mm110) REVERT: Q 18 ASP cc_start: 0.8151 (p0) cc_final: 0.7666 (p0) REVERT: Q 95 GLN cc_start: 0.8183 (mm110) cc_final: 0.7908 (mp10) REVERT: R 26 ARG cc_start: 0.6514 (mtt90) cc_final: 0.6193 (mtt90) REVERT: R 28 LYS cc_start: 0.6060 (mptt) cc_final: 0.5808 (mptt) REVERT: R 38 ARG cc_start: 0.8103 (tpt90) cc_final: 0.7648 (tpt90) REVERT: R 84 LYS cc_start: 0.8196 (tptp) cc_final: 0.7606 (pptt) REVERT: R 93 LYS cc_start: 0.8418 (tttt) cc_final: 0.8013 (tttp) REVERT: S 18 ASP cc_start: 0.7299 (p0) cc_final: 0.6671 (p0) REVERT: S 21 VAL cc_start: 0.8834 (m) cc_final: 0.8590 (p) REVERT: S 26 ARG cc_start: 0.7350 (mtt180) cc_final: 0.6936 (ttm110) REVERT: S 38 ARG cc_start: 0.8279 (tpt90) cc_final: 0.7706 (tpt90) REVERT: S 59 ARG cc_start: 0.7609 (mmt-90) cc_final: 0.7385 (mmm-85) REVERT: S 72 LYS cc_start: 0.8546 (tptt) cc_final: 0.7902 (tppt) REVERT: S 93 LYS cc_start: 0.8052 (tttt) cc_final: 0.7539 (tptp) REVERT: T 25 MET cc_start: 0.7633 (ttm) cc_final: 0.6756 (tmm) REVERT: T 28 LYS cc_start: 0.8055 (tptp) cc_final: 0.7621 (ttpt) REVERT: T 56 GLU cc_start: 0.7861 (mm-30) cc_final: 0.7476 (mm-30) REVERT: T 59 ARG cc_start: 0.8152 (tpp-160) cc_final: 0.7408 (tpp80) REVERT: T 72 LYS cc_start: 0.8576 (tmtt) cc_final: 0.8027 (tptp) REVERT: T 78 GLU cc_start: 0.8230 (tp30) cc_final: 0.7880 (tp30) REVERT: T 79 LYS cc_start: 0.9031 (mmtm) cc_final: 0.8662 (mmmt) REVERT: U 18 ASP cc_start: 0.7264 (p0) cc_final: 0.6759 (p0) REVERT: U 59 ARG cc_start: 0.7782 (mpt180) cc_final: 0.7381 (mmt-90) REVERT: U 78 GLU cc_start: 0.8121 (tt0) cc_final: 0.7775 (tm-30) REVERT: U 93 LYS cc_start: 0.8358 (tttt) cc_final: 0.7860 (tptp) REVERT: U 100 GLU cc_start: 0.7945 (mp0) cc_final: 0.7652 (mp0) REVERT: V 24 ASP cc_start: 0.7749 (m-30) cc_final: 0.6695 (t0) REVERT: V 32 ARG cc_start: 0.7489 (tmt-80) cc_final: 0.6894 (tpt90) REVERT: V 38 ARG cc_start: 0.6411 (tmm160) cc_final: 0.5938 (tmm160) outliers start: 0 outliers final: 0 residues processed: 329 average time/residue: 0.4970 time to fit residues: 211.8719 Evaluate side-chains 282 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 131 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 63 optimal weight: 9.9990 chunk 41 optimal weight: 10.0000 chunk 134 optimal weight: 7.9990 chunk 144 optimal weight: 1.9990 chunk 104 optimal weight: 5.9990 chunk 19 optimal weight: 0.0070 chunk 166 optimal weight: 8.9990 chunk 192 optimal weight: 9.9990 overall best weight: 2.1804 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6578 moved from start: 0.6438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16478 Z= 0.246 Angle : 0.718 8.236 22198 Z= 0.357 Chirality : 0.051 0.159 2684 Planarity : 0.004 0.035 2904 Dihedral : 5.601 21.642 2376 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 17.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.39 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.58 (0.13), residues: 1232 loop : -3.31 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS U 68 PHE 0.008 0.001 PHE T 105 TYR 0.011 0.001 TYR O 14 ARG 0.007 0.000 ARG E 59 *********************** 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 326 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 326 time to evaluate : 1.905 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: A 61 GLU cc_start: 0.4768 (mp0) cc_final: 0.3735 (tm-30) REVERT: A 72 LYS cc_start: 0.8097 (tmtt) cc_final: 0.7676 (tmtt) REVERT: A 91 GLN cc_start: 0.7042 (mp10) cc_final: 0.6208 (tm-30) REVERT: B 72 LYS cc_start: 0.8115 (tmtt) cc_final: 0.7705 (tmtt) REVERT: B 91 GLN cc_start: 0.7265 (mp10) cc_final: 0.6222 (tm-30) REVERT: C 20 GLU cc_start: 0.7574 (mp0) cc_final: 0.7262 (tm-30) REVERT: C 24 ASP cc_start: 0.7648 (m-30) cc_final: 0.6700 (t0) REVERT: C 32 ARG cc_start: 0.7193 (tpt90) cc_final: 0.6861 (tpt90) REVERT: C 38 ARG cc_start: 0.6376 (tmm160) cc_final: 0.5884 (ttp80) REVERT: C 78 GLU cc_start: 0.5472 (pt0) cc_final: 0.4892 (mm-30) REVERT: D 24 ASP cc_start: 0.6864 (t0) cc_final: 0.6512 (t0) REVERT: D 78 GLU cc_start: 0.8044 (tt0) cc_final: 0.7697 (tm-30) REVERT: D 93 LYS cc_start: 0.8403 (tttt) cc_final: 0.7924 (tptp) REVERT: D 100 GLU cc_start: 0.8360 (mp0) cc_final: 0.8009 (mp0) REVERT: E 25 MET cc_start: 0.7256 (ttm) cc_final: 0.6488 (tmm) REVERT: E 72 LYS cc_start: 0.8709 (tttt) cc_final: 0.8118 (tptp) REVERT: E 79 LYS cc_start: 0.9112 (mmtm) cc_final: 0.8690 (mmpt) REVERT: F 26 ARG cc_start: 0.7407 (mtt180) cc_final: 0.6953 (ttm110) REVERT: F 32 ARG cc_start: 0.7611 (tpt-90) cc_final: 0.7384 (tpt-90) REVERT: F 38 ARG cc_start: 0.8205 (tpt90) cc_final: 0.7709 (tpt90) REVERT: F 59 ARG cc_start: 0.7884 (mmt90) cc_final: 0.7490 (mmm-85) REVERT: F 70 GLU cc_start: 0.7923 (mt-10) cc_final: 0.7284 (mp0) REVERT: G 38 ARG cc_start: 0.8153 (tpt90) cc_final: 0.7507 (tpt90) REVERT: G 74 GLU cc_start: 0.7746 (pp20) cc_final: 0.7104 (pm20) REVERT: G 84 LYS cc_start: 0.8086 (tptp) cc_final: 0.7523 (pptt) REVERT: G 93 LYS cc_start: 0.8324 (tttt) cc_final: 0.7982 (tttp) REVERT: H 18 ASP cc_start: 0.8273 (p0) cc_final: 0.7755 (p0) REVERT: H 24 ASP cc_start: 0.7319 (t0) cc_final: 0.6993 (t0) REVERT: H 95 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8141 (mp10) REVERT: I 25 MET cc_start: 0.6983 (ttm) cc_final: 0.5990 (tmm) REVERT: I 79 LYS cc_start: 0.8425 (mmtt) cc_final: 0.8098 (mmmt) REVERT: I 93 LYS cc_start: 0.7710 (tttt) cc_final: 0.6968 (mmtm) REVERT: I 95 GLN cc_start: 0.8657 (mm110) cc_final: 0.8325 (mm110) REVERT: J 25 MET cc_start: 0.7570 (ttm) cc_final: 0.6874 (tmm) REVERT: J 38 ARG cc_start: 0.8038 (tpt90) cc_final: 0.7611 (tpt90) REVERT: J 44 GLU cc_start: 0.8098 (mt-10) cc_final: 0.7845 (mt-10) REVERT: J 63 ARG cc_start: 0.7183 (mmt-90) cc_final: 0.6838 (mpt180) REVERT: J 66 LEU cc_start: 0.7844 (mm) cc_final: 0.7599 (mm) REVERT: J 72 LYS cc_start: 0.8413 (tttt) cc_final: 0.7974 (ttpp) REVERT: J 93 LYS cc_start: 0.7596 (tttt) cc_final: 0.6561 (mmtm) REVERT: K 59 ARG cc_start: 0.7463 (mmt-90) cc_final: 0.7074 (mmt180) REVERT: K 72 LYS cc_start: 0.8389 (tttt) cc_final: 0.7782 (mptt) REVERT: K 74 GLU cc_start: 0.6874 (mt-10) cc_final: 0.6568 (mp0) REVERT: K 93 LYS cc_start: 0.7510 (tttt) cc_final: 0.7253 (mtpt) REVERT: K 95 GLN cc_start: 0.8024 (mm-40) cc_final: 0.7072 (tp40) REVERT: L 18 ASP cc_start: 0.7333 (p0) cc_final: 0.6668 (p0) REVERT: L 20 GLU cc_start: 0.7583 (mp0) cc_final: 0.7037 (mm-30) REVERT: L 79 LYS cc_start: 0.8050 (mppt) cc_final: 0.7778 (mppt) REVERT: M 18 ASP cc_start: 0.7484 (p0) cc_final: 0.7250 (p0) REVERT: M 20 GLU cc_start: 0.7938 (mp0) cc_final: 0.7730 (mp0) REVERT: M 38 ARG cc_start: 0.7373 (tpt90) cc_final: 0.7131 (tpt90) REVERT: M 93 LYS cc_start: 0.7702 (tttt) cc_final: 