Starting phenix.real_space_refine on Fri Feb 6 00:35:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iy4_60984/02_2026/9iy4_60984.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iy4_60984/02_2026/9iy4_60984.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9iy4_60984/02_2026/9iy4_60984.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iy4_60984/02_2026/9iy4_60984.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9iy4_60984/02_2026/9iy4_60984.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iy4_60984/02_2026/9iy4_60984.map" } resolution = 2.0 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= 0.009 sd= 0.094 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: 5 Type Number sf(0) Gaussians P 42 5.49 5 S 42 5.16 5 C 13328 2.51 5 N 3934 2.21 5 O 4102 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 21448 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1481 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1481 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 9, 'TRANS': 179} Chain: "A" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 51 Unusual residues: {'ACO': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L, M, N Time building chain proxies: 1.93, per 1000 atoms: 0.09 Number of scatterers: 21448 At special positions: 0 Unit cell: (127.143, 125.481, 93.903, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 42 16.00 P 42 15.00 O 4102 8.00 N 3934 7.00 C 13328 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: 1.39 Conformation dependent library (CDL) restraints added in 815.3 milliseconds 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4648 Finding SS restraints... Secondary structure from input PDB file: 126 helices and 14 sheets defined 43.9% alpha, 28.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 35 through 43 Processing helix chain 'A' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG A 108 " --> pdb=" O ALA A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU A 115 " --> pdb=" O GLY A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 152 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY A 190 " --> pdb=" O SER A 186 " (cutoff:3.500A) Processing helix chain 'B' and resid 22 through 24 No H-bonds generated for 'chain 'B' and resid 22 through 24' Processing helix chain 'B' and resid 25 through 34 Processing helix chain 'B' and resid 35 through 43 Processing helix chain 'B' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG B 108 " --> pdb=" O ALA B 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 105 through 108' Processing helix chain 'B' and resid 111 through 127 removed outlier: 3.578A pdb=" N GLU B 115 " --> pdb=" O GLY B 111 " (cutoff:3.500A) Processing helix chain 'B' and resid 141 through 152 Processing helix chain 'B' and resid 178 through 182 Processing helix chain 'B' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY B 190 " --> pdb=" O SER B 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 22 through 24 No H-bonds generated for 'chain 'C' and resid 22 through 24' Processing helix chain 'C' and resid 25 through 34 Processing helix chain 'C' and resid 35 through 43 Processing helix chain 'C' and resid 49 through 63 removed outlier: 4.236A pdb=" N GLY C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG C 108 " --> pdb=" O ALA C 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 105 through 108' Processing helix chain 'C' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU C 115 " --> pdb=" O GLY C 111 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 152 Processing helix chain 'C' and resid 178 through 182 Processing helix chain 'C' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY C 190 " --> pdb=" O SER C 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 22 through 24 No H-bonds generated for 'chain 'D' and resid 22 through 24' Processing helix chain 'D' and resid 25 through 34 Processing helix chain 'D' and resid 35 through 43 Processing helix chain 'D' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 108 removed outlier: 4.082A pdb=" N ARG D 108 " --> pdb=" O ALA D 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 105 through 108' Processing helix chain 'D' and resid 111 through 127 removed outlier: 3.578A pdb=" N GLU D 115 " --> pdb=" O GLY D 111 " (cutoff:3.500A) Processing helix chain 'D' and resid 141 through 152 Processing helix chain 'D' and resid 178 through 182 Processing helix chain 'D' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 22 through 24 No H-bonds generated for 'chain 'E' and resid 22 through 24' Processing helix chain 'E' and resid 25 through 34 Processing helix chain 'E' and resid 35 through 43 Processing helix chain 'E' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS E 59 " --> pdb=" O GLU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG E 108 " --> pdb=" O ALA E 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 105 through 108' Processing helix chain 'E' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU E 115 " --> pdb=" O GLY E 111 " (cutoff:3.500A) Processing helix chain 'E' and resid 141 through 152 Processing helix chain 'E' and resid 178 through 182 Processing helix chain 'E' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'F' and resid 22 through 24 No H-bonds generated for 'chain 'F' and resid 22 through 24' Processing helix chain 'F' and resid 25 through 34 Processing helix chain 'F' and resid 35 through 43 Processing helix chain 'F' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG F 108 " --> pdb=" O ALA F 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 105 through 108' Processing helix chain 'F' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU F 115 " --> pdb=" O GLY F 111 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 152 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY F 190 " --> pdb=" O SER F 186 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 24 No H-bonds generated for 'chain 'G' and resid 22 through 24' Processing helix chain 'G' and resid 25 through 34 Processing helix chain 'G' and resid 35 through 43 Processing helix chain 'G' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG G 108 " --> pdb=" O ALA G 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 105 through 108' Processing helix chain 'G' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU G 115 " --> pdb=" O GLY G 111 " (cutoff:3.500A) Processing helix chain 'G' and resid 141 through 152 Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'G' and resid 186 through 193 removed outlier: 3.610A pdb=" N GLY G 190 " --> pdb=" O SER G 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 22 through 24 No H-bonds generated for 'chain 'H' and resid 22 through 24' Processing helix chain 'H' and