Starting phenix.real_space_refine on Thu Mar 5 07:14:39 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7l85_23222/03_2026/7l85_23222.cif Found real_map, /net/cci-nas-00/data/ceres_data/7l85_23222/03_2026/7l85_23222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7l85_23222/03_2026/7l85_23222.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7l85_23222/03_2026/7l85_23222.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7l85_23222/03_2026/7l85_23222.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7l85_23222/03_2026/7l85_23222.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 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 36 5.16 5 C 13104 2.51 5 N 3552 2.21 5 O 3864 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 48 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 20556 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 907 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 8, 'TRANS': 109} Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 806 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 6, 'TRANS': 97} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, V, X, D, F, H, J, L, N, P, R, T, W, Y Time building chain proxies: 2.08, per 1000 atoms: 0.10 Number of scatterers: 20556 At special positions: 0 Unit cell: (126.5, 127.65, 125.35, 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 36 16.00 O 3864 8.00 N 3552 7.00 C 13104 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.49 Conformation dependent library (CDL) restraints added in 891.1 milliseconds 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5040 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 24 sheets defined 36.5% alpha, 26.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'B' and resid 16 through 35 Processing helix chain 'B' and resid 39 through 41 No H-bonds generated for 'chain 'B' and resid 39 through 41' Processing helix chain 'B' and resid 58 through 64 removed outlier: 4.121A pdb=" N ALA B 62 " --> pdb=" O PHE B 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA B 63 " --> pdb=" O PRO B 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 58 through 64' Processing helix chain 'B' and resid 100 through 104 Processing helix chain 'B' and resid 110 through 116 removed outlier: 3.541A pdb=" N VAL B 113 " --> pdb=" O ASN B 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 26 Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 92 through 102 Processing helix chain 'C' and resid 16 through 35 Processing helix chain 'C' and resid 39 through 41 No H-bonds generated for 'chain 'C' and resid 39 through 41' Processing helix chain 'C' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA C 62 " --> pdb=" O PHE C 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA C 63 " --> pdb=" O PRO C 59 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ARG C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 58 through 64' Processing helix chain 'C' and resid 100 through 104 Processing helix chain 'C' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL C 113 " --> pdb=" O ASN C 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 12 through 26 Processing helix chain 'D' and resid 64 through 76 Processing helix chain 'D' and resid 92 through 102 Processing helix chain 'E' and resid 16 through 35 Processing helix chain 'E' and resid 39 through 41 No H-bonds generated for 'chain 'E' and resid 39 through 41' Processing helix chain 'E' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA E 62 " --> pdb=" O PHE E 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA E 63 " --> pdb=" O PRO E 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG E 64 " --> pdb=" O ALA E 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 58 through 64' Processing helix chain 'E' and resid 100 through 104 Processing helix chain 'E' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL E 113 " --> pdb=" O ASN E 110 " (cutoff:3.500A) Processing helix chain 'F' and resid 12 through 26 Processing helix chain 'F' and resid 64 through 76 Processing helix chain 'F' and resid 92 through 102 Processing helix chain 'G' and resid 16 through 35 Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 58 through 64 removed outlier: 4.121A pdb=" N ALA G 62 " --> pdb=" O PHE G 58 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA G 63 " --> pdb=" O PRO G 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 58 through 64' Processing helix chain 'G' and resid 100 through 104 Processing helix chain 'G' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL G 113 " --> pdb=" O ASN G 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 12 through 26 Processing helix chain 'H' and resid 64 through 76 Processing helix chain 'H' and resid 92 through 102 Processing helix chain 'I' and resid 16 through 35 Processing helix chain 'I' and resid 39 through 41 No H-bonds generated for 'chain 'I' and resid 39 through 41' Processing helix chain 'I' and resid 58 through 64 removed outlier: 4.121A pdb=" N ALA I 62 " --> pdb=" O PHE I 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA I 63 " --> pdb=" O PRO I 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG I 64 " --> pdb=" O ALA I 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 58 through 64' Processing helix chain 'I' and resid 100 through 104 Processing helix chain 'I' and resid 110 through 116 removed outlier: 3.539A pdb=" N VAL I 113 " --> pdb=" O ASN I 110 " (cutoff:3.500A) Processing helix chain 'J' and resid 12 through 26 Processing helix chain 'J' and resid 64 through 76 Processing helix chain 'J' and resid 92 through 102 Processing helix chain 'K' and resid 16 through 35 Processing helix chain 'K' and resid 39 through 41 No H-bonds generated for 'chain 'K' and resid 39 through 41' Processing helix chain 'K' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA K 62 " --> pdb=" O PHE K 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA K 63 " --> pdb=" O PRO K 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG K 64 " --> pdb=" O ALA K 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 58 through 64' Processing helix chain 'K' and resid 100 through 104 Processing helix chain 'K' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL K 113 " --> pdb=" O ASN K 110 " (cutoff:3.500A) Processing helix chain 'L' and resid 12 through 26 Processing helix chain 'L' and resid 64 through 76 Processing helix chain 'L' and resid 92 through 102 Processing helix chain 'M' and resid 16 through 35 Processing helix chain 'M' and resid 39 through 41 No H-bonds generated for 'chain 'M' and resid 39 through 41' Processing helix chain 'M' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA M 62 " --> pdb=" O PHE M 58 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA M 63 " --> pdb=" O PRO M 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG M 64 " --> pdb=" O ALA M 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 58 through 64' Processing helix chain 'M' and resid 100 through 104 Processing helix chain 'M' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL M 113 " --> pdb=" O ASN M 110 " (cutoff:3.500A) Processing helix chain 'N' and resid 12 through 26 Processing helix chain 'N' and resid 64 through 76 Processing helix chain 'N' and resid 92 through 102 Processing helix chain 'O' and resid 16 through 35 Processing helix chain 'O' and resid 39 through 41 No H-bonds generated for 'chain 'O' and resid 39 through 41' Processing helix chain 'O' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA O 62 " --> pdb=" O PHE O 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA O 63 " --> pdb=" O PRO O 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG O 64 " --> pdb=" O ALA O 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'O' and resid 58 through 64' Processing helix chain 'O' and resid 100 through 104 Processing helix chain 'O' and resid 110 through 116 removed outlier: 3.539A pdb=" N VAL O 113 " --> pdb=" O ASN O 110 " (cutoff:3.500A) Processing helix chain 'P' and resid 12 through 26 Processing helix chain 'P' and resid 64 through 76 Processing helix chain 'P' and resid 92 through 102 Processing helix chain 'Q' and resid 16 through 35 Processing helix chain 'Q' and resid 39 through 41 No H-bonds generated for 'chain 'Q' and resid 39 through 41' Processing helix chain 'Q' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA Q 62 " --> pdb=" O PHE Q 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA Q 63 " --> pdb=" O PRO Q 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ARG Q 64 " --> pdb=" O ALA Q 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 58 through 64' Processing helix chain 'Q' and resid 100 through 104 Processing helix chain 'Q' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL Q 113 " --> pdb=" O ASN Q 110 " (cutoff:3.500A) Processing helix chain 'R' and resid 12 through 26 Processing helix chain 'R' and resid 64 through 76 Processing helix chain 'R' and resid 92 through 102 Processing helix chain 'S' and resid 16 through 35 Processing helix chain 'S' and resid 39 through 41 No H-bonds generated for 'chain 'S' and resid 39 through 41' Processing helix chain 'S' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA S 62 " --> pdb=" O PHE S 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA S 63 " --> pdb=" O PRO S 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG S 64 " --> pdb=" O ALA S 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'S' and