Starting phenix.real_space_refine on Tue Oct 27 11:11:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9nav_49204/10_2026/9nav_49204.cif Found real_map, /net/cci-nas-00/data/ceres_data/9nav_49204/10_2026/9nav_49204.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9nav_49204/10_2026/9nav_49204.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9nav_49204/10_2026/9nav_49204.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9nav_49204/10_2026/9nav_49204.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9nav_49204/10_2026/9nav_49204.map" } resolution = 3.81 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= 0.002 sd= 0.026 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 92 5.16 5 C 15420 2.51 5 N 4156 2.21 5 O 4602 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 28 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 24270 Number of models: 1 Model: "" Number of chains: 5 Chain: "G" Number of atoms: 2093 Number of conformers: 1 Conformer: "" Number of residues, atoms: 267, 2093 Classifications: {'peptide': 267} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 248} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASN:plan1': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "H" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 791 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 10} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 45 Unresolved non-hydrogen dihedrals: 31 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 3, 'ASN:plan1': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 23 Chain: "A" Number of atoms: 4197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 549, 4197 Classifications: {'peptide': 549} Link IDs: {'PCIS': 2, 'PTRANS': 31, 'TRANS': 515} Chain breaks: 3 Chain: "B" Number of atoms: 2528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 335, 2528 Classifications: {'peptide': 335} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 313} Chain breaks: 3 Chain: "C" Number of atoms: 2526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 334, 2526 Classifications: {'peptide': 334} Link IDs: {'PCIS': 1, 'PTRANS': 19, 'TRANS': 313} Chain breaks: 3 Restraints were copied for chains: I, J, D, E, F Time building chain proxies: 8.24, per 1000 atoms: 0.34 Number of scatterers: 24270 At special positions: 0 Unit cell: (114.352, 174.304, 168.753, 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 92 16.00 O 4602 8.00 N 4156 7.00 C 15420 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=13, symmetry=0 Simple disulfide: pdb=" SG CYS G 96 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 198 " - pdb=" SG CYS G 252 " distance=2.03 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 80 " distance=2.03 Simple disulfide: pdb=" SG CYS I 96 " - pdb=" SG CYS I 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 198 " - pdb=" SG CYS I 252 " distance=2.03 Simple disulfide: pdb=" SG CYS J 25 " - pdb=" SG CYS J 80 " distance=2.03 Simple disulfide: pdb=" SG CYS A 82 " - pdb=" SG CYS A 254 " distance=2.03 Simple disulfide: pdb=" SG CYS A 637 " - pdb=" SG CYS D 637 " distance=2.03 Simple disulfide: pdb=" SG CYS B 82 " - pdb=" SG CYS B 254 " distance=2.03 Simple disulfide: pdb=" SG CYS C 82 " - pdb=" SG CYS C 254 " distance=2.03 Simple disulfide: pdb=" SG CYS D 82 " - pdb=" SG CYS D 254 " distance=2.03 Simple disulfide: pdb=" SG CYS E 82 " - pdb=" SG CYS E 254 " distance=2.03 Simple disulfide: pdb=" SG CYS F 82 " - pdb=" SG CYS F 254 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.60 Conformation dependent library (CDL) restraints added in 1.1 seconds 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5812 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 54 sheets defined 17.4% alpha, 41.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.71 Creating SS restraints... Processing helix chain 'G' and resid 49 through 54 removed outlier: 3.535A pdb=" N VAL G 52 " --> pdb=" O GLY G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 81 removed outlier: 4.484A pdb=" N GLU G 62 " --> pdb=" O SER G 58 " (cutoff:3.500A) Processing helix chain 'G' and resid 131 through 143 removed outlier: 3.738A pdb=" N GLN G 143 " --> pdb=" O GLN G 139 " (cutoff:3.500A) Processing helix chain 'G' and resid 146 through 157 Processing helix chain 'G' and resid 157 through 170 Processing helix chain 'G' and resid 170 through 175 Processing helix chain 'I' and resid 49 through 54 removed outlier: 3.535A pdb=" N VAL I 52 " --> pdb=" O GLY I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 58 through 81 removed outlier: 4.484A pdb=" N GLU I 62 " --> pdb=" O SER I 58 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 143 removed outlier: 3.738A pdb=" N