Starting phenix.real_space_refine on Sat Feb 7 00:29:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v0g_64664/02_2026/9v0g_64664.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v0g_64664/02_2026/9v0g_64664.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v0g_64664/02_2026/9v0g_64664.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v0g_64664/02_2026/9v0g_64664.map" model { file = "/net/cci-nas-00/data/ceres_data/9v0g_64664/02_2026/9v0g_64664.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v0g_64664/02_2026/9v0g_64664.cif" } resolution = 2.46 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= 0.001 sd= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 18320 2.51 5 N 5088 2.21 5 O 5312 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.03s 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: 28816 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 1399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1399 Classifications: {'peptide': 180} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 170} Chain: "E" Number of atoms: 2203 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2203 Classifications: {'peptide': 277} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 263} Restraints were copied for chains: B, L, K, I, J, C, D, G, F, H, M, P, N, O Time building chain proxies: 2.76, per 1000 atoms: 0.10 Number of scatterers: 28816 At special positions: 0 Unit cell: (173.55, 170.95, 118.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 5312 8.00 N 5088 7.00 C 18320 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: 2.30 Conformation dependent library (CDL) restraints added in 1.2 seconds 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6832 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 24 sheets defined 51.4% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'A' and resid 11 through 22 removed outlier: 3.696A pdb=" N ARG A 16 " --> pdb=" O SER A 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL A 21 " --> pdb=" O GLU A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 59 removed outlier: 3.569A pdb=" N ALA A 51 " --> pdb=" O ILE A 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE A 52 " --> pdb=" O ARG A 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA A 57 " --> pdb=" O ALA A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 87 removed outlier: 4.031A pdb=" N PHE A 85 " --> pdb=" O LEU A 81 " (cutoff:3.500A) Processing helix chain 'A' and resid 91 through 95 Processing helix chain 'A' and resid 158 through 163 Processing helix chain 'A' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG A 170 " --> pdb=" O SER A 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS A 172 " --> pdb=" O LEU A 168 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR A 173 " --> pdb=" O GLY A 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 11 through 22 removed outlier: 3.697A pdb=" N ARG B 16 " --> pdb=" O SER B 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 21 " --> pdb=" O GLU B 17 " (cutoff:3.500A) Processing helix chain 'B' and resid 42 through 59 removed outlier: 3.570A pdb=" N ALA B 51 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE B 52 " --> pdb=" O ARG B 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA B 57 " --> pdb=" O ALA B 53 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 87 removed outlier: 4.030A pdb=" N PHE B 85 " --> pdb=" O LEU B 81 " (cutoff:3.500A) Processing helix chain 'B' and resid 91 through 95 Processing helix chain 'B' and resid 158 through 163 Processing helix chain 'B' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG B 170 " --> pdb=" O SER B 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS B 172 " --> pdb=" O LEU B 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR B 173 " --> pdb=" O GLY B 169 " (cutoff:3.500A) Processing helix chain 'L' and resid 11 through 22 removed outlier: 3.695A pdb=" N ARG L 16 " --> pdb=" O SER L 12 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL L 21 " --> pdb=" O GLU L 17 " (cutoff:3.500A) Processing helix chain 'L' and resid 42 through 59 removed outlier: 3.569A pdb=" N ALA L 51 " --> pdb=" O ILE L 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE L 52 " --> pdb=" O ARG L 48 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N ALA L 57 " --> pdb=" O ALA L 53 " (cutoff:3.500A) Processing helix chain 'L' and resid 81 through 87 removed outlier: 4.030A pdb=" N PHE L 85 " --> pdb=" O LEU L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 91 through 95 Processing helix chain 'L' and resid 158 through 163 Processing helix chain 'L' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG L 170 " --> pdb=" O SER L 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR L 173 " --> pdb=" O GLY L 169 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 22 removed outlier: 3.697A pdb=" N ARG K 16 " --> pdb=" O SER K 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL K 21 " --> pdb=" O GLU K 17 " (cutoff:3.500A) Processing helix chain 'K' and resid 42 through 59 removed outlier: 3.571A pdb=" N ALA K 51 " --> pdb=" O ILE K 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE K 52 " --> pdb=" O ARG K 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA K 57 " --> pdb=" O ALA K 53 " (cutoff:3.500A) Processing helix chain 'K' and resid 81 through 87 removed outlier: 4.031A pdb=" N PHE K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) Processing helix chain 'K' and resid 91 through 95 Processing helix chain 'K' and resid 158 through 163 Processing helix chain 'K' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG K 170 " --> pdb=" O SER K 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS K 172 " --> pdb=" O LEU K 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR K 173 " --> pdb=" O GLY K 169 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 22 removed outlier: 3.696A pdb=" N ARG I 16 " --> pdb=" O SER I 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL I 21 " --> pdb=" O GLU I 17 " (cutoff:3.500A) Processing helix chain 'I' and resid 42 through 59 removed outlier: 3.570A pdb=" N ALA I 51 " --> pdb=" O ILE I 47 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE I 52 " --> pdb=" O ARG I 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA I 57 " --> pdb=" O ALA I 53 " (cutoff:3.500A) Processing helix chain 'I' and resid 81 through 87 removed outlier: 4.031A pdb=" N PHE I 85 " --> pdb=" O LEU I 81 " (cutoff:3.500A) Processing helix chain 'I' and resid 91 through 95 Processing helix chain 'I' and resid 158 through 163 Processing helix chain 'I' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG I 170 " --> pdb=" O SER I 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS I 172 " --> pdb=" O LEU I 168 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR I 173 " --> pdb=" O GLY I 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 22 removed outlier: 3.696A pdb=" N ARG J 16 " --> pdb=" O SER J 12 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL J 21 " --> pdb=" O GLU J 17 " (cutoff:3.500A) Processing helix chain 'J' and resid 42 through 59 removed outlier: 3.570A pdb=" N ALA J 51 " --> pdb=" O ILE J 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE J 52 " --> pdb=" O ARG J 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA J 57 " --> pdb=" O ALA J 53 " (cutoff:3.500A) Processing helix chain 'J' and resid 81 through 87 removed outlier: 4.030A pdb=" N PHE J 85 " --> pdb=" O LEU J 81 " (cutoff:3.500A) Processing helix chain 'J' and resid 91 through 95 Processing helix chain 'J' and resid 158 through 163 Processing helix chain 'J' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG J 170 " --> pdb=" O SER J 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS J 172 " --> pdb=" O LEU J 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR J 173 " --> pdb=" O GLY J 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 22 removed outlier: 3.696A pdb=" N ARG C 16 " --> pdb=" O SER C 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL C 21 " --> pdb=" O GLU C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 59 removed outlier: 3.570A pdb=" N ALA C 51 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N ILE C 52 " --> pdb=" O ARG C 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 87 removed outlier: 4.030A pdb=" N PHE C 85 " --> pdb=" O LEU C 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 95 Processing helix chain 'C' and resid 158 through 163 Processing helix chain 'C' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG C 170 " --> pdb=" O SER C 166 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N HIS C 172 " --> pdb=" O LEU C 168 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR C 173 " --> pdb=" O GLY C 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 11 through 22 removed outlier: 3.697A pdb=" N ARG D 16 " --> pdb=" O SER D 12 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL D 21 " --> pdb=" O GLU D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 59 removed outlier: 3.569A pdb=" N ALA D 51 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N ILE D 52 " --> pdb=" O ARG D 48 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 57 " --> pdb=" O ALA D 53 " (cutoff:3.500A) Processing helix chain 'D' and resid 81 through 87 removed outlier: 4.031A pdb=" N PHE D 85 " --> pdb=" O LEU D 81 " (cutoff:3.500A) Processing helix chain 'D' and resid 91 through 95 Processing helix chain 'D' and resid 158 through 163 Processing helix chain 'D' and resid 166 through 180 removed outlier: 3.727A pdb=" N ARG D 170 " --> pdb=" O SER D 166 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N HIS D 172 " --> pdb=" O LEU D 168 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N THR D 173 " --> pdb=" O GLY D 169 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 19 Proline residue: E 11 - end of helix removed outlier: 3.545A pdb=" N GLU E 16 " --> pdb=" O LEU E 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU E 19 " --> pdb=" O LYS E 15 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 Proline residue: E 33 - end of helix Processing helix chain 'E' and resid 39 through 47 Processing helix chain 'E' and resid 48 through 51 Processing helix chain 'E' and resid 53 through 58 removed outlier: 3.512A pdb=" N ASP E 58 " --> pdb=" O PRO E 54 " (cutoff:3.500A) Processing helix chain 'E' and resid 59 through 61 No H-bonds generated for 'chain 'E' and resid 59 through 61' Processing helix chain 'E' and resid 62 through 74 Processing helix chain 'E' and resid 74 through 90 removed outlier: 3.713A pdb=" N LEU E 78 " --> pdb=" O ALA E 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 91 through 101 removed outlier: 3.785A pdb=" N LYS E 100 " --> pdb=" O ALA E 96 " (cutoff:3.500A) Processing helix chain 'E' and resid 101 through 109 Processing helix chain 