resid 58 through 64' Processing helix chain 'S' and resid 100 through 104 Processing helix chain 'S' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL S 113 " --> pdb=" O ASN S 110 " (cutoff:3.500A) Processing helix chain 'T' and resid 12 through 26 Processing helix chain 'T' and resid 64 through 76 Processing helix chain 'T' and resid 92 through 102 Processing helix chain 'V' and resid 16 through 35 Processing helix chain 'V' and resid 39 through 41 No H-bonds generated for 'chain 'V' and resid 39 through 41' Processing helix chain 'V' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA V 62 " --> pdb=" O PHE V 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA V 63 " --> pdb=" O PRO V 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG V 64 " --> pdb=" O ALA V 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'V' and resid 58 through 64' Processing helix chain 'V' and resid 100 through 104 Processing helix chain 'V' and resid 110 through 116 removed outlier: 3.539A pdb=" N VAL V 113 " --> pdb=" O ASN V 110 " (cutoff:3.500A) Processing helix chain 'W' and resid 12 through 26 Processing helix chain 'W' and resid 64 through 76 Processing helix chain 'W' and resid 92 through 102 Processing helix chain 'X' and resid 16 through 35 Processing helix chain 'X' and resid 39 through 41 No H-bonds generated for 'chain 'X' and resid 39 through 41' Processing helix chain 'X' and resid 58 through 64 removed outlier: 4.120A pdb=" N ALA X 62 " --> pdb=" O PHE X 58 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ALA X 63 " --> pdb=" O PRO X 59 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ARG X 64 " --> pdb=" O ALA X 60 " (cutoff:3.500A) No H-bonds generated for 'chain 'X' and resid 58 through 64' Processing helix chain 'X' and resid 100 through 104 Processing helix chain 'X' and resid 110 through 116 removed outlier: 3.540A pdb=" N VAL X 113 " --> pdb=" O ASN X 110 " (cutoff:3.500A) Processing helix chain 'Y' and resid 12 through 26 Processing helix chain 'Y' and resid 64 through 76 Processing helix chain 'Y' and resid 92 through 102 Processing sheet with id=AA1, first strand: chain 'B' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA B 45 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL B 107 " --> pdb=" O GLY B 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG B 7 " --> pdb=" O VAL B 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU B 109 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA B 9 " --> pdb=" O LEU B 109 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'W' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS A 31 " --> pdb=" O LYS A 59 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N GLU Y 90 " --> pdb=" O ALA A 85 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS Y 31 " --> pdb=" O LYS Y 59 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU W 90 " --> pdb=" O ALA Y 85 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 90 through 91 removed outlier: 3.530A pdb=" N GLU A 90 " --> pdb=" O ALA W 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS W 31 " --> pdb=" O LYS W 59 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA C 45 " --> pdb=" O LEU C 94 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL C 107 " --> pdb=" O GLY C 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG C 7 " --> pdb=" O VAL C 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU C 109 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA C 9 " --> pdb=" O LEU C 109 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'R' and resid 47 through 51 removed outlier: 3.527A pdb=" N CYS D 31 " --> pdb=" O LYS D 59 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLU T 90 " --> pdb=" O ALA D 85 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS T 31 " --> pdb=" O LYS T 59 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU R 90 " --> pdb=" O ALA T 85 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 90 through 91 removed outlier: 3.549A pdb=" N GLU D 90 " --> pdb=" O ALA R 85 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N CYS R 31 " --> pdb=" O LYS R 59 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA E 45 " --> pdb=" O LEU E 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL E 107 " --> pdb=" O GLY E 5 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG E 7 " --> pdb=" O VAL E 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU E 109 " --> pdb=" O ARG E 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA E 9 " --> pdb=" O LEU E 109 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 90 through 91 removed outlier: 3.527A pdb=" N GLU J 90 " --> pdb=" O ALA F 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS F 31 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'F' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS J 31 " --> pdb=" O LYS J 59 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU N 90 " --> pdb=" O ALA J 85 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 90 through 91 removed outlier: 3.562A pdb=" N GLU F 90 " --> pdb=" O ALA N 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS N 31 " --> pdb=" O LYS N 59 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'G' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA G 45 " --> pdb=" O LEU G 94 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL G 107 " --> pdb=" O GLY G 5 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG G 7 " --> pdb=" O VAL G 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU G 109 " --> pdb=" O ARG G 7 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ALA G 9 " --> pdb=" O LEU G 109 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 47 through 51 removed outlier: 3.528A pdb=" N CYS H 31 " --> pdb=" O LYS H 59 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU P 90 " --> pdb=" O ALA H 85 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 47 through 51 removed outlier: 3.529A pdb=" N CYS P 31 " --> pdb=" O LYS P 59 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N GLU L 90 " --> pdb=" O ALA P 85 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 90 through 91 removed outlier: 3.530A pdb=" N GLU H 90 " --> pdb=" O ALA L 85 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N CYS L 31 " --> pdb=" O LYS L 59 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'I' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA I 45 " --> pdb=" O LEU I 94 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL I 107 " --> pdb=" O GLY I 5 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N ARG I 7 " --> pdb=" O VAL I 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU I 109 " --> pdb=" O ARG I 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA I 9 " --> pdb=" O LEU I 109 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'K' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA K 45 " --> pdb=" O LEU K 94 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL K 107 " --> pdb=" O GLY K 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG K 7 " --> pdb=" O VAL K 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU K 109 " --> pdb=" O ARG K 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA K 9 " --> pdb=" O LEU K 109 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'M' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA M 45 " --> pdb=" O LEU M 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL M 107 " --> pdb=" O GLY M 5 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ARG M 7 " --> pdb=" O VAL M 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU M 109 " --> pdb=" O ARG M 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA M 9 " --> pdb=" O LEU M 109 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'O' and resid 73 through 77 removed outlier: 3.626A pdb=" N ALA O 45 " --> pdb=" O LEU O 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL O 107 " --> pdb=" O GLY O 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG O 7 " --> pdb=" O VAL O 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU O 109 " --> pdb=" O ARG O 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA O 9 " --> pdb=" O LEU O 109 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'Q' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA Q 45 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) removed outlier: 8.987A pdb=" N VAL Q 107 " --> pdb=" O GLY Q 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG Q 7 " --> pdb=" O VAL Q 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU Q 109 " --> pdb=" O ARG Q 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA Q 9 " --> pdb=" O LEU Q 109 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'S' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA S 45 " --> pdb=" O LEU S 94 " (cutoff:3.500A) removed outlier: 8.990A pdb=" N VAL S 107 " --> pdb=" O GLY S 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG S 7 " --> pdb=" O VAL S 107 " (cutoff:3.500A) removed outlier: 8.276A pdb=" N LEU S 109 " --> pdb=" O ARG S 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA S 9 " --> pdb=" O LEU S 109 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'V' and resid 73 through 77 removed outlier: 3.625A pdb=" N ALA V 45 " --> pdb=" O LEU V 94 " (cutoff:3.500A) removed outlier: 8.988A pdb=" N VAL V 107 " --> pdb=" O GLY V 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG V 7 " --> pdb=" O VAL V 107 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N LEU V 109 " --> pdb=" O ARG V 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA V 9 " --> pdb=" O LEU V 109 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'X' and resid 73 through 77 removed outlier: 3.627A pdb=" N ALA X 45 " --> pdb=" O LEU X 94 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N VAL X 107 " --> pdb=" O GLY X 5 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N ARG X 7 " --> pdb=" O VAL X 107 " (cutoff:3.500A) removed outlier: 8.277A pdb=" N LEU X 109 " --> pdb=" O ARG X 7 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N ALA X 9 " --> pdb=" O LEU X 109 " (cutoff:3.500A) 1116 hydrogen bonds defined for protein. 