GLN I 143 " --> pdb=" O GLN I 139 " (cutoff:3.500A) Processing helix chain 'I' and resid 146 through 157 Processing helix chain 'I' and resid 157 through 170 Processing helix chain 'I' and resid 170 through 175 Processing helix chain 'A' and resid 61 through 73 removed outlier: 3.550A pdb=" N VAL A 65 " --> pdb=" O VAL A 61 " (cutoff:3.500A) Processing helix chain 'A' and resid 109 through 113 removed outlier: 3.887A pdb=" N VAL A 113 " --> pdb=" O PRO A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 131 Processing helix chain 'A' and resid 172 through 177 Processing helix chain 'A' and resid 195 through 199 Processing helix chain 'A' and resid 261 through 266 removed outlier: 3.873A pdb=" N VAL A 265 " --> pdb=" O PRO A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 349 removed outlier: 3.598A pdb=" N VAL A 346 " --> pdb=" O PHE A 342 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 379 Processing helix chain 'A' and resid 620 through 624 removed outlier: 3.991A pdb=" N VAL A 624 " --> pdb=" O LYS A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 72 removed outlier: 3.583A pdb=" N ILE B 64 " --> pdb=" O ARG B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 195 through 200 removed outlier: 3.894A pdb=" N GLY B 200 " --> pdb=" O SER B 197 " (cutoff:3.500A) Processing helix chain 'B' and resid 214 through 219 Processing helix chain 'B' and resid 261 through 267 removed outlier: 3.596A pdb=" N VAL B 265 " --> pdb=" O PRO B 262 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU B 267 " --> pdb=" O LEU B 264 " (cutoff:3.500A) Processing helix chain 'B' and resid 295 through 304 removed outlier: 3.553A pdb=" N ARG B 304 " --> pdb=" O THR B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 349 removed outlier: 4.313A pdb=" N VAL B 346 " --> pdb=" O PHE B 342 " (cutoff:3.500A) Processing helix chain 'B' and resid 372 through 379 Processing helix chain 'C' and resid 60 through 72 Processing helix chain 'C' and resid 123 through 131 Processing helix chain 'C' and resid 172 through 179 Processing helix chain 'C' and resid 195 through 199 Processing helix chain 'C' and resid 261 through 267 removed outlier: 3.863A pdb=" N VAL C 265 " --> pdb=" O PRO C 262 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU C 267 " --> pdb=" O LEU C 264 " (cutoff:3.500A) Processing helix chain 'C' and resid 295 through 304 removed outlier: 3.581A pdb=" N ARG C 299 " --> pdb=" O SER C 295 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 349 removed outlier: 3.958A pdb=" N GLY C 349 " --> pdb=" O LEU C 345 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 379 Processing helix chain 'D' and resid 61 through 73 removed outlier: 3.550A pdb=" N VAL D 65 " --> pdb=" O VAL D 61 " (cutoff:3.500A) Processing helix chain 'D' and resid 109 through 113 removed outlier: 3.886A pdb=" N VAL D 113 " --> pdb=" O PRO D 110 " (cutoff:3.500A) Processing helix chain 'D' and resid 123 through 131 Processing helix chain 'D' and resid 172 through 177 Processing helix chain 'D' and resid 195 through 199 Processing helix chain 'D' and resid 261 through 266 removed outlier: 3.874A pdb=" N VAL D 265 " --> pdb=" O PRO D 262 " (cutoff:3.500A) Processing helix chain 'D' and resid 342 through 349 removed outlier: 3.598A pdb=" N VAL D 346 " --> pdb=" O PHE D 342 " (cutoff:3.500A) Processing helix chain 'D' and resid 372 through 379 Processing helix chain 'D' and resid 620 through 624 removed outlier: 3.992A pdb=" N VAL D 624 " --> pdb=" O LYS D 621 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 72 removed outlier: 3.582A pdb=" N ILE E 64 " --> pdb=" O ARG E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 123 through 131 Processing helix chain 'E' and resid 195 through 200 removed outlier: 3.895A pdb=" N GLY E 200 " --> pdb=" O SER E 197 " (cutoff:3.500A) Processing helix chain 'E' and resid 214 through 219 Processing helix chain 'E' and resid 261 through 267 removed outlier: 3.595A pdb=" N VAL E 265 " --> pdb=" O PRO E 262 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU E 267 " --> pdb=" O LEU E 264 " (cutoff:3.500A) Processing helix chain 'E' and resid 295 through 304 removed outlier: 3.554A pdb=" N ARG E 304 " --> pdb=" O THR E 300 " (cutoff:3.500A) Processing helix chain 'E' and resid 342 through 349 removed outlier: 4.314A pdb=" N VAL E 346 " --> pdb=" O PHE E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 372 through 379 Processing helix chain 'F' and resid 60 through 72 Processing helix chain 'F' and resid 123 through 131 Processing helix chain 'F' and resid 172 through 179 Processing helix chain 'F' and resid 195 through 199 Processing helix chain 'F' and resid 261 through 267 removed outlier: 