resid 25 through 34 Processing helix chain 'H' and resid 35 through 43 Processing helix chain 'H' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY H 58 " --> pdb=" O ARG H 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG H 108 " --> pdb=" O ALA H 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 105 through 108' Processing helix chain 'H' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU H 115 " --> pdb=" O GLY H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 141 through 152 Processing helix chain 'H' and resid 178 through 182 Processing helix chain 'H' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY H 190 " --> pdb=" O SER H 186 " (cutoff:3.500A) Processing helix chain 'I' and resid 22 through 24 No H-bonds generated for 'chain 'I' and resid 22 through 24' Processing helix chain 'I' and resid 25 through 34 Processing helix chain 'I' and resid 35 through 43 Processing helix chain 'I' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS I 59 " --> pdb=" O GLU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG I 108 " --> pdb=" O ALA I 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 105 through 108' Processing helix chain 'I' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU I 115 " --> pdb=" O GLY I 111 " (cutoff:3.500A) Processing helix chain 'I' and resid 141 through 152 Processing helix chain 'I' and resid 178 through 182 Processing helix chain 'I' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY I 190 " --> pdb=" O SER I 186 " (cutoff:3.500A) Processing helix chain 'J' and resid 22 through 24 No H-bonds generated for 'chain 'J' and resid 22 through 24' Processing helix chain 'J' and resid 25 through 34 Processing helix chain 'J' and resid 35 through 43 Processing helix chain 'J' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 4.053A pdb=" N HIS J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 108 removed outlier: 4.080A pdb=" N ARG J 108 " --> pdb=" O ALA J 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 105 through 108' Processing helix chain 'J' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU J 115 " --> pdb=" O GLY J 111 " (cutoff:3.500A) Processing helix chain 'J' and resid 141 through 152 Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'J' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY J 190 " --> pdb=" O SER J 186 " (cutoff:3.500A) Processing helix chain 'K' and resid 22 through 24 No H-bonds generated for 'chain 'K' and resid 22 through 24' Processing helix chain 'K' and resid 25 through 34 Processing helix chain 'K' and resid 35 through 43 Processing helix chain 'K' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG K 108 " --> pdb=" O ALA K 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 105 through 108' Processing helix chain 'K' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU K 115 " --> pdb=" O GLY K 111 " (cutoff:3.500A) Processing helix chain 'K' and resid 141 through 152 Processing helix chain 'K' and resid 178 through 182 Processing helix chain 'K' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY K 190 " --> pdb=" O SER K 186 " (cutoff:3.500A) Processing helix chain 'L' and resid 22 through 24 No H-bonds generated for 'chain 'L' and resid 22 through 24' Processing helix chain 'L' and resid 25 through 34 Processing helix chain 'L' and resid 35 through 43 Processing helix chain 'L' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 108 removed outlier: 4.080A pdb=" N ARG L 108 " --> pdb=" O ALA L 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 105 through 108' Processing helix chain 'L' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU L 115 " --> pdb=" O GLY L 111 " (cutoff:3.500A) Processing helix chain 'L' and resid 141 through 152 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY L 190 " --> pdb=" O SER L 186 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 24 No H-bonds generated for 'chain 'M' and resid 22 through 24' Processing helix chain 'M' and resid 25 through 34 Processing helix chain 'M' and resid 35 through 43 Processing helix chain 'M' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY M 58 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N HIS M 59 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 108 removed outlier: 4.082A pdb=" N ARG M 108 " --> pdb=" O ALA M 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'M' and resid 105 through 108' Processing helix chain 'M' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU M 115 " --> pdb=" O GLY M 111 " (cutoff:3.500A) Processing helix chain 'M' and resid 141 through 152 Processing helix chain 'M' and resid 178 through 182 Processing helix chain 'M' and resid 186 through 193 removed outlier: 3.609A pdb=" N GLY M 190 " --> pdb=" O SER M 186 " (cutoff:3.500A) Processing helix chain 'N' and resid 22 through 24 No H-bonds generated for 'chain 'N' and resid 22 through 24' Processing helix chain 'N' and resid 25 through 34 Processing helix chain 'N' and resid 35 through 43 Processing helix chain 'N' and resid 49 through 63 removed outlier: 4.235A pdb=" N GLY N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N HIS N 59 " --> pdb=" O GLU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 108 removed outlier: 4.081A pdb=" N ARG N 108 " --> pdb=" O ALA N 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'N' and resid 105 through 108' Processing helix chain 'N' and resid 111 through 127 removed outlier: 3.579A pdb=" N GLU N 115 " --> pdb=" O GLY N 111 " (cutoff:3.500A) Processing helix chain 'N' and resid 141 through 152 Processing helix chain 'N' and resid 178 through 182 Processing helix chain 'N' and resid 186 through 193 removed outlier: 3.610A pdb=" N GLY N 190 " --> pdb=" O SER N 186 " (cutoff:3.500A) Processing sheet with id=1, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY A 84 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP A 74 " --> pdb=" O PRO A 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA A 136 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE A 101 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU A 138 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU A 103 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG A 168 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER A 162 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL A 170 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG A 160 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU A 172 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU A 158 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU A 174 " --> pdb=" O ILE A 156 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'B' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY B 84 " --> pdb=" O VAL