3024 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: 3.18 Time building geometry restraints manager: 2.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 4436 1.31 - 1.43: 4397 1.43 - 1.56: 11996 1.56 - 1.68: 15 1.68 - 1.80: 60 Bond restraints: 20904 Sorted by residual: bond pdb=" CB TYR P 95 " pdb=" CG TYR P 95 " ideal model delta sigma weight residual 1.512 1.418 0.094 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR N 95 " pdb=" CG TYR N 95 " ideal model delta sigma weight residual 1.512 1.418 0.094 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR T 95 " pdb=" CG TYR T 95 " ideal model delta sigma weight residual 1.512 1.419 0.093 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR D 95 " pdb=" CG TYR D 95 " ideal model delta sigma weight residual 1.512 1.419 0.093 2.20e-02 2.07e+03 1.81e+01 bond pdb=" CB TYR H 95 " pdb=" CG TYR H 95 " ideal model delta sigma weight residual 1.512 1.419 0.093 2.20e-02 2.07e+03 1.80e+01 ... (remaining 20899 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 22392 1.85 - 3.70: 4934 3.70 - 5.55: 976 5.55 - 7.40: 210 7.40 - 9.25: 24 Bond angle restraints: 28536 Sorted by residual: angle pdb=" C THR Q 99 " pdb=" N PRO Q 100 " pdb=" CA PRO Q 100 " ideal model delta sigma weight residual 119.78 126.91 -7.13 1.03e+00 9.43e-01 4.80e+01 angle pdb=" C THR E 99 " pdb=" N PRO E 100 " pdb=" CA PRO E 100 " ideal model delta sigma weight residual 119.78 126.89 -7.11 1.03e+00 9.43e-01 4.76e+01 angle pdb=" C THR K 99 " pdb=" N PRO K 100 " pdb=" CA PRO K 100 " ideal model delta sigma weight residual 119.78 126.88 -7.10 1.03e+00 9.43e-01 4.76e+01 angle pdb=" C THR O 99 " pdb=" N PRO O 100 " pdb=" CA PRO O 100 " ideal model delta sigma weight residual 119.78 126.88 -7.10 1.03e+00 9.43e-01 4.75e+01 angle pdb=" C THR G 99 " pdb=" N PRO G 100 " pdb=" CA PRO G 100 " ideal model delta sigma weight residual 119.78 126.87 -7.09 1.03e+00 9.43e-01 4.73e+01 ... (remaining 28531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.83: 12365 15.83 - 31.66: 343 31.66 - 47.49: 60 47.49 - 63.32: 24 63.32 - 79.15: 36 Dihedral angle restraints: 12828 sinusoidal: 5088 harmonic: 7740 Sorted by residual: dihedral pdb=" C LEU T 99 " pdb=" N LEU T 99 " pdb=" CA LEU T 99 " pdb=" CB LEU T 99 " ideal model delta harmonic sigma weight residual -122.60 -114.32 -8.28 0 2.50e+00 1.60e-01 1.10e+01 dihedral pdb=" C LEU D 99 " pdb=" N LEU D 99 " pdb=" CA LEU D 99 " pdb=" CB LEU D 99 " ideal model delta harmonic sigma weight residual -122.60 -114.33 -8.27 0 2.50e+00 1.60e-01 1.09e+01 dihedral pdb=" C LEU F 99 " pdb=" N LEU F 99 " pdb=" CA LEU F 99 " pdb=" CB LEU F 99 " ideal model delta harmonic sigma weight residual -122.60 -114.34 -8.26 0 2.50e+00 1.60e-01 1.09e+01 ... (remaining 12825 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.069: 1797 0.069 - 0.139: 1059 0.139 - 0.208: 564 0.208 - 0.278: 84 0.278 - 0.347: 12 Chirality restraints: 3516 Sorted by residual: chirality pdb=" CA PHE D 65 " pdb=" N PHE D 65 " pdb=" C PHE D 65 " pdb=" CB PHE D 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.01e+00 chirality pdb=" CA PHE L 65 " pdb=" N PHE L 65 " pdb=" C PHE L 65 " pdb=" CB PHE L 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.00e+00 chirality pdb=" CA PHE R 65 " pdb=" N PHE R 65 " pdb=" C PHE R 65 " pdb=" CB PHE R 65 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.99e+00 ... (remaining 3513 not shown) Planarity restraints: 3660 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL K 50 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C VAL K 50 " -0.041 2.00e-02 2.50e+03 pdb=" O VAL K 50 " 0.015 2.00e-02 2.50e+03 pdb=" N THR K 51 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL I 50 " -0.012 2.00e-02 2.50e+03 2.37e-02 5.59e+00 pdb=" C VAL I 50 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL I 50 " -0.015 2.00e-02 2.50e+03 pdb=" N THR I 51 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL V 50 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.59e+00 pdb=" C VAL V 50 " 0.041 2.00e-02 2.50e+03 pdb=" O VAL V 50 " -0.015 2.00e-02 2.50e+03 pdb=" N THR V 51 " -0.014 2.00e-02 2.50e+03 ... (remaining 3657 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 8066 2.87 - 3.38: 18735 3.38 - 3.89: 35040 3.89 - 4.39: 41795 4.39 - 4.90: 69355 Nonbonded interactions: 172991 Sorted by model distance: nonbonded pdb=" N ASP S 53 " pdb=" OD1 ASP S 53 " model vdw 2.365 3.120 nonbonded pdb=" N ASP C 53 " pdb=" OD1 ASP C 53 " model vdw 2.365 3.120 nonbonded pdb=" N ASP Q 53 " pdb=" OD1 ASP Q 53 " model vdw 2.365 3.120 nonbonded pdb=" N ASP I 53 " pdb=" OD1 ASP I 53 " model vdw 2.365 3.120 nonbonded pdb=" N ASP E 53 " pdb=" OD1 ASP E 53 " model vdw 2.365 3.120 ... (remaining 172986 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: 0.06 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' selection = chain 'V' selection = chain 'X' } ncs_group { reference = chain 'A' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' selection = chain 'W' selection = chain 'Y' } 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 individual isotropic 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: 12.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 15.920 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:9.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 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 : 0.025 0.116 20904 Z= 1.379 Angle : 1.676 9.251 28536 Z= 1.148 Chirality : 0.102 0.347 3516 Planarity : 0.008 0.040 3660 Dihedral : 9.891 79.155 7788 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2616 helix: -0.47 (0.15), residues: 888 sheet: 0.89 (0.18), residues: 840 loop : 1.83 (0.21), residues: 888 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG N 100 TYR 0.032 0.006 TYR L 78 PHE 0.016 0.007 PHE M 58 TRP 0.015 0.005 TRP H 98 HIS 0.005 0.001 HIS F 21 Details of bonding type rmsd covalent geometry : bond 0.02548 (20904) covalent geometry : angle 1.67569 (28536) hydrogen bonds : bond 0.13722 ( 1116) hydrogen bonds : angle 6.79817 ( 3024) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 608 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 608 time to evaluate : 0.614 Fit side-chains revert: symmetry clash REVERT: D 42 TYR cc_start: 0.9348 (p90) cc_final: 0.9098 (p90) REVERT: G 26 GLU cc_start: 0.8689 (tt0) cc_final: 0.8485 (tt0) REVERT: K 70 ARG cc_start: 0.8184 (mtt90) cc_final: 0.7946 (mmt180) REVERT: O 26 GLU cc_start: 0.8595 (tt0) cc_final: 0.8370 (tt0) REVERT: O 75 SER cc_start: 0.8974 (p) cc_final: 0.8573 (m) REVERT: V 114 ARG cc_start: 0.8159 (ptp-170) cc_final: 0.7774 (ptm160) REVERT: X 68 MET cc_start: 0.9107 (mtp) cc_final: 0.8683 (mtm) outliers start: 0 outliers final: 0 residues processed: 608 average time/residue: 1.0204 time to fit residues: 666.5305 Evaluate side-chains 390 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 390 time to evaluate : 0.788 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 0.6980 chunk 194 optimal weight: 0.5980 chunk 227 optimal weight: 0.9990 chunk 107 optimal weight: 0.8980 chunk 10 optimal weight: 0.7980 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 0.7980 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 21 HIS ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 35 ASN ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 92 ASN H 21 HIS ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 ASN ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 96 ASN ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 HIS ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 21 HIS T 52 HIS ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 21 HIS W 33 ASN ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 52 HIS ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.088798 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2630 r_free = 0.2630 target = 0.074366 restraints weight = 27162.284| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 1.80 r_work: 0.2524 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2384 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2384 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.3155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 20904 Z= 0.182 Angle : 0.595 8.204 28536 Z= 0.311 Chirality : 0.050 0.160 3516 Planarity : 0.006 0.040 3660 Dihedral : 4.266 13.781 2892 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.79 % Allowed : 11.51 % Favored : 86.