3.863A pdb=" N VAL F 265 " --> pdb=" O PRO F 262 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N LEU F 267 " --> pdb=" O LEU F 264 " (cutoff:3.500A) Processing helix chain 'F' and resid 295 through 304 removed outlier: 3.581A pdb=" N ARG F 299 " --> pdb=" O SER F 295 " (cutoff:3.500A) Processing helix chain 'F' and resid 342 through 349 removed outlier: 3.957A pdb=" N GLY F 349 " --> pdb=" O LEU F 345 " (cutoff:3.500A) Processing helix chain 'F' and resid 372 through 379 Processing sheet with id=AA1, first strand: chain 'G' and resid 46 through 47 removed outlier: 6.552A pdb=" N GLY G 28 " --> pdb=" O TYR G 35 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER G 37 " --> pdb=" O VAL G 26 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL G 26 " --> pdb=" O SER G 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN G 39 " --> pdb=" O PHE G 24 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE G 24 " --> pdb=" O ASN G 39 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ASP G 121 " --> pdb=" O PRO G 106 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA G 108 " --> pdb=" O ASN G 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN G 119 " --> pdb=" O ALA G 108 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE G 110 " --> pdb=" O PHE G 117 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 181 through 187 removed outlier: 3.530A pdb=" N PHE G 201 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG G 183 " --> pdb=" O SER G 199 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N SER G 199 " --> pdb=" O ARG G 183 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS G 185 " --> pdb=" O THR G 197 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N THR G 197 " --> pdb=" O LYS G 185 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ARG G 187 " --> pdb=" O VAL G 195 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL G 195 " --> pdb=" O ARG G 187 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE G 234 " --> pdb=" O SER G 202 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N SER G 237 " --> pdb=" O ASP G 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 217 through 218 removed outlier: 3.924A pdb=" N VAL G 254 " --> pdb=" O LEU G 263 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N LEU G 263 " --> pdb=" O VAL G 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 6 through 11 removed outlier: 3.690A pdb=" N PHE H 70 " --> pdb=" O ASN H 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 23 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 68 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS H 25 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR H 66 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE H 62 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N TYR H 67 " --> pdb=" O GLU H 50 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLU H 50 " --> pdb=" O TYR H 67 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 6 through 11 removed outlier: 3.690A pdb=" N PHE H 70 " --> pdb=" O ASN H 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU H 23 " --> pdb=" O THR H 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR H 68 " --> pdb=" O LEU H 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS H 25 " --> pdb=" O TYR H 66 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N TYR H 66 " --> pdb=" O CYS H 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE H 62 " --> pdb=" O GLY H 29 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 36 through 40 removed outlier: 3.609A pdb=" N ALA H 79 " --> pdb=" O LEU H 40 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 46 through 47 removed outlier: 6.552A pdb=" N GLY I 28 " --> pdb=" O TYR I 35 " (cutoff:3.500A) removed outlier: 4.563A pdb=" N SER I 37 " --> pdb=" O VAL I 26 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL I 26 " --> pdb=" O SER I 37 " (cutoff:3.500A) removed outlier: 4.664A pdb=" N ASN I 39 " --> pdb=" O PHE I 24 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N PHE I 24 " --> pdb=" O ASN I 39 " (cutoff:3.500A) removed outlier: 9.526A pdb=" N ASP I 121 " --> pdb=" O PRO I 106 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N ALA I 108 " --> pdb=" O ASN I 119 " (cutoff:3.500A) removed outlier: 4.978A pdb=" N ASN I 119 " --> pdb=" O ALA I 108 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N PHE I 110 " --> pdb=" O PHE I 117 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 181 through 187 removed outlier: 3.529A pdb=" N PHE I 201 " --> pdb=" O SER I 181 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ARG I 183 " --> pdb=" O SER I 199 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N SER I 199 " --> pdb=" O ARG I 