B 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP B 74 " --> pdb=" O PRO B 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA B 136 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE B 101 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU B 138 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU B 103 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N ARG B 168 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER B 162 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL B 170 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG B 160 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU B 172 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU B 158 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU B 174 " --> pdb=" O ILE B 156 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'C' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY C 84 " --> pdb=" O VAL C 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP C 74 " --> pdb=" O PRO C 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA C 136 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE C 101 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU C 138 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU C 103 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG C 168 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER C 162 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL C 170 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG C 160 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU C 172 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU C 158 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU C 174 " --> pdb=" O ILE C 156 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'D' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY D 84 " --> pdb=" O VAL D 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP D 74 " --> pdb=" O PRO D 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA D 136 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE D 101 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU D 138 " --> pdb=" O ILE D 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU D 103 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG D 168 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER D 162 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL D 170 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG D 160 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU D 172 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU D 158 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU D 174 " --> pdb=" O ILE D 156 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'E' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY E 84 " --> pdb=" O VAL E 72 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP E 74 " --> pdb=" O PRO E 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA E 136 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE E 101 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU E 138 " --> pdb=" O ILE E 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU E 103 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG E 168 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER E 162 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL E 170 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG E 160 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU E 172 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU E 158 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU E 174 " --> pdb=" O ILE E 156 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'F' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY F 84 " --> pdb=" O VAL F 72 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP F 74 " --> pdb=" O PRO F 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA F 136 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE F 101 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU F 138 " --> pdb=" O ILE F 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU F 103 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG F 168 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER F 162 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL F 170 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N ARG F 160 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU F 172 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU F 158 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU F 174 " --> pdb=" O ILE F 156 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'G' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY G 84 " --> pdb=" O VAL G 72 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP G 74 " --> pdb=" O PRO G 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA G 136 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE G 101 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU G 138 " --> pdb=" O ILE G 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU G 103 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG G 168 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER G 162 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL G 170 " --> pdb=" O ARG G 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG G 160 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU G 172 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU G 158 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU G 174 " --> pdb=" O ILE G 156 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY H 84 " --> pdb=" O VAL H 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP H 74 " --> pdb=" O PRO H 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA H 136 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE H 101 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU H 138 " --> pdb=" O ILE H 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU H 103 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG H 168 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER H 162 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL H 170 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG H 160 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU H 172 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU H 158 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU H 174 " --> pdb=" O ILE H 156 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'I' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY I 84 " --> pdb=" O VAL I 72 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASP I 74 " --> pdb=" O PRO I 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA I 136 " --> pdb=" O PHE I 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE I 101 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU I 138 " --> pdb=" O ILE I 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU I 103 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N ARG I 168 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER I 162 " --> pdb=" O ARG I 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL I 170 " --> pdb=" O ARG I 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG I 160 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU I 172 " --> pdb=" O GLU I 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU I 158 " --> pdb=" O GLU I 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU I 174 " --> pdb=" O ILE I 156 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'J' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY J 84 " --> pdb=" O VAL J 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP J 74 " --> pdb=" O PRO J 82 " (cutoff:3.500A) removed outlier: 5.005A pdb=" N ALA J 136 " --> pdb=" O PHE J 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE J 101 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU J 138 " --> pdb=" O ILE J 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU J 103 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N ARG J 168 " --> pdb=" O SER J 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER J 162 " --> pdb=" O ARG J 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL J 170 " --> pdb=" O ARG J 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG J 160 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU J 172 " --> pdb=" O GLU J 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU J 158 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU J 174 " --> pdb=" O ILE J 156 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'K' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY K 84 " --> pdb=" O VAL K 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP K 74 " --> pdb=" O PRO K 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA K 136 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE K 101 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU K 138 " --> pdb=" O ILE K 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU K 103 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N ARG K 168 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER K 162 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL K 170 " --> pdb=" O ARG K 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG K 160 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU K 172 " --> pdb=" O GLU K 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU K 158 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU K 174 " --> pdb=" O ILE K 156 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'L' and resid 11 through 12 removed outlier: 3.773A pdb=" N GLY L 84 " --> pdb=" O VAL L 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP L 74 " --> pdb=" O PRO L 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA L 136 " --> pdb=" O PHE L 99 " (cutoff:3.500A) removed outlier: 8.060A pdb=" N ILE L 101 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU L 138 " --> pdb=" O ILE L 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU L 103 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG L 168 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER L 162 " --> pdb=" O ARG L 168 " (cutoff:3.500A) removed outlier: 7.545A pdb=" N VAL L 170 " --> pdb=" O ARG L 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG L 160 " --> pdb=" O VAL L 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU L 172 " --> pdb=" O GLU L 158 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N GLU L 158 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU L 174 " --> pdb=" O ILE L 156 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'M' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY M 84 " --> pdb=" O VAL M 72 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASP M 74 " --> pdb=" O PRO M 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA M 136 " --> pdb=" O PHE M 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE M 101 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU M 138 " --> pdb=" O ILE M 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU M 103 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 11.012A pdb=" N ARG M 168 " --> pdb=" O SER M 162 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N SER M 162 " --> pdb=" O ARG M 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL M 170 " --> pdb=" O ARG M 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG M 160 " --> pdb=" O VAL M 170 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLU M 172 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU M 158 " --> pdb=" O GLU M 172 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N LEU M 174 " --> pdb=" O ILE M 156 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'N' and resid 11 through 12 removed outlier: 3.772A pdb=" N GLY N 84 " --> pdb=" O VAL N 72 " (cutoff:3.500A) removed outlier: 6.075A pdb=" N ASP N 74 " --> pdb=" O PRO N 82 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N ALA N 136 " --> pdb=" O PHE N 99 " (cutoff:3.500A) removed outlier: 8.061A pdb=" N ILE N 101 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 10.293A pdb=" N LEU N 138 " --> pdb=" O ILE N 101 " (cutoff:3.500A) removed outlier: 14.630A pdb=" N LEU N 103 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 11.011A pdb=" N ARG N 168 " --> pdb=" O SER N 162 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER N 162 " --> pdb=" O ARG N 168 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N VAL N 170 " --> pdb=" O ARG N 160 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N ARG N 160 " --> pdb=" O VAL N 170 " (cutoff:3.500A) removed outlier: 6.268A pdb=" N GLU N 172 " --> pdb=" O GLU N 158 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N GLU N 158 " --> pdb=" O GLU N 172 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU N 174 " --> pdb=" O ILE N 156 " (cutoff:3.500A) 1064 hydrogen bonds defined for protein. 2982 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: 3.56 Time building geometry restraints manager: 2.