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.16), residues: 2616 helix: 1.45 (0.17), residues: 816 sheet: 0.91 (0.18), residues: 756 loop : 1.17 (0.20), residues: 1044 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG K 64 TYR 0.010 0.002 TYR O 108 PHE 0.013 0.002 PHE K 58 TRP 0.013 0.002 TRP J 98 HIS 0.004 0.001 HIS T 52 Details of bonding type rmsd covalent geometry : bond 0.00421 (20904) covalent geometry : angle 0.59505 (28536) hydrogen bonds : bond 0.04717 ( 1116) hydrogen bonds : angle 4.86219 ( 3024) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 508 time to evaluate : 0.800 Fit side-chains REVERT: B 14 GLU cc_start: 0.8350 (pt0) cc_final: 0.8132 (pt0) REVERT: A 42 TYR cc_start: 0.9395 (p90) cc_final: 0.9190 (p90) REVERT: A 67 LYS cc_start: 0.8550 (mmmt) cc_final: 0.8050 (mppt) REVERT: A 70 GLU cc_start: 0.7817 (mm-30) cc_final: 0.7490 (mp0) REVERT: C 38 GLN cc_start: 0.8529 (OUTLIER) cc_final: 0.8013 (OUTLIER) REVERT: C 52 GLU cc_start: 0.7795 (mp0) cc_final: 0.7590 (mp0) REVERT: C 64 ARG cc_start: 0.8166 (mtt-85) cc_final: 0.7932 (mtt90) REVERT: C 103 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7777 (mtp180) REVERT: D 70 GLU cc_start: 0.7950 (mt-10) cc_final: 0.7485 (mp0) REVERT: E 70 ARG cc_start: 0.8337 (mtp85) cc_final: 0.8087 (mtp180) REVERT: F 67 LYS cc_start: 0.8446 (mmmt) cc_final: 0.7713 (mppt) REVERT: G 26 GLU cc_start: 0.8964 (tt0) cc_final: 0.8521 (tt0) REVERT: G 38 GLN cc_start: 0.8458 (OUTLIER) cc_final: 0.8226 (mm-40) REVERT: G 105 ARG cc_start: 0.8571 (mmt-90) cc_final: 0.8327 (mmt180) REVERT: H 42 TYR cc_start: 0.9297 (p90) cc_final: 0.9004 (p90) REVERT: I 77 ARG cc_start: 0.8220 (OUTLIER) cc_final: 0.8015 (mtt180) REVERT: J 53 GLU cc_start: 0.8802 (OUTLIER) cc_final: 0.8507 (mm-30) REVERT: K 70 ARG cc_start: 0.8347 (mtt90) cc_final: 0.7849 (mmt180) REVERT: L 94 GLU cc_start: 0.8303 (mp0) cc_final: 0.7551 (mp0) REVERT: L 102 ASN cc_start: 0.8798 (OUTLIER) cc_final: 0.8542 (m110) REVERT: M 33 GLU cc_start: 0.7900 (mt-10) cc_final: 0.7635 (mt-10) REVERT: N 70 GLU cc_start: 0.7680 (OUTLIER) cc_final: 0.7099 (mp0) REVERT: O 26 GLU cc_start: 0.8925 (tt0) cc_final: 0.8507 (tt0) REVERT: O 52 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7325 (tp30) REVERT: O 77 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7324 (ttt-90) REVERT: O 116 ARG cc_start: 0.7810 (ttm110) cc_final: 0.7526 (ttp-170) REVERT: P 18 LYS cc_start: 0.8592 (tptt) cc_final: 0.8127 (ttpt) REVERT: P 42 TYR cc_start: 0.9331 (p90) cc_final: 0.8872 (p90) REVERT: P 70 GLU cc_start: 0.7708 (mp0) cc_final: 0.7253 (mp0) REVERT: Q 70 ARG cc_start: 0.8173 (mtt-85) cc_final: 0.7790 (mtt-85) REVERT: Q 115 LEU cc_start: 0.8861 (pp) cc_final: 0.8593 (pp) REVERT: R 70 GLU cc_start: 0.7818 (mm-30) cc_final: 0.7443 (mp0) REVERT: T 18 LYS cc_start: 0.8392 (tptt) cc_final: 0.7926 (ttmt) REVERT: T 67 LYS cc_start: 0.8431 (mmmt) cc_final: 0.7911 (mtmm) REVERT: V 14 GLU cc_start: 0.8449 (pt0) cc_final: 0.8226 (pt0) REVERT: V 41 GLU cc_start: 0.8630 (mt-10) cc_final: 0.8207 (mp0) REVERT: V 75 SER cc_start: 0.9220 (p) cc_final: 0.8903 (m) REVERT: V 114 ARG cc_start: 0.8461 (ptp-170) cc_final: 0.8059 (ptp-170) REVERT: W 70 GLU cc_start: 0.7838 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: W 94 GLU cc_start: 0.8281 (mp0) cc_final: 0.7910 (mp0) REVERT: Y 67 LYS cc_start: 0.8584 (mttt) cc_final: 0.8258 (mttt) outliers start: 40 outliers final: 4 residues processed: 518 average time/residue: 0.9210 time to fit residues: 515.9656 Evaluate side-chains 434 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 422 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain I residue 77 ARG Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain L residue 102 ASN Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 33 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 224 optimal weight: 1.9990 chunk 113 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 231 optimal weight: 0.6980 chunk 180 optimal weight: 0.6980 chunk 149 optimal weight: 0.9980 chunk 128 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 52 HIS ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 102 ASN ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.086450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.071605 restraints weight = 27049.258| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 1.89 r_work: 0.2672 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2527 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.3643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 20904 Z= 0.196 Angle : 0.564 9.057 28536 Z= 0.291 Chirality : 0.050 0.148 3516 Planarity : 0.006 0.039 3660 Dihedral : 4.072 13.252 2892 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 2.87 % Allowed : 13.66 % Favored : 83.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.18 (0.16), residues: 2616 helix: 1.36 (0.17), residues: 816 sheet: 0.29 (0.18), residues: 696 loop : 0.91 (0.19), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 64 TYR 0.012 0.002 TYR Y 95 PHE 0.011 0.002 PHE V 58 TRP 0.009 0.001 TRP J 98 HIS 0.004 0.001 HIS D 21 Details of bonding type rmsd covalent geometry : bond 0.00467 (20904) covalent geometry : angle 0.56404 (28536) hydrogen bonds : bond 0.04609 ( 1116) hydrogen bonds : angle 4.57701 ( 3024) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 483 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 419 time to evaluate : 0.766 Fit side-chains REVERT: A 67 LYS cc_start: 0.8707 (mmmt) cc_final: 0.8259 (mppt) REVERT: A 70 GLU cc_start: 0.7931 (mm-30) cc_final: 0.7559 (mp0) REVERT: C 38 GLN cc_start: 0.8540 (OUTLIER) cc_final: 0.8229 (mp10) REVERT: C 52 GLU cc_start: 0.8066 (mp0) cc_final: 0.7815 (mp0) REVERT: D 67 LYS cc_start: 0.8781 (mmmt) cc_final: 0.8253 (mppt) REVERT: E 61 GLU cc_start: 0.8313 (mm-30) cc_final: 0.7717 (mt-10) REVERT: E 70 ARG cc_start: 0.8535 (mtp85) cc_final: 0.8318 (mtp180) REVERT: F 67 LYS cc_start: 0.8658 (mmmt) cc_final: 0.8112 (mtmm) REVERT: G 38 GLN cc_start: 0.8691 (OUTLIER) cc_final: 0.8440 (mm-40) REVERT: G 41 GLU cc_start: 0.8782 (mt-10) cc_final: 0.8556 (mp0) REVERT: H 42 TYR cc_start: 0.9410 (p90) cc_final: 0.9185 (p90) REVERT: J 70 GLU cc_start: 0.8050 (OUTLIER) cc_final: 0.7610 (mp0) REVERT: K 70 ARG cc_start: 0.8560 (mtt90) cc_final: 0.8053 (mmt180) REVERT: K 114 ARG cc_start: 0.8573 (OUTLIER) cc_final: 0.8107 (ptp-110) REVERT: L 100 ARG cc_start: 0.8898 (mtm110) cc_final: 0.8675 (mtm110) REVERT: N 70 GLU cc_start: 0.7643 (OUTLIER) cc_final: 0.7215 (mp0) REVERT: O 26 GLU cc_start: 0.9018 (tt0) cc_final: 0.8626 (tt0) REVERT: O 77 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7583 (ttt-90) REVERT: O 116 ARG cc_start: 0.7929 (ttm110) cc_final: 0.7667 (ttp-170) REVERT: P 18 LYS cc_start: 0.8701 (tptt) cc_final: 0.8243 (ttpt) REVERT: P 42 TYR cc_start: 0.9461 (p90) cc_final: 0.8940 (p90) REVERT: P 53 GLU cc_start: 0.8593 (OUTLIER) cc_final: 0.8058 (mt-10) REVERT: P 70 GLU cc_start: 0.7797 (mp0) cc_final: 0.7425 (mp0) REVERT: Q 70 ARG cc_start: 0.8496 (mtt-85) cc_final: 0.8120 (mtt-85) REVERT: Q 115 LEU cc_start: 0.9103 (pp) cc_final: 0.8806 (pp) REVERT: R 70 GLU cc_start: 0.7872 (mm-30) cc_final: 0.7546 (mp0) REVERT: T 18 LYS cc_start: 0.8561 (tptt) cc_final: 0.8101 (ttmt) REVERT: T 67 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8085 (mtmm) REVERT: V 14 GLU cc_start: 0.8549 (pt0) cc_final: 0.8311 (pt0) REVERT: V 41 GLU cc_start: 0.8788 (mt-10) cc_final: 0.8418 (mp0) REVERT: V 53 ASP cc_start: 0.9010 (OUTLIER) cc_final: 0.8521 (p0) REVERT: V 75 SER cc_start: 0.9204 (OUTLIER) cc_final: 0.8995 (m) REVERT: V 78 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7517 (tp30) REVERT: W 70 GLU cc_start: 0.7877 (OUTLIER) cc_final: 0.7448 (mp0) REVERT: X 114 ARG cc_start: 0.8666 (OUTLIER) cc_final: 0.8432 (mtm110) REVERT: Y 67 LYS cc_start: 0.8771 (mttt) cc_final: 0.8454 (mttt) outliers start: 64 outliers final: 12 residues processed: 437 average time/residue: 0.9754 time to fit residues: 458.9362 Evaluate side-chains 426 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 403 time to evaluate : 0.700 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain R residue 47 SER Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 75 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 114 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 191 optimal weight: 0.9980 chunk 182 optimal weight: 1.9990 chunk 126 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 239 optimal weight: 0.9980 chunk 60 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 114 optimal weight: 1.9990 chunk 243 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 52 HIS ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.086147 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2586 r_free = 0.2586 target = 0.071125 restraints weight = 27261.900| |-----------------------------------------------------------------------------| r_work (start): 0.2759 rms_B_bonded: 1.93 r_work: 0.2617 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.2474 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.2474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8691 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 20904 Z= 0.206 Angle : 0.565 8.185 28536 Z= 0.288 Chirality : 0.050 0.148 3516 Planarity : 0.006 0.039 3660 Dihedral : 4.076 13.567 2892 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.06 % Favored : 96.90 % Rotamer: Outliers : 2.78 % Allowed : 14.34 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.87 (0.16), residues: 2616 helix: 1.24 (0.17), residues: 816 sheet: 0.07 (0.18), residues: 708 loop : 0.64 (0.19), residues: 1092 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 64 TYR 0.013 0.002 TYR