0.7126 (mtpp) REVERT: N 59 ARG cc_start: 0.7595 (mmt-90) cc_final: 0.7204 (mmm-85) REVERT: N 72 LYS cc_start: 0.8562 (tttt) cc_final: 0.7971 (mptt) REVERT: N 93 LYS cc_start: 0.7786 (tttt) cc_final: 0.7500 (mtpt) REVERT: N 95 GLN cc_start: 0.8236 (mm-40) cc_final: 0.7240 (tp40) REVERT: O 38 ARG cc_start: 0.8034 (tpt90) cc_final: 0.7576 (tpt90) REVERT: O 44 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7714 (mt-10) REVERT: O 59 ARG cc_start: 0.7375 (mmm-85) cc_final: 0.6956 (ptm160) REVERT: O 63 ARG cc_start: 0.7100 (mmt-90) cc_final: 0.6876 (mpt180) REVERT: O 72 LYS cc_start: 0.8269 (tttt) cc_final: 0.7865 (ttpp) REVERT: O 78 GLU cc_start: 0.7728 (mt-10) cc_final: 0.6991 (tm-30) REVERT: O 93 LYS cc_start: 0.7433 (tttt) cc_final: 0.6704 (mtpp) REVERT: P 25 MET cc_start: 0.7281 (ttm) cc_final: 0.6225 (tmm) REVERT: P 32 ARG cc_start: 0.7660 (ttt90) cc_final: 0.7126 (ttm-80) REVERT: P 79 LYS cc_start: 0.8563 (mmtt) cc_final: 0.8026 (mmmt) REVERT: P 93 LYS cc_start: 0.7859 (tttt) cc_final: 0.7553 (tttp) REVERT: P 95 GLN cc_start: 0.8696 (mm110) cc_final: 0.8371 (mm110) REVERT: Q 18 ASP cc_start: 0.8102 (p0) cc_final: 0.7625 (p0) REVERT: Q 95 GLN cc_start: 0.8181 (mm110) cc_final: 0.7954 (mm-40) REVERT: R 26 ARG cc_start: 0.6644 (mtt90) cc_final: 0.6329 (mtt90) REVERT: R 38 ARG cc_start: 0.8085 (tpt90) cc_final: 0.7616 (tpt90) REVERT: R 84 LYS cc_start: 0.8140 (tptp) cc_final: 0.7584 (pptt) REVERT: R 93 LYS cc_start: 0.8470 (tttt) cc_final: 0.8060 (tttp) REVERT: S 18 ASP cc_start: 0.7232 (p0) cc_final: 0.6828 (p0) REVERT: S 21 VAL cc_start: 0.8811 (m) cc_final: 0.8608 (p) REVERT: S 26 ARG cc_start: 0.7321 (mtt180) cc_final: 0.6921 (ttm110) REVERT: S 38 ARG cc_start: 0.8271 (tpt90) cc_final: 0.7700 (tpt90) REVERT: S 59 ARG cc_start: 0.7592 (mmt-90) cc_final: 0.7389 (mmm-85) REVERT: S 72 LYS cc_start: 0.8403 (tptt) cc_final: 0.7743 (tppt) REVERT: S 93 LYS cc_start: 0.8027 (tttt) cc_final: 0.7493 (tptp) REVERT: T 25 MET cc_start: 0.7657 (ttm) cc_final: 0.6761 (tmm) REVERT: T 28 LYS cc_start: 0.8113 (tptp) cc_final: 0.7695 (ttpt) REVERT: T 56 GLU cc_start: 0.7930 (mm-30) cc_final: 0.7330 (mm-30) REVERT: T 59 ARG cc_start: 0.8184 (tpp-160) cc_final: 0.7781 (tpp80) REVERT: T 72 LYS cc_start: 0.8595 (tmtt) cc_final: 0.8060 (tptp) REVERT: T 78 GLU cc_start: 0.8240 (tp30) cc_final: 0.7907 (tp30) REVERT: T 79 LYS cc_start: 0.9038 (mmtm) cc_final: 0.8654 (mmmt) REVERT: U 18 ASP cc_start: 0.7265 (p0) cc_final: 0.6792 (p0) REVERT: U 54 ARG cc_start: 0.7853 (tmm-80) cc_final: 0.7169 (ttp80) REVERT: U 59 ARG cc_start: 0.7801 (mpt180) cc_final: 0.7326 (mmt-90) REVERT: U 78 GLU cc_start: 0.8145 (tt0) cc_final: 0.7767 (tm-30) REVERT: U 93 LYS cc_start: 0.8395 (tttt) cc_final: 0.7830 (mptt) REVERT: U 100 GLU cc_start: 0.7929 (mp0) cc_final: 0.7607 (mp0) REVERT: V 24 ASP cc_start: 0.7753 (m-30) cc_final: 0.6611 (t0) REVERT: V 32 ARG cc_start: 0.7347 (tmt-80) cc_final: 0.6793 (tpt90) REVERT: V 38 ARG cc_start: 0.6445 (tmm160) cc_final: 0.6033 (tmm160) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.4798 time to fit residues: 199.5130 Evaluate side-chains 282 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 203 optimal weight: 0.9990 chunk 185 optimal weight: 6.9990 chunk 197 optimal weight: 10.0000 chunk 118 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 155 optimal weight: 0.7980 chunk 60 optimal weight: 10.0000 chunk 178 optimal weight: 0.9990 chunk 186 optimal weight: 10.0000 chunk 196 optimal weight: 7.9990 chunk 129 optimal weight: 3.