'E' and resid 124 through 131 removed outlier: 3.757A pdb=" N LEU E 128 " --> pdb=" O VAL E 124 " (cutoff:3.500A) Processing helix chain 'E' and resid 140 through 146 removed outlier: 3.513A pdb=" N PHE E 144 " --> pdb=" O SER E 140 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE E 168 " --> pdb=" O PRO E 165 " (cutoff:3.500A) Processing helix chain 'E' and resid 171 through 178 Processing helix chain 'E' and resid 183 through 193 removed outlier: 3.687A pdb=" N ALA E 191 " --> pdb=" O GLN E 187 " (cutoff:3.500A) Processing helix chain 'E' and resid 209 through 224 removed outlier: 3.548A pdb=" N ASN E 218 " --> pdb=" O TRP E 214 " (cutoff:3.500A) Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.511A pdb=" N ILE E 250 " --> pdb=" O VAL E 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN E 253 " --> pdb=" O ASP E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL E 270 " --> pdb=" O LYS E 266 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE E 277 " --> pdb=" O LEU E 273 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA E 278 " --> pdb=" O LEU E 274 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 19 Proline residue: G 11 - end of helix removed outlier: 3.545A pdb=" N GLU G 16 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU G 19 " --> pdb=" O LYS G 15 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 35 Proline residue: G 33 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'G' and resid 48 through 51 Processing helix chain 'G' and resid 53 through 58 removed outlier: 3.513A pdb=" N ASP G 58 " --> pdb=" O PRO G 54 " (cutoff:3.500A) Processing helix chain 'G' and resid 59 through 61 No H-bonds generated for 'chain 'G' and resid 59 through 61' Processing helix chain 'G' and resid 62 through 74 Processing helix chain 'G' and resid 74 through 90 removed outlier: 3.712A pdb=" N LEU G 78 " --> pdb=" O ALA G 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP G 90 " --> pdb=" O SER G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 101 removed outlier: 3.784A pdb=" N LYS G 100 " --> pdb=" O ALA G 96 " (cutoff:3.500A) Processing helix chain 'G' and resid 101 through 109 Processing helix chain 'G' and resid 124 through 131 removed outlier: 3.756A pdb=" N LEU G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 140 through 146 removed outlier: 3.514A pdb=" N PHE G 144 " --> pdb=" O SER G 140 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE G 168 " --> pdb=" O PRO G 165 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 178 Processing helix chain 'G' and resid 183 through 193 removed outlier: 3.686A pdb=" N ALA G 191 " --> pdb=" O GLN G 187 " (cutoff:3.500A) Processing helix chain 'G' and resid 209 through 224 removed outlier: 3.548A pdb=" N ASN G 218 " --> pdb=" O TRP G 214 " (cutoff:3.500A) Processing helix chain 'G' and resid 246 through 253 removed outlier: 3.511A pdb=" N ILE G 250 " --> pdb=" O VAL G 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN G 253 " --> pdb=" O ASP G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL G 270 " --> pdb=" O LYS G 266 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE G 277 " --> pdb=" O LEU G 273 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA G 278 " --> pdb=" O LEU G 274 " (cutoff:3.500A) Processing helix chain 'F' and resid 5 through 19 Proline residue: F 11 - end of helix removed outlier: 3.545A pdb=" N GLU F 16 " --> pdb=" O LEU F 12 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU F 19 " --> pdb=" O LYS F 15 " (cutoff:3.500A) Processing helix chain 'F' and resid 28 through 35 Proline residue: F 33 - end of helix Processing helix chain 'F' and resid 39 through 47 Processing helix chain 'F' and resid 48 through 51 Processing helix chain 'F' and resid 53 through 58 removed outlier: 3.512A pdb=" N ASP F 58 " --> pdb=" O PRO F 54 " (cutoff:3.500A) Processing helix chain 'F' and resid 59 through 61 No H-bonds generated for 'chain 'F' and resid 59 through 61' Processing helix chain 'F' and resid 62 through 74 Processing helix chain 'F' and resid 74 through 90 removed outlier: 3.712A pdb=" N LEU F 78 " --> pdb=" O ALA F 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP F 90 " --> pdb=" O SER F 86 " (cutoff:3.500A) Processing helix chain 'F' and resid 91 through 101 removed outlier: 3.785A pdb=" N LYS F 100 " --> pdb=" O ALA F 96 " (cutoff:3.500A) Processing helix chain 'F' and resid 101 through 109 Processing helix chain 'F' and resid 124 through 131 removed outlier: 3.757A pdb=" N LEU F 128 " --> pdb=" O VAL F 124 " (cutoff:3.500A) Processing helix chain 'F' and resid 140 through 146 removed outlier: 3.514A pdb=" N PHE F 144 " --> pdb=" O SER F 140 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE F 168 " --> pdb=" O PRO F 165 " (cutoff:3.500A) Processing helix chain 'F' and resid 171 through 178 Processing helix chain 'F' and resid 183 through 193 removed outlier: 3.686A pdb=" N ALA F 191 " --> pdb=" O GLN F 187 " (cutoff:3.500A) Processing helix chain 'F' and resid 209 through 224 removed outlier: 3.548A pdb=" N ASN F 218 " --> pdb=" O TRP F 214 " (cutoff:3.500A) Processing helix chain 'F' and resid 246 through 253 removed outlier: 3.511A pdb=" N ILE F 250 " --> pdb=" O VAL F 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN F 253 " --> pdb=" O ASP F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL F 270 " --> pdb=" O LYS F 266 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE F 277 " --> pdb=" O LEU F 273 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA F 278 " --> pdb=" O LEU F 274 " (cutoff:3.500A) Processing helix chain 'H' and resid 5 through 19 Proline residue: H 11 - end of helix removed outlier: 3.544A pdb=" N GLU H 16 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU H 19 " --> pdb=" O LYS H 15 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 35 Proline residue: H 33 - end of helix Processing helix chain 'H' and resid 39 through 47 Processing helix chain 'H' and resid 48 through 51 Processing helix chain 'H' and resid 53 through 58 removed outlier: 3.512A pdb=" N ASP H 58 " --> pdb=" O PRO H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 61 No H-bonds generated for 'chain 'H' and resid 59 through 61' Processing helix chain 'H' and resid 62 through 74 Processing helix chain 'H' and resid 74 through 90 removed outlier: 3.713A pdb=" N LEU H 78 " --> pdb=" O ALA H 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP H 90 " --> pdb=" O SER H 86 " (cutoff:3.500A) Processing helix chain 'H' and resid 91 through 101 removed outlier: 3.784A pdb=" N LYS H 100 " --> pdb=" O ALA H 96 " (cutoff:3.500A) Processing helix chain 'H' and resid 101 through 109 Processing helix chain 'H' and resid 124 through 131 removed outlier: 3.757A pdb=" N LEU H 128 " --> pdb=" O VAL H 124 " (cutoff:3.500A) Processing helix chain 'H' and resid 140 through 146 removed outlier: 3.514A pdb=" N PHE H 144 " --> pdb=" O SER H 140 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE H 168 " --> pdb=" O PRO H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 178 Processing helix chain 'H' and resid 183 through 193 removed outlier: 3.686A pdb=" N ALA H 191 " --> pdb=" O GLN H 187 " (cutoff:3.500A) Processing helix chain 'H' and resid 209 through 224 removed outlier: 3.549A pdb=" N ASN H 218 " --> pdb=" O TRP H 214 " (cutoff:3.500A) Processing helix chain 'H' and resid 246 through 253 removed outlier: 3.511A pdb=" N ILE H 250 " --> pdb=" O VAL H 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN H 253 " --> pdb=" O ASP H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL H 270 " --> pdb=" O LYS H 266 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE H 277 " --> pdb=" O LEU H 273 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA H 278 " --> pdb=" O LEU H 274 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 19 Proline residue: M 11 - end of helix removed outlier: 3.544A pdb=" N GLU M 16 " --> pdb=" O LEU M 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU M 19 " --> pdb=" O LYS M 15 " (cutoff:3.500A) Processing helix chain 'M' and resid 28 through 35 Proline residue: M 33 - end of helix Processing helix chain 'M' and resid 39 through 47 Processing helix chain 'M' and resid 48 through 51 Processing helix chain 'M' and resid 53 through 58 removed outlier: 3.512A pdb=" N ASP M 58 " --> pdb=" O PRO M 54 " (cutoff:3.500A) Processing helix chain 'M' and resid 59 through 61 No H-bonds generated for 'chain 'M' and resid 59 through 61' Processing helix chain 'M' and resid 62 through 74 Processing helix chain 'M' and resid 74 through 90 removed outlier: 3.712A pdb=" N LEU M 78 " --> pdb=" O ALA M 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) Processing helix chain 'M' and resid 91 through 101 removed outlier: 3.784A pdb=" N LYS M 100 " --> pdb=" O ALA M 96 " (cutoff:3.500A) Processing helix chain 'M' and resid 101 through 109 Processing helix chain 'M' and resid 124 through 131 removed outlier: 3.756A pdb=" N LEU M 128 " --> pdb=" O VAL M 124 " (cutoff:3.500A) Processing helix chain 'M' and resid 140 through 146 removed outlier: 3.513A pdb=" N PHE M 144 " --> pdb=" O SER M 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE M 168 " --> pdb=" O PRO M 165 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 178 Processing helix chain 'M' and resid 183 through 193 removed outlier: 3.686A pdb=" N ALA M 191 " --> pdb=" O GLN M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 209 through 224 removed outlier: 3.549A pdb=" N ASN M 218 " --> pdb=" O TRP M 214 " (cutoff:3.500A) Processing helix chain 'M' and resid 246 through 253 removed outlier: 3.510A pdb=" N ILE M 250 " --> pdb=" O VAL M 246 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLN M 253 " --> pdb=" O ASP M 249 " (cutoff:3.500A) Processing helix chain 'M' and resid 265 through 278 removed outlier: 3.534A pdb=" N VAL M 270 " --> pdb=" O LYS M 266 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE M 277 " --> pdb=" O LEU M 273 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N ALA M 278 " --> pdb=" O LEU M 274 " (cutoff:3.500A) Processing helix chain 'P' and resid 5 through 19 Proline residue: P 11 - end of helix removed outlier: 3.545A pdb=" N GLU P 16 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N GLU P 19 " --> pdb=" O LYS P 15 " (cutoff:3.500A) Processing helix chain 'P' and resid 28 through 35 Proline residue: P 33 - end of helix Processing helix chain 'P' and resid 39 through 47 Processing helix chain 'P' and resid 48 through 51 Processing helix chain 'P' and resid 53 through 58 removed outlier: 3.513A pdb=" N ASP P 58 " --> pdb=" O PRO P 54 " (cutoff:3.500A) Processing helix chain 'P' and resid 59 through 61 No H-bonds generated for 'chain 'P' and resid 59 through 61' Processing helix chain 'P' and resid 62 through 74 Processing helix chain 'P' and resid 74 through 90 removed