Starting phenix.real_space_refine on Fri Feb 6 00:26:47 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9iy3_60983/02_2026/9iy3_60983.cif Found real_map, /net/cci-nas-00/data/ceres_data/9iy3_60983/02_2026/9iy3_60983.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9iy3_60983/02_2026/9iy3_60983.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9iy3_60983/02_2026/9iy3_60983.map" model { file = "/net/cci-nas-00/data/ceres_data/9iy3_60983/02_2026/9iy3_60983.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9iy3_60983/02_2026/9iy3_60983.cif" } resolution = 2.17 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= 0.008 sd= 0.075 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 13300 2.51 5 N 3934 2.21 5 O 4088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 42 residue(s): 0.02s 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: 21406 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: 48 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 48 Unusual residues: {'COA': 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: 1.82, per 1000 atoms: 0.09 Number of scatterers: 21406 At special positions: 0 Unit cell: (127.143, 124.65, 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 4088 8.00 N 3934 7.00 C 13300 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: 1.63 Conformation dependent library (CDL) restraints added in 772.4 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: 0.84 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: 4.148A pdb=" N GLY A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 removed outlier: 4.091A 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: 3.652A 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: 3.506A 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: 4.149A pdb=" N GLY B 58 " --> pdb=" O ARG B 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS B 59 " --> pdb=" O GLU B 55 " (cutoff:3.500A) Processing helix chain 'B' and resid 105 through 108 removed outlier: 4.092A 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: 3.652A 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: 3.507A 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: 4.148A pdb=" N GLY C 58 " --> pdb=" O ARG C 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS C 59 " --> pdb=" O GLU C 55 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 removed outlier: 4.092A 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: 3.653A 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: 3.506A 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: 4.149A pdb=" N GLY D 58 " --> pdb=" O ARG D 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS D 59 " --> pdb=" O GLU D 55 " (cutoff:3.500A) Processing helix chain 'D' and resid 105 through 108 removed outlier: 4.091A 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: 3.651A 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: 3.507A 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: 4.149A pdb=" N GLY E 58 " --> pdb=" O ARG E 54 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS E 59 " --> pdb=" O GLU E 55 " (cutoff:3.500A) Processing helix chain 'E' and resid 105 through 108 removed outlier: 4.091A 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: 3.652A 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: 3.506A 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: 4.149A pdb=" N GLY F 58 " --> pdb=" O ARG F 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS F 59 " --> pdb=" O GLU F 55 " (cutoff:3.500A) Processing helix chain 'F' and resid 105 through 108 removed outlier: 4.092A 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: 3.652A 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: 3.507A 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: 4.149A pdb=" N GLY G 58 " --> pdb=" O ARG G 54 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS G 59 " --> pdb=" O GLU G 55 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 108 removed outlier: 4.092A 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: 3.652A 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: 3.506A 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: 4.148A pdb=" N GLY H 58 " --> pdb=" O ARG H 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS H 59 " --> pdb=" O GLU H 55 " (cutoff:3.500A) Processing helix chain 'H' and resid 105 through 108 removed outlier: 4.091A 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: 3.652A 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: 3.506A 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: 4.149A pdb=" N GLY I 58 " --> pdb=" O ARG I 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS I 59 " --> pdb=" O GLU I 55 " (cutoff:3.500A) Processing helix chain 'I' and resid 105 through 108 removed outlier: 4.092A 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: 3.652A 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: 3.507A 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: 4.148A pdb=" N GLY J 58 " --> pdb=" O ARG J 54 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N HIS J 59 " --> pdb=" O GLU J 55 " (cutoff:3.500A) Processing helix chain 'J' and resid 105 through 108 removed outlier: 4.092A 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: 3.653A 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: 3.506A 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: 4.148A pdb=" N GLY K 58 " --> pdb=" O ARG K 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS K 59 " --> pdb=" O GLU K 55 " (cutoff:3.500A) Processing helix chain 'K' and resid 105 through 108 removed outlier: 4.092A 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: 3.651A 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: 3.506A 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: 4.148A pdb=" N GLY L 58 " --> pdb=" O ARG L 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS L 59 " --> pdb=" O GLU L 55 " (cutoff:3.500A) Processing helix chain 'L' and resid 105 through 108 removed outlier: 4.091A 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: 3.652A 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: 3.506A 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: 4.149A pdb=" N GLY M 58 " --> pdb=" O ARG M 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS M 59 " --> pdb=" O GLU M 55 " (cutoff:3.500A) Processing helix chain 'M' and resid 105 through 108 removed outlier: 4.092A 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: 3.652A 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: 3.506A 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: 4.148A pdb=" N GLY N 58 " --> pdb=" O ARG N 54 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N HIS N 59 " --> pdb=" O GLU N 55 " (cutoff:3.500A) Processing helix chain 'N' and resid 105 through 108 removed outlier: 4.092A 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: 3.652A 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: 3.506A 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: 6.578A pdb=" N LEU A 68 " --> pdb=" O ALA A 87 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA A 87 " --> pdb=" O LEU A 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE A 70 " --> pdb=" O THR A 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR A 85 " --> pdb=" O PHE A 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL A 72 " --> pdb=" O VAL A 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY A 97 " --> pdb=" O HIS A 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA A 136 " --> pdb=" O GLY A 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE A 99 " --> pdb=" O ALA A 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU A 138 " --> pdb=" O PHE A 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE A 101 " --> pdb=" O LEU A 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG A 168 " --> pdb=" O SER A 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER A 162 " --> pdb=" O ARG A 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL A 170 " --> pdb=" O ARG A 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG A 160 " --> pdb=" O VAL A 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU A 172 " --> pdb=" O GLU A 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU A 158 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU B 68 " --> pdb=" O ALA B 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA B 87 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE B 70 " --> pdb=" O THR B 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR B 85 " --> pdb=" O PHE B 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL B 72 " --> pdb=" O VAL B 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY B 97 " --> pdb=" O HIS B 134 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ALA B 136 " --> pdb=" O GLY B 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE B 99 " --> pdb=" O ALA B 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU B 138 " --> pdb=" O PHE B 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE B 101 " --> pdb=" O LEU B 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG B 168 " --> pdb=" O SER B 162 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N SER B 162 " --> pdb=" O ARG B 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL B 170 " --> pdb=" O ARG B 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG B 160 " --> pdb=" O VAL B 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU B 172 " --> pdb=" O GLU B 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU B 158 " --> pdb=" O GLU B 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.579A pdb=" N LEU C 68 " --> pdb=" O ALA C 87 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA C 87 " --> pdb=" O LEU C 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE C 70 " --> pdb=" O THR C 85 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR C 85 " --> pdb=" O PHE C 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL C 72 " --> pdb=" O VAL C 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY C 97 " --> pdb=" O HIS C 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA C 136 " --> pdb=" O GLY C 97 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE C 99 " --> pdb=" O ALA C 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU C 138 " --> pdb=" O PHE C 99 " (cutoff:3.500A) removed outlier: 12.580A pdb=" N ILE C 101 " --> pdb=" O LEU C 138 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ARG C 168 " --> pdb=" O SER C 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER C 162 " --> pdb=" O ARG C 168 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL C 170 " --> pdb=" O ARG C 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG C 160 " --> pdb=" O VAL C 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU C 172 " --> pdb=" O GLU C 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU C 158 " --> pdb=" O GLU C 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU D 68 " --> pdb=" O ALA D 87 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA D 87 " --> pdb=" O LEU D 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE D 70 " --> pdb=" O THR D 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR D 85 " --> pdb=" O PHE D 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL D 72 " --> pdb=" O VAL D 83 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY D 97 " --> pdb=" O HIS D 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA D 136 " --> pdb=" O GLY D 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE D 99 " --> pdb=" O ALA D 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU D 138 " --> pdb=" O PHE D 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE D 101 " --> pdb=" O LEU D 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG D 168 " --> pdb=" O SER D 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER D 162 " --> pdb=" O ARG D 168 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL D 170 " --> pdb=" O ARG D 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG D 160 " --> pdb=" O VAL D 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU D 172 " --> pdb=" O GLU D 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU D 158 " --> pdb=" O GLU D 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.579A pdb=" N LEU E 68 " --> pdb=" O ALA E 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA E 87 " --> pdb=" O LEU E 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE E 70 " --> pdb=" O THR E 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR E 85 " --> pdb=" O PHE E 70 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL E 72 " --> pdb=" O VAL E 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY E 97 " --> pdb=" O HIS E 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA E 136 " --> pdb=" O GLY E 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE E 99 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU E 138 " --> pdb=" O PHE E 99 " (cutoff:3.500A) removed outlier: 12.580A pdb=" N ILE E 101 " --> pdb=" O LEU E 138 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ARG E 168 " --> pdb=" O SER E 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER E 162 " --> pdb=" O ARG E 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 170 " --> pdb=" O ARG E 160 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG E 160 " --> pdb=" O VAL E 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU E 172 " --> pdb=" O GLU E 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU E 158 " --> pdb=" O GLU E 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU F 68 " --> pdb=" O ALA F 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA F 87 " --> pdb=" O LEU F 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE F 70 " --> pdb=" O THR F 85 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR F 85 " --> pdb=" O PHE F 70 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL F 72 " --> pdb=" O VAL F 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY F 97 " --> pdb=" O HIS F 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA F 136 " --> pdb=" O GLY F 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE F 99 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU F 138 " --> pdb=" O PHE F 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE F 101 " --> pdb=" O LEU F 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG F 168 " --> pdb=" O SER F 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER F 162 " --> pdb=" O ARG F 168 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL F 170 " --> pdb=" O ARG F 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG F 160 " --> pdb=" O VAL F 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU F 172 " --> pdb=" O GLU F 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU F 158 " --> pdb=" O GLU F 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU G 68 " --> pdb=" O ALA G 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA G 87 " --> pdb=" O LEU G 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE G 70 " --> pdb=" O THR G 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR G 85 " --> pdb=" O PHE G 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL G 72 " --> pdb=" O VAL G 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY G 97 " --> pdb=" O HIS G 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA G 136 " --> pdb=" O GLY G 97 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE G 99 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU G 138 " --> pdb=" O PHE G 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE G 101 " --> pdb=" O LEU G 138 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ARG G 168 " --> pdb=" O SER G 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER G 162 " --> pdb=" O ARG G 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL G 170 " --> pdb=" O ARG G 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG G 160 " --> pdb=" O VAL G 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU G 172 " --> pdb=" O GLU G 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU G 158 " --> pdb=" O GLU G 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU H 68 " --> pdb=" O ALA H 87 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA H 87 " --> pdb=" O LEU H 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE H 70 " --> pdb=" O THR H 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR H 85 " --> pdb=" O PHE H 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL H 72 " --> pdb=" O VAL H 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY H 97 " --> pdb=" O HIS H 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA H 136 " --> pdb=" O GLY H 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE H 99 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU H 138 " --> pdb=" O PHE H 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE H 101 " --> pdb=" O LEU H 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG H 168 " --> pdb=" O SER H 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER H 162 " --> pdb=" O ARG H 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL H 170 " --> pdb=" O ARG H 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG H 160 " --> pdb=" O VAL H 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU H 172 " --> pdb=" O GLU H 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU H 158 " --> pdb=" O GLU H 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU I 68 " --> pdb=" O ALA I 87 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA I 87 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE I 70 " --> pdb=" O THR I 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR I 85 " --> pdb=" O PHE I 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL I 72 " --> pdb=" O VAL I 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY I 97 " --> pdb=" O HIS I 134 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ALA I 136 " --> pdb=" O GLY I 97 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE I 99 " --> pdb=" O ALA I 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU I 138 " --> pdb=" O PHE I 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE I 101 " --> pdb=" O LEU I 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG I 168 " --> pdb=" O SER I 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER I 162 " --> pdb=" O ARG I 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL I 170 " --> pdb=" O ARG I 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG I 160 " --> pdb=" O VAL I 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU I 172 " --> pdb=" O GLU I 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU I 158 " --> pdb=" O GLU I 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.579A pdb=" N LEU J 68 " --> pdb=" O ALA J 87 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N ALA J 87 " --> pdb=" O LEU J 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE J 70 " --> pdb=" O THR J 85 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR J 85 " --> pdb=" O PHE J 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL J 72 " --> pdb=" O VAL J 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY J 97 " --> pdb=" O HIS J 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA J 136 " --> pdb=" O GLY J 97 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE J 99 " --> pdb=" O ALA J 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU J 138 " --> pdb=" O PHE J 99 " (cutoff:3.500A) removed outlier: 12.580A pdb=" N ILE J 101 " --> pdb=" O LEU J 138 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ARG J 168 " --> pdb=" O SER J 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER J 162 " --> pdb=" O ARG J 168 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL J 170 " --> pdb=" O ARG J 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG J 160 " --> pdb=" O VAL J 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU J 172 " --> pdb=" O GLU J 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU J 158 " --> pdb=" O GLU J 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.579A pdb=" N LEU K 68 " --> pdb=" O ALA K 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA K 87 " --> pdb=" O LEU K 68 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE K 70 " --> pdb=" O THR K 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR K 85 " --> pdb=" O PHE K 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL K 72 " --> pdb=" O VAL K 83 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY K 97 " --> pdb=" O HIS K 134 " (cutoff:3.500A) removed outlier: 8.333A pdb=" N ALA K 136 " --> pdb=" O GLY K 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE K 99 " --> pdb=" O ALA K 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU K 138 " --> pdb=" O PHE K 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE K 101 " --> pdb=" O LEU K 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG K 168 " --> pdb=" O SER K 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER K 162 " --> pdb=" O ARG K 168 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL K 170 " --> pdb=" O ARG K 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG K 160 " --> pdb=" O VAL K 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU K 172 " --> pdb=" O GLU K 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU K 158 " --> pdb=" O GLU K 172 " (cutoff:3.500A) removed outlier: 6.691A 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: 