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4203 1.32 - 1.44: 5805 1.44 - 1.56: 11776 1.56 - 1.68: 126 1.68 - 1.80: 70 Bond restraints: 21980 Sorted by residual: bond pdb=" C6A ACO B 200 " pdb=" N6A ACO B 200 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.00e-02 1.00e+04 2.15e+01 bond pdb=" C6A ACO E 200 " pdb=" N6A ACO E 200 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.00e-02 1.00e+04 2.15e+01 bond pdb=" C6A ACO J 200 " pdb=" N6A ACO J 200 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.00e-02 1.00e+04 2.14e+01 bond pdb=" C6A ACO C 200 " pdb=" N6A ACO C 200 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.00e-02 1.00e+04 2.14e+01 bond pdb=" C6A ACO I 200 " pdb=" N6A ACO I 200 " ideal model delta sigma weight residual 1.337 1.383 -0.046 1.00e-02 1.00e+04 2.14e+01 ... (remaining 21975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.46: 29848 5.46 - 10.93: 98 10.93 - 16.39: 28 16.39 - 21.86: 0 21.86 - 27.32: 14 Bond angle restraints: 29988 Sorted by residual: angle pdb=" P1A ACO B 200 " pdb=" O3A ACO B 200 " pdb=" P2A ACO B 200 " ideal model delta sigma weight residual 136.83 109.51 27.32 1.00e+00 1.00e+00 7.47e+02 angle pdb=" P1A ACO D 200 " pdb=" O3A ACO D 200 " pdb=" P2A ACO D 200 " ideal model delta sigma weight residual 136.83 109.51 27.32 1.00e+00 1.00e+00 7.46e+02 angle pdb=" P1A ACO J 200 " pdb=" O3A ACO J 200 " pdb=" P2A ACO J 200 " ideal model delta sigma weight residual 136.83 109.52 27.31 1.00e+00 1.00e+00 7.46e+02 angle pdb=" P1A ACO M 200 " pdb=" O3A ACO M 200 " pdb=" P2A ACO M 200 " ideal model delta sigma weight residual 136.83 109.53 27.30 1.00e+00 1.00e+00 7.45e+02 angle pdb=" P1A ACO N 200 " pdb=" O3A ACO N 200 " pdb=" P2A ACO N 200 " ideal model delta sigma weight residual 136.83 109.53 27.30 1.00e+00 1.00e+00 7.45e+02 ... (remaining 29983 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.07: 11508 15.07 - 30.13: 812 30.13 - 45.20: 525 45.20 - 60.27: 147 60.27 - 75.33: 14 Dihedral angle restraints: 13006 sinusoidal: 5642 harmonic: 7364 Sorted by residual: dihedral pdb=" CG ARG N 44 " pdb=" CD ARG N 44 " pdb=" NE ARG N 44 " pdb=" CZ ARG N 44 " ideal model delta sinusoidal sigma weight residual 90.00 133.35 -43.35 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG G 44 " pdb=" CD ARG G 44 " pdb=" NE ARG G 44 " pdb=" CZ ARG G 44 " ideal model delta sinusoidal sigma weight residual 90.00 133.35 -43.35 2 1.50e+01 4.44e-03 1.01e+01 dihedral pdb=" CG ARG I 44 " pdb=" CD ARG I 44 " pdb=" NE ARG I 44 " pdb=" CZ ARG I 44 " ideal model delta sinusoidal sigma weight residual 90.00 133.32 -43.32 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 13003 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 1842 0.033 - 0.066: 804 0.066 - 0.099: 349 0.099 - 0.132: 141 0.132 - 0.165: 14 Chirality restraints: 3150 Sorted by residual: chirality pdb=" C1B ACO N 200 " pdb=" C2B ACO N 200 " pdb=" N9A ACO N 200 " pdb=" O4B ACO N 200 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.17 2.00e-01 2.50e+01 6.82e-01 chirality pdb=" C1B ACO C 200 " pdb=" C2B ACO C 200 " pdb=" N9A ACO C 200 " pdb=" O4B ACO C 200 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.76e-01 chirality pdb=" C1B ACO I 200 " pdb=" C2B ACO I 200 " pdb=" N9A ACO I 200 " pdb=" O4B ACO I 200 " both_signs ideal model delta sigma weight residual False 2.41 2.57 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 3147 not shown) Planarity restraints: 3920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP J 35 " 0.019 5.00e-02 4.00e+02 2.88e-02 1.32e+00 pdb=" N PRO J 36 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO J 36 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO J 36 " 0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 35 " -0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO C 36 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO C 36 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO C 36 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP F 35 " 0.019 5.00e-02 4.00e+02 2.87e-02 1.32e+00 pdb=" N PRO F 36 " -0.050 5.00e-02 4.00e+02 pdb=" CA PRO F 36 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO F 36 " 0.016 5.00e-02 4.00e+02 ... (remaining 3917 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 4071 2.77 - 3.30: 19302 3.30 - 3.84: 36037 3.84 - 4.37: 45803 4.37 - 4.90: 76841 Nonbonded interactions: 182054 Sorted by model distance: nonbonded pdb=" O6A ACO G 200 " pdb=" OAP ACO G 200 " model vdw 2.238 3.040 nonbonded pdb=" O6A ACO N 200 " pdb=" OAP ACO N 200 " model vdw 2.238 3.040 nonbonded pdb=" O6A ACO F 200 " pdb=" OAP ACO F 200 " model vdw 2.238 3.040 nonbonded pdb=" O6A ACO E 200 " pdb=" OAP ACO E 200 " model vdw 2.238 3.040 nonbonded pdb=" O6A ACO L 200 " pdb=" OAP ACO L 200 " model vdw 2.238 3.040 ... (remaining 182049 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.240 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 15.740 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 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 : 0.007 0.078 21980 Z= 0.368 Angle : 1.112 27.323 29988 Z= 0.923 Chirality : 0.046 0.165 3150 Planarity : 0.005 0.030 3920 Dihedral : 15.080 75.332 8358 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.59 (0.15), residues: 2618 helix: 1.39 (0.15), residues: 924 sheet: 0.40 (0.19), residues: 658 loop : -0.45 (0.17), residues: 1036 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 95 TYR 0.016 0.002 TYR H 57 PHE 0.018 0.003 PHE J 164 TRP 0.009 0.002 TRP B 10 HIS 0.005 0.002 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00717 (21980) covalent geometry : angle 1.11160 (29988) hydrogen bonds : bond 0.14184 ( 1064) hydrogen bonds : angle 6.80396 ( 2982) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 310 time to evaluate : 0.597 Fit side-chains REVERT: E 57 TYR cc_start: 0.8158 (t80) cc_final: 0.7834 (t80) REVERT: L 57 TYR cc_start: 0.8156 (t80) cc_final: 0.7832 (t80) outliers start: 0 outliers final: 0 residues processed: 310 average time/residue: 0.5225 time to fit residues: 186.5008 Evaluate side-chains 285 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 0.664 ------------------------------------------------------------------------------- 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: 3.9990 chunk 98 optimal weight: 3.9990 chunk 194 optimal weight: 6.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 247 optimal weight: 1.9990 chunk 130 optimal weight: 6.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 overall best weight: 1.1582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.129281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.116900 restraints weight = 26008.089| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 1.44 r_work: 0.3629 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3499 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21980 Z= 0.131 Angle : 0.508 4.284 29988 Z= 0.273 Chirality : 0.041 0.126 3150 Planarity : 0.005 0.030 3920 Dihedral : 16.292 64.614 3724 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 1.