183 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LYS I 185 " --> pdb=" O THR I 197 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N THR I 197 " --> pdb=" O LYS I 185 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ARG I 187 " --> pdb=" O VAL I 195 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N VAL I 195 " --> pdb=" O ARG I 187 " (cutoff:3.500A) removed outlier: 5.741A pdb=" N PHE I 234 " --> pdb=" O SER I 202 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N SER I 237 " --> pdb=" O ASP I 225 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 217 through 218 removed outlier: 3.924A pdb=" N VAL I 254 " --> pdb=" O LEU I 263 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N LEU I 263 " --> pdb=" O VAL I 254 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 6 through 11 removed outlier: 3.690A pdb=" N PHE J 70 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU J 23 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR J 68 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS J 25 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR J 66 " --> pdb=" O CYS J 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE J 62 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N TYR J 67 " --> pdb=" O GLU J 50 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N GLU J 50 " --> pdb=" O TYR J 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'J' and resid 6 through 11 removed outlier: 3.690A pdb=" N PHE J 70 " --> pdb=" O ASN J 21 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N LEU J 23 " --> pdb=" O THR J 68 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N THR J 68 " --> pdb=" O LEU J 23 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS J 25 " --> pdb=" O TYR J 66 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR J 66 " --> pdb=" O CYS J 25 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N PHE J 62 " --> pdb=" O GLY J 29 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'J' and resid 36 through 40 removed outlier: 3.609A pdb=" N ALA J 79 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 81 through 92 removed outlier: 3.775A pdb=" N SER A 251 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 87 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 247 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR A 91 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 245 " --> pdb=" O THR A 91 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 81 through 92 removed outlier: 3.775A pdb=" N SER A 251 " --> pdb=" O ALA A 85 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 87 " --> pdb=" O LEU A 249 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N VAL A 247 " --> pdb=" O LEU A 89 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR A 91 " --> pdb=" O PHE A 245 " (cutoff:3.500A) removed outlier: 7.021A pdb=" N PHE A 245 " --> pdb=" O THR A 91 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N CYS A 254 " --> pdb=" O LYS A 136 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR A 256 " --> pdb=" O MET A 134 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N TYR A 258 " --> pdb=" O TYR A 132 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR A 132 " --> pdb=" O TYR A 258 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 101 through 107 removed outlier: 6.744A pdb=" N ILE A 102 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR A 227 " --> pdb=" O ILE A 102 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA A 104 " --> pdb=" O ILE A 225 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N VAL A 160 " --> pdb=" O LEU A 182 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU A 182 " --> pdb=" O VAL A 160 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'A' and resid 269 through 280 removed outlier: 5.892A pdb=" N SER A 366 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N LEU A 355 " --> pdb=" O THR A 322 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N THR A 322 " --> pdb=" O LEU A 355 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL A 398 " --> pdb=" O PRO A 276 " (cutoff:3.500A) removed outlier: 5.671A pdb=" N THR A 400 " --> pdb=" O GLN A 274 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN A 274 " --> pdb=" O THR A 400 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'A' and resid 285 through 286 removed outlier: 4.114A pdb=" N SER A 285 " --> pdb=" O CYS A 384 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'A' and resid 474 through 477 removed outlier: 6.831A pdb=" N HIS A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 508 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL A 518 " --> pdb=" O LYS A 542 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS A 542 " --> pdb=" O VAL A 518 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA A 520 " --> pdb=" O LEU A 540 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU A 540 " --> pdb=" O ALA A 520 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS A 522 " --> pdb=" O LEU A 538 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N TRP A 587 " --> pdb=" O ILE A 484 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR A 591 " --> pdb=" O GLY A 480 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY A 480 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 489 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'A' and resid 474 through 477 removed outlier: 6.831A pdb=" N HIS A 474 " --> pdb=" O LYS A 470 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL A 508 " --> pdb=" O LYS A 515 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N GLN A 523 " --> pdb=" O GLU A 639 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N GLU A 639 " --> pdb=" O GLN A 523 " (cutoff:3.500A) removed outlier: 13.946A pdb=" N VAL A 525 " --> pdb=" O CYS A 637 " (cutoff:3.500A) removed outlier: 17.817A pdb=" N CYS A 637 " --> pdb=" O VAL A 525 " (cutoff:3.500A) removed outlier: 23.956A pdb=" N ALA A 527 " --> pdb=" O GLN A 635 " (cutoff:3.500A) removed outlier: 28.121A pdb=" N GLN A 635 " --> pdb=" O ALA A 527 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ASP A 488 " --> pdb=" O VAL A 435 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER A 486 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N TRP A 489 " --> pdb=" O SER A 497 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'A' and resid 453 through 454 removed outlier: 3.563A pdb=" N VAL A 549 " --> pdb=" O ILE A 580 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN A 551 " --> pdb=" O ALA A 578 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA A 578 " --> pdb=" O ASN A 551 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'A' and resid 556 through 557 Processing sheet with id=AC5, first strand: chain 'B' and resid 81 through 92 removed outlier: 4.038A pdb=" N ILE B 81 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN B 83 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 253 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 85 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL B 247 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 91 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 245 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU B 140 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE B 192 " --> pdb=" O VAL B 142 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU B 144 " --> pdb=" O ALA B 190 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 190 " --> pdb=" O LEU B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 81 through 92 removed outlier: 4.038A pdb=" N ILE B 81 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN B 83 " --> pdb=" O TRP B 253 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP B 253 " --> pdb=" O GLN B 83 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ALA B 85 " --> pdb=" O SER B 251 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL B 247 " --> pdb=" O LEU B 89 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N THR B 91 " --> pdb=" O PHE B 245 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N PHE B 245 " --> pdb=" O THR B 91 " (cutoff:3.500A) removed outlier: 6.944A pdb=" N PHE B 255 " --> pdb=" O TRP B 135 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP B 135 " --> pdb=" O PHE B 255 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY B 257 " --> pdb=" O SER B 133 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 101 through 107 removed outlier: 5.795A pdb=" N ILE B 102 " --> pdb=" O THR B 227 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR B 227 " --> pdb=" O ILE B 102 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N ALA B 104 " --> pdb=" O ILE B 225 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 153 through 154 Processing sheet with id=AC9, first strand: chain 'B' and resid 269 through 280 removed outlier: 5.996A pdb=" N SER B 366 " --> pdb=" O ILE B 356 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ILE B 356 " --> pdb=" O SER B 366 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N LEU B 355 " --> pdb=" O THR B 322 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N THR B 322 " --> pdb=" O LEU B 355 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N THR B 401 " --> pdb=" O THR B 329 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU B 402 " --> pdb=" O ASN B 273 " (cutoff:3.500A) removed outlier: 5.401A pdb=" N ASN B 273 " --> pdb=" O LEU B 402 