6.578A pdb=" N LEU L 68 " --> pdb=" O ALA L 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA L 87 " --> pdb=" O LEU L 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE L 70 " --> pdb=" O THR L 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR L 85 " --> pdb=" O PHE L 70 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N VAL L 72 " --> pdb=" O VAL L 83 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N GLY L 97 " --> pdb=" O HIS L 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA L 136 " --> pdb=" O GLY L 97 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE L 99 " --> pdb=" O ALA L 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU L 138 " --> pdb=" O PHE L 99 " (cutoff:3.500A) removed outlier: 12.580A pdb=" N ILE L 101 " --> pdb=" O LEU L 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG L 168 " --> pdb=" O SER L 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER L 162 " --> pdb=" O ARG L 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL L 170 " --> pdb=" O ARG L 160 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ARG L 160 " --> pdb=" O VAL L 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU L 172 " --> pdb=" O GLU L 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU L 158 " --> pdb=" O GLU L 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU M 68 " --> pdb=" O ALA M 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA M 87 " --> pdb=" O LEU M 68 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N PHE M 70 " --> pdb=" O THR M 85 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N THR M 85 " --> pdb=" O PHE M 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL M 72 " --> pdb=" O VAL M 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY M 97 " --> pdb=" O HIS M 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA M 136 " --> pdb=" O GLY M 97 " (cutoff:3.500A) removed outlier: 7.936A pdb=" N PHE M 99 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU M 138 " --> pdb=" O PHE M 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE M 101 " --> pdb=" O LEU M 138 " (cutoff:3.500A) removed outlier: 10.960A pdb=" N ARG M 168 " --> pdb=" O SER M 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER M 162 " --> pdb=" O ARG M 168 " (cutoff:3.500A) removed outlier: 7.628A pdb=" N VAL M 170 " --> pdb=" O ARG M 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG M 160 " --> pdb=" O VAL M 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU M 172 " --> pdb=" O GLU M 158 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N GLU M 158 " --> pdb=" O GLU M 172 " (cutoff:3.500A) removed outlier: 6.692A 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: 6.578A pdb=" N LEU N 68 " --> pdb=" O ALA N 87 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N ALA N 87 " --> pdb=" O LEU N 68 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N PHE N 70 " --> pdb=" O THR N 85 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N THR N 85 " --> pdb=" O PHE N 70 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N VAL N 72 " --> pdb=" O VAL N 83 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N GLY N 97 " --> pdb=" O HIS N 134 " (cutoff:3.500A) removed outlier: 8.332A pdb=" N ALA N 136 " --> pdb=" O GLY N 97 " (cutoff:3.500A) removed outlier: 7.937A pdb=" N PHE N 99 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N LEU N 138 " --> pdb=" O PHE N 99 " (cutoff:3.500A) removed outlier: 12.579A pdb=" N ILE N 101 " --> pdb=" O LEU N 138 " (cutoff:3.500A) removed outlier: 10.961A pdb=" N ARG N 168 " --> pdb=" O SER N 162 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N SER N 162 " --> pdb=" O ARG N 168 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL N 170 " --> pdb=" O ARG N 160 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ARG N 160 " --> pdb=" O VAL N 170 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLU N 172 " --> pdb=" O GLU N 158 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N GLU N 158 " --> pdb=" O GLU N 172 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N LEU N 174 " --> pdb=" O ILE N 156 " (cutoff:3.500A) 994 hydrogen bonds defined for protein. 2730 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: 3.27 Time building geometry restraints manager: 2.15 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 4629 1.33 - 1.45: 5473 1.45 - 1.57: 11654 1.57 - 1.69: 126 1.69 - 1.81: 56 Bond restraints: 21938 Sorted by residual: bond pdb=" O5A COA G 501 " pdb=" P2A COA G 501 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" O5A COA N 501 " pdb=" P2A COA N 501 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" O5A COA K 501 " pdb=" P2A COA K 501 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" O5A COA D 501 " pdb=" P2A COA D 501 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.48e+01 bond pdb=" O5A COA E 501 " pdb=" P2A COA E 501 " ideal model delta sigma weight residual 1.491 1.609 -0.118 2.00e-02 2.50e+03 3.47e+01 ... (remaining 21933 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.68: 29638 4.68 - 9.35: 210 9.35 - 14.03: 42 14.03 - 18.70: 28 18.70 - 23.38: 14 Bond angle restraints: 29932 Sorted by residual: angle pdb=" P1A COA J 501 " pdb=" O3A COA J 501 " pdb=" P2A COA J 501 " ideal model delta sigma weight residual 135.11 111.73 23.38 3.00e+00 1.11e-01 6.07e+01 angle pdb=" P1A COA N 501 " pdb=" O3A COA N 501 " pdb=" P2A COA N 501 " ideal model delta sigma weight residual 135.11 111.75 23.36 3.00e+00 1.11e-01 6.06e+01 angle pdb=" P1A COA C 501 " pdb=" O3A COA C 501 " pdb=" P2A COA C 501 " ideal model delta sigma weight residual 135.11 111.75 23.36 3.00e+00 1.11e-01 6.06e+01 angle pdb=" P1A COA H 501 " pdb=" O3A COA H 501 " pdb=" P2A COA H 501 " ideal model delta sigma weight residual 135.11 111.76 23.35 3.00e+00 1.11e-01 6.06e+01 angle pdb=" P1A COA A 501 " pdb=" O3A COA A 501 " pdb=" P2A COA A 501 " ideal model delta sigma weight residual 135.11 111.76 23.35 3.00e+00 1.11e-01 6.06e+01 ... (remaining 29927 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.84: 11997 16.84 - 33.67: 771 33.67 - 50.51: 168 50.51 - 67.35: 84 67.35 - 84.18: 98 Dihedral angle restraints: 13118 sinusoidal: 5754 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 90.00 133.25 -43.25 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG M 44 " pdb=" CD ARG M 44 " pdb=" NE ARG M 44 " pdb=" CZ ARG M 44 " ideal model delta sinusoidal sigma weight residual 90.00 133.25 -43.25 2 1.50e+01 4.44e-03 1.00e+01 dihedral pdb=" CG ARG B 44 " pdb=" CD ARG B 44 " pdb=" NE ARG B 44 " pdb=" CZ ARG B 44 " ideal model delta sinusoidal sigma weight residual 90.00 133.23 -43.23 2 1.50e+01 4.44e-03 1.00e+01 ... (remaining 13115 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 2820 0.068 - 0.135: 302 0.135 - 0.203: 0 0.203 - 0.270: 0 0.270 - 0.338: 28 Chirality restraints: 3150 Sorted by residual: chirality pdb=" C2B COA G 501 " pdb=" C1B COA G 501 " pdb=" C3B COA G 501 " pdb=" O2B COA G 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C2B COA N 501 " pdb=" C1B COA N 501 " pdb=" C3B COA N 501 " pdb=" O2B COA N 