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 0.28 % Allowed : 6.91 % Favored : 92.81 % 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: 0.70 (0.15), residues: 2618 helix: 1.66 (0.16), residues: 966 sheet: 0.36 (0.19), residues: 658 loop : -0.60 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG N 62 TYR 0.013 0.001 TYR J 57 PHE 0.011 0.002 PHE G 164 TRP 0.004 0.001 TRP I 32 HIS 0.003 0.001 HIS J 134 Details of bonding type rmsd covalent geometry : bond 0.00308 (21980) covalent geometry : angle 0.50815 (29988) hydrogen bonds : bond 0.03501 ( 1064) hydrogen bonds : angle 4.81875 ( 2982) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 294 time to evaluate : 0.639 Fit side-chains REVERT: C 57 TYR cc_start: 0.8263 (t80) cc_final: 0.8008 (t80) REVERT: E 57 TYR cc_start: 0.8255 (t80) cc_final: 0.7979 (t80) REVERT: L 57 TYR cc_start: 0.8261 (t80) cc_final: 0.7976 (t80) outliers start: 6 outliers final: 0 residues processed: 294 average time/residue: 0.5848 time to fit residues: 196.5288 Evaluate side-chains 290 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 46 optimal weight: 10.0000 chunk 196 optimal weight: 2.9990 chunk 221 optimal weight: 6.9990 chunk 217 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 7.9990 chunk 148 optimal weight: 8.9990 chunk 144 optimal weight: 3.9990 chunk 128 optimal weight: 5.9990 chunk 54 optimal weight: 8.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3804 r_free = 0.3804 target = 0.122631 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.110134 restraints weight = 26221.951| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 1.45 r_work: 0.3530 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.061 21980 Z= 0.400 Angle : 0.731 7.185 29988 Z= 0.392 Chirality : 0.052 0.154 3150 Planarity : 0.007 0.052 3920 Dihedral : 16.516 70.111 3724 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.23 % Allowed : 8.23 % Favored : 90.54 % 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: 0.13 (0.14), residues: 2618 helix: 1.00 (0.15), residues: 952 sheet: 0.47 (0.19), residues: 644 loop : -0.99 (0.15), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG H 95 TYR 0.020 0.003 TYR L 123 PHE 0.021 0.003 PHE G 21 TRP 0.014 0.003 TRP A 30 HIS 0.008 0.002 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00993 (21980) covalent geometry : angle 0.73058 (29988) hydrogen bonds : bond 0.05248 ( 1064) hydrogen bonds : angle 5.58673 ( 2982) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 309 time to evaluate : 0.766 Fit side-chains REVERT: M 180 GLU cc_start: 0.8109 (pm20) cc_final: 0.7886 (pm20) outliers start: 26 outliers final: 20 residues processed: 319 average time/residue: 0.5514 time to fit residues: 200.9416 Evaluate side-chains 322 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 302 time to evaluate : 0.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 119 LEU Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain C residue 119 LEU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain F residue 115 GLU Chi-restraints excluded: chain G residue 119 LEU Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain J residue 119 LEU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain M residue 115 GLU Chi-restraints excluded: chain N residue 119 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 93 optimal weight: 0.4980 chunk 89 optimal weight: 3.9990 chunk 163 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 192 optimal weight: 0.8980 chunk 237 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 233 optimal weight: 0.8980 chunk 224 optimal weight: 0.7980 chunk 220 optimal weight: 3.9990 chunk 128 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.116713 restraints weight = 26048.316| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 1.46 r_work: 0.3619 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3493 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3493 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8313 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 21980 Z= 0.107 Angle : 0.459 4.201 29988 Z= 0.249 Chirality : 0.040 0.125 3150 Planarity : 0.004 0.031 3920 Dihedral : 15.482 69.387 3724 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 2.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % Rotamer: Outliers : 1.99 % Allowed : 7.38 % Favored : 90.63 % 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: 0.57 (0.15), residues: 2618 helix: 1.64 (0.16), residues: 980 sheet: 0.34 (0.19), residues: 658 loop : -0.85 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 62 TYR 0.013 0.001 TYR J 57 PHE 0.007 0.001 PHE B 99 TRP 0.004 0.001 TRP G 30 HIS 0.002 0.001 HIS N 126 Details of bonding type rmsd covalent geometry : bond 0.00245 (21980) covalent geometry : angle 0.45858 (29988) hydrogen bonds : bond 0.02840 ( 1064) hydrogen bonds : angle 4.57161 ( 2982) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 310 time to evaluate : 0.634 Fit side-chains REVERT: A 57 TYR cc_start: 0.8250 (t80) cc_final: 0.8049 (t80) outliers start: 42 outliers final: 8 residues processed: 334 average time/residue: 0.5878 time to fit residues: 226.1455 Evaluate side-chains 302 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 294 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 SER Chi-restraints excluded: chain C residue 49 SER Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain H residue 37 SER Chi-restraints excluded: chain J residue 49 SER Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain M residue 81 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 6 optimal weight: 3.9990 chunk 214 optimal weight: 3.9990 chunk 229 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 97 optimal weight: 0.5980 chunk 115 optimal weight: 4.9990 chunk 231 optimal weight: 9.9990 chunk 234 optimal weight: 0.9990 chunk 91 optimal weight: 7.9990 chunk 166 optimal weight: 2.9990 chunk 10 optimal weight: 6.9990 overall best weight: 2.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN C 67 GLN H 67 GLN J 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.125364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.112742 restraints weight = 26040.850| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 1.46 r_work: 0.3564 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3433 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.1630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 21980 Z= 0.212 Angle : 0.550 4.841 29988 Z= 0.296 Chirality : 0.043 0.120 3150 Planarity : 0.005 0.037 3920 Dihedral : 15.524 70.603 3724 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 1.42 % Allowed : 8.70 % Favored : 89.88 % 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: 0.45 (0.15), residues: 2618 helix: 1.47 (0.16), residues: 966 sheet: 0.40 (0.20), residues: 658 loop : -0.91 (0.16), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 62 TYR 0.014 0.002 TYR J 57 PHE 0.017 0.002 PHE A 21 TRP 0.008 0.001 TRP A 30 HIS 0.004 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00522 (21980) covalent geometry : angle 0.55045 (29988) hydrogen bonds : bond 0.03753 ( 1064) hydrogen bonds : angle 4.94265 ( 2982) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 307 time to evaluate : 0.535 Fit side-chains REVERT: A 57 TYR cc_start: 0.8321 (t80) cc_final: 0.8114 (t80) outliers start: 30 outliers final: 24 residues processed: 328 average time/residue: 0.5950 time to fit residues: 223.4663 Evaluate side-chains 331 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 307 time to evaluate : 0.