outlier: 3.713A pdb=" N LEU P 78 " --> pdb=" O ALA P 74 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ASP P 90 " --> pdb=" O SER P 86 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 101 removed outlier: 3.785A pdb=" N LYS P 100 " --> pdb=" O ALA P 96 " (cutoff:3.500A) Processing helix chain 'P' and resid 101 through 109 Processing helix chain 'P' and resid 124 through 131 removed outlier: 3.757A pdb=" N LEU P 128 " --> pdb=" O VAL P 124 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 146 removed outlier: 3.513A pdb=" N PHE P 144 " --> pdb=" O SER P 140 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE P 168 " --> pdb=" O PRO P 165 " (cutoff:3.500A) Processing helix chain 'P' and resid 171 through 178 Processing helix chain 'P' and resid 183 through 193 removed outlier: 3.687A pdb=" N ALA P 191 " --> pdb=" O GLN P 187 " (cutoff:3.500A) Processing helix chain 'P' and resid 209 through 224 removed outlier: 3.549A pdb=" N ASN P 218 " --> pdb=" O TRP P 214 " (cutoff:3.500A) Processing helix chain 'P' and resid 246 through 253 removed outlier: 3.511A pdb=" N ILE P 250 " --> pdb=" O VAL P 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN P 253 " --> pdb=" O ASP P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL P 270 " --> pdb=" O LYS P 266 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE P 277 " --> pdb=" O LEU P 273 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA P 278 " --> pdb=" O LEU P 274 " (cutoff:3.500A) Processing helix chain 'N' and resid 5 through 19 Proline residue: N 11 - end of helix removed outlier: 3.545A pdb=" N GLU N 16 " --> pdb=" O LEU N 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU N 19 " --> pdb=" O LYS N 15 " (cutoff:3.500A) Processing helix chain 'N' and resid 28 through 35 Proline residue: N 33 - end of helix Processing helix chain 'N' and resid 39 through 47 Processing helix chain 'N' and resid 48 through 51 Processing helix chain 'N' and resid 53 through 58 removed outlier: 3.512A pdb=" N ASP N 58 " --> pdb=" O PRO N 54 " (cutoff:3.500A) Processing helix chain 'N' and resid 59 through 61 No H-bonds generated for 'chain 'N' and resid 59 through 61' Processing helix chain 'N' and resid 62 through 74 Processing helix chain 'N' and resid 74 through 90 removed outlier: 3.713A pdb=" N LEU N 78 " --> pdb=" O ALA N 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP N 90 " --> pdb=" O SER N 86 " (cutoff:3.500A) Processing helix chain 'N' and resid 91 through 101 removed outlier: 3.785A pdb=" N LYS N 100 " --> pdb=" O ALA N 96 " (cutoff:3.500A) Processing helix chain 'N' and resid 101 through 109 Processing helix chain 'N' and resid 124 through 131 removed outlier: 3.757A pdb=" N LEU N 128 " --> pdb=" O VAL N 124 " (cutoff:3.500A) Processing helix chain 'N' and resid 140 through 146 removed outlier: 3.514A pdb=" N PHE N 144 " --> pdb=" O SER N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE N 168 " --> pdb=" O PRO N 165 " (cutoff:3.500A) Processing helix chain 'N' and resid 171 through 178 Processing helix chain 'N' and resid 183 through 193 removed outlier: 3.687A pdb=" N ALA N 191 " --> pdb=" O GLN N 187 " (cutoff:3.500A) Processing helix chain 'N' and resid 209 through 224 removed outlier: 3.549A pdb=" N ASN N 218 " --> pdb=" O TRP N 214 " (cutoff:3.500A) Processing helix chain 'N' and resid 246 through 253 removed outlier: 3.511A pdb=" N ILE N 250 " --> pdb=" O VAL N 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN N 253 " --> pdb=" O ASP N 249 " (cutoff:3.500A) Processing helix chain 'N' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL N 270 " --> pdb=" O LYS N 266 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ILE N 277 " --> pdb=" O LEU N 273 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA N 278 " --> pdb=" O LEU N 274 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 19 Proline residue: O 11 - end of helix removed outlier: 3.544A pdb=" N GLU O 16 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N GLU O 19 " --> pdb=" O LYS O 15 " (cutoff:3.500A) Processing helix chain 'O' and resid 28 through 35 Proline residue: O 33 - end of helix Processing helix chain 'O' and resid 39 through 47 Processing helix chain 'O' and resid 48 through 51 Processing helix chain 'O' and resid 53 through 58 removed outlier: 3.512A pdb=" N ASP O 58 " --> pdb=" O PRO O 54 " (cutoff:3.500A) Processing helix chain 'O' and resid 59 through 61 No H-bonds generated for 'chain 'O' and resid 59 through 61' Processing helix chain 'O' and resid 62 through 74 Processing helix chain 'O' and resid 74 through 90 removed outlier: 3.712A pdb=" N LEU O 78 " --> pdb=" O ALA O 74 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ASP O 90 " --> pdb=" O SER O 86 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 101 removed outlier: 3.784A pdb=" N LYS O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) Processing helix chain 'O' and resid 101 through 109 Processing helix chain 'O' and resid 124 through 131 removed outlier: 3.757A pdb=" N LEU O 128 " --> pdb=" O VAL O 124 " (cutoff:3.500A) Processing helix chain 'O' and resid 140 through 146 removed outlier: 3.514A pdb=" N PHE O 144 " --> pdb=" O SER O 140 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 168 removed outlier: 3.502A pdb=" N ILE O 168 " --> pdb=" O PRO O 165 " (cutoff:3.500A) Processing helix chain 'O' and resid 171 through 178 Processing helix chain 'O' and resid 183 through 193 removed outlier: 3.686A pdb=" N ALA O 191 " --> pdb=" O GLN O 187 " (cutoff:3.500A) Processing helix chain 'O' and resid 209 through 224 removed outlier: 3.549A pdb=" N ASN O 218 " --> pdb=" O TRP O 214 " (cutoff:3.500A) Processing helix chain 'O' and resid 246 through 253 removed outlier: 3.510A pdb=" N ILE O 250 " --> pdb=" O VAL O 246 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N GLN O 253 " --> pdb=" O ASP O 249 " (cutoff:3.500A) Processing helix chain 'O' and resid 265 through 278 removed outlier: 3.533A pdb=" N VAL O 270 " --> pdb=" O LYS O 266 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ILE O 277 " --> pdb=" O LEU O 273 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N ALA O 278 " --> pdb=" O LEU O 274 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP A 5 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 31 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR A 7 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP A 5 " --> pdb=" O GLY A 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU A 31 " --> pdb=" O TRP A 5 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR A 7 " --> pdb=" O LEU A 31 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU A 65 " --> pdb=" O ASN A 8 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP B 5 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 31 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B 7 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU B 65 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP B 5 " --> pdb=" O GLY B 29 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU B 31 " --> pdb=" O TRP B 5 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR B 7 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU B 65 " --> pdb=" O ASN B 8 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP L 5 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU L 31 " --> pdb=" O TRP L 5 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR L 7 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU L 65 " --> pdb=" O ASN L 8 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP L 5 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU L 31 " --> pdb=" O TRP L 5 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR L 7 " --> pdb=" O LEU L 31 " (cutoff:3.500A) removed outlier: 4.823A pdb=" N GLU L 65 " --> pdb=" O ASN L 8 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP K 5 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU K 31 " --> pdb=" O TRP K 5 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR K 7 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU K 65 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP K 5 " --> pdb=" O GLY K 29 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU K 31 " --> pdb=" O TRP K 5 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR K 7 " --> pdb=" O LEU K 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU K 65 " --> pdb=" O ASN K 8 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP I 5 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU I 31 " --> pdb=" O TRP I 5 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR I 7 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU I 65 " --> pdb=" O ASN I 8 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP I 5 " --> pdb=" O GLY I 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU I 31 " --> pdb=" O TRP I 5 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR I 7 " --> pdb=" O LEU I 31 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N GLU I 65 " --> pdb=" O ASN I 8 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP J 5 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU J 31 " --> pdb=" O TRP J 5 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR J 7 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU J 65 " --> pdb=" O ASN J 8 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP J 5 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N LEU J 31 " --> pdb=" O TRP J 5 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR J 7 " --> pdb=" O LEU J 31 " (cutoff:3.500A) removed outlier: 4.821A pdb=" N GLU J 65 " --> pdb=" O ASN J 8 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 28 through 31 removed outlier: 6.634A pdb=" N TRP C 5 " --> pdb=" O GLY C 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU C 31 " --> pdb=" O TRP C 5 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N TYR C 7 " --> pdb=" O LEU C 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU C 65 " --> pdb=" O ASN C 8 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP D 5 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU D 31 " --> pdb=" O TRP D 5 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR D 7 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU D 65 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 28 through 31 removed outlier: 6.633A pdb=" N TRP D 5 " --> pdb=" O GLY D 29 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N LEU D 31 " --> pdb=" O TRP D 5 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR D 7 " --> pdb=" O LEU D 31 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N GLU D 65 " --> pdb=" O ASN D 8 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA E 136 " --> pdb=" O VAL E 155 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS E 157 " --> pdb=" O ALA E 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU E 138 " --> pdb=" O LYS E 157 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU E 22 " --> pdb=" O THR E 114 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR E 116 " --> pdb=" O LEU E 22 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'G' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA G 136 " --> pdb=" O VAL G 155 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS G 157 " --> pdb=" O ALA G 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU G 138 " --> pdb=" O LYS G 157 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU G 22 " --> pdb=" O THR G 114 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR G 116 " --> pdb=" O LEU G 22 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA F 136 " --> pdb=" O VAL F 155 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS F 157 " --> pdb=" O ALA F 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU F 138 " --> pdb=" O LYS F 157 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU F 22 " --> pdb=" O THR F 114 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR F 116 " --> pdb=" O LEU F 22 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'H' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA H 136 " --> pdb=" O VAL H 155 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS H 157 " --> pdb=" O ALA H 136 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU H 138 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU H 22 " --> pdb=" O THR H 114 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR H 116 " --> pdb=" O LEU H 22 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'M' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA M 136 " --> pdb=" O VAL M 155 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N LYS M 157 " --> pdb=" O ALA M 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU M 138 " --> pdb=" O LYS M 157 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU M 22 " --> pdb=" O THR M 114 " (cutoff:3.500A) removed outlier: 8.125A pdb=" N TYR M 116 " --> pdb=" O LEU M 22 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'P' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA P 136 " --> pdb=" O VAL P 155 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS P 157 " --> pdb=" O ALA P 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU P 138 " --> pdb=" O LYS P 157 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU P 22 " --> pdb=" O THR P 114 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR P 116 " --> pdb=" O LEU P 22 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'N' and resid 135 through 138 removed outlier: 5.868A pdb=" N ALA N 136 " --> pdb=" O VAL N 155 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS N 157 " --> pdb=" O ALA N 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU N 138 " --> pdb=" O LYS N 157 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N LEU N 22 " --> pdb=" O THR N 114 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR N 116 " --> pdb=" O LEU N 22 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'O' and resid 135 through 138 removed outlier: 5.867A pdb=" N ALA O 136 " --> pdb=" O VAL O 155 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N LYS O 157 " --> pdb=" O ALA O 136 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N LEU O 138 " --> pdb=" O LYS O 157 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU O 22 " --> pdb=" O THR O 114 " (cutoff:3.500A) removed outlier: 8.124A pdb=" N TYR O 116 " --> pdb=" O LEU O 22 " (cutoff:3.500A) 1240 hydrogen bonds defined for protein. 3552 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: 5.09 Time building geometry restraints manager: 2.92 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9499 1.34 - 1.45: 4798 1.45 - 1.57: 14999 1.57 - 1.69: 0 1.69 - 1.81: 144 Bond restraints: 29440 Sorted by residual: bond pdb=" C ILE C 129 " pdb=" N ALA C 130 " ideal model delta sigma weight residual 1.331 1.248 0.083 2.83e-02 1.25e+03 8.58e+00 bond pdb=" C ILE I 129 " pdb=" N ALA I 130 " ideal model delta sigma weight residual 1.331 1.248 0.083 2.83e-02 1.25e+03 8.52e+00 bond pdb=" C ILE D 129 " pdb=" N ALA D 130 " ideal model delta sigma weight residual 1.331 1.249 0.082 2.83e-02 1.25e+03 8.50e+00 bond pdb=" C ILE A 129 " pdb=" N ALA A 130 " ideal model delta sigma weight residual 1.331 1.249 0.082 2.83e-02 1.25e+03 8.45e+00 bond pdb=" C ILE L 129 " pdb=" N ALA L 130 " ideal model delta sigma weight residual 1.331 1.249 0.082 2.83e-02 1.25e+03 8.43e+00 ... (remaining 29435 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.11: 38511 2.11 - 4.23: 1128 4.23 - 6.34: 161 6.34 - 8.46: 80 8.46 - 10.57: 8 Bond angle restraints: 39888 Sorted by residual: angle pdb=" C PHE L 139 " pdb=" N HIS L 140 " pdb=" CA HIS L 140 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C PHE I 139 " pdb=" N HIS I 140 " pdb=" CA HIS I 140 " ideal model delta sigma weight residual 121.54 132.11 -10.57 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C PHE J 139 " pdb=" N HIS J 140 " pdb=" CA HIS J 140 " ideal model delta sigma weight residual 121.54 132.10 -10.56 1.91e+00 2.74e-01 3.06e+01 angle pdb=" C PHE A 139 " pdb=" N HIS A 140 " pdb=" CA HIS A 140 " ideal model delta sigma weight residual 121.54 132.09 -10.55 1.91e+00 2.74e-01 3.05e+01 angle pdb=" C PHE B 139 " pdb=" N HIS B 140 " pdb=" CA HIS B 140 " ideal model delta sigma weight residual 121.54 132.07 -10.53 1.91e+00 2.74e-01 3.04e+01 ... (remaining 39883 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.51: 16298 11.51 - 23.01: 1030 23.01 - 34.52: 304 34.52 - 46.03: 88 46.03 - 57.54: 8 Dihedral angle restraints: 17728 sinusoidal: 7168 harmonic: 10560 Sorted by residual: dihedral pdb=" CA PHE E 52 " pdb=" C PHE E 52 " pdb=" N GLU E 53 " pdb=" CA GLU E 53 " ideal model delta harmonic sigma weight residual 180.00 161.92 18.08 0 5.00e+00 4.00e-02 1.31e+01 dihedral pdb=" CA PHE P 52 " pdb=" C PHE P 52 " pdb=" N GLU P 53 " pdb=" CA GLU P 53 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA PHE F 52 " pdb=" C PHE F 52 " pdb=" N GLU F 53 " pdb=" CA GLU F 53 " ideal model delta harmonic sigma weight residual 180.00 161.94 18.06 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 17725 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 2557 0.041 - 0.083: 1262 0.083 - 0.124: 483 0.124 - 0.166: 114 0.166 - 0.207: 24 Chirality restraints: 4440 Sorted by residual: chirality pdb=" CB VAL D 62 " pdb=" CA VAL D 62 " pdb=" CG1 VAL D 62 " pdb=" CG2 VAL D 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL B 62 " pdb=" CA VAL B 62 " pdb=" CG1 VAL B 62 " pdb=" CG2 VAL B 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB VAL K 62 " pdb=" CA VAL K 62 " pdb=" CG1 VAL K 62 " pdb=" CG2 VAL K 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.07e+00 ... (remaining 4437 not shown) Planarity restraints: 5200 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE L 154 " -0.022 2.00e-02 2.50e+03 2.33e-02 9.50e+00 pdb=" CG PHE L 154 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE L 154 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE L 154 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE L 154 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE L 154 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE L 154 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE D 154 " -0.022 2.00e-02 2.50e+03 2.33e-02 9.50e+00 pdb=" CG PHE D 154 " 0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE D 154 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE D 154 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE D 154 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE D 154 " -0.010 2.00e-02 2.50e+03 pdb=" CZ PHE D 154 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 154 " 0.022 2.00e-02 2.50e+03 2.33e-02 9.46e+00 pdb=" CG PHE A 154 " -0.054 2.00e-02 2.50e+03 pdb=" CD1 PHE A 154 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 PHE A 154 " 0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 154 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 154 " 0.010 2.00e-02 2.50e+03 pdb=" CZ PHE A 154 " -0.001 2.00e-02 2.50e+03 ... (remaining 5197 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 7667 2.79 - 3.32: 24677 3.32 - 3.85: 47118 3.85 - 4.37: 58994 4.37 - 4.90: 99710 Nonbonded interactions: 238166 Sorted by model distance: nonbonded pdb=" OH TYR O 116 " pdb=" OD2 ASP O 192 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR F 116 " pdb=" OD2 ASP F 192 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR H 116 " pdb=" OD2 ASP H 192 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR N 116 " pdb=" OD2 ASP N 192 " model vdw 2.265 3.040 nonbonded pdb=" OH TYR M 116 " pdb=" OD2 ASP M 192 " model vdw 2.265 3.040 ... (remaining 238161 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: 0.10 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'L' selection = chain 'K' selection = chain 'I' selection = chain 'J' selection = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = chain 'G' selection = chain 'F' selection = chain 'H' selection = chain 'M' selection = chain 'P' selection = chain 'N' selection = chain 'O' } 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: 5.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.700 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 21.150 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.100 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 29440 Z= 0.333 Angle : 0.896 10.570 39888 Z= 0.485 Chirality : 0.055 0.207 4440 Planarity : 0.008 0.070 5200 Dihedral : 9.345 57.537 10896 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 3.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -4.77 (0.10), residues: 3624 helix: -4.09 (0.05), residues: 1648 sheet: -1.39 (0.17), residues: 688 loop : -2.51 (0.13), residues: 1288 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 102 TYR 0.020 0.004 TYR K 112 PHE 0.054 0.004 PHE L 154 TRP 0.018 0.003 TRP J 141 HIS 0.019 0.003 HIS D 140 Details of bonding type rmsd covalent geometry : bond 0.00810 (29440) covalent geometry : angle 0.89641 (39888) hydrogen bonds : bond 0.29405 ( 1224) hydrogen bonds : angle 8.96726 ( 3552) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 694 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 694 time to evaluate : 0.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 58 ASP cc_start: 0.8482 (t70) cc_final: 0.8227 (t0) REVERT: F 100 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8668 (mttp) REVERT: H 95 GLU cc_start: 0.8217 (mt-10) cc_final: 0.7972 (mt-10) REVERT: M 122 LYS cc_start: 0.8929 (pttt) cc_final: 0.8719 (pttt) REVERT: P 122 LYS cc_start: 0.8952 (pttt) cc_final: 0.8603 (pttt) outliers start: 0 outliers final: 0 residues processed: 694 average time/residue: 0.8280 time to fit residues: 648.2295 Evaluate side-chains 366 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 366 time to evaluate : 0.