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.85e+00 chirality pdb=" C2B COA F 501 " pdb=" C1B COA F 501 " pdb=" C3B COA F 501 " pdb=" O2B COA F 501 " both_signs ideal model delta sigma weight residual False -2.40 -2.74 0.34 2.00e-01 2.50e+01 2.83e+00 ... (remaining 3147 not shown) Planarity restraints: 3906 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL D 178 " -0.022 5.00e-02 4.00e+02 3.29e-02 1.73e+00 pdb=" N PRO D 179 " 0.057 5.00e-02 4.00e+02 pdb=" CA PRO D 179 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 179 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL G 178 " 0.022 5.00e-02 4.00e+02 3.28e-02 1.72e+00 pdb=" N PRO G 179 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO G 179 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO G 179 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL F 178 " 0.022 5.00e-02 4.00e+02 3.27e-02 1.71e+00 pdb=" N PRO F 179 " -0.057 5.00e-02 4.00e+02 pdb=" CA PRO F 179 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO F 179 " 0.018 5.00e-02 4.00e+02 ... (remaining 3903 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 5393 2.80 - 3.32: 19397 3.32 - 3.85: 35728 3.85 - 4.37: 45023 4.37 - 4.90: 75367 Nonbonded interactions: 180908 Sorted by model distance: nonbonded pdb=" OD2 ASP F 74 " pdb=" NH2 ARG F 110 " model vdw 2.275 3.120 nonbonded pdb=" O PHE C 21 " pdb=" OH TYR C 57 " model vdw 2.275 3.040 nonbonded pdb=" O PHE J 21 " pdb=" OH TYR J 57 " model vdw 2.275 3.040 nonbonded pdb=" OD2 ASP J 74 " pdb=" NH2 ARG J 110 " model vdw 2.275 3.120 nonbonded pdb=" OD2 ASP C 74 " pdb=" NH2 ARG C 110 " model vdw 2.275 3.120 ... (remaining 180903 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.220 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 15.490 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 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 0.118 21938 Z= 0.348 Angle : 1.151 23.379 29932 Z= 0.430 Chirality : 0.050 0.338 3150 Planarity : 0.004 0.033 3906 Dihedral : 14.895 84.183 8470 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 0.65 (0.15), residues: 2618 helix: 1.41 (0.16), residues: 938 sheet: 0.20 (0.19), residues: 658 loop : -0.21 (0.18), residues: 1022 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 31 TYR 0.016 0.001 TYR D 57 PHE 0.007 0.001 PHE I 21 TRP 0.005 0.001 TRP D 165 HIS 0.004 0.001 HIS C 107 Details of bonding type rmsd covalent geometry : bond 0.00702 (21938) covalent geometry : angle 1.15079 (29932) hydrogen bonds : bond 0.15965 ( 994) hydrogen bonds : angle 6.55374 ( 2730) *********************** 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 332 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 332 time to evaluate : 0.740 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.5372 time to fit residues: 204.9136 Evaluate side-chains 288 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 288 time to evaluate : 0.803 ------------------------------------------------------------------------------- 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: 10.0000 chunk 98 optimal weight: 10.0000 chunk 194 optimal weight: 0.7980 chunk 227 optimal weight: 0.7980 chunk 107 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.6980 chunk 247 optimal weight: 5.9990 chunk 130 optimal weight: 2.9990 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 8.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN F 34 GLN H 34 GLN I 34 GLN M 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.106957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.091640 restraints weight = 27591.109| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 1.75 r_work: 0.3204 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.1453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 21938 Z= 0.132 Angle : 0.524 4.526 29932 Z= 0.267 Chirality : 0.041 0.124 3150 Planarity : 0.004 0.027 3906 Dihedral : 15.543 89.195 3836 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 1.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 1.04 % Allowed : 3.31 % Favored : 95.65 % 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: 0.80 (0.15), residues: 2618 helix: 1.89 (0.16), residues: 966 sheet: 0.02 (0.18), residues: 658 loop : -0.37 (0.17), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG L 62 TYR 0.013 0.001 TYR G 57 PHE 0.011 0.001 PHE N 164 TRP 0.006 0.001 TRP B 30 HIS 0.004 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00307 (21938) covalent geometry : angle 0.52408 (29932) hydrogen bonds : bond 0.03469 ( 994) hydrogen bonds : angle 4.55078 ( 2730) *********************** 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 298 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 276 time to evaluate : 0.822 Fit side-chains REVERT: B 24 ASP cc_start: 0.8284 (m-30) cc_final: 0.8049 (OUTLIER) REVERT: E 24 ASP cc_start: 0.8466 (m-30) cc_final: 0.8205 (OUTLIER) REVERT: G 149 GLU cc_start: 0.8611 (OUTLIER) cc_final: 0.8409 (mt-10) REVERT: I 24 ASP cc_start: 0.8284 (m-30) cc_final: 0.8066 (t0) REVERT: L 24 ASP cc_start: 0.8468 (m-30) cc_final: 0.8205 (OUTLIER) REVERT: N 149 GLU cc_start: 0.8616 (OUTLIER) cc_final: 0.8415 (mt-10) outliers start: 22 outliers final: 13 residues processed: 294 average time/residue: 0.6425 time to fit residues: 212.6862 Evaluate side-chains 271 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 259 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 149 GLU Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 149 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 158 optimal weight: 0.7980 chunk 216 optimal weight: 1.9990 chunk 203 optimal weight: 5.9990 chunk 199 optimal weight: 5.9990 chunk 244 optimal weight: 3.9990 chunk 116 optimal weight: 8.9990 chunk 106 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 chunk 208 optimal weight: 9.9990 chunk 112 optimal weight: 10.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.102367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.087502 restraints weight = 28099.534| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.72 r_work: 0.3132 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2969 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.2024 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 21938 Z= 0.224 Angle : 0.570 4.489 29932 Z= 0.293 Chirality : 0.044 0.121 3150 Planarity : 0.004 0.032 3906 Dihedral : 15.460 84.363 3836 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 1.