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE B 404 " --> pdb=" O THR B 271 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR B 271 " --> pdb=" O PHE B 404 " (cutoff:3.500A) removed outlier: 7.095A pdb=" N GLN B 406 " --> pdb=" O LYS B 269 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N LYS B 269 " --> pdb=" O GLN B 406 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 84 through 92 removed outlier: 5.094A pdb=" N THR C 86 " --> pdb=" O SER C 251 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N SER C 251 " --> pdb=" O THR C 86 " (cutoff:3.500A) removed outlier: 5.722A pdb=" N THR C 88 " --> pdb=" O LEU C 249 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N LEU C 249 " --> pdb=" O THR C 88 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY C 90 " --> pdb=" O VAL C 247 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN C 141 " --> pdb=" O ALA C 250 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA C 190 " --> pdb=" O LEU C 144 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 101 through 107 removed outlier: 5.977A pdb=" N ILE C 102 " --> pdb=" O THR C 227 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR C 227 " --> pdb=" O ILE C 102 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA C 104 " --> pdb=" O ILE C 225 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 132 through 134 removed outlier: 7.875A pdb=" N GLY C 257 " --> pdb=" O SER C 133 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 153 through 154 Processing sheet with id=AD5, first strand: chain 'C' and resid 269 through 280 removed outlier: 3.523A pdb=" N THR C 278 " --> pdb=" O ASN C 290 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU C 280 " --> pdb=" O ILE C 288 " (cutoff:3.500A) removed outlier: 5.164A pdb=" N SER C 366 " --> pdb=" O ILE C 356 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP C 351 " --> pdb=" O TRP C 324 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N TRP C 324 " --> pdb=" O TRP C 351 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL C 353 " --> pdb=" O THR C 322 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR C 322 " --> pdb=" O VAL C 353 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU C 355 " --> pdb=" O SER C 320 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR C 401 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N VAL C 275 " --> pdb=" O THR C 400 " (cutoff:3.500A) removed outlier: 5.419A pdb=" N LEU C 402 " --> pdb=" O ASN C 273 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ASN C 273 " --> pdb=" O LEU C 402 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N PHE C 404 " --> pdb=" O THR C 271 " (cutoff:3.500A) removed outlier: 5.112A pdb=" N THR C 271 " --> pdb=" O PHE C 404 " (cutoff:3.500A) removed outlier: 7.537A pdb=" N GLN C 406 " --> pdb=" O LYS C 269 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS C 269 " --> pdb=" O GLN C 406 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 285 through 286 removed outlier: 4.106A pdb=" N SER C 285 " --> pdb=" O CYS C 384 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 81 through 92 removed outlier: 3.775A pdb=" N SER D 251 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 87 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 247 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR D 91 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE D 245 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 81 through 92 removed outlier: 3.775A pdb=" N SER D 251 " --> pdb=" O ALA D 85 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 87 " --> pdb=" O LEU D 249 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N VAL D 247 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N THR D 91 " --> pdb=" O PHE D 245 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N PHE D 245 " --> pdb=" O THR D 91 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N CYS D 254 " --> pdb=" O LYS D 136 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N THR D 256 " --> pdb=" O MET D 134 " (cutoff:3.500A) removed outlier: 6.462A pdb=" N TYR D 258 " --> pdb=" O TYR D 132 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N TYR D 132 " --> pdb=" O TYR D 258 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 101 through 107 removed outlier: 6.744A pdb=" N ILE D 102 " --> pdb=" O THR D 227 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N THR D 227 " --> pdb=" O ILE D 102 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N ALA D 104 " --> pdb=" O ILE D 225 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N VAL D 160 " --> pdb=" O LEU D 182 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N LEU D 182 " --> pdb=" O VAL D 160 