T 42 PHE 0.010 0.002 PHE V 58 TRP 0.006 0.001 TRP J 98 HIS 0.004 0.001 HIS A 52 Details of bonding type rmsd covalent geometry : bond 0.00500 (20904) covalent geometry : angle 0.56480 (28536) hydrogen bonds : bond 0.04507 ( 1116) hydrogen bonds : angle 4.51483 ( 3024) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 462 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 400 time to evaluate : 0.867 Fit side-chains REVERT: B 103 ARG cc_start: 0.8144 (mtm-85) cc_final: 0.7814 (mtm110) REVERT: A 67 LYS cc_start: 0.8695 (mmmt) cc_final: 0.8245 (mppt) REVERT: C 33 GLU cc_start: 0.8617 (tt0) cc_final: 0.8393 (tt0) REVERT: C 38 GLN cc_start: 0.8614 (OUTLIER) cc_final: 0.8257 (mp10) REVERT: E 61 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7704 (mt-10) REVERT: F 42 TYR cc_start: 0.9363 (p90) cc_final: 0.9116 (p90) REVERT: F 67 LYS cc_start: 0.8708 (mmmt) cc_final: 0.8166 (mtmm) REVERT: G 38 GLN cc_start: 0.8627 (OUTLIER) cc_final: 0.7968 (mp10) REVERT: G 41 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8510 (mp0) REVERT: H 42 TYR cc_start: 0.9412 (p90) cc_final: 0.9184 (p90) REVERT: I 114 ARG cc_start: 0.8694 (OUTLIER) cc_final: 0.8256 (ttp-110) REVERT: J 70 GLU cc_start: 0.8038 (OUTLIER) cc_final: 0.7606 (mp0) REVERT: K 70 ARG cc_start: 0.8610 (mtt90) cc_final: 0.8242 (mtt-85) REVERT: K 114 ARG cc_start: 0.8599 (OUTLIER) cc_final: 0.8088 (ptp-110) REVERT: L 67 LYS cc_start: 0.8643 (mppt) cc_final: 0.8423 (mppt) REVERT: L 70 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7862 (mp0) REVERT: M 42 GLU cc_start: 0.8647 (OUTLIER) cc_final: 0.8269 (mt-10) REVERT: M 114 ARG cc_start: 0.8617 (OUTLIER) cc_final: 0.8345 (ptp-110) REVERT: N 70 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7073 (mp0) REVERT: O 77 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.7581 (ttt-90) REVERT: O 116 ARG cc_start: 0.7986 (ttm110) cc_final: 0.7604 (ttp-170) REVERT: P 18 LYS cc_start: 0.8714 (tptt) cc_final: 0.8218 (ttpt) REVERT: P 42 TYR cc_start: 0.9462 (p90) cc_final: 0.9242 (p90) REVERT: P 53 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.8092 (mt-10) REVERT: P 70 GLU cc_start: 0.7829 (mp0) cc_final: 0.7424 (mp0) REVERT: Q 70 ARG cc_start: 0.8539 (mtt-85) cc_final: 0.8144 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8449 (OUTLIER) cc_final: 0.8094 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.7745 (ptp-110) REVERT: R 70 GLU cc_start: 0.7842 (mm-30) cc_final: 0.7468 (mp0) REVERT: S 64 ARG cc_start: 0.8412 (mpt90) cc_final: 0.8179 (mpt90) REVERT: S 114 ARG cc_start: 0.8815 (OUTLIER) cc_final: 0.8612 (ttp-110) REVERT: T 18 LYS cc_start: 0.8555 (tptt) cc_final: 0.8088 (ttmt) REVERT: T 67 LYS cc_start: 0.8531 (mmmt) cc_final: 0.8042 (mtmm) REVERT: V 14 GLU cc_start: 0.8595 (pt0) cc_final: 0.8367 (pt0) REVERT: V 41 GLU cc_start: 0.8765 (mt-10) cc_final: 0.8391 (mp0) REVERT: V 53 ASP cc_start: 0.9014 (OUTLIER) cc_final: 0.8510 (p0) REVERT: V 75 SER cc_start: 0.9221 (OUTLIER) cc_final: 0.8932 (m) REVERT: V 78 GLU cc_start: 0.8106 (mm-30) cc_final: 0.7756 (tp30) REVERT: W 70 GLU cc_start: 0.7805 (OUTLIER) cc_final: 0.7321 (mp0) REVERT: X 114 ARG cc_start: 0.8648 (OUTLIER) cc_final: 0.8407 (mtm110) REVERT: Y 67 LYS cc_start: 0.8787 (mttt) cc_final: 0.8467 (mttt) outliers start: 62 outliers final: 21 residues processed: 418 average time/residue: 0.9874 time to fit residues: 444.5060 Evaluate side-chains 435 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 397 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain H residue 50 SER Chi-restraints excluded: chain I residue 30 LYS Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 52 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 114 ARG Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain V residue 75 SER Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 30 LYS Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 114 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 121 optimal weight: 0.8980 chunk 218 optimal weight: 0.0870 chunk 240 optimal weight: 1.9990 chunk 99 optimal weight: 0.4980 chunk 158 optimal weight: 1.9990 chunk 217 optimal weight: 0.7980 chunk 95 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 176 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 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 = 0.2837 r_free = 0.2837 target = 0.087432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2608 r_free = 0.2608 target = 0.072421 restraints weight = 27101.934| |-----------------------------------------------------------------------------| r_work (start): 0.2947 rms_B_bonded: 1.95 r_work: 0.2801 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.3975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20904 Z= 0.149 Angle : 0.516 8.757 28536 Z= 0.263 Chirality : 0.048 0.147 3516 Planarity : 0.005 0.034 3660 Dihedral : 3.905 13.152 2892 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.13 % Favored : 96.79 % Rotamer: Outliers : 2.91 % Allowed : 14.11 % Favored : 82.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.98 (0.16), residues: 2616 helix: 1.36 (0.17), residues: 816 sheet: -0.02 (0.17), residues: 780 loop : 0.87 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 64 TYR 0.013 0.002 TYR T 42 PHE 0.009 0.002 PHE T 65 TRP 0.005 0.001 TRP B 95 HIS 0.003 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00354 (20904) covalent geometry : angle 0.51555 (28536) hydrogen bonds : bond 0.04052 ( 1116) hydrogen bonds : angle 4.44465 ( 3024) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 472 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 407 time to evaluate : 0.852 Fit side-chains REVERT: B 103 ARG cc_start: 0.8143 (mtm-85) cc_final: 0.7818 (mtm110) REVERT: C 33 GLU cc_start: 0.8613 (tt0) cc_final: 0.8403 (tt0) REVERT: C 38 GLN cc_start: 0.8643 (OUTLIER) cc_final: 0.8295 (mp10) REVERT: E 61 GLU cc_start: 0.8320 (mm-30) cc_final: 0.7686 (mt-10) REVERT: F 42 TYR cc_start: 0.9359 (p90) cc_final: 0.9151 (p90) REVERT: F 67 LYS cc_start: 0.8700 (mmmt) cc_final: 0.8221 (mtmm) REVERT: G 38 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8152 (mp10) REVERT: G 41 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8511 (mp0) REVERT: G 115 LEU cc_start: 0.9138 (OUTLIER) cc_final: 0.8676 (pp) REVERT: I 114 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.8266 (ttp-110) REVERT: J 70 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7611 (mp0) REVERT: K 64 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7673 (mtt180) REVERT: K 70 ARG cc_start: 0.8597 (mtt90) cc_final: 0.8235 (mtt-85) REVERT: K 114 ARG cc_start: 0.8555 (OUTLIER) cc_final: 0.8014 (ptp-110) REVERT: L 70 GLU cc_start: 0.8290 (mt-10) cc_final: 0.7857 (mp0) REVERT: M 30 LYS cc_start: 0.9022 (OUTLIER) cc_final: 0.8452 (mmmt) REVERT: M 42 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8319 (mt-10) REVERT: N 70 GLU cc_start: 0.7558 (OUTLIER) cc_final: 0.7065 (mp0) REVERT: O 41 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8370 (mp0) REVERT: O 52 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7197 (tp30) REVERT: O 77 ARG cc_start: 0.8181 (OUTLIER) cc_final: 0.7296 (ttt-90) REVERT: O 116 ARG cc_start: 0.7972 (ttm110) cc_final: 0.7597 (ttp-170) REVERT: P 18 LYS cc_start: 0.8684 (tptt) cc_final: 0.8247 (ttpt) REVERT: P 42 TYR cc_start: 0.9464 (p90) cc_final: 0.9253 (p90) REVERT: P 53 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8011 (mt-10) REVERT: P 70 GLU cc_start: 0.7789 (mp0) cc_final: 0.7403 (mp0) REVERT: Q 41 GLU cc_start: 0.8699 (OUTLIER) cc_final: 0.8381 (mp0) REVERT: Q 70 ARG cc_start: 0.8546 (mtt-85) cc_final: 0.8170 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8443 (OUTLIER) cc_final: 0.8012 (ttt-90) REVERT: R 51 ASP cc_start: 0.8443 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: R 70 GLU cc_start: 0.7815 (mm-30) cc_final: 0.7454 (mp0) REVERT: S 64 ARG cc_start: 0.8467 (mpt90) cc_final: 0.8246 (mpt90) REVERT: T 18 LYS cc_start: 0.8487 (tptt) cc_final: 0.8057 (ttmt) REVERT: T 67 LYS cc_start: 0.8516 (mmmt) cc_final: 0.8032 (mtmm) REVERT: V 14 GLU cc_start: 0.8548 (pt0) cc_final: 0.8318 (pt0) REVERT: V 41 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8371 (mp0) REVERT: V 53 ASP cc_start: 0.8964 (OUTLIER) cc_final: 0.8461 (p0) REVERT: V 78 GLU cc_start: 0.8073 (mm-30) cc_final: 0.7558 (tp30) REVERT: W 70 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7355 (mp0) REVERT: Y 18 LYS cc_start: 0.8780 (tptt) cc_final: 0.8286 (ttpt) REVERT: Y 67 LYS cc_start: 0.8789 (mttt) cc_final: 0.8455 (mttt) outliers start: 65 outliers final: 15 residues processed: 427 average time/residue: 0.9954 time to fit residues: 458.2687 Evaluate side-chains 429 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 397 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain R residue 51 ASP Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 63 ASP Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 103 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 137 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 229 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 31 optimal weight: 0.5980 chunk 247 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 92 ASN ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 52 HIS ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.086234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.071381 restraints weight = 27024.035| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 1.92 r_work: 0.2774 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2631 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8791 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20904 Z= 0.160 Angle : 0.526 8.089 28536 Z= 0.267 Chirality : 0.048 0.147 3516 Planarity : 0.005 0.044 3660 Dihedral : 3.897 13.469 2892 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.51 % Allowed : 15.68 % Favored : 81.