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.95 % Favored : 99.05 % Rotamer: Outliers : 2.18 % Allowed : 3.78 % Favored : 94.04 % 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: 0.79 (0.15), residues: 2618 helix: 1.91 (0.16), residues: 966 sheet: -0.05 (0.18), residues: 658 loop : -0.38 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG M 95 TYR 0.011 0.002 TYR E 57 PHE 0.011 0.002 PHE B 164 TRP 0.008 0.001 TRP A 30 HIS 0.005 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00548 (21938) covalent geometry : angle 0.57021 (29932) hydrogen bonds : bond 0.04010 ( 994) hydrogen bonds : angle 4.55580 ( 2730) *********************** 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 310 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 264 time to evaluate : 0.611 Fit side-chains REVERT: A 24 ASP cc_start: 0.8471 (m-30) cc_final: 0.8177 (OUTLIER) REVERT: B 62 ARG cc_start: 0.8018 (OUTLIER) cc_final: 0.7645 (mtm-85) REVERT: D 62 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7706 (mtm-85) REVERT: E 24 ASP cc_start: 0.8439 (m-30) cc_final: 0.8232 (t0) REVERT: H 24 ASP cc_start: 0.8467 (m-30) cc_final: 0.8174 (OUTLIER) REVERT: I 62 ARG cc_start: 0.8028 (OUTLIER) cc_final: 0.7657 (mtm-85) REVERT: K 62 ARG cc_start: 0.8151 (OUTLIER) cc_final: 0.7706 (mtm-85) REVERT: L 24 ASP cc_start: 0.8446 (m-30) cc_final: 0.8225 (t0) outliers start: 46 outliers final: 18 residues processed: 300 average time/residue: 0.6452 time to fit residues: 218.4233 Evaluate side-chains 272 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 252 time to evaluate : 0.786 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain E residue 81 VAL Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain L residue 81 VAL Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 49 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 245 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 137 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 195 optimal weight: 7.9990 chunk 16 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 183 optimal weight: 5.9990 chunk 232 optimal weight: 0.9990 chunk 47 optimal weight: 0.9990 chunk 242 optimal weight: 0.7980 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104586 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.089690 restraints weight = 28240.418| |-----------------------------------------------------------------------------| r_work (start): 0.3305 rms_B_bonded: 1.75 r_work: 0.3170 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.2156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 21938 Z= 0.116 Angle : 0.481 4.447 29932 Z= 0.248 Chirality : 0.040 0.121 3150 Planarity : 0.004 0.029 3906 Dihedral : 14.941 83.422 3836 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 1.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.14 % Allowed : 6.29 % Favored : 92.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.00 (0.16), residues: 2618 helix: 2.31 (0.17), residues: 966 sheet: -0.08 (0.18), residues: 658 loop : -0.40 (0.18), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG L 62 TYR 0.008 0.001 TYR L 57 PHE 0.007 0.001 PHE G 21 TRP 0.005 0.001 TRP F 30 HIS 0.002 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00273 (21938) covalent geometry : angle 0.48077 (29932) hydrogen bonds : bond 0.03045 ( 994) hydrogen bonds : angle 4.25994 ( 2730) *********************** 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 290 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 266 time to evaluate : 0.644 Fit side-chains REVERT: A 24 ASP cc_start: 0.8474 (m-30) cc_final: 0.8173 (t0) REVERT: B 62 ARG cc_start: 0.7977 (OUTLIER) cc_final: 0.7597 (mtm-85) REVERT: D 62 ARG cc_start: 0.8133 (OUTLIER) cc_final: 0.7677 (mtm-85) REVERT: E 24 ASP cc_start: 0.8412 (m-30) cc_final: 0.8200 (t0) REVERT: H 24 ASP cc_start: 0.8454 (m-30) cc_final: 0.8165 (t0) REVERT: I 62 ARG cc_start: 0.7982 (OUTLIER) cc_final: 0.7606 (mtm-85) REVERT: K 62 ARG cc_start: 0.8131 (OUTLIER) cc_final: 0.7672 (mtm-85) outliers start: 24 outliers final: 12 residues processed: 284 average time/residue: 0.6652 time to fit residues: 210.9193 Evaluate side-chains 274 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 258 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 191 PHE Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 24 ASP Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 191 PHE Chi-restraints excluded: chain N residue 49 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 165 optimal weight: 0.9980 chunk 170 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 189 optimal weight: 3.9990 chunk 143 optimal weight: 0.8980 chunk 217 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 30 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 174 optimal weight: 2.9990 chunk 111 optimal weight: 0.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN D 34 GLN F 34 GLN H 34 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3297 r_free = 0.3297 target = 0.089502 restraints weight = 27531.693| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 1.75 r_work: 0.3164 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 21938 Z= 0.131 Angle : 0.492 4.604 29932 Z= 0.253 Chirality : 0.040 0.120 3150 Planarity : 0.004 0.030 3906 Dihedral : 14.766 82.103 3836 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.73 % Favored : 99.27 % Rotamer: Outliers : 1.61 % Allowed : 6.76 % Favored : 91.63 % 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: 1.04 (0.16), residues: 2618 helix: 2.42 (0.16), residues: 966 sheet: -0.11 (0.18), residues: 658 loop : -0.44 (0.19), residues: 994 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 110 TYR 0.008 0.001 TYR J 57 PHE 0.008 0.001 PHE E 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 0.00311 (21938) covalent geometry : angle 0.49193 (29932) hydrogen bonds : bond 0.03095 ( 994) hydrogen bonds : angle 4.19590 ( 2730) *********************** 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 296 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 262 time to evaluate : 0.776 Fit side-chains REVERT: A 24 ASP cc_start: 0.8431 (m-30) cc_final: 0.8162 (t0) REVERT: B 62 ARG cc_start: 0.7978 (OUTLIER) cc_final: 0.7578 (mtm-85) REVERT: D 62 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7666 (mtm-85) REVERT: H 24 ASP cc_start: 0.8461 (m-30) cc_final: 0.8165 (t0) REVERT: I 62 ARG cc_start: 0.7993 (OUTLIER) cc_final: 0.7599 (mtm-85) REVERT: K 62 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7665 (mtm-85) outliers start: 34 outliers final: 16 residues processed: 290 average time/residue: 0.6252 time to fit residues: 203.9665 Evaluate side-chains 277 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 257 time to evaluate : 0.800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 85 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 241 optimal weight: 5.9990 chunk 127 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 223 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 155 optimal weight: 2.9990 chunk 148 optimal weight: 7.9990 chunk 249 optimal weight: 10.0000 chunk 133 optimal weight: 0.1980 chunk 57 optimal weight: 5.9990 overall best weight: 2.4388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN D 34 GLN F 34 GLN H 34 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.087561 restraints weight = 27400.387| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.78 r_work: 0.3128 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8747 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 21938 Z= 0.202 Angle : 0.555 5.512 29932 Z= 0.286 Chirality : 0.042 0.120 3150 Planarity : 0.004 0.032 3906 Dihedral : 14.705 76.389 3836 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 1.