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 197 optimal weight: 0.9980 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 2.9990 chunk 244 optimal weight: 0.7980 chunk 183 optimal weight: 0.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 172 HIS J 150 GLN ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 79 GLN E 255 ASN G 255 ASN F 223 GLN H 223 GLN H 255 ASN M 255 ASN P 255 ASN N 255 ASN O 255 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.116488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.071096 restraints weight = 45535.558| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.36 r_work: 0.2714 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2600 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8913 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 29440 Z= 0.139 Angle : 0.619 8.365 39888 Z= 0.316 Chirality : 0.043 0.165 4440 Planarity : 0.006 0.047 5200 Dihedral : 4.631 27.880 4024 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 3.01 % Allowed : 11.11 % Favored : 85.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -2.58 (0.11), residues: 3624 helix: -1.51 (0.11), residues: 1688 sheet: -1.29 (0.17), residues: 688 loop : -1.94 (0.14), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG M 105 TYR 0.017 0.002 TYR J 112 PHE 0.017 0.002 PHE O 70 TRP 0.013 0.001 TRP A 86 HIS 0.008 0.001 HIS I 66 Details of bonding type rmsd covalent geometry : bond 0.00319 (29440) covalent geometry : angle 0.61887 (39888) hydrogen bonds : bond 0.03854 ( 1224) hydrogen bonds : angle 5.29628 ( 3552) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 441 time to evaluate : 1.165 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.8156 (t0) cc_final: 0.7717 (t70) REVERT: A 139 PHE cc_start: 0.7658 (p90) cc_final: 0.7234 (p90) REVERT: A 157 MET cc_start: 0.7253 (mtt) cc_final: 0.6560 (ttm) REVERT: A 162 LYS cc_start: 0.8299 (ttmt) cc_final: 0.7998 (tttt) REVERT: B 42 ASP cc_start: 0.8083 (t0) cc_final: 0.7565 (t70) REVERT: L 34 LYS cc_start: 0.8973 (ttmm) cc_final: 0.8726 (mmmm) REVERT: L 139 PHE cc_start: 0.7638 (p90) cc_final: 0.7014 (p90) REVERT: L 154 PHE cc_start: 0.5963 (m-80) cc_final: 0.5255 (m-80) REVERT: L 157 MET cc_start: 0.7457 (mtt) cc_final: 0.7020 (ttm) REVERT: K 139 PHE cc_start: 0.7624 (p90) cc_final: 0.7329 (p90) REVERT: K 154 PHE cc_start: 0.5686 (m-80) cc_final: 0.4936 (m-80) REVERT: K 157 MET cc_start: 0.6890 (mtt) cc_final: 0.6284 (ttm) REVERT: K 170 ARG cc_start: 0.8152 (mtm-85) cc_final: 0.7879 (mtm-85) REVERT: I 139 PHE cc_start: 0.7630 (p90) cc_final: 0.7396 (p90) REVERT: I 157 MET cc_start: 0.7074 (mtt) cc_final: 0.6611 (ttm) REVERT: I 170 ARG cc_start: 0.8158 (mtm-85) cc_final: 0.7873 (mtm-85) REVERT: J 139 PHE cc_start: 0.7603 (p90) cc_final: 0.7022 (p90) REVERT: J 154 PHE cc_start: 0.5964 (m-80) cc_final: 0.5127 (m-80) REVERT: J 157 MET cc_start: 0.7513 (mtt) cc_final: 0.6966 (ttm) REVERT: C 19 GLN cc_start: 0.9220 (OUTLIER) cc_final: 0.8964 (mt0) REVERT: C 42 ASP cc_start: 0.8122 (t0) cc_final: 0.7635 (t70) REVERT: C 139 PHE cc_start: 0.7617 (p90) cc_final: 0.7293 (p90) REVERT: C 157 MET cc_start: 0.7200 (mtt) cc_final: 0.6609 (ttm) REVERT: C 162 LYS cc_start: 0.8345 (ttmt) cc_final: 0.8085 (tttt) REVERT: D 42 ASP cc_start: 0.8059 (t0) cc_final: 0.7521 (t70) REVERT: D 139 PHE cc_start: 0.7613 (p90) cc_final: 0.7402 (p90) REVERT: E 58 ASP cc_start: 0.9110 (t70) cc_final: 0.8797 (t0) REVERT: G 62 ARG cc_start: 0.8727 (mtp85) cc_final: 0.8525 (mtp85) REVERT: F 186 ASP cc_start: 0.9238 (m-30) cc_final: 0.9006 (m-30) REVERT: F 252 GLN cc_start: 0.9401 (OUTLIER) cc_final: 0.9179 (tt0) REVERT: H 32 LYS cc_start: 0.9311 (tppp) cc_final: 0.9079 (tptm) REVERT: H 166 ASP cc_start: 0.8927 (OUTLIER) cc_final: 0.8631 (p0) REVERT: H 252 GLN cc_start: 0.9412 (OUTLIER) cc_final: 0.9197 (tt0) REVERT: M 18 ARG cc_start: 0.8667 (OUTLIER) cc_final: 0.8141 (mtm-85) REVERT: M 161 THR cc_start: 0.9106 (OUTLIER) cc_final: 0.8892 (t) REVERT: P 38 ASP cc_start: 0.8383 (t0) cc_final: 0.7977 (t0) outliers start: 91 outliers final: 33 residues processed: 503 average time/residue: 0.7487 time to fit residues: 428.5293 Evaluate side-chains 404 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 365 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 SER Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 25 SER Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 36 THR Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain C residue 12 SER Chi-restraints excluded: chain C residue 19 GLN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 25 SER Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 105 ARG Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain F residue 252 GLN Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain M residue 18 ARG Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain O residue 113 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 338 optimal weight: 0.8980 chunk 164 optimal weight: 2.9990 chunk 54 optimal weight: 10.0000 chunk 232 optimal weight: 5.9990 chunk 152 optimal weight: 5.9990 chunk 332 optimal weight: 4.9990 chunk 57 optimal weight: 7.9990 chunk 173 optimal weight: 4.9990 chunk 331 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 140 HIS L 150 GLN L 172 HIS I 66 HIS J 140 HIS J 172 HIS C 140 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS F 223 GLN F 255 ASN H 223 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.067647 restraints weight = 45403.291| |-----------------------------------------------------------------------------| r_work (start): 0.2773 rms_B_bonded: 2.31 r_work: 0.2637 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2521 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2521 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8958 moved from start: 0.3118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 29440 Z= 0.167 Angle : 0.594 7.293 39888 Z= 0.301 Chirality : 0.044 0.156 4440 Planarity : 0.005 0.040 5200 Dihedral : 4.538 30.354 4024 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 5.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.80 % Allowed : 12.30 % Favored : 83.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.47 (0.12), residues: 3624 helix: -0.35 (0.12), residues: 1704 sheet: -1.09 (0.17), residues: 688 loop : -1.58 (0.14), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG O 62 TYR 0.018 0.002 TYR J 112 PHE 0.017 0.002 PHE K 145 TRP 0.010 0.001 TRP I 141 HIS 0.011 0.001 HIS L 20 Details of bonding type rmsd covalent geometry : bond 0.00397 (29440) covalent geometry : angle 0.59407 (39888) hydrogen bonds : bond 0.03659 ( 1224) hydrogen bonds : angle 4.84978 ( 3552) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 504 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 115 poor density : 389 time to evaluate : 0.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 42 ASP cc_start: 0.7976 (t0) cc_final: 0.7540 (t70) REVERT: A 139 PHE cc_start: 0.7454 (p90) cc_final: 0.7065 (p90) REVERT: A 157 MET cc_start: 0.7282 (mtt) cc_final: 0.6561 (ttm) REVERT: A 160 ASP cc_start: 0.8542 (t70) cc_final: 0.8285 (t0) REVERT: A 162 LYS cc_start: 0.8256 (ttmt) cc_final: 0.7972 (tttt) REVERT: B 95 GLU cc_start: 0.7887 (mm-30) cc_final: 0.7353 (pp20) REVERT: L 34 LYS cc_start: 0.9064 (ttmm) cc_final: 0.8861 (mmmm) REVERT: K 50 LYS cc_start: 0.9150 (OUTLIER) cc_final: 0.8753 (mttt) REVERT: K 65 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8108 (pp20) REVERT: K 139 PHE cc_start: 0.7577 (p90) cc_final: 0.7284 (p90) REVERT: K 157 MET cc_start: 0.6992 (mtt) cc_final: 0.6248 (ttm) REVERT: K 170 ARG cc_start: 0.8067 (mtm-85) cc_final: 0.7764 (mtm-85) REVERT: I 65 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8147 (pp20) REVERT: I 157 MET cc_start: 0.7114 (mtt) cc_final: 0.6541 (ttm) REVERT: I 170 ARG cc_start: 0.8092 (mtm-85) cc_final: 0.7765 (mtm-85) REVERT: C 42 ASP cc_start: 0.7934 (t0) cc_final: 0.7481 (t70) REVERT: C 139 PHE cc_start: 0.7433 (p90) cc_final: 0.7115 (p90) REVERT: C 157 MET cc_start: 0.7216 (mtt) cc_final: 0.6614 (ttm) REVERT: C 160 ASP cc_start: 0.8564 (t70) cc_final: 0.8300 (t0) REVERT: C 162 LYS cc_start: 0.8308 (ttmt) cc_final: 0.8071 (tttt) REVERT: E 58 ASP cc_start: 0.9120 (t70) cc_final: 0.8810 (t0) REVERT: E 95 GLU cc_start: 0.8883 (mt-10) cc_final: 0.8675 (mm-30) REVERT: E 161 THR cc_start: 0.9169 (OUTLIER) cc_final: 0.8900 (t) REVERT: E 163 ASP cc_start: 0.9265 (OUTLIER) cc_final: 0.9026 (p0) REVERT: G 95 GLU cc_start: 0.8870 (mt-10) cc_final: 0.8638 (mm-30) REVERT: G 156 ILE cc_start: 0.9467 (OUTLIER) cc_final: 0.9192 (mt) REVERT: F 166 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8692 (p0) REVERT: H 252 GLN cc_start: 0.9432 (OUTLIER) cc_final: 0.9229 (tt0) REVERT: M 38 ASP cc_start: 0.8525 (t0) cc_final: 0.8096 (t0) REVERT: M 156 ILE cc_start: 0.9433 (OUTLIER) cc_final: 0.9170 (mp) REVERT: N 156 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9035 (mm) REVERT: N 161 THR cc_start: 0.9174 (OUTLIER) cc_final: 0.8964 (p) REVERT: O 156 ILE cc_start: 0.9490 (OUTLIER) cc_final: 0.9056 (mm) REVERT: O 161 THR cc_start: 0.9166 (OUTLIER) cc_final: 0.8956 (p) outliers start: 115 outliers final: 43 residues processed: 472 average time/residue: 0.6999 time to fit residues: 379.2824 Evaluate side-chains 396 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 340 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 ASN Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 96 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 96 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 36 THR Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 11 ASN Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 96 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 11 ASN Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 168 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 96 VAL Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 161 THR Chi-restraints excluded: chain E residue 163 ASP Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 252 GLN Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 156 ILE Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain N residue 156 ILE Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain O residue 156 ILE Chi-restraints excluded: chain O residue 161 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 237 optimal weight: 2.9990 chunk 262 optimal weight: 5.9990 chunk 215 optimal weight: 0.9990 chunk 153 optimal weight: 4.9990 chunk 46 optimal weight: 20.0000 chunk 98 optimal weight: 5.9990 chunk 245 optimal weight: 2.9990 chunk 284 optimal weight: 0.0670 chunk 34 optimal weight: 0.0000 chunk 24 optimal weight: 3.9990 chunk 68 optimal weight: 8.9990 overall best weight: 1.4128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 140 HIS B 140 HIS L 140 HIS L 172 HIS J 140 HIS J 172 HIS C 20 HIS C 140 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS F 223 GLN F 253 GLN H 223 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114448 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.069025 restraints weight = 45092.307| |-----------------------------------------------------------------------------| r_work (start): 0.2806 rms_B_bonded: 2.30 r_work: 0.2672 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2557 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8961 moved from start: 0.3376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 29440 Z= 0.118 Angle : 0.542 6.770 39888 Z= 0.274 Chirality : 0.042 0.148 4440 Planarity : 0.004 0.037 5200 Dihedral : 4.267 31.219 4024 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 2.68 % Allowed : 14.62 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.90 (0.13), residues: 3624 helix: 0.20 (0.12), residues: 1720 sheet: -0.93 (0.17), residues: 688 loop : -1.38 (0.15), residues: 1216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 77 TYR 0.015 0.002 TYR L 112 PHE 0.014 0.001 PHE D 145 TRP 0.007 0.001 TRP B 141 HIS 0.010 0.001 HIS A 20 Details of bonding type rmsd covalent geometry : bond 0.00276 (29440) covalent geometry : angle 0.54250 (39888) hydrogen bonds : bond 0.02868 ( 1224) hydrogen bonds : angle 4.59564 ( 3552) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 376 time to evaluate : 1.