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.95 (0.16), residues: 2616 helix: 1.35 (0.17), residues: 816 sheet: -0.06 (0.17), residues: 780 loop : 0.86 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 64 TYR 0.014 0.002 TYR T 42 PHE 0.009 0.002 PHE T 65 TRP 0.004 0.001 TRP T 98 HIS 0.003 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00384 (20904) covalent geometry : angle 0.52624 (28536) hydrogen bonds : bond 0.04099 ( 1116) hydrogen bonds : angle 4.44298 ( 3024) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 459 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 403 time to evaluate : 0.825 Fit side-chains REVERT: B 103 ARG cc_start: 0.8206 (mtm-85) cc_final: 0.7882 (mtm110) REVERT: A 70 GLU cc_start: 0.7913 (mm-30) cc_final: 0.7488 (mp0) REVERT: C 38 GLN cc_start: 0.8710 (OUTLIER) cc_final: 0.8350 (mp10) REVERT: E 61 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7885 (mt-10) REVERT: F 42 TYR cc_start: 0.9407 (p90) cc_final: 0.9192 (p90) REVERT: F 67 LYS cc_start: 0.8816 (mmmt) cc_final: 0.8412 (mtmm) REVERT: G 38 GLN cc_start: 0.8721 (OUTLIER) cc_final: 0.8519 (mm-40) REVERT: G 41 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8591 (mp0) REVERT: G 115 LEU cc_start: 0.9229 (OUTLIER) cc_final: 0.8776 (pp) REVERT: I 114 ARG cc_start: 0.8674 (OUTLIER) cc_final: 0.8286 (ttp-110) REVERT: J 70 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7712 (mp0) REVERT: K 61 GLU cc_start: 0.8541 (mt-10) cc_final: 0.8089 (mm-30) REVERT: K 64 ARG cc_start: 0.8263 (mtt-85) cc_final: 0.7785 (mtt180) REVERT: K 70 ARG cc_start: 0.8659 (mtt90) cc_final: 0.8360 (mtt-85) REVERT: K 114 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8072 (ptp-110) REVERT: L 70 GLU cc_start: 0.8398 (mt-10) cc_final: 0.8071 (mp0) REVERT: M 30 LYS cc_start: 0.9095 (OUTLIER) cc_final: 0.8664 (mmmt) REVERT: M 42 GLU cc_start: 0.8628 (OUTLIER) cc_final: 0.8351 (mt-10) REVERT: M 114 ARG cc_start: 0.8606 (OUTLIER) cc_final: 0.8326 (ptp-110) REVERT: N 70 GLU cc_start: 0.7709 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: O 77 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7654 (ttt-90) REVERT: O 116 ARG cc_start: 0.8096 (ttm110) cc_final: 0.7752 (ttp-170) REVERT: P 18 LYS cc_start: 0.8783 (tptt) cc_final: 0.8419 (ttpt) REVERT: P 40 SER cc_start: 0.9177 (t) cc_final: 0.8965 (m) REVERT: P 53 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.8025 (mt-10) REVERT: P 70 GLU cc_start: 0.7907 (OUTLIER) cc_final: 0.7595 (mp0) REVERT: Q 41 GLU cc_start: 0.8741 (OUTLIER) cc_final: 0.8487 (mp0) REVERT: Q 70 ARG cc_start: 0.8623 (mtt-85) cc_final: 0.8279 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8488 (OUTLIER) cc_final: 0.8133 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8609 (OUTLIER) cc_final: 0.7826 (ptp-110) REVERT: Q 115 LEU cc_start: 0.9269 (OUTLIER) cc_final: 0.8984 (pp) REVERT: R 70 GLU cc_start: 0.7912 (mm-30) cc_final: 0.7622 (mp0) REVERT: R 73 LYS cc_start: 0.9046 (mttp) cc_final: 0.8840 (mttm) REVERT: T 18 LYS cc_start: 0.8681 (tptt) cc_final: 0.8312 (ttmt) REVERT: T 67 LYS cc_start: 0.8625 (mmmt) cc_final: 0.8225 (mtmm) REVERT: V 14 GLU cc_start: 0.8595 (pt0) cc_final: 0.8365 (pt0) REVERT: V 41 GLU cc_start: 0.8808 (mt-10) cc_final: 0.8501 (mp0) REVERT: V 53 ASP cc_start: 0.9034 (OUTLIER) cc_final: 0.8565 (p0) REVERT: W 70 GLU cc_start: 0.7946 (OUTLIER) cc_final: 0.7567 (mp0) REVERT: Y 18 LYS cc_start: 0.8876 (tptt) cc_final: 0.8445 (ttpt) REVERT: Y 67 LYS cc_start: 0.8879 (mttt) cc_final: 0.8608 (mttt) outliers start: 56 outliers final: 17 residues processed: 418 average time/residue: 1.0207 time to fit residues: 458.6405 Evaluate side-chains 427 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 391 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 215 optimal weight: 0.9980 chunk 130 optimal weight: 0.9990 chunk 155 optimal weight: 0.6980 chunk 183 optimal weight: 2.9990 chunk 233 optimal weight: 0.9990 chunk 66 optimal weight: 1.9990 chunk 163 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 chunk 173 optimal weight: 0.2980 chunk 139 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.086428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2589 r_free = 0.2589 target = 0.071699 restraints weight = 27068.408| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.89 r_work: 0.2799 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2657 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20904 Z= 0.167 Angle : 0.531 7.795 28536 Z= 0.269 Chirality : 0.048 0.146 3516 Planarity : 0.005 0.037 3660 Dihedral : 3.919 13.231 2892 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.29 % Favored : 96.67 % Rotamer: Outliers : 2.46 % Allowed : 15.86 % Favored : 81.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), residues: 2616 helix: 1.33 (0.17), residues: 816 sheet: -0.09 (0.17), residues: 780 loop : 0.85 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG V 64 TYR 0.015 0.002 TYR T 42 PHE 0.009 0.002 PHE T 65 TRP 0.004 0.001 TRP C 95 HIS 0.003 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00401 (20904) covalent geometry : angle 0.53068 (28536) hydrogen bonds : bond 0.04113 ( 1116) hydrogen bonds : angle 4.43885 ( 3024) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 397 time to evaluate : 0.737 Fit side-chains REVERT: B 68 MET cc_start: 0.9378 (mtt) cc_final: 0.9169 (mtt) REVERT: B 103 ARG cc_start: 0.8034 (mtm-85) cc_final: 0.7683 (mtm110) REVERT: A 70 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7255 (mp0) REVERT: C 38 GLN cc_start: 0.8685 (OUTLIER) cc_final: 0.8313 (mp10) REVERT: E 61 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7680 (mt-10) REVERT: F 42 TYR cc_start: 0.9358 (p90) cc_final: 0.9131 (p90) REVERT: F 67 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8225 (mtmm) REVERT: G 38 GLN cc_start: 0.8687 (OUTLIER) cc_final: 0.8486 (mm-40) REVERT: G 41 GLU cc_start: 0.8795 (mt-10) cc_final: 0.8431 (mp0) REVERT: G 115 LEU cc_start: 0.9144 (OUTLIER) cc_final: 0.8795 (pp) REVERT: I 114 ARG cc_start: 0.8672 (OUTLIER) cc_final: 0.8252 (ttp-110) REVERT: J 53 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.8295 (mt-10) REVERT: J 70 GLU cc_start: 0.7992 (OUTLIER) cc_final: 0.7687 (mp0) REVERT: K 61 GLU cc_start: 0.8432 (mt-10) cc_final: 0.7884 (mm-30) REVERT: K 64 ARG cc_start: 0.8139 (mtt-85) cc_final: 0.7641 (mtt180) REVERT: K 70 ARG cc_start: 0.8559 (mtt90) cc_final: 0.8204 (mtt-85) REVERT: K 114 ARG cc_start: 0.8554 (OUTLIER) cc_final: 0.8033 (ptp-110) REVERT: L 70 GLU cc_start: 0.8173 (mt-10) cc_final: 0.7723 (mp0) REVERT: M 30 LYS cc_start: 0.8948 (OUTLIER) cc_final: 0.8420 (mmmt) REVERT: M 42 GLU cc_start: 0.8592 (OUTLIER) cc_final: 0.8364 (mt-10) REVERT: M 114 ARG cc_start: 0.8601 (OUTLIER) cc_final: 0.8322 (ptp-110) REVERT: N 70 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.6976 (mp0) REVERT: O 64 ARG cc_start: 0.8282 (mmt180) cc_final: 0.7941 (mmt90) REVERT: O 77 ARG cc_start: 0.8177 (OUTLIER) cc_final: 0.7549 (ttt-90) REVERT: O 116 ARG cc_start: 0.7966 (ttm110) cc_final: 0.7564 (ttp-170) REVERT: P 18 LYS cc_start: 0.8671 (tptt) cc_final: 0.8211 (ttpt) REVERT: P 40 SER cc_start: 0.9216 (t) cc_final: 0.8952 (m) REVERT: P 53 GLU cc_start: 0.8513 (OUTLIER) cc_final: 0.7950 (mt-10) REVERT: P 70 GLU cc_start: 0.7737 (OUTLIER) cc_final: 0.7372 (mp0) REVERT: Q 41 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8409 (mp0) REVERT: Q 70 ARG cc_start: 0.8540 (mtt-85) cc_final: 0.8162 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8413 (OUTLIER) cc_final: 0.8055 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8588 (OUTLIER) cc_final: 0.7788 (ptp-110) REVERT: Q 115 LEU cc_start: 0.9127 (OUTLIER) cc_final: 0.8817 (pp) REVERT: R 70 GLU cc_start: 0.7699 (mm-30) cc_final: 0.7318 (mp0) REVERT: T 18 LYS cc_start: 0.8546 (tptt) cc_final: 0.8116 (ttmt) REVERT: T 67 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8006 (mtmm) REVERT: V 14 GLU cc_start: 0.8590 (pt0) cc_final: 0.8336 (pt0) REVERT: V 41 GLU cc_start: 0.8692 (mt-10) cc_final: 0.8350 (mp0) REVERT: V 53 ASP cc_start: 0.8963 (OUTLIER) cc_final: 0.8454 (p0) REVERT: V 78 GLU cc_start: 0.8058 (mm-30) cc_final: 0.7562 (tp30) REVERT: W 70 GLU cc_start: 0.7763 (OUTLIER) cc_final: 0.7349 (mp0) REVERT: X 116 ARG cc_start: 0.7945 (ttm-80) cc_final: 0.7724 (ttm-80) REVERT: Y 18 LYS cc_start: 0.8757 (tptt) cc_final: 0.8252 (ttpt) REVERT: Y 67 LYS cc_start: 0.8776 (mttt) cc_final: 0.8440 (mttt) outliers start: 55 outliers final: 20 residues processed: 412 average time/residue: 1.0176 time to fit residues: 451.1282 Evaluate side-chains 434 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 394 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 38 GLN Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 19 optimal weight: 0.8980 chunk 203 optimal weight: 2.9990 chunk 12 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 70 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 168 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 209 optimal weight: 0.9990 chunk 83 optimal weight: 0.7980 chunk 192 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 92 ASN Y 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.086576 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.071737 restraints weight = 27076.460| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 1.91 r_work: 0.2789 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.4110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 20904 Z= 0.178 Angle : 0.540 7.639 28536 Z= 0.274 Chirality : 0.049 0.146 3516 Planarity : 0.005 0.035 3660 Dihedral : 3.965 13.373 2892 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.42 % Allowed : 16.17 % Favored : 81.