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.42 % Allowed : 7.05 % Favored : 91.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 2.23 (0.16), residues: 980 sheet: -0.20 (0.18), residues: 658 loop : -0.62 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 110 TYR 0.010 0.001 TYR B 123 PHE 0.010 0.001 PHE L 21 TRP 0.007 0.001 TRP A 30 HIS 0.005 0.001 HIS B 126 Details of bonding type rmsd covalent geometry : bond 0.00493 (21938) covalent geometry : angle 0.55513 (29932) hydrogen bonds : bond 0.03651 ( 994) hydrogen bonds : angle 4.33335 ( 2730) *********************** 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 293 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 263 time to evaluate : 0.828 Fit side-chains REVERT: A 24 ASP cc_start: 0.8449 (m-30) cc_final: 0.8173 (t0) REVERT: B 62 ARG cc_start: 0.8054 (OUTLIER) cc_final: 0.7641 (mtm-85) REVERT: D 62 ARG cc_start: 0.8154 (OUTLIER) cc_final: 0.7676 (mtm-85) REVERT: E 14 ASP cc_start: 0.7772 (p0) cc_final: 0.7492 (p0) REVERT: H 24 ASP cc_start: 0.8464 (m-30) cc_final: 0.8176 (t0) REVERT: I 62 ARG cc_start: 0.8069 (OUTLIER) cc_final: 0.7659 (mtm-85) REVERT: K 62 ARG cc_start: 0.8159 (OUTLIER) cc_final: 0.7681 (mtm-85) REVERT: L 14 ASP cc_start: 0.7786 (p0) cc_final: 0.7498 (p0) outliers start: 30 outliers final: 16 residues processed: 289 average time/residue: 0.6571 time to fit residues: 213.2386 Evaluate side-chains 285 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 265 time to evaluate : 0.762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 62 ARG Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 62 ARG Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 89 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 149 optimal weight: 1.9990 chunk 250 optimal weight: 0.9990 chunk 240 optimal weight: 0.5980 chunk 136 optimal weight: 5.9990 chunk 154 optimal weight: 7.9990 chunk 122 optimal weight: 0.8980 chunk 112 optimal weight: 7.9990 chunk 148 optimal weight: 4.9990 chunk 242 optimal weight: 2.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.104700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.089420 restraints weight = 27250.768| |-----------------------------------------------------------------------------| r_work (start): 0.3293 rms_B_bonded: 1.78 r_work: 0.3159 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.2996 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 21938 Z= 0.128 Angle : 0.497 5.749 29932 Z= 0.257 Chirality : 0.040 0.119 3150 Planarity : 0.004 0.030 3906 Dihedral : 14.263 74.327 3836 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 2.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Rotamer: Outliers : 1.66 % Allowed : 7.19 % Favored : 91.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.92 (0.16), residues: 2618 helix: 2.43 (0.16), residues: 980 sheet: -0.16 (0.18), residues: 658 loop : -0.70 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 110 TYR 0.008 0.001 TYR M 57 PHE 0.007 0.001 PHE J 21 TRP 0.005 0.001 TRP D 30 HIS 0.002 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00303 (21938) covalent geometry : angle 0.49718 (29932) hydrogen bonds : bond 0.03020 ( 994) hydrogen bonds : angle 4.19310 ( 2730) *********************** 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 297 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 262 time to evaluate : 0.771 Fit side-chains REVERT: A 24 ASP cc_start: 0.8433 (m-30) cc_final: 0.8162 (t0) REVERT: D 62 ARG cc_start: 0.8119 (OUTLIER) cc_final: 0.7636 (mtm-85) REVERT: D 115 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7682 (tm-30) REVERT: H 24 ASP cc_start: 0.8424 (m-30) cc_final: 0.8156 (t0) REVERT: K 62 ARG cc_start: 0.8123 (OUTLIER) cc_final: 0.7642 (mtm-85) REVERT: K 115 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7678 (tm-30) outliers start: 35 outliers final: 15 residues processed: 291 average time/residue: 0.6726 time to fit residues: 218.8986 Evaluate side-chains 282 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 263 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 115 GLU Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 115 GLU Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 2 optimal weight: 3.9990 chunk 122 optimal weight: 2.9990 chunk 161 optimal weight: 2.9990 chunk 103 optimal weight: 0.8980 chunk 113 optimal weight: 8.9990 chunk 130 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 239 optimal weight: 8.9990 chunk 200 optimal weight: 0.9980 chunk 190 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN B 67 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN I 67 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.103003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3269 r_free = 0.3269 target = 0.087932 restraints weight = 27103.675| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.74 r_work: 0.3135 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2976 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.2976 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 21938 Z= 0.198 Angle : 0.554 4.724 29932 Z= 0.285 Chirality : 0.042 0.143 3150 Planarity : 0.004 0.032 3906 Dihedral : 14.138 70.374 3836 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 2.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.69 % Favored : 99.31 % Rotamer: Outliers : 1.61 % Allowed : 7.71 % Favored : 90.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.16), residues: 2618 helix: 2.26 (0.16), residues: 980 sheet: -0.23 (0.18), residues: 658 loop : -0.68 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.009 0.001 TYR I 123 PHE 0.009 0.001 PHE L 21 TRP 0.006 0.001 TRP H 30 HIS 0.004 0.001 HIS I 126 Details of bonding type rmsd covalent geometry : bond 0.00482 (21938) covalent geometry : angle 0.55371 (29932) hydrogen bonds : bond 0.03546 ( 994) hydrogen bonds : angle 4.30404 ( 2730) *********************** 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 302 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 268 time to evaluate : 0.707 Fit side-chains REVERT: A 24 ASP cc_start: 0.8402 (m-30) cc_final: 0.8166 (t0) REVERT: D 62 ARG cc_start: 0.8147 (OUTLIER) cc_final: 0.7671 (mtm-85) REVERT: H 24 ASP cc_start: 0.8409 (m-30) cc_final: 0.8164 (t0) REVERT: K 62 ARG cc_start: 0.8166 (OUTLIER) cc_final: 0.7695 (mtm-85) outliers start: 34 outliers final: 22 residues processed: 300 average time/residue: 0.6536 time to fit residues: 219.7162 Evaluate side-chains 293 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 269 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 179 optimal weight: 2.9990 chunk 228 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 125 optimal weight: 4.9990 chunk 115 optimal weight: 0.5980 chunk 42 optimal weight: 0.9990 chunk 154 optimal weight: 8.9990 chunk 247 optimal weight: 5.9990 chunk 95 optimal weight: 4.9990 chunk 28 optimal weight: 8.9990 chunk 199 optimal weight: 7.9990 overall best weight: 2.