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 157 MET cc_start: 0.7217 (mtt) cc_final: 0.6757 (ttm) REVERT: B 95 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7209 (pp20) REVERT: L 139 PHE cc_start: 0.7743 (p90) cc_final: 0.6942 (p90) REVERT: K 50 LYS cc_start: 0.9127 (OUTLIER) cc_final: 0.8752 (mttt) REVERT: K 65 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: K 139 PHE cc_start: 0.7627 (p90) cc_final: 0.7263 (p90) REVERT: K 154 PHE cc_start: 0.5290 (m-80) cc_final: 0.4387 (m-80) REVERT: K 157 MET cc_start: 0.6935 (mtt) cc_final: 0.6316 (ttm) REVERT: K 170 ARG cc_start: 0.8120 (mtm-85) cc_final: 0.7829 (mtm-85) REVERT: I 50 LYS cc_start: 0.9155 (OUTLIER) cc_final: 0.8766 (mttt) REVERT: I 65 GLU cc_start: 0.8446 (OUTLIER) cc_final: 0.8161 (pp20) REVERT: I 157 MET cc_start: 0.7061 (mtt) cc_final: 0.6564 (ttm) REVERT: I 170 ARG cc_start: 0.8133 (mtm-85) cc_final: 0.7826 (mtm-85) REVERT: C 139 PHE cc_start: 0.7625 (p90) cc_final: 0.7168 (p90) REVERT: C 157 MET cc_start: 0.7157 (mtt) cc_final: 0.6805 (ttm) REVERT: D 139 PHE cc_start: 0.7762 (p90) cc_final: 0.7018 (p90) REVERT: E 58 ASP cc_start: 0.9098 (t70) cc_final: 0.8787 (t0) REVERT: G 156 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9210 (mt) REVERT: M 38 ASP cc_start: 0.8484 (t0) cc_final: 0.8060 (t0) REVERT: P 186 ASP cc_start: 0.9196 (m-30) cc_final: 0.8936 (m-30) outliers start: 81 outliers final: 35 residues processed: 432 average time/residue: 0.8671 time to fit residues: 424.8905 Evaluate side-chains 391 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 351 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain A residue 164 SER Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 69 optimal weight: 5.9990 chunk 282 optimal weight: 0.8980 chunk 171 optimal weight: 6.9990 chunk 332 optimal weight: 3.9990 chunk 135 optimal weight: 8.9990 chunk 203 optimal weight: 0.9990 chunk 213 optimal weight: 4.9990 chunk 340 optimal weight: 1.9990 chunk 158 optimal weight: 0.8980 chunk 173 optimal weight: 6.9990 chunk 54 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 140 HIS L 172 HIS K 20 HIS J 140 HIS J 172 HIS C 20 HIS C 140 HIS D 140 HIS F 223 GLN H 223 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.113875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.068433 restraints weight = 45162.304| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.31 r_work: 0.2671 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2556 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8971 moved from start: 0.3536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 29440 Z= 0.132 Angle : 0.542 6.579 39888 Z= 0.274 Chirality : 0.042 0.146 4440 Planarity : 0.004 0.037 5200 Dihedral : 4.213 24.178 4024 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.24 % Allowed : 14.62 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.50 (0.13), residues: 3624 helix: 0.56 (0.13), residues: 1704 sheet: -0.77 (0.18), residues: 688 loop : -1.16 (0.15), residues: 1232 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG M 77 TYR 0.016 0.002 TYR L 112 PHE 0.017 0.001 PHE L 145 TRP 0.009 0.001 TRP D 141 HIS 0.008 0.001 HIS L 140 Details of bonding type rmsd covalent geometry : bond 0.00315 (29440) covalent geometry : angle 0.54189 (39888) hydrogen bonds : bond 0.02948 ( 1224) hydrogen bonds : angle 4.54851 ( 3552) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 468 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 370 time to evaluate : 1.502 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 154 PHE cc_start: 0.5317 (m-80) cc_final: 0.4713 (m-80) REVERT: A 157 MET cc_start: 0.7180 (mtt) cc_final: 0.6871 (ttm) REVERT: B 95 GLU cc_start: 0.7934 (mm-30) cc_final: 0.7051 (pp20) REVERT: L 154 PHE cc_start: 0.5488 (OUTLIER) cc_final: 0.4583 (m-10) REVERT: K 50 LYS cc_start: 0.9124 (OUTLIER) cc_final: 0.8772 (mttt) REVERT: K 65 GLU cc_start: 0.8460 (OUTLIER) cc_final: 0.8109 (pp20) REVERT: K 134 ARG cc_start: 0.8066 (mtm180) cc_final: 0.7303 (ptp-110) REVERT: K 154 PHE cc_start: 0.5326 (m-80) cc_final: 0.4506 (m-80) REVERT: K 157 MET cc_start: 0.6932 (mtt) cc_final: 0.6554 (ttm) REVERT: K 170 ARG cc_start: 0.8115 (mtm-85) cc_final: 0.7847 (mtm-85) REVERT: I 50 LYS cc_start: 0.9163 (OUTLIER) cc_final: 0.8766 (mttt) REVERT: I 65 GLU cc_start: 0.8455 (OUTLIER) cc_final: 0.8167 (pp20) REVERT: I 157 MET cc_start: 0.7032 (mtt) cc_final: 0.6759 (ttm) REVERT: I 170 ARG cc_start: 0.8149 (mtm-85) cc_final: 0.7841 (mtm-85) REVERT: J 154 PHE cc_start: 0.5700 (m-80) cc_final: 0.4629 (m-10) REVERT: J 157 MET cc_start: 0.6967 (pmm) cc_final: 0.6668 (ptp) REVERT: C 157 MET cc_start: 0.7132 (mtt) cc_final: 0.6889 (ttm) REVERT: D 95 GLU cc_start: 0.7900 (mm-30) cc_final: 0.7078 (pp20) REVERT: D 139 PHE cc_start: 0.7694 (p90) cc_final: 0.7270 (p90) REVERT: D 161 GLU cc_start: 0.8746 (mt-10) cc_final: 0.8282 (mp0) REVERT: E 58 ASP cc_start: 0.9127 (t70) cc_final: 0.8833 (t0) REVERT: E 156 ILE cc_start: 0.9442 (OUTLIER) cc_final: 0.9161 (mt) REVERT: G 156 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9212 (mt) REVERT: F 111 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8786 (t70) REVERT: F 166 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8660 (p0) REVERT: H 166 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8626 (p0) REVERT: M 38 ASP cc_start: 0.8540 (t0) cc_final: 0.8099 (t0) REVERT: M 55 GLU cc_start: 0.8850 (mp0) cc_final: 0.8612 (mp0) REVERT: P 38 ASP cc_start: 0.8611 (t0) cc_final: 0.8158 (t0) REVERT: P 177 GLN cc_start: 0.9146 (tm-30) cc_final: 0.8719 (tp-100) REVERT: P 186 ASP cc_start: 0.9193 (m-30) cc_final: 0.8952 (m-30) outliers start: 98 outliers final: 46 residues processed: 434 average time/residue: 0.8436 time to fit residues: 416.3849 Evaluate side-chains 399 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 343 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 47 ILE Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 20 HIS Chi-restraints excluded: chain L residue 21 VAL Chi-restraints excluded: chain L residue 25 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 154 PHE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 25 SER Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain M residue 103 MET Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 185 optimal weight: 3.9990 chunk 240 optimal weight: 4.9990 chunk 58 optimal weight: 9.9990 chunk 83 optimal weight: 10.0000 chunk 153 optimal weight: 4.9990 chunk 233 optimal weight: 3.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 130 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 140 HIS L 172 HIS J 140 HIS J 172 HIS C 140 HIS D 140 HIS F 223 GLN H 223 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.111268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.065778 restraints weight = 45253.651| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 2.29 r_work: 0.2623 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9025 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 29440 Z= 0.223 Angle : 0.594 6.619 39888 Z= 0.302 Chirality : 0.045 0.152 4440 Planarity : 0.005 0.040 5200 Dihedral : 4.528 36.581 4024 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.31 % Allowed : 15.11 % Favored : 81.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.31 (0.13), residues: 3624 helix: 0.68 (0.13), residues: 1688 sheet: -0.67 (0.18), residues: 688 loop : -1.01 (0.16), residues: 1248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG M 77 TYR 0.018 0.002 TYR L 112 PHE 0.011 0.002 PHE C 85 TRP 0.012 0.001 TRP B 141 HIS 0.007 0.001 HIS L 140 Details of bonding type rmsd covalent geometry : bond 0.00543 (29440) covalent geometry : angle 0.59449 (39888) hydrogen bonds : bond 0.03594 ( 1224) hydrogen bonds : angle 4.77295 ( 3552) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 355 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 95 GLU cc_start: 0.7956 (mm-30) cc_final: 0.6830 (pp20) REVERT: B 139 PHE cc_start: 0.7777 (p90) cc_final: 0.7536 (p90) REVERT: L 154 PHE cc_start: 0.5201 (m-10) cc_final: 0.4898 (m-10) REVERT: L 157 MET cc_start: 0.6953 (ptp) cc_final: 0.6686 (ptp) REVERT: K 50 LYS cc_start: 0.9187 (OUTLIER) cc_final: 0.8793 (mttt) REVERT: K 65 GLU cc_start: 0.8529 (OUTLIER) cc_final: 0.8119 (pp20) REVERT: K 157 MET cc_start: 0.6958 (mtt) cc_final: 0.6638 (ttm) REVERT: K 170 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7887 (mtm-85) REVERT: I 50 LYS cc_start: 0.9183 (OUTLIER) cc_final: 0.8764 (mttt) REVERT: I 65 GLU cc_start: 0.8554 (OUTLIER) cc_final: 0.8150 (pp20) REVERT: I 157 MET cc_start: 0.7022 (mtt) cc_final: 0.6790 (ttm) REVERT: I 170 ARG cc_start: 0.8132 (mtm-85) cc_final: 0.7857 (mtm-85) REVERT: J 154 PHE cc_start: 0.5519 (m-80) cc_final: 0.4629 (m-80) REVERT: C 42 ASP cc_start: 0.8105 (t0) cc_final: 0.7624 (t70) REVERT: D 95 GLU cc_start: 0.7922 (mm-30) cc_final: 0.6876 (pp20) REVERT: D 134 ARG cc_start: 0.6738 (OUTLIER) cc_final: 0.6092 (ptm160) REVERT: D 139 PHE cc_start: 0.7957 (p90) cc_final: 0.7533 (p90) REVERT: D 161 GLU cc_start: 0.8835 (mt-10) cc_final: 0.8400 (mp0) REVERT: E 58 ASP cc_start: 0.9190 (t70) cc_final: 0.8886 (t0) REVERT: E 156 ILE cc_start: 0.9474 (OUTLIER) cc_final: 0.9197 (mt) REVERT: G 156 ILE cc_start: 0.9485 (OUTLIER) cc_final: 0.9226 (mt) REVERT: F 161 THR cc_start: 0.9198 (OUTLIER) cc_final: 0.8994 (p) REVERT: F 166 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8669 (p0) REVERT: H 166 ASP cc_start: 0.8876 (OUTLIER) cc_final: 0.8655 (p0) REVERT: P 156 ILE cc_start: 0.9469 (OUTLIER) cc_final: 0.9191 (mp) outliers start: 100 outliers final: 47 residues processed: 425 average time/residue: 0.8743 time to fit residues: 421.6000 Evaluate side-chains 386 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 328 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 25 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 134 ARG Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain L residue 134 ARG Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 47 ILE Chi-restraints excluded: chain K residue 50 LYS Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain J residue 134 ARG Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 25 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 47 ILE Chi-restraints excluded: chain D residue 134 ARG Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 161 THR Chi-restraints excluded: chain F residue 166 ASP Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain P residue 156 ILE Chi-restraints excluded: chain P residue 161 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 35 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 108 optimal weight: 10.0000 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.0370 chunk 139 optimal weight: 10.0000 chunk 170 optimal weight: 0.5980 chunk 203 optimal weight: 0.6980 chunk 253 optimal weight: 2.9990 chunk 214 optimal weight: 1.9990 chunk 197 optimal weight: 0.7980 overall best weight: 0.8260 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 140 HIS L 172 HIS K 66 HIS J 140 HIS J 172 HIS C 140 HIS D 140 HIS F 223 GLN H 223 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.114526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.069307 restraints weight = 44952.131| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 2.30 r_work: 0.2692 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2576 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.2576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.3872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 29440 Z= 0.100 Angle : 0.525 6.167 39888 Z= 0.265 Chirality : 0.042 0.182 4440 Planarity : 0.004 0.038 5200 Dihedral : 4.146 38.272 4024 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 2.55 % Allowed : 16.53 % Favored : 80.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.07 (0.14), residues: 3624 helix: 0.95 (0.13), residues: 1672 sheet: -0.63 (0.18), residues: 688 loop : -0.93 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG P 77 TYR 0.015 0.001 TYR D 112 PHE 0.022 0.001 PHE L 145 TRP 0.009 0.001 TRP B 141 HIS 0.008 0.001 HIS L 140 Details of bonding type rmsd covalent geometry : bond 0.00225 (29440) covalent geometry : angle 0.52502 (39888) hydrogen bonds : bond 0.02670 ( 1224) hydrogen bonds : angle 4.52505 ( 3552) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 367 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 14 LYS cc_start: 0.8873 (mttt) cc_final: 0.8481 (mtmm) REVERT: B 95 GLU cc_start: 0.7937 (mm-30) cc_final: 0.6832 (pp20) REVERT: B 139 PHE cc_start: 0.7790 (p90) cc_final: 0.7536 (p90) REVERT: B 161 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8322 (pt0) REVERT: L 154 PHE cc_start: 0.5182 (m-10) cc_final: 0.4858 (m-10) REVERT: L 157 MET cc_start: 0.6983 (ptp) cc_final: 0.6698 (ptp) REVERT: K 65 GLU cc_start: 0.8444 (OUTLIER) cc_final: 0.8120 (pp20) REVERT: K 170 ARG cc_start: 0.8099 (mtm-85) cc_final: 0.7831 (mtm-85) REVERT: I 50 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8742 (mttt) REVERT: I 65 GLU cc_start: 0.8478 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: I 154 PHE cc_start: 0.5364 (m-80) cc_final: 0.4689 (m-10) REVERT: D 14 LYS cc_start: 0.9022 (mttt) cc_final: 0.8574 (mtmm) REVERT: D 95 GLU cc_start: 0.7906 (mm-30) cc_final: 0.6851 (pp20) REVERT: D 139 PHE cc_start: 0.7964 (p90) cc_final: 0.7474 (p90) REVERT: D 161 GLU cc_start: 0.8821 (mt-10) cc_final: 0.8368 (mp0) REVERT: E 58 ASP cc_start: 0.9106 (t70) cc_final: 0.8798 (t0) REVERT: E 156 ILE cc_start: 0.9423 (OUTLIER) cc_final: 0.9144 (mt) REVERT: G 58 ASP cc_start: 0.8912 (t70) cc_final: 0.8674 (t0) REVERT: G 95 GLU cc_start: 0.8888 (mt-10) cc_final: 0.8652 (mm-30) REVERT: G 156 ILE cc_start: 0.9452 (OUTLIER) cc_final: 0.9212 (mt) REVERT: M 55 GLU cc_start: 0.8836 (mp0) cc_final: 0.8568 (mp0) REVERT: M 177 GLN cc_start: 0.9162 (tm-30) cc_final: 0.8731 (tp-100) REVERT: M 186 ASP cc_start: 0.9182 (m-30) cc_final: 0.8958 (m-30) REVERT: P 186 ASP cc_start: 0.9193 (m-30) cc_final: 0.8969 (m-30) outliers start: 77 outliers final: 40 residues processed: 427 average time/residue: 0.8558 time to fit residues: 413.8090 Evaluate side-chains 375 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 330 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain K residue 12 SER Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 12 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 12 SER Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 23 optimal weight: 8.9990 chunk 185 optimal weight: 5.9990 chunk 229 optimal weight: 4.9990 chunk 306 optimal weight: 6.9990 chunk 10 optimal weight: 9.9990 chunk 167 optimal weight: 10.0000 chunk 234 optimal weight: 0.0770 chunk 12 optimal weight: 4.9990 chunk 8 optimal weight: 1.9990 chunk 255 optimal weight: 0.3980 chunk 254 optimal weight: 5.9990 overall best weight: 2.4944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 140 HIS I 172 HIS J 140 HIS C 140 HIS D 140 HIS F 223 GLN H 223 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.112126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.066806 restraints weight = 45266.433| |-----------------------------------------------------------------------------| r_work (start): 0.2778 rms_B_bonded: 2.29 r_work: 0.2643 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2528 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8990 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29440 Z= 0.169 Angle : 0.568 6.546 39888 Z= 0.288 Chirality : 0.044 0.164 4440 Planarity : 0.005 0.041 5200 Dihedral : 4.273 31.753 4024 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer: Outliers : 2.22 % Allowed : 17.20 % Favored : 80.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.01 (0.14), residues: 3624 helix: 0.93 (0.13), residues: 1664 sheet: -0.57 (0.18), residues: 688 loop : -0.81 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG P 77 TYR 0.016 0.002 TYR L 112 PHE 0.010 0.001 PHE A 85 TRP 0.009 0.001 TRP B 141 HIS 0.011 0.001 HIS L 140 Details of bonding type rmsd covalent geometry : bond 0.00406 (29440) covalent geometry : angle 0.56847 (39888) hydrogen bonds : bond 0.03226 ( 1224) hydrogen bonds : angle 4.65991 ( 3552) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 410 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 343 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 163 LEU cc_start: 0.8517 (tt) cc_final: 0.8229 (mt) REVERT: B 139 PHE cc_start: 0.7849 (p90) cc_final: 0.7641 (p90) REVERT: B 161 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8427 (pt0) REVERT: L 157 MET cc_start: 0.7089 (ptp) cc_final: 0.6836 (ptp) REVERT: K 65 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8113 (pp20) REVERT: K 170 ARG cc_start: 0.8126 (mtm-85) cc_final: 0.7862 (mtm-85) REVERT: I 50 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8749 (mttt) REVERT: I 65 GLU cc_start: 0.8512 (OUTLIER) cc_final: 0.8143 (pp20) REVERT: I 161 GLU cc_start: 0.8869 (mt-10) cc_final: 0.8578 (mp0) REVERT: J 157 MET cc_start: 0.7472 (ptp) cc_final: 0.7214 (ttm) REVERT: C 161 GLU cc_start: 0.9067 (mt-10) cc_final: 0.8805 (mp0) REVERT: C 163 LEU cc_start: 0.8526 (tt) cc_final: 0.8229 (mt) REVERT: D 14 LYS cc_start: 0.9029 (mttt) cc_final: 0.8581 (mtmm) REVERT: D 139 PHE cc_start: 0.8002 (p90) cc_final: 0.7530 (p90) REVERT: D 158 SER cc_start: 0.8448 (OUTLIER) cc_final: 0.7760 (t) REVERT: D 161 GLU cc_start: 0.8806 (mt-10) cc_final: 0.8505 (mp0) REVERT: E 38 ASP cc_start: 0.8546 (OUTLIER) cc_final: 0.8102 (t0) REVERT: E 58 ASP cc_start: 0.9161 (t70) cc_final: 0.8855 (t0) REVERT: E 156 ILE cc_start: 0.9446 (OUTLIER) cc_final: 0.9168 (mt) REVERT: G 38 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8108 (t0) REVERT: G 58 ASP cc_start: 0.8962 (t70) cc_final: 0.8738 (t0) REVERT: G 156 ILE cc_start: 0.9472 (OUTLIER) cc_final: 0.9217 (mt) REVERT: F 122 LYS cc_start: 0.9082 (OUTLIER) cc_final: 0.7988 (pptt) REVERT: M 177 GLN cc_start: 0.9189 (tm-30) cc_final: 0.8776 (tp-100) outliers start: 67 outliers final: 39 residues processed: 393 average time/residue: 0.8264 time to fit residues: 368.4219 Evaluate side-chains 374 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 326 time to evaluate : 1.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 19 GLN Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 65 GLU Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain G residue 19 GLU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain F residue 122 LYS Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain N residue 208 THR Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 37 optimal weight: 0.9990 chunk 340 optimal weight: 0.8980 chunk 252 optimal weight: 5.9990 chunk 312 optimal weight: 2.9990 chunk 220 optimal weight: 4.9990 chunk 298 optimal weight: 7.9990 chunk 139 optimal weight: 5.9990 chunk 238 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 79 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 140 HIS ** K 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 172 HIS J 140 HIS C 20 HIS C 140 HIS D 140 HIS F 223 GLN H 223 GLN O 230 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.113008 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.067951 restraints weight = 45075.296| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.28 r_work: 0.2666 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8975 moved from start: 0.4045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 29440 Z= 0.133 Angle : 0.552 8.851 39888 Z= 0.278 Chirality : 0.043 0.163 4440 Planarity : 0.004 0.041 5200 Dihedral : 4.207 41.020 4024 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 2.08 % Allowed : 17.79 % Favored : 80.