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.88 (0.16), residues: 2616 helix: 1.29 (0.17), residues: 816 sheet: -0.11 (0.17), residues: 780 loop : 0.83 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG O 114 TYR 0.015 0.002 TYR T 42 PHE 0.009 0.002 PHE T 65 TRP 0.004 0.001 TRP T 98 HIS 0.003 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00430 (20904) covalent geometry : angle 0.54021 (28536) hydrogen bonds : bond 0.04187 ( 1116) hydrogen bonds : angle 4.44619 ( 3024) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 403 time to evaluate : 0.698 Fit side-chains REVERT: B 103 ARG cc_start: 0.8154 (mtm-85) cc_final: 0.7844 (mtm110) REVERT: A 70 GLU cc_start: 0.7885 (mm-30) cc_final: 0.7434 (mp0) REVERT: C 38 GLN cc_start: 0.8698 (OUTLIER) cc_final: 0.8364 (mp10) REVERT: E 61 GLU cc_start: 0.8387 (mm-30) cc_final: 0.7842 (mt-10) REVERT: F 42 TYR cc_start: 0.9394 (p90) cc_final: 0.9149 (p90) REVERT: F 67 LYS cc_start: 0.8864 (mmmt) cc_final: 0.8408 (mtmm) REVERT: G 41 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8508 (mp0) REVERT: G 115 LEU cc_start: 0.9243 (OUTLIER) cc_final: 0.8930 (pp) REVERT: I 114 ARG cc_start: 0.8682 (OUTLIER) cc_final: 0.8262 (ttp-110) REVERT: J 53 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8341 (mt-10) REVERT: J 70 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7804 (mp0) REVERT: K 61 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8032 (mm-30) REVERT: K 64 ARG cc_start: 0.8244 (mtt-85) cc_final: 0.7773 (mtt180) REVERT: K 70 ARG cc_start: 0.8616 (mtt90) cc_final: 0.8306 (mtt-85) REVERT: K 114 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.8073 (ptp-110) REVERT: L 70 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7925 (mp0) REVERT: M 30 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8611 (mmmt) REVERT: M 42 GLU cc_start: 0.8669 (OUTLIER) cc_final: 0.8454 (mt-10) REVERT: M 114 ARG cc_start: 0.8620 (OUTLIER) cc_final: 0.8317 (ptp-110) REVERT: N 70 GLU cc_start: 0.7633 (OUTLIER) cc_final: 0.7148 (mp0) REVERT: O 64 ARG cc_start: 0.8380 (mmt180) cc_final: 0.8051 (mmt90) REVERT: O 77 ARG cc_start: 0.8247 (OUTLIER) cc_final: 0.7632 (ttt-90) REVERT: O 116 ARG cc_start: 0.8039 (ttm110) cc_final: 0.7668 (ttp-170) REVERT: P 18 LYS cc_start: 0.8770 (tptt) cc_final: 0.8365 (ttpt) REVERT: P 40 SER cc_start: 0.9179 (t) cc_final: 0.8950 (m) REVERT: P 53 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: P 70 GLU cc_start: 0.7865 (OUTLIER) cc_final: 0.7558 (mp0) REVERT: Q 41 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8458 (mp0) REVERT: Q 70 ARG cc_start: 0.8592 (mtt-85) cc_final: 0.8240 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8160 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.7664 (ptp-110) REVERT: Q 115 LEU cc_start: 0.9250 (OUTLIER) cc_final: 0.8950 (pp) REVERT: R 70 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7514 (mp0) REVERT: T 18 LYS cc_start: 0.8657 (tptt) cc_final: 0.8269 (ttmt) REVERT: T 67 LYS cc_start: 0.8604 (mmmt) cc_final: 0.8185 (mtmm) REVERT: V 14 GLU cc_start: 0.8622 (pt0) cc_final: 0.8377 (pt0) REVERT: V 38 GLN cc_start: 0.8483 (OUTLIER) cc_final: 0.7518 (mp10) REVERT: V 41 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8518 (mp0) REVERT: V 53 ASP cc_start: 0.9035 (OUTLIER) cc_final: 0.8558 (p0) REVERT: W 70 GLU cc_start: 0.7898 (OUTLIER) cc_final: 0.7508 (mp0) REVERT: Y 18 LYS cc_start: 0.8855 (tptt) cc_final: 0.8402 (ttpt) REVERT: Y 67 LYS cc_start: 0.8865 (mttt) cc_final: 0.8579 (mttt) outliers start: 54 outliers final: 23 residues processed: 419 average time/residue: 1.0047 time to fit residues: 453.4640 Evaluate side-chains 443 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 400 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 38 GLN Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain C residue 52 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 53 ASP Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 38 GLN Chi-restraints excluded: chain V residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 114 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 223 optimal weight: 0.7980 chunk 169 optimal weight: 1.9990 chunk 233 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 chunk 227 optimal weight: 0.4980 chunk 230 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 187 optimal weight: 1.9990 chunk 192 optimal weight: 1.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2819 r_free = 0.2819 target = 0.086626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.071971 restraints weight = 27071.617| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 1.88 r_work: 0.2808 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.4176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 20904 Z= 0.156 Angle : 0.525 8.336 28536 Z= 0.267 Chirality : 0.048 0.147 3516 Planarity : 0.005 0.046 3660 Dihedral : 3.900 13.164 2892 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.25 % Favored : 96.71 % Rotamer: Outliers : 2.28 % Allowed : 16.26 % Favored : 81.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.90 (0.16), residues: 2616 helix: 1.34 (0.17), residues: 816 sheet: -0.12 (0.17), residues: 780 loop : 0.85 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG V 64 TYR 0.015 0.001 TYR T 42 PHE 0.010 0.002 PHE T 65 TRP 0.004 0.001 TRP P 98 HIS 0.003 0.001 HIS R 21 Details of bonding type rmsd covalent geometry : bond 0.00373 (20904) covalent geometry : angle 0.52524 (28536) hydrogen bonds : bond 0.04011 ( 1116) hydrogen bonds : angle 4.42550 ( 3024) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 458 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 407 time to evaluate : 0.641 Fit side-chains REVERT: B 103 ARG cc_start: 0.8016 (mtm-85) cc_final: 0.7675 (mtm110) REVERT: A 70 GLU cc_start: 0.7720 (mm-30) cc_final: 0.7362 (mp0) REVERT: E 61 GLU cc_start: 0.8322 (mm-30) cc_final: 0.7678 (mt-10) REVERT: F 42 TYR cc_start: 0.9349 (p90) cc_final: 0.9083 (p90) REVERT: F 67 LYS cc_start: 0.8735 (mmmt) cc_final: 0.8258 (mtmm) REVERT: G 41 GLU cc_start: 0.8705 (mt-10) cc_final: 0.8341 (mp0) REVERT: G 115 LEU cc_start: 0.9107 (OUTLIER) cc_final: 0.8794 (pp) REVERT: I 114 ARG cc_start: 0.8665 (OUTLIER) cc_final: 0.8279 (ttp-110) REVERT: J 53 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.8266 (mt-10) REVERT: J 70 GLU cc_start: 0.8013 (OUTLIER) cc_final: 0.7706 (mp0) REVERT: K 64 ARG cc_start: 0.8147 (mtt-85) cc_final: 0.7675 (mtt180) REVERT: K 70 ARG cc_start: 0.8551 (mtt90) cc_final: 0.8186 (mtt-85) REVERT: K 114 ARG cc_start: 0.8545 (OUTLIER) cc_final: 0.8031 (ptp-110) REVERT: L 70 GLU cc_start: 0.8160 (mt-10) cc_final: 0.7742 (mp0) REVERT: M 14 GLU cc_start: 0.8365 (pt0) cc_final: 0.7917 (mt-10) REVERT: M 30 LYS cc_start: 0.8992 (OUTLIER) cc_final: 0.8419 (mmmt) REVERT: M 42 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.8369 (mt-10) REVERT: M 114 ARG cc_start: 0.8592 (OUTLIER) cc_final: 0.8299 (ptp-110) REVERT: N 70 GLU cc_start: 0.7445 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: O 52 GLU cc_start: 0.8152 (OUTLIER) cc_final: 0.7189 (tp30) REVERT: O 64 ARG cc_start: 0.8312 (mmt180) cc_final: 0.7968 (mmt90) REVERT: O 77 ARG cc_start: 0.8185 (OUTLIER) cc_final: 0.7297 (ttt-90) REVERT: O 116 ARG cc_start: 0.7933 (ttm110) cc_final: 0.7541 (ttp-170) REVERT: P 18 LYS cc_start: 0.8672 (tptt) cc_final: 0.8211 (ttpt) REVERT: P 40 SER cc_start: 0.9207 (t) cc_final: 0.8941 (m) REVERT: P 53 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: P 70 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7351 (mp0) REVERT: Q 41 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8407 (mp0) REVERT: Q 61 GLU cc_start: 0.8329 (mt-10) cc_final: 0.8064 (mm-30) REVERT: Q 70 ARG cc_start: 0.8528 (mtt-85) cc_final: 0.8152 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8417 (OUTLIER) cc_final: 0.8055 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8542 (OUTLIER) cc_final: 0.7714 (ptp-110) REVERT: Q 115 LEU cc_start: 0.9120 (OUTLIER) cc_final: 0.8798 (pp) REVERT: R 70 GLU cc_start: 0.7719 (mm-30) cc_final: 0.7338 (mp0) REVERT: R 73 LYS cc_start: 0.8899 (mttp) cc_final: 0.8658 (mmtm) REVERT: T 18 LYS cc_start: 0.8537 (tptt) cc_final: 0.8113 (ttmt) REVERT: T 67 LYS cc_start: 0.8495 (mmmt) cc_final: 0.8012 (mtmm) REVERT: V 14 GLU cc_start: 0.8575 (pt0) cc_final: 0.8320 (pt0) REVERT: V 41 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8415 (mp0) REVERT: V 42 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8227 (mt-10) REVERT: V 53 ASP cc_start: 0.8958 (OUTLIER) cc_final: 0.8460 (p0) REVERT: V 78 GLU cc_start: 0.8071 (mm-30) cc_final: 0.7732 (tp30) REVERT: W 70 GLU cc_start: 0.7753 (OUTLIER) cc_final: 0.7310 (mp0) REVERT: Y 18 LYS cc_start: 0.8751 (tptt) cc_final: 