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN B 67 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN I 67 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.102775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.088232 restraints weight = 27611.073| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.70 r_work: 0.3148 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2986 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2986 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8733 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 21938 Z= 0.180 Angle : 0.539 4.876 29932 Z= 0.278 Chirality : 0.042 0.141 3150 Planarity : 0.004 0.032 3906 Dihedral : 13.780 69.330 3836 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.51 % Allowed : 8.18 % Favored : 90.30 % 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: 0.79 (0.16), residues: 2618 helix: 2.24 (0.16), residues: 980 sheet: -0.21 (0.18), residues: 658 loop : -0.69 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG I 110 TYR 0.008 0.001 TYR M 57 PHE 0.008 0.001 PHE G 21 TRP 0.006 0.001 TRP H 30 HIS 0.004 0.001 HIS I 126 Details of bonding type rmsd covalent geometry : bond 0.00436 (21938) covalent geometry : angle 0.53851 (29932) hydrogen bonds : bond 0.03372 ( 994) hydrogen bonds : angle 4.29648 ( 2730) *********************** 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 298 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 266 time to evaluate : 0.842 Fit side-chains REVERT: A 24 ASP cc_start: 0.8412 (m-30) cc_final: 0.8179 (t0) REVERT: D 62 ARG cc_start: 0.8144 (OUTLIER) cc_final: 0.7664 (mtm-85) REVERT: H 24 ASP cc_start: 0.8419 (m-30) cc_final: 0.8178 (t0) REVERT: K 62 ARG cc_start: 0.8157 (OUTLIER) cc_final: 0.7684 (mtm-85) outliers start: 32 outliers final: 22 residues processed: 296 average time/residue: 0.7316 time to fit residues: 242.3114 Evaluate side-chains 289 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 265 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 159 optimal weight: 7.9990 chunk 157 optimal weight: 3.9990 chunk 162 optimal weight: 0.9980 chunk 112 optimal weight: 7.9990 chunk 100 optimal weight: 8.9990 chunk 149 optimal weight: 5.9990 chunk 232 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 176 optimal weight: 0.7980 chunk 111 optimal weight: 3.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN B 67 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN I 67 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.103372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.088140 restraints weight = 26943.614| |-----------------------------------------------------------------------------| r_work (start): 0.3273 rms_B_bonded: 1.77 r_work: 0.3139 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.2975 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 21938 Z= 0.183 Angle : 0.549 4.917 29932 Z= 0.283 Chirality : 0.042 0.151 3150 Planarity : 0.004 0.032 3906 Dihedral : 13.537 68.371 3836 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 1.51 % Allowed : 8.28 % Favored : 90.21 % 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: 0.77 (0.16), residues: 2618 helix: 2.22 (0.16), residues: 980 sheet: -0.23 (0.18), residues: 658 loop : -0.68 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.009 0.001 TYR F 42 PHE 0.009 0.001 PHE L 21 TRP 0.006 0.001 TRP K 30 HIS 0.004 0.001 HIS H 126 Details of bonding type rmsd covalent geometry : bond 0.00443 (21938) covalent geometry : angle 0.54857 (29932) hydrogen bonds : bond 0.03435 ( 994) hydrogen bonds : angle 4.32409 ( 2730) ********************** 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 299 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 267 time to evaluate : 0.809 Fit side-chains REVERT: A 24 ASP cc_start: 0.8438 (m-30) cc_final: 0.8172 (t0) REVERT: D 62 ARG cc_start: 0.8145 (OUTLIER) cc_final: 0.7660 (mtm-85) REVERT: H 24 ASP cc_start: 0.8432 (m-30) cc_final: 0.8165 (t0) REVERT: K 62 ARG cc_start: 0.8156 (OUTLIER) cc_final: 0.7676 (mtm-85) outliers start: 32 outliers final: 22 residues processed: 297 average time/residue: 0.6833 time to fit residues: 227.1276 Evaluate side-chains 294 residues out of total 2114 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 270 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 192 VAL Chi-restraints excluded: chain B residue 85 THR Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 137 VAL Chi-restraints excluded: chain D residue 62 ARG Chi-restraints excluded: chain D residue 85 THR Chi-restraints excluded: chain F residue 85 THR Chi-restraints excluded: chain G residue 49 SER Chi-restraints excluded: chain G residue 85 THR Chi-restraints excluded: chain G residue 115 GLU Chi-restraints excluded: chain H residue 81 VAL Chi-restraints excluded: chain H residue 85 THR Chi-restraints excluded: chain H residue 192 VAL Chi-restraints excluded: chain I residue 85 THR Chi-restraints excluded: chain J residue 85 THR Chi-restraints excluded: chain J residue 137 VAL Chi-restraints excluded: chain K residue 62 ARG Chi-restraints excluded: chain K residue 85 THR Chi-restraints excluded: chain M residue 85 THR Chi-restraints excluded: chain N residue 49 SER Chi-restraints excluded: chain N residue 85 THR Chi-restraints excluded: chain N residue 115 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 252 random chunks: chunk 116 optimal weight: 7.9990 chunk 12 optimal weight: 0.2980 chunk 229 optimal weight: 4.9990 chunk 167 optimal weight: 2.9990 chunk 57 optimal weight: 3.9990 chunk 228 optimal weight: 0.7980 chunk 19 optimal weight: 8.9990 chunk 160 optimal weight: 3.9990 chunk 146 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 231 optimal weight: 9.9990 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 34 GLN B 34 GLN B 67 GLN D 34 GLN F 34 GLN H 34 GLN I 34 GLN I 67 GLN K 34 GLN M 34 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.103756 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.089105 restraints weight = 27605.361| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 1.72 r_work: 0.3158 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2997 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2997 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.2619 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 21938 Z= 0.145 Angle : 0.516 4.960 29932 Z= 0.267 Chirality : 0.040 0.141 3150 Planarity : 0.004 0.031 3906 Dihedral : 13.149 69.210 3836 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 2.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.37 % Allowed : 8.66 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.85 (0.16), residues: 2618 helix: 2.32 (0.16), residues: 980 sheet: -0.18 (0.18), residues: 658 loop : -0.68 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 110 TYR 0.011 0.001 TYR F 42 PHE 0.007 0.001 PHE D 21 TRP 0.004 0.001 TRP H 30 HIS 0.003 0.001 HIS A 126 Details of bonding type rmsd covalent geometry : bond 0.00346 (21938) covalent geometry : angle 0.51564 (29932) hydrogen bonds : bond 0.03099 ( 994) hydrogen bonds : angle 4.25375 ( 2730) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7221.60 seconds wall clock time: 123 minutes 19.93 seconds (7399.93 seconds total)