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AE2, first strand: chain 'D' and resid 269 through 280 removed outlier: 5.893A pdb=" N SER D 366 " --> pdb=" O ILE D 356 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LEU D 355 " --> pdb=" O THR D 322 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N THR D 322 " --> pdb=" O LEU D 355 " (cutoff:3.500A) removed outlier: 5.955A pdb=" N VAL D 398 " --> pdb=" O PRO D 276 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N THR D 400 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLN D 274 " --> pdb=" O THR D 400 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 285 through 286 removed outlier: 4.114A pdb=" N SER D 285 " --> pdb=" O CYS D 384 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 474 through 477 removed outlier: 6.832A pdb=" N HIS D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 508 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N VAL D 518 " --> pdb=" O LYS D 542 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N LYS D 542 " --> pdb=" O VAL D 518 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N ALA D 520 " --> pdb=" O LEU D 540 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N LEU D 540 " --> pdb=" O ALA D 520 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS D 522 " --> pdb=" O LEU D 538 " (cutoff:3.500A) removed outlier: 4.233A pdb=" N TRP D 587 " --> pdb=" O ILE D 484 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR D 591 " --> pdb=" O GLY D 480 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLY D 480 " --> pdb=" O THR D 591 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP D 489 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 474 through 477 removed outlier: 6.832A pdb=" N HIS D 474 " --> pdb=" O LYS D 470 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N VAL D 508 " --> pdb=" O LYS D 515 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N GLN D 523 " --> pdb=" O GLU D 639 " (cutoff:3.500A) removed outlier: 9.462A pdb=" N GLU D 639 " --> pdb=" O GLN D 523 " (cutoff:3.500A) removed outlier: 13.946A pdb=" N VAL D 525 " --> pdb=" O CYS D 637 " (cutoff:3.500A) removed outlier: 17.818A pdb=" N CYS D 637 " --> pdb=" O VAL D 525 " (cutoff:3.500A) removed outlier: 23.956A pdb=" N ALA D 527 " --> pdb=" O GLN D 635 " (cutoff:3.500A) removed outlier: 28.122A pdb=" N GLN D 635 " --> pdb=" O ALA D 527 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ASP D 488 " --> pdb=" O VAL D 435 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER D 486 " --> pdb=" O THR D 437 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N TRP D 489 " --> pdb=" O SER D 497 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 453 through 454 removed outlier: 3.563A pdb=" N VAL D 549 " --> pdb=" O ILE D 580 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASN D 551 " --> pdb=" O ALA D 578 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA D 578 " --> pdb=" O ASN D 551 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 556 through 557 Processing sheet with id=AE8, first strand: chain 'E' and resid 81 through 92 removed outlier: 4.039A pdb=" N ILE E 81 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN E 83 " --> pdb=" O TRP E 253 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP E 253 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA E 85 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL E 247 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR E 91 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE E 245 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LEU E 140 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N PHE E 192 " --> pdb=" O VAL E 142 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 144 " --> pdb=" O ALA E 190 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA E 190 " --> pdb=" O LEU E 144 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 81 through 92 removed outlier: 4.039A pdb=" N ILE E 81 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N GLN E 83 " --> pdb=" O TRP E 253 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TRP E 253 " --> pdb=" O GLN E 83 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N ALA E 85 " --> pdb=" O SER E 251 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N VAL E 247 " --> pdb=" O LEU E 89 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N THR E 91 " --> pdb=" O PHE E 245 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N PHE E 245 " --> pdb=" O THR E 91 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N PHE E 255 " --> pdb=" O TRP E 135 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N TRP E 135 " --> pdb=" O PHE E 255 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N GLY E 257 " --> pdb=" O SER E 133 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'E' and resid 101 through 107 removed outlier: 5.795A pdb=" N ILE E 102 " --> pdb=" O THR E 227 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N THR E 227 " --> pdb=" O ILE E 102 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ALA E 104 " --> pdb=" O ILE E 225 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AF3, first strand: chain 'E' and resid 269 through 280 removed outlier: 5.996A pdb=" N SER E 366 " --> pdb=" O ILE E 356 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ILE E 356 " --> pdb=" O SER E 366 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU E 355 " --> pdb=" O THR E 322 " (cutoff:3.500A) removed outlier: 5.880A pdb=" N THR E 322 " --> pdb=" O LEU E 355 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N THR E 401 " --> pdb=" O THR E 329 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU E 402 " --> pdb=" O ASN E 273 " (cutoff:3.500A) removed outlier: 5.399A pdb=" N ASN E 273 " --> pdb=" O LEU E 402 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N PHE E 404 " --> pdb=" O THR E 271 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N THR E 271 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N GLN E 406 " --> pdb=" O LYS E 269 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LYS E 269 " --> pdb=" O GLN E 406 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'F' and resid 84 through 92 removed outlier: 5.094A pdb=" N THR F 86 " --> pdb=" O SER F 251 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N SER F 251 " --> pdb=" O THR F 86 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N THR F 88 " --> pdb=" O LEU F 249 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU F 249 " --> pdb=" O THR F 88 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY F 90 " --> pdb=" O VAL F 247 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASN F 141 " --> pdb=" O ALA F 250 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA F 190 " --> pdb=" O LEU F 144 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'F' and resid 101 through 107 removed outlier: 5.978A pdb=" N ILE F 102 " --> pdb=" O THR F 227 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N THR F 227 " --> pdb=" O ILE F 102 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA F 104 " --> pdb=" O ILE F 225 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 132 through 134 removed outlier: 7.875A pdb=" N GLY F 257 " --> pdb=" O SER F 133 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 153 through 154 Processing sheet with id=AF8, first strand: chain 'F' and resid 269 through 280 removed outlier: 3.523A pdb=" N THR F 278 " --> pdb=" O ASN F 290 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU F 280 " --> pdb=" O ILE F 288 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N SER F 366 " --> pdb=" O ILE F 356 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N TRP F 351 " --> pdb=" O TRP F 324 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N TRP F 324 " --> pdb=" O TRP F 351 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N VAL F 353 " --> pdb=" O THR F 322 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N THR F 322 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N LEU F 355 " --> pdb=" O SER F 320 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N THR F 401 " --> pdb=" O THR F 329 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N VAL F 398 " --> pdb=" O PRO F 276 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N THR F 400 " --> pdb=" O GLN F 274 " (cutoff:3.500A) removed outlier: 4.453A pdb=" N GLN F 274 " --> pdb=" O THR F 400 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'F' and resid 285 through 286 removed outlier: 4.106A pdb=" N SER F 285 " --> pdb=" O CYS F 384 " (cutoff:3.500A) 947 hydrogen bonds defined for protein. 2472 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: 5.10 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 7440 1.34 - 1.46: 4994 1.46 - 1.58: 12304 1.58 - 1.70: 0 1.70 - 1.82: 142 Bond restraints: 24880 Sorted by residual: bond pdb=" CB TRP E 344 " pdb=" CG TRP E 344 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.94e+00 bond pdb=" CB TRP B 344 " pdb=" CG TRP B 344 " ideal model delta sigma weight residual 1.498 1.455 0.043 3.10e-02 1.04e+03 1.88e+00 bond pdb=" CA GLN E 121 " pdb=" CB GLN E 121 " ideal model delta sigma weight residual 1.531 1.575 -0.045 3.28e-02 9.30e+02 1.86e+00 bond pdb=" CA GLN B 121 " pdb=" CB GLN B 121 " ideal model delta sigma weight residual 1.531 1.575 -0.044 3.28e-02 9.30e+02 1.83e+00 bond pdb=" CB LYS C 195 " pdb=" CG LYS C 195 " ideal model delta sigma weight residual 1.520 1.557 -0.