0.8253 (ttpt) REVERT: Y 67 LYS cc_start: 0.8778 (mttt) cc_final: 0.8441 (mttt) outliers start: 51 outliers final: 19 residues processed: 422 average time/residue: 1.0034 time to fit residues: 455.8203 Evaluate side-chains 438 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 399 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 52 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 52 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 114 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 90 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 212 optimal weight: 1.9990 chunk 125 optimal weight: 0.9990 chunk 101 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 112 optimal weight: 0.2980 chunk 158 optimal weight: 0.9990 chunk 154 optimal weight: 0.8980 chunk 127 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 92 ASN ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 102 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.085940 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2582 r_free = 0.2582 target = 0.071222 restraints weight = 27240.145| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.88 r_work: 0.2662 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8702 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 20904 Z= 0.179 Angle : 0.547 8.087 28536 Z= 0.277 Chirality : 0.049 0.147 3516 Planarity : 0.005 0.039 3660 Dihedral : 3.970 13.421 2892 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 2.15 % Allowed : 16.67 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2616 helix: 1.28 (0.17), residues: 816 sheet: -0.15 (0.17), residues: 780 loop : 0.81 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG O 114 TYR 0.017 0.002 TYR T 42 PHE 0.009 0.002 PHE E 48 TRP 0.004 0.001 TRP T 98 HIS 0.004 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00432 (20904) covalent geometry : angle 0.54732 (28536) hydrogen bonds : bond 0.04183 ( 1116) hydrogen bonds : angle 4.45783 ( 3024) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5232 Ramachandran restraints generated. 2616 Oldfield, 0 Emsley, 2616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 454 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 406 time to evaluate : 0.765 Fit side-chains REVERT: B 103 ARG cc_start: 0.8059 (mtm-85) cc_final: 0.7721 (mtm110) REVERT: A 70 GLU cc_start: 0.7790 (mm-30) cc_final: 0.7437 (mp0) REVERT: E 14 GLU cc_start: 0.8253 (pt0) cc_final: 0.8041 (mt-10) REVERT: E 61 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7739 (mt-10) REVERT: F 42 TYR cc_start: 0.9383 (p90) cc_final: 0.9129 (p90) REVERT: F 67 LYS cc_start: 0.8769 (mmmt) cc_final: 0.8313 (mtmm) REVERT: F 70 GLU cc_start: 0.7696 (mp0) cc_final: 0.7466 (mm-30) REVERT: G 41 GLU cc_start: 0.8723 (mt-10) cc_final: 0.8374 (mp0) REVERT: G 115 LEU cc_start: 0.9158 (OUTLIER) cc_final: 0.8912 (pp) REVERT: I 14 GLU cc_start: 0.8349 (pt0) cc_final: 0.8069 (mt-10) REVERT: I 114 ARG cc_start: 0.8679 (OUTLIER) cc_final: 0.8273 (ttp-110) REVERT: J 53 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8339 (mt-10) REVERT: J 70 GLU cc_start: 0.8046 (OUTLIER) cc_final: 0.7754 (mp0) REVERT: K 64 ARG cc_start: 0.8175 (mtt-85) cc_final: 0.7706 (mtt180) REVERT: K 70 ARG cc_start: 0.8571 (mtt90) cc_final: 0.8222 (mtt-85) REVERT: K 114 ARG cc_start: 0.8579 (OUTLIER) cc_final: 0.8069 (ptp-110) REVERT: L 70 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7823 (mp0) REVERT: M 14 GLU cc_start: 0.8296 (pt0) cc_final: 0.7814 (mt-10) REVERT: M 30 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8499 (mmmt) REVERT: M 42 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8445 (mt-10) REVERT: M 114 ARG cc_start: 0.8603 (OUTLIER) cc_final: 0.8291 (ptp-110) REVERT: N 70 GLU cc_start: 0.7519 (OUTLIER) cc_final: 0.7040 (mp0) REVERT: O 64 ARG cc_start: 0.8346 (mmt180) cc_final: 0.8009 (mmt90) REVERT: O 77 ARG cc_start: 0.8222 (OUTLIER) cc_final: 0.7470 (ttt-90) REVERT: O 116 ARG cc_start: 0.7974 (ttm110) cc_final: 0.7593 (ttp-170) REVERT: P 18 LYS cc_start: 0.8738 (tptt) cc_final: 0.8280 (ttpt) REVERT: P 40 SER cc_start: 0.9199 (t) cc_final: 0.8954 (m) REVERT: P 53 GLU cc_start: 0.8520 (OUTLIER) cc_final: 0.7953 (mt-10) REVERT: P 70 GLU cc_start: 0.7803 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: Q 41 GLU cc_start: 0.8721 (OUTLIER) cc_final: 0.8412 (mp0) REVERT: Q 61 GLU cc_start: 0.8346 (mt-10) cc_final: 0.8109 (mm-30) REVERT: Q 70 ARG cc_start: 0.8576 (mtt-85) cc_final: 0.8214 (mtt-85) REVERT: Q 77 ARG cc_start: 0.8426 (OUTLIER) cc_final: 0.8075 (ttt-90) REVERT: Q 114 ARG cc_start: 0.8537 (OUTLIER) cc_final: 0.7625 (ptp-110) REVERT: Q 115 LEU cc_start: 0.9179 (OUTLIER) cc_final: 0.8870 (pp) REVERT: R 70 GLU cc_start: 0.7786 (mm-30) cc_final: 0.7431 (mp0) REVERT: T 18 LYS cc_start: 0.8609 (tptt) cc_final: 0.8183 (ttmt) REVERT: T 67 LYS cc_start: 0.8540 (mmmt) cc_final: 0.8077 (mtmm) REVERT: V 14 GLU cc_start: 0.8556 (pt0) cc_final: 0.8308 (pt0) REVERT: V 38 GLN cc_start: 0.8619 (OUTLIER) cc_final: 0.7758 (mp10) REVERT: V 41 GLU cc_start: 0.8784 (mt-10) cc_final: 0.8450 (mp0) REVERT: V 53 ASP cc_start: 0.9024 (OUTLIER) cc_final: 0.8526 (p0) REVERT: V 78 GLU cc_start: 0.8086 (mm-30) cc_final: 0.7615 (tp30) REVERT: W 70 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7373 (mp0) REVERT: X 14 GLU cc_start: 0.8410 (pt0) cc_final: 0.8165 (mt-10) REVERT: Y 18 LYS cc_start: 0.8792 (tptt) cc_final: 0.8304 (ttpt) REVERT: Y 67 LYS cc_start: 0.8813 (mttt) cc_final: 0.8494 (mttt) outliers start: 48 outliers final: 21 residues processed: 421 average time/residue: 1.0065 time to fit residues: 456.0071 Evaluate side-chains 446 residues out of total 2232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 406 time to evaluate : 0.912 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 42 GLU Chi-restraints excluded: chain C residue 42 GLU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain E residue 42 GLU Chi-restraints excluded: chain E residue 53 ASP Chi-restraints excluded: chain F residue 69 LYS Chi-restraints excluded: chain G residue 42 GLU Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain I residue 42 GLU Chi-restraints excluded: chain I residue 114 ARG Chi-restraints excluded: chain J residue 53 GLU Chi-restraints excluded: chain J residue 70 GLU Chi-restraints excluded: chain K residue 42 GLU Chi-restraints excluded: chain K residue 114 ARG Chi-restraints excluded: chain L residue 50 SER Chi-restraints excluded: chain M residue 30 LYS Chi-restraints excluded: chain M residue 42 GLU Chi-restraints excluded: chain M residue 114 ARG Chi-restraints excluded: chain N residue 70 GLU Chi-restraints excluded: chain O residue 42 GLU Chi-restraints excluded: chain O residue 77 ARG Chi-restraints excluded: chain P residue 53 GLU Chi-restraints excluded: chain P residue 70 GLU Chi-restraints excluded: chain P residue 99 LEU Chi-restraints excluded: chain Q residue 41 GLU Chi-restraints excluded: chain Q residue 77 ARG Chi-restraints excluded: chain Q residue 114 ARG Chi-restraints excluded: chain Q residue 115 LEU Chi-restraints excluded: chain S residue 42 GLU Chi-restraints excluded: chain S residue 115 LEU Chi-restraints excluded: chain V residue 13 GLU Chi-restraints excluded: chain V residue 38 GLN Chi-restraints excluded: chain V residue 42 GLU Chi-restraints excluded: chain V residue 53 ASP Chi-restraints excluded: chain W residue 50 SER Chi-restraints excluded: chain W residue 70 GLU Chi-restraints excluded: chain X residue 33 GLU Chi-restraints excluded: chain X residue 42 GLU Chi-restraints excluded: chain X residue 102 ASP Chi-restraints excluded: chain X residue 114 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 125 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 118 optimal weight: 0.6980 chunk 161 optimal weight: 0.9990 chunk 156 optimal weight: 0.8980 chunk 83 optimal weight: 0.5980 chunk 246 optimal weight: 0.0670 chunk 104 optimal weight: 0.9980 chunk 205 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 overall best weight: 0.6518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 102 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.086120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2578 r_free = 0.2578 target = 0.071262 restraints weight = 27099.228| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 1.92 r_work: 0.2753 rms_B_bonded: 2.40 restraints_weight: 0.5000 r_work: 0.2609 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.4210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 20904 Z= 0.162 Angle : 0.533 7.879 28536 Z= 0.271 Chirality : 0.048 0.147 3516 Planarity : 0.005 0.038 3660 Dihedral : 3.921 13.247 2892 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.25 % Favored : 96.67 % Rotamer: Outliers : 2.02 % Allowed : 17.03 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.86 (0.16), residues: 2616 helix: 1.32 (0.17), residues: 816 sheet: -0.15 (0.17), residues: 780 loop : 0.81 (0.20), residues: 1020 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 64 TYR 0.015 0.002 TYR T 42 PHE 0.010 0.002 PHE Y 65 TRP 0.004 0.001 TRP P 98 HIS 0.003 0.001 HIS N 21 Details of bonding type rmsd covalent geometry : bond 0.00390 (20904) covalent geometry : angle 0.53287 (28536) hydrogen bonds : bond 0.04024 ( 1116) hydrogen bonds : angle 4.43625 ( 3024) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 8558.62 seconds wall clock time: 145 minutes 52.57 seconds (8752.57 seconds total)