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 50 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 chunk 84 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 185 optimal weight: 2.9990 chunk 249 optimal weight: 8.9990 chunk 186 optimal weight: 4.9990 chunk 5 optimal weight: 0.0770 chunk 189 optimal weight: 5.9990 chunk 132 optimal weight: 0.7980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN J 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.129678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.117179 restraints weight = 26033.618| |-----------------------------------------------------------------------------| r_work (start): 0.3725 rms_B_bonded: 1.46 r_work: 0.3629 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8309 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 21980 Z= 0.101 Angle : 0.442 4.211 29988 Z= 0.240 Chirality : 0.039 0.124 3150 Planarity : 0.004 0.031 3920 Dihedral : 14.485 69.309 3724 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.56 % Allowed : 8.99 % Favored : 89.45 % 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: 0.81 (0.16), residues: 2618 helix: 1.98 (0.17), residues: 966 sheet: 0.42 (0.19), residues: 658 loop : -0.80 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 62 TYR 0.012 0.001 TYR J 57 PHE 0.006 0.001 PHE K 99 TRP 0.004 0.001 TRP F 30 HIS 0.001 0.000 HIS G 126 Details of bonding type rmsd covalent geometry : bond 0.00233 (21980) covalent geometry : angle 0.44177 (29988) hydrogen bonds : bond 0.02636 ( 1064) hydrogen bonds : angle 4.40582 ( 2982) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 305 time to evaluate : 0.854 Fit side-chains REVERT: A 57 TYR cc_start: 0.8273 (t80) cc_final: 0.8073 (t80) REVERT: F 14 ASP cc_start: 0.6638 (p0) cc_final: 0.6335 (p0) REVERT: M 14 ASP cc_start: 0.6685 (p0) cc_final: 0.6380 (p0) outliers start: 33 outliers final: 23 residues processed: 319 average time/residue: 0.6090 time to fit residues: 222.3950 Evaluate side-chains 323 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 300 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 4 optimal weight: 0.9990 chunk 183 optimal weight: 0.0060 chunk 102 optimal weight: 6.9990 chunk 133 optimal weight: 3.9990 chunk 119 optimal weight: 5.9990 chunk 154 optimal weight: 9.9990 chunk 38 optimal weight: 5.9990 chunk 236 optimal weight: 6.9990 chunk 174 optimal weight: 4.9990 chunk 48 optimal weight: 7.9990 chunk 85 optimal weight: 1.9990 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 67 GLN H 67 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.125700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.113218 restraints weight = 26076.279| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.46 r_work: 0.3571 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 21980 Z= 0.204 Angle : 0.536 4.693 29988 Z= 0.289 Chirality : 0.042 0.118 3150 Planarity : 0.005 0.036 3920 Dihedral : 14.627 71.182 3724 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.42 % Allowed : 8.99 % Favored : 89.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.15), residues: 2618 helix: 1.62 (0.16), residues: 966 sheet: 0.49 (0.20), residues: 658 loop : -0.87 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 95 TYR 0.015 0.002 TYR L 57 PHE 0.017 0.002 PHE B 21 TRP 0.008 0.001 TRP H 30 HIS 0.004 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00501 (21980) covalent geometry : angle 0.53649 (29988) hydrogen bonds : bond 0.03612 ( 1064) hydrogen bonds : angle 4.83323 ( 2982) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 351 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 321 time to evaluate : 0.777 Fit side-chains outliers start: 30 outliers final: 26 residues processed: 340 average time/residue: 0.6584 time to fit residues: 254.2825 Evaluate side-chains 336 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 310 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 108 optimal weight: 2.9990 chunk 112 optimal weight: 0.9990 chunk 120 optimal weight: 4.9990 chunk 134 optimal weight: 7.9990 chunk 96 optimal weight: 2.9990 chunk 224 optimal weight: 3.9990 chunk 189 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 chunk 195 optimal weight: 0.0770 chunk 13 optimal weight: 1.9990 chunk 188 optimal weight: 4.9990 overall best weight: 1.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN F 67 GLN H 67 GLN J 67 GLN M 67 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3850 r_free = 0.3850 target = 0.126512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.114075 restraints weight = 26063.234| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 1.45 r_work: 0.3584 rms_B_bonded: 1.85 restraints_weight: 0.5000 r_work: 0.3453 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3453 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.1844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 21980 Z= 0.165 Angle : 0.509 4.099 29988 Z= 0.275 Chirality : 0.041 0.119 3150 Planarity : 0.005 0.035 3920 Dihedral : 14.232 71.310 3724 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.61 % Allowed : 9.93 % Favored : 88.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.61 (0.15), residues: 2618 helix: 1.67 (0.16), residues: 966 sheet: 0.48 (0.20), residues: 658 loop : -0.88 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 15 TYR 0.015 0.002 TYR L 57 PHE 0.013 0.002 PHE N 21 TRP 0.006 0.001 TRP A 30 HIS 0.003 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00400 (21980) covalent geometry : angle 0.50866 (29988) hydrogen bonds : bond 0.03293 ( 1064) hydrogen bonds : angle 4.68638 ( 2982) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 310 time to evaluate : 0.858 Fit side-chains REVERT: E 115 GLU cc_start: 0.7651 (OUTLIER) cc_final: 0.7171 (tm-30) REVERT: L 115 GLU cc_start: 0.7657 (OUTLIER) cc_final: 0.7185 (tm-30) outliers start: 34 outliers final: 25 residues processed: 326 average time/residue: 0.6196 time to fit residues: 230.9793 Evaluate side-chains 334 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 307 time to evaluate : 0.663 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain C residue 115 GLU Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain E residue 115 