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6598 moved from start: 0.6639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 16478 Z= 0.294 Angle : 0.748 8.200 22198 Z= 0.378 Chirality : 0.052 0.164 2684 Planarity : 0.004 0.050 2904 Dihedral : 5.851 21.902 2376 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.67 % Favored : 87.33 % 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: -5.44 (0.16), residues: 2178 helix: None (None), residues: 0 sheet: -3.63 (0.13), residues: 1232 loop : -3.31 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS J 68 PHE 0.011 0.002 PHE E 105 TYR 0.015 0.002 TYR O 14 ARG 0.008 0.001 ARG E 59 *********************** 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 320 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 320 time to evaluate : 1.862 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: 0.8109 (tmtt) cc_final: 0.7678 (tmtt) REVERT: B 72 LYS cc_start: 0.8134 (tmtt) cc_final: 0.7677 (tmtt) REVERT: C 20 GLU cc_start: 0.7613 (mp0) cc_final: 0.7280 (tm-30) REVERT: C 24 ASP cc_start: 0.7674 (m-30) cc_final: 0.6742 (t0) REVERT: C 38 ARG cc_start: 0.6373 (tmm160) cc_final: 0.5775 (ttp80) REVERT: C 78 GLU cc_start: 0.5302 (pt0) cc_final: 0.4719 (mm-30) REVERT: C 88 PHE cc_start: 0.5234 (t80) cc_final: 0.4836 (t80) REVERT: D 24 ASP cc_start: 0.7006 (t0) cc_final: 0.6736 (t0) REVERT: D 78 GLU cc_start: 0.7973 (tt0) cc_final: 0.7663 (tm-30) REVERT: D 93 LYS cc_start: 0.8445 (tttt) cc_final: 0.7974 (tptp) REVERT: D 100 GLU cc_start: 0.8363 (mp0) cc_final: 0.7952 (mp0) REVERT: E 25 MET cc_start: 0.7636 (ttm) cc_final: 0.6597 (tmm) REVERT: E 26 ARG cc_start: 0.7057 (tpt-90) cc_final: 0.6450 (ptp90) REVERT: E 72 LYS cc_start: 0.8698 (tttt) cc_final: 0.8094 (tptp) REVERT: E 79 LYS cc_start: 0.9106 (mmtm) cc_final: 0.8707 (mmpt) REVERT: F 20 GLU cc_start: 0.8074 (mp0) cc_final: 0.7755 (mp0) REVERT: F 26 ARG cc_start: 0.7546 (mtt180) cc_final: 0.6951 (ttm110) REVERT: F 38 ARG cc_start: 0.8215 (tpt90) cc_final: 0.7692 (tpt90) REVERT: F 59 ARG cc_start: 0.7827 (mmt90) cc_final: 0.7451 (mmm-85) REVERT: G 38 ARG cc_start: 0.8224 (tpt90) cc_final: 0.7653 (tpt90) REVERT: G 74 GLU cc_start: 0.7739 (pp20) cc_final: 0.7466 (pp20) REVERT: G 84 LYS cc_start: 0.8130 (tptp) cc_final: 0.7574 (pptt) REVERT: G 93 LYS cc_start: 0.8278 (tttt) cc_final: 0.7948 (tttp) REVERT: H 18 ASP cc_start: 0.8315 (p0) cc_final: 0.7824 (p0) REVERT: H 24 ASP cc_start: 0.7359 (t0) cc_final: 0.7029 (t0) REVERT: I 25 MET cc_start: 0.7068 (ttm) cc_final: 0.6012 (tmm) REVERT: I 79 LYS cc_start: 0.8500 (mmtt) cc_final: 0.7981 (mmmt) REVERT: I 93 LYS cc_start: 0.7705 (tttt) cc_final: 0.6914 (mmtm) REVERT: I 95 GLN cc_start: 0.8663 (mm110) cc_final: 0.8341 (mm110) REVERT: J 25 MET cc_start: 0.7552 (ttm) cc_final: 0.6844 (tmm) REVERT: J 38 ARG cc_start: 0.8061 (tpt90) cc_final: 0.7663 (tpt90) REVERT: J 59 ARG cc_start: 0.7823 (mmm-85) cc_final: 0.7384 (ptm160) REVERT: J 63 ARG cc_start: 0.7217 (mmt-90) cc_final: 0.6861 (mpt180) REVERT: J 66 LEU cc_start: 0.7893 (mm) cc_final: 0.7668 (mm) REVERT: J 72 LYS cc_start: 0.8442 (tttt) cc_final: 0.7972 (ttmm) REVERT: J 93 LYS cc_start: 0.7632 (tttt) cc_final: 0.6835 (mtpp) REVERT: K 59 ARG cc_start: 0.7460 (mmt-90) cc_final: 0.7048 (mmt180) REVERT: K 72 LYS cc_start: 0.8459 (tttt) cc_final: 0.7781 (mtmm) REVERT: K 74 GLU cc_start: 0.6883 (mt-10) cc_final: 0.6553 (mp0) REVERT: K 78 GLU cc_start: 0.7508 (tp30) cc_final: 0.6556 (tm-30) REVERT: K 93 LYS cc_start: 0.7511 (tttt) cc_final: 0.7275 (mtpt) REVERT: K 95 GLN cc_start: 0.8068 (mm-40) cc_final: 0.7214 (tp40) REVERT: L 18 ASP cc_start: 0.7345 (p0) cc_final: 0.6627 (p0) REVERT: L 20 GLU cc_start: 0.7653 (mp0) cc_final: 0.7413 (mp0) REVERT: M 18 ASP cc_start: 0.7475 (p0) cc_final: 0.7209 (p0) REVERT: M 20 GLU cc_start: 0.7958 (mp0) cc_final: 0.7700 (mp0) REVERT: M 38 ARG cc_start: 0.7473 (tpt90) cc_final: 0.7151 (tpt90) REVERT: M 79 LYS cc_start: 0.7882 (mppt) cc_final: 0.7435 (mmtt) REVERT: M 93 LYS cc_start: 0.7744 (tttt) cc_final: 0.7177 (mtpp) REVERT: N 59 ARG cc_start: 0.7598 (mmt-90) cc_final: 0.7213 (mmm-85) REVERT: N 72 LYS cc_start: 0.8582 (tttt) cc_final: 0.7935 (mtmm) REVERT: N 93 LYS cc_start: 0.7793 (tttt) cc_final: 0.7498 (mtpt) REVERT: N 95 GLN cc_start: 0.8239 (mm-40) cc_final: 0.7309 (tp-100) REVERT: O 25 MET cc_start: 0.7432 (ttt) cc_final: 0.6558 (tmm) REVERT: O 38 ARG cc_start: 0.8089 (tpt90) cc_final: 0.7642 (tpt90) REVERT: O 59 ARG cc_start: 0.7349 (mmm-85) cc_final: 0.6932 (ptm160) REVERT: O 63 ARG cc_start: 0.7171 (mmt-90) cc_final: 0.6917 (mpt180) REVERT: O 72 LYS cc_start: 0.8231 (tttt) cc_final: 0.7763 (ttmm) REVERT: O 78 GLU cc_start: 0.7784 (mt-10) cc_final: 0.7019 (tm-30) REVERT: O 93 LYS cc_start: 0.7483 (tttt) cc_final: 0.6733 (mtpp) REVERT: P 25 MET cc_start: 0.7345 (ttm) cc_final: 0.6212 (tmm) REVERT: P 32 ARG cc_start: 0.7702 (ttt90) cc_final: 0.7175 (ttm-80) REVERT: P 79 LYS cc_start: 0.8602 (mmtt) cc_final: 0.8302 (mmmt) REVERT: P 93 LYS cc_start: 0.7947 (tttt) cc_final: 0.7096 (mmtm) REVERT: P 95 GLN cc_start: 0.8714 (mm110) cc_final: 0.8400 (mm110) REVERT: Q 18 ASP cc_start: 0.8216 (p0) cc_final: 0.7700 (p0) REVERT: Q 95 GLN cc_start: 0.8195 (mm110) cc_final: 0.7864 (mp10) REVERT: R 28 LYS cc_start: 0.6315 (mptt) cc_final: 0.5917 (mptt) REVERT: R 38 ARG cc_start: 0.8110 (tpt90) cc_final: 0.7543 (tpt90) REVERT: R 84 LYS cc_start: 0.8161 (tptp) cc_final: 0.7593 (pptt) REVERT: R 93 LYS cc_start: 0.8479 (tttt) cc_final: 0.8091 (tttp) REVERT: S 18 ASP cc_start: 0.7289 (p0) cc_final: 0.6980 (p0) REVERT: S 21 VAL cc_start: 0.8805 (m) cc_final: 0.8591 (p) REVERT: S 26 ARG cc_start: 0.7458 (mtt180) cc_final: 0.7131 (ttm110) REVERT: S 28 LYS cc_start: 0.7186 (mptt) cc_final: 0.6947 (mmtm) REVERT: S 38 ARG cc_start: 0.8295 (tpt90) cc_final: 0.7733 (tpt90) REVERT: S 59 ARG cc_start: 0.7596 (mmt-90) cc_final: 0.7379 (mmm-85) REVERT: S 72 LYS cc_start: 0.8399 (tptt) cc_final: 0.7756 (tppt) REVERT: S 79 LYS cc_start: 0.8033 (mppt) cc_final: 0.7784 (mmtm) REVERT: S 93 LYS cc_start: 0.7999 (tttt) cc_final: 0.7508 (tptp) REVERT: T 25 MET cc_start: 0.7750 (ttm) cc_final: 0.6745 (tmm) REVERT: T 28 LYS cc_start: 0.8089 (tptp) cc_final: 0.7683 (ttpt) REVERT: T 72 LYS cc_start: 0.8574 (tmtt) cc_final: 0.8139 (tptp) REVERT: T 78 GLU cc_start: 0.8250 (tp30) cc_final: 0.7918 (tp30) REVERT: T 79 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8531 (mmmt) REVERT: U 18 ASP cc_start: 0.7271 (p0) cc_final: 0.6776 (p0) REVERT: U 93 LYS cc_start: 0.8457 (tttt) cc_final: 0.7978 (tptp) REVERT: U 100 GLU cc_start: 0.7999 (mp0) cc_final: 0.7728 (mp0) REVERT: V 24 ASP cc_start: 0.7779 (m-30) cc_final: 0.6680 (t0) REVERT: V 38 ARG cc_start: 0.6444 (tmm160) cc_final: 0.6069 (tmm160) outliers start: 0 outliers final: 0 residues processed: 320 average time/residue: 0.4837 time to fit residues: 196.9103 Evaluate side-chains 281 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 281 time to evaluate : 1.