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.07 (0.14), residues: 3624 helix: 1.00 (0.13), residues: 1672 sheet: -0.53 (0.18), residues: 688 loop : -0.79 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG P 77 TYR 0.015 0.002 TYR L 112 PHE 0.025 0.001 PHE L 145 TRP 0.008 0.001 TRP B 141 HIS 0.011 0.001 HIS L 140 Details of bonding type rmsd covalent geometry : bond 0.00317 (29440) covalent geometry : angle 0.55197 (39888) hydrogen bonds : bond 0.02965 ( 1224) hydrogen bonds : angle 4.61151 ( 3552) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 351 time to evaluate : 1.142 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.9063 (mt-10) cc_final: 0.8813 (mp0) REVERT: A 163 LEU cc_start: 0.8476 (tt) cc_final: 0.8264 (mt) REVERT: A 164 SER cc_start: 0.9135 (t) cc_final: 0.8868 (m) REVERT: B 14 LYS cc_start: 0.8867 (mttt) cc_final: 0.8478 (mtmm) REVERT: B 139 PHE cc_start: 0.7870 (p90) cc_final: 0.7606 (p90) REVERT: B 161 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8429 (pt0) REVERT: L 157 MET cc_start: 0.7195 (ptp) cc_final: 0.6938 (ptp) REVERT: K 163 LEU cc_start: 0.8670 (tt) cc_final: 0.8439 (tp) REVERT: I 50 LYS cc_start: 0.9133 (OUTLIER) cc_final: 0.8726 (mttt) REVERT: I 65 GLU cc_start: 0.8490 (OUTLIER) cc_final: 0.8131 (pp20) REVERT: I 161 GLU cc_start: 0.8974 (mt-10) cc_final: 0.8633 (mp0) REVERT: I 163 LEU cc_start: 0.8708 (tt) cc_final: 0.8505 (tp) REVERT: J 139 PHE cc_start: 0.7849 (p90) cc_final: 0.7647 (p90) REVERT: J 157 MET cc_start: 0.7483 (ptp) cc_final: 0.7269 (ttm) REVERT: C 161 GLU cc_start: 0.9098 (mt-10) cc_final: 0.8848 (mp0) REVERT: C 164 SER cc_start: 0.9131 (t) cc_final: 0.8858 (m) REVERT: D 14 LYS cc_start: 0.9032 (mttt) cc_final: 0.8583 (mtmm) REVERT: D 139 PHE cc_start: 0.7989 (p90) cc_final: 0.7536 (p90) REVERT: D 158 SER cc_start: 0.8525 (OUTLIER) cc_final: 0.7693 (t) REVERT: D 161 GLU cc_start: 0.8812 (mt-10) cc_final: 0.8501 (mp0) REVERT: E 38 ASP cc_start: 0.8542 (OUTLIER) cc_final: 0.8148 (t0) REVERT: E 58 ASP cc_start: 0.9126 (t70) cc_final: 0.8827 (t0) REVERT: E 156 ILE cc_start: 0.9439 (OUTLIER) cc_final: 0.9173 (mt) REVERT: G 38 ASP cc_start: 0.8554 (OUTLIER) cc_final: 0.8159 (t0) REVERT: G 58 ASP cc_start: 0.8944 (t70) cc_final: 0.8724 (t0) REVERT: G 156 ILE cc_start: 0.9459 (OUTLIER) cc_final: 0.9218 (mt) REVERT: M 177 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8755 (tp-100) REVERT: P 186 ASP cc_start: 0.9184 (m-30) cc_final: 0.8969 (m-30) outliers start: 63 outliers final: 41 residues processed: 398 average time/residue: 0.8471 time to fit residues: 381.4368 Evaluate side-chains 378 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 330 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 12 SER Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain L residue 12 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 12 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 39 LEU Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain H residue 6 LEU Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 23 optimal weight: 2.9990 chunk 324 optimal weight: 0.8980 chunk 311 optimal weight: 0.7980 chunk 321 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 178 optimal weight: 0.9990 chunk 194 optimal weight: 8.9990 chunk 218 optimal weight: 5.9990 chunk 172 optimal weight: 1.9990 chunk 237 optimal weight: 6.9990 chunk 138 optimal weight: 10.0000 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS A 140 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 20 HIS L 140 HIS K 20 HIS ** K 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 140 HIS C 20 HIS C 140 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS F 223 GLN H 223 GLN O 230 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.113033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.068557 restraints weight = 45008.188| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.24 r_work: 0.2678 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2564 rms_B_bonded: 3.92 restraints_weight: 0.2500 r_work (final): 0.2564 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8988 moved from start: 0.4156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29440 Z= 0.124 Angle : 0.549 8.092 39888 Z= 0.277 Chirality : 0.042 0.164 4440 Planarity : 0.004 0.048 5200 Dihedral : 4.127 42.057 4024 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 2.08 % Allowed : 17.96 % Favored : 79.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.13 (0.14), residues: 3624 helix: 1.04 (0.13), residues: 1672 sheet: -0.51 (0.18), residues: 688 loop : -0.73 (0.16), residues: 1264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG M 77 TYR 0.015 0.002 TYR D 112 PHE 0.013 0.001 PHE C 139 TRP 0.007 0.001 TRP L 86 HIS 0.011 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00295 (29440) covalent geometry : angle 0.54851 (39888) hydrogen bonds : bond 0.02900 ( 1224) hydrogen bonds : angle 4.58160 ( 3552) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7248 Ramachandran restraints generated. 3624 Oldfield, 0 Emsley, 3624 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 424 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 361 time to evaluate : 1.237 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 161 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8769 (mp0) REVERT: A 162 LYS cc_start: 0.7691 (tptt) cc_final: 0.7486 (tttt) REVERT: A 164 SER cc_start: 0.9181 (t) cc_final: 0.8931 (m) REVERT: B 14 LYS cc_start: 0.8864 (mttt) cc_final: 0.8485 (mtmm) REVERT: B 139 PHE cc_start: 0.7910 (p90) cc_final: 0.7684 (p90) REVERT: B 161 GLU cc_start: 0.8777 (mt-10) cc_final: 0.8436 (pt0) REVERT: L 157 MET cc_start: 0.7254 (ptp) cc_final: 0.7013 (ptp) REVERT: K 163 LEU cc_start: 0.8685 (tt) cc_final: 0.8439 (tp) REVERT: I 50 LYS cc_start: 0.9156 (OUTLIER) cc_final: 0.8743 (mttt) REVERT: I 65 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8146 (pp20) REVERT: I 142 ASP cc_start: 0.5773 (m-30) cc_final: 0.5322 (m-30) REVERT: I 161 GLU cc_start: 0.8943 (mt-10) cc_final: 0.8627 (mp0) REVERT: I 163 LEU cc_start: 0.8766 (tt) cc_final: 0.8502 (tp) REVERT: J 139 PHE cc_start: 0.7858 (p90) cc_final: 0.7654 (p90) REVERT: C 161 GLU cc_start: 0.9013 (mt-10) cc_final: 0.8801 (mp0) REVERT: C 164 SER cc_start: 0.9113 (t) cc_final: 0.8895 (m) REVERT: D 139 PHE cc_start: 0.7957 (p90) cc_final: 0.7601 (p90) REVERT: E 38 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8123 (t0) REVERT: E 58 ASP cc_start: 0.9092 (t70) cc_final: 0.8786 (t0) REVERT: E 156 ILE cc_start: 0.9453 (OUTLIER) cc_final: 0.9182 (mt) REVERT: G 38 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8152 (t0) REVERT: G 58 ASP cc_start: 0.8924 (t70) cc_final: 0.8706 (t0) REVERT: G 156 ILE cc_start: 0.9473 (OUTLIER) cc_final: 0.9226 (mt) REVERT: H 111 ASP cc_start: 0.9026 (OUTLIER) cc_final: 0.8800 (t70) REVERT: H 166 ASP cc_start: 0.8803 (OUTLIER) cc_final: 0.8599 (p0) REVERT: M 177 GLN cc_start: 0.9159 (tm-30) cc_final: 0.8780 (tp-100) REVERT: P 186 ASP cc_start: 0.9170 (m-30) cc_final: 0.8945 (m-30) outliers start: 63 outliers final: 38 residues processed: 401 average time/residue: 0.7958 time to fit residues: 363.0750 Evaluate side-chains 380 residues out of total 3024 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 334 time to evaluate : 1.064 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 VAL Chi-restraints excluded: chain B residue 21 VAL Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain B residue 158 SER Chi-restraints excluded: chain L residue 41 VAL Chi-restraints excluded: chain L residue 122 ILE Chi-restraints excluded: chain K residue 21 VAL Chi-restraints excluded: chain K residue 25 SER Chi-restraints excluded: chain K residue 41 VAL Chi-restraints excluded: chain K residue 166 SER Chi-restraints excluded: chain I residue 21 VAL Chi-restraints excluded: chain I residue 41 VAL Chi-restraints excluded: chain I residue 50 LYS Chi-restraints excluded: chain I residue 65 GLU Chi-restraints excluded: chain I residue 166 SER Chi-restraints excluded: chain J residue 21 VAL Chi-restraints excluded: chain J residue 41 VAL Chi-restraints excluded: chain J residue 122 ILE Chi-restraints excluded: chain C residue 21 VAL Chi-restraints excluded: chain C residue 41 VAL Chi-restraints excluded: chain C residue 91 THR Chi-restraints excluded: chain C residue 163 LEU Chi-restraints excluded: chain D residue 19 GLN Chi-restraints excluded: chain D residue 21 VAL Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 158 SER Chi-restraints excluded: chain E residue 38 ASP Chi-restraints excluded: chain E residue 156 ILE Chi-restraints excluded: chain E residue 208 THR Chi-restraints excluded: chain G residue 6 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 156 ILE Chi-restraints excluded: chain G residue 161 THR Chi-restraints excluded: chain G residue 208 THR Chi-restraints excluded: chain F residue 6 LEU Chi-restraints excluded: chain F residue 14 LYS Chi-restraints excluded: chain F residue 111 ASP Chi-restraints excluded: chain F residue 118 THR Chi-restraints excluded: chain H residue 111 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain H residue 161 THR Chi-restraints excluded: chain H residue 166 ASP Chi-restraints excluded: chain M residue 161 THR Chi-restraints excluded: chain N residue 161 THR Chi-restraints excluded: chain O residue 161 THR Chi-restraints excluded: chain O residue 208 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 360 random chunks: chunk 219 optimal weight: 0.9980 chunk 249 optimal weight: 0.8980 chunk 296 optimal weight: 0.8980 chunk 261 optimal weight: 5.9990 chunk 288 optimal weight: 5.9990 chunk 221 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 333 optimal weight: 7.9990 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 10.0000 chunk 183 optimal weight: 0.5980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 20 HIS ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 140 HIS L 20 HIS L 140 HIS K 20 HIS ** K 66 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 20 HIS ** D 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 140 HIS F 223 GLN H 223 GLN O 230 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.113321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.068504 restraints weight = 45266.974| |-----------------------------------------------------------------------------| r_work (start): 0.2810 rms_B_bonded: 2.29 r_work: 0.2677 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8967 moved from start: 0.4207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 29440 Z= 0.122 Angle : 0.549 8.207 39888 Z= 0.277 Chirality : 0.042 0.163 4440 Planarity : 0.004 0.037 5200 Dihedral : 4.157 42.507 4024 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.05 % Allowed : 18.12 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: 0.19 (0.14), residues: 3624 helix: 1.09 (0.13), residues: 1664 sheet: -0.50 (0.18), residues: 688 loop : -0.66 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG N 62 TYR 0.015 0.002 TYR D 112 PHE 0.027 0.001 PHE L 145 TRP 0.012 0.001 TRP L 86 HIS 0.010 0.001 HIS J 140 Details of bonding type rmsd covalent geometry : bond 0.00287 (29440) covalent geometry : angle 0.54853 (39888) hydrogen bonds : bond 0.02858 ( 1224) hydrogen bonds : angle 4.57378 ( 3552) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14202.56 seconds wall clock time: 241 minutes 22.00 seconds (14482.00 seconds total)