GLU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain I residue 119 LEU Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain J residue 115 GLU Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain L residue 115 GLU Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 15 optimal weight: 10.0000 chunk 239 optimal weight: 3.9990 chunk 159 optimal weight: 8.9990 chunk 223 optimal weight: 0.7980 chunk 158 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 240 optimal weight: 1.9990 chunk 170 optimal weight: 5.9990 chunk 133 optimal weight: 0.9990 chunk 144 optimal weight: 0.2980 chunk 212 optimal weight: 0.8980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 67 GLN F 67 GLN J 67 GLN M 67 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.129244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.116921 restraints weight = 25966.426| |-----------------------------------------------------------------------------| r_work (start): 0.3716 rms_B_bonded: 1.45 r_work: 0.3624 rms_B_bonded: 1.84 restraints_weight: 0.5000 r_work: 0.3500 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8306 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 21980 Z= 0.105 Angle : 0.452 4.210 29988 Z= 0.246 Chirality : 0.039 0.121 3150 Planarity : 0.004 0.039 3920 Dihedral : 13.480 70.151 3724 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 1.23 % Allowed : 10.41 % Favored : 88.36 % 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: 2618 helix: 1.94 (0.16), residues: 980 sheet: 0.47 (0.19), residues: 658 loop : -0.77 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 15 TYR 0.015 0.001 TYR E 57 PHE 0.009 0.001 PHE L 21 TRP 0.004 0.001 TRP L 30 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00240 (21980) covalent geometry : angle 0.45175 (29988) hydrogen bonds : bond 0.02651 ( 1064) hydrogen bonds : angle 4.37483 ( 2982) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 304 time to evaluate : 0.836 Fit side-chains outliers start: 26 outliers final: 22 residues processed: 315 average time/residue: 0.6074 time to fit residues: 218.6536 Evaluate side-chains 325 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 303 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 69 optimal weight: 1.9990 chunk 180 optimal weight: 0.0060 chunk 196 optimal weight: 0.9980 chunk 179 optimal weight: 0.9990 chunk 154 optimal weight: 0.6980 chunk 147 optimal weight: 0.9980 chunk 101 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 248 optimal weight: 0.9980 chunk 242 optimal weight: 4.9990 chunk 188 optimal weight: 6.9990 overall best weight: 0.7396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.130197 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3732 r_free = 0.3732 target = 0.117800 restraints weight = 26129.073| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 1.46 r_work: 0.3634 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.3508 rms_B_bonded: 3.30 restraints_weight: 0.2500 r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 21980 Z= 0.100 Angle : 0.443 4.270 29988 Z= 0.240 Chirality : 0.039 0.121 3150 Planarity : 0.004 0.039 3920 Dihedral : 12.799 70.700 3724 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.28 % Allowed : 9.98 % Favored : 88.74 % 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: 1.04 (0.16), residues: 2618 helix: 2.22 (0.17), residues: 966 sheet: 0.51 (0.19), residues: 658 loop : -0.71 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 15 TYR 0.016 0.001 TYR N 57 PHE 0.008 0.001 PHE L 21 TRP 0.004 0.001 TRP M 30 HIS 0.002 0.000 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00228 (21980) covalent geometry : angle 0.44340 (29988) hydrogen bonds : bond 0.02573 ( 1064) hydrogen bonds : angle 4.26526 ( 2982) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5236 Ramachandran restraints generated. 2618 Oldfield, 0 Emsley, 2618 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 300 time to evaluate : 0.840 Fit side-chains REVERT: G 14 ASP cc_start: 0.6760 (p0) cc_final: 0.6552 (p0) outliers start: 27 outliers final: 20 residues processed: 307 average time/residue: 0.6702 time to fit residues: 233.1970 Evaluate side-chains 310 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 290 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 81 VAL Chi-restraints excluded: chain C residue 96 THR Chi-restraints excluded: chain D residue 37 SER Chi-restraints excluded: chain D residue 96 THR Chi-restraints excluded: chain E residue 96 THR Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain I residue 81 VAL Chi-restraints excluded: chain I residue 96 THR Chi-restraints excluded: chain J residue 81 VAL Chi-restraints excluded: chain J residue 96 THR Chi-restraints excluded: chain K residue 37 SER Chi-restraints excluded: chain K residue 96 THR Chi-restraints excluded: chain L residue 96 THR Chi-restraints excluded: chain M residue 81 VAL Chi-restraints excluded: chain M residue 96 THR Chi-restraints excluded: chain N residue 96 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 91 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 chunk 101 optimal weight: 3.9990 chunk 73 optimal weight: 9.9990 chunk 183 optimal weight: 0.7980 chunk 198 optimal weight: 5.9990 chunk 223 optimal weight: 0.9980 chunk 192 optimal weight: 3.9990 chunk 85 optimal weight: 0.9980 chunk 5 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 67 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.127522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.115077 restraints weight = 26110.029| |-----------------------------------------------------------------------------| r_work (start): 0.3695 rms_B_bonded: 1.45 r_work: 0.3596 rms_B_bonded: 1.87 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8347 moved from start: 0.1992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21980 Z= 0.144 Angle : 0.490 4.173 29988 Z= 0.264 Chirality : 0.041 0.120 3150 Planarity : 0.005 0.042 3920 Dihedral : 13.053 71.021 3724 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 3.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.18 % Allowed : 9.89 % Favored : 88.93 % 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: 2618 helix: 1.91 (0.16), residues: 980 sheet: 0.54 (0.20), residues: 658 loop : -0.73 (0.17), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 15 TYR 0.016 0.002 TYR G 57 PHE 0.012 0.002 PHE L 21 TRP 0.007 0.001 TRP I 30 HIS 0.003 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00346 (21980) covalent geometry : angle 0.48951 (29988) hydrogen bonds : bond 0.03095 ( 1064) hydrogen bonds : angle 4.52160 ( 2982) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9002.62 seconds wall clock time: 153 minutes 25.13 seconds (9205.13 seconds total)