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 208 optimal weight: 10.0000 chunk 127 optimal weight: 0.7980 chunk 99 optimal weight: 6.9990 chunk 145 optimal weight: 5.9990 chunk 219 optimal weight: 30.0000 chunk 201 optimal weight: 2.9990 chunk 174 optimal weight: 10.0000 chunk 18 optimal weight: 4.9990 chunk 134 optimal weight: 1.9990 chunk 107 optimal weight: 0.9980 chunk 138 optimal weight: 2.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 95 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.6686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 16478 Z= 0.231 Angle : 0.732 8.332 22198 Z= 0.361 Chirality : 0.051 0.163 2684 Planarity : 0.003 0.034 2904 Dihedral : 5.468 21.363 2376 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.31 % Favored : 91.69 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -3.51 (0.13), residues: 1232 loop : -3.28 (0.16), residues: 946 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 68 PHE 0.008 0.001 PHE H 105 TYR 0.009 0.001 TYR J 14 ARG 0.009 0.000 ARG E 59 ********************** 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 324 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 324 time to evaluate : 1.950 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: 0.8096 (tmtt) cc_final: 0.7662 (tmtt) REVERT: A 91 GLN cc_start: 0.7040 (mp10) cc_final: 0.6255 (tm-30) REVERT: B 72 LYS cc_start: 0.8105 (tmtt) cc_final: 0.7697 (tmtt) REVERT: C 20 GLU cc_start: 0.7569 (mp0) cc_final: 0.7296 (tm-30) REVERT: C 24 ASP cc_start: 0.7646 (m-30) cc_final: 0.6695 (t0) REVERT: C 30 GLN cc_start: 0.7984 (tt0) cc_final: 0.7424 (tm-30) REVERT: C 38 ARG cc_start: 0.6327 (tmm160) cc_final: 0.5833 (ttp80) REVERT: C 78 GLU cc_start: 0.5292 (pt0) cc_final: 0.4817 (mm-30) REVERT: C 88 PHE cc_start: 0.5321 (t80) cc_final: 0.4845 (t80) REVERT: D 24 ASP cc_start: 0.6978 (t0) cc_final: 0.6631 (t0) REVERT: D 78 GLU cc_start: 0.7985 (tt0) cc_final: 0.7548 (tm-30) REVERT: D 93 LYS cc_start: 0.8432 (tttt) cc_final: 0.8039 (tptt) REVERT: D 100 GLU cc_start: 0.8276 (mp0) cc_final: 0.7891 (mp0) REVERT: E 25 MET cc_start: 0.7257 (ttm) cc_final: 0.6393 (tmm) REVERT: E 26 ARG cc_start: 0.6965 (tpt-90) cc_final: 0.6429 (ptp90) REVERT: E 72 LYS cc_start: 0.8743 (tttt) cc_final: 0.8205 (tptp) REVERT: E 79 LYS cc_start: 0.9135 (mmtm) cc_final: 0.8845 (mmmt) REVERT: F 26 ARG cc_start: 0.7828 (mtt180) cc_final: 0.6953 (ttm110) REVERT: F 32 ARG cc_start: 0.7610 (tpt-90) cc_final: 0.7344 (tpt-90) REVERT: F 38 ARG cc_start: 0.8182 (tpt90) cc_final: 0.7673 (tpt90) REVERT: F 59 ARG cc_start: 0.7912 (mmt90) cc_final: 0.7517 (mmm-85) REVERT: G 38 ARG cc_start: 0.8179 (tpt90) cc_final: 0.7615 (tpt90) REVERT: G 79 LYS cc_start: 0.8652 (tttp) cc_final: 0.8418 (tmmt) REVERT: G 84 LYS cc_start: 0.8107 (tptp) cc_final: 0.7556 (pptt) REVERT: G 93 LYS cc_start: 0.8327 (tttt) cc_final: 0.7986 (tttp) REVERT: H 18 ASP cc_start: 0.8314 (p0) cc_final: 0.7688 (p0) REVERT: H 20 GLU cc_start: 0.8034 (mp0) cc_final: 0.7748 (mp0) REVERT: H 24 ASP cc_start: 0.7397 (t0) cc_final: 0.7042 (t0) REVERT: I 25 MET cc_start: 0.7032 (ttm) cc_final: 0.5963 (tmm) REVERT: I 79 LYS cc_start: 0.8430 (mmtt) cc_final: 0.7907 (mmmt) REVERT: I 93 LYS cc_start: 0.7738 (tttt) cc_final: 0.6987 (mmtm) REVERT: I 95 GLN cc_start: 0.8645 (mm110) cc_final: 0.8344 (mm110) REVERT: J 25 MET cc_start: 0.7606 (ttm) cc_final: 0.6843 (tmm) REVERT: J 38 ARG cc_start: 0.8012 (tpt90) cc_final: 0.7611 (tpt90) REVERT: J 44 GLU cc_start: 0.8036 (mt-10) cc_final: 0.7809 (mt-10) REVERT: J 59 ARG cc_start: 0.7688 (mmm-85) cc_final: 0.7311 (ptm160) REVERT: J 63 ARG cc_start: 0.7242 (mmt-90) cc_final: 0.7014 (mmt-90) REVERT: J 66 LEU cc_start: 0.7705 (mm) cc_final: 0.7461 (mm) REVERT: J 72 LYS cc_start: 0.8396 (tttt) cc_final: 0.7845 (ttpp) REVERT: J 93 LYS cc_start: 0.7578 (tttt) cc_final: 0.6802 (mtpp) REVERT: K 59 ARG cc_start: 0.7444 (mmt-90) cc_final: 0.7006 (mmm-85) REVERT: K 72 LYS cc_start: 0.8385 (tttt) cc_final: 0.7809 (mptt) REVERT: K 74 GLU cc_start: 0.6833 (mt-10) cc_final: 0.6526 (mp0) REVERT: K 78 GLU cc_start: 0.7523 (tp30) cc_final: 0.6539 (tm-30) REVERT: K 93 LYS cc_start: 0.7397 (tttt) cc_final: 0.7168 (mtpt) REVERT: K 95 GLN cc_start: 0.8052 (mm-40) cc_final: 0.7009 (tp40) REVERT: L 18 ASP cc_start: 0.7390 (p0) cc_final: 0.6687 (p0) REVERT: L 20 GLU cc_start: 0.7256 (mp0) cc_final: 0.6754 (mm-30) REVERT: L 79 LYS cc_start: 0.8109 (mppt) cc_final: 0.7820 (mppt) REVERT: M 18 ASP cc_start: 0.7440 (p0) cc_final: 0.7226 (p0) REVERT: M 38 ARG cc_start: 0.7560 (tpt90) cc_final: 0.7175 (tpt90) REVERT: N 59 ARG cc_start: 0.7560 (mmt-90) cc_final: 0.7180 (mmm-85) REVERT: N 72 LYS cc_start: 0.8558 (tttt) cc_final: 0.7983 (mptt) REVERT: N 93 LYS cc_start: 0.7693 (tttt) cc_final: 0.7411 (mtpt) REVERT: N 95 GLN cc_start: 0.8160 (mm-40) cc_final: 0.7014 (tp40) REVERT: O 25 MET cc_start: 0.7240 (ttt) cc_final: 0.6531 (tmm) REVERT: O 38 ARG cc_start: 0.8058 (tpt90) cc_final: 0.7594 (tpt90) REVERT: O 44 GLU cc_start: 0.7959 (mt-10) cc_final: 0.7618 (mt-10) REVERT: O 59 ARG cc_start: 0.7309 (mmm-85) cc_final: 0.6972 (ptm160) REVERT: O 66 LEU cc_start: 0.7681 (mm) cc_final: 0.7441 (mm) REVERT: O 72 LYS cc_start: 0.8209 (tttt) cc_final: 0.7659 (ttpp) REVERT: O 78 GLU cc_start: 0.7719 (mt-10) cc_final: 0.7000 (tm-30) REVERT: O 93 LYS cc_start: 0.7406 (tttt) cc_final: 0.6653 (mtpp) REVERT: P 25 MET cc_start: 0.7255 (ttm) cc_final: 0.6146 (tmm) REVERT: P 32 ARG cc_start: 0.7669 (ttt90) cc_final: 0.7129 (ttm-80) REVERT: P 79 LYS cc_start: 0.8551 (mmtt) cc_final: 0.8042 (mmmt) REVERT: P 93 LYS cc_start: 0.7917 (tttt) cc_final: 0.7100 (mmtm) REVERT: P 95 GLN cc_start: 0.8702 (mm110) cc_final: 0.8406 (mm110) REVERT: Q 18 ASP cc_start: 0.8032 (p0) cc_final: 0.7553 (p0) REVERT: R 28 LYS cc_start: 0.6300 (mptt) cc_final: 0.6015 (mptt) REVERT: R 38 ARG cc_start: 0.8088 (tpt90) cc_final: 0.7478 (tpt90) REVERT: R 66 LEU cc_start: 0.8267 (mm) cc_final: 0.7901 (mp) REVERT: R 79 LYS cc_start: 0.8716 (pptt) cc_final: 0.8488 (tmmt) REVERT: R 84 LYS cc_start: 0.8141 (tptp) cc_final: 0.7590 (pptt) REVERT: R 93 LYS cc_start: 0.8422 (tttt) cc_final: 0.8027 (tttp) REVERT: S 18 ASP cc_start: 0.7178 (p0) cc_final: 0.6860 (p0) REVERT: S 21 VAL cc_start: 0.8857 (m) cc_final: 0.8593 (p) REVERT: S 26 ARG cc_start: 0.7547 (mtt180) cc_final: 0.7004 (ttm110) REVERT: S 38 ARG cc_start: 0.8273 (tpt90) cc_final: 0.7693 (tpt90) REVERT: S 72 LYS cc_start: 0.8427 (tptt) cc_final: 0.7759 (tppt) REVERT: S 79 LYS cc_start: 0.8282 (mppt) cc_final: 0.8025 (tptt) REVERT: S 93 LYS cc_start: 0.8029 (tttt) cc_final: 0.7498 (tptp) REVERT: T 25 MET cc_start: 0.7605 (ttm) cc_final: 0.6731 (tmm) REVERT: T 28 LYS cc_start: 0.8117 (tptp) cc_final: 0.7809 (ttpt) REVERT: T 72 LYS cc_start: 0.8575 (tmtt) cc_final: 0.8127 (tptp) REVERT: T 78 GLU cc_start: 0.8315 (tp30) cc_final: 0.8023 (tp30) REVERT: T 79 LYS cc_start: 0.9025 (mmtm) cc_final: 0.8571 (mmmt) REVERT: U 18 ASP cc_start: 0.7321 (p0) cc_final: 0.6869 (p0) REVERT: U 54 ARG cc_start: 0.7900 (tmm-80) cc_final: 0.7327 (ttp80) REVERT: U 78 GLU cc_start: 0.8281 (tt0) cc_final: 0.7787 (tm-30) REVERT: U 93 LYS cc_start: 0.8397 (tttt) cc_final: 0.7897 (mptt) REVERT: U 100 GLU cc_start: 0.7955 (mp0) cc_final: 0.7588 (mp0) REVERT: V 24 ASP cc_start: 0.7723 (m-30) cc_final: 0.6618 (t0) REVERT: V 38 ARG cc_start: 0.6431 (tmm160) cc_final: 0.6063 (tmm160) outliers start: 0 outliers final: 0 residues processed: 324 average time/residue: 0.4786 time to fit residues: 197.3222 Evaluate side-chains 269 residues out of total 1694 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 269 time to evaluate : 1.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 220 random chunks: chunk 185 optimal weight: 3.9990 chunk 53 optimal weight: 0.0980 chunk 160 optimal weight: 9.9990 chunk 25 optimal weight: 30.0000 chunk 48 optimal weight: 20.0000 chunk 174 optimal weight: 10.0000 chunk 73 optimal weight: 7.9990 chunk 179 optimal weight: 9.9990 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 10.0000 chunk 153 optimal weight: 9.9990 overall best weight: 6.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 68 HIS ** 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 = 0.4824 r_free = 0.4824 target = 0.107088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4272 r_free = 0.4272 target = 0.081170 restraints weight = 33926.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.082124 restraints weight = 24018.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.082800 restraints weight = 18833.122| |-----------------------------------------------------------------------------| r_work (final): 0.4305 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.7280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.067 16478 Z= 0.609 Angle : 0.987 9.006 22198 Z= 0.522 Chirality : 0.058 0.209 2684 Planarity : 0.007 0.082 2904 Dihedral : 7.617 27.001 2376 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 26.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.73 % Favored : 77.27 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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: -6.12 (0.15), residues: 2178 helix: None (None), residues: 0 sheet: -4.37 (0.11), residues: 1276 loop : -3.19 (0.17), residues: 902 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.015 0.003 HIS J 68 PHE 0.027 0.004 PHE Q 105 TYR 0.026 0.003 TYR O 14 ARG 0.010 0.001 ARG T 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4151.80 seconds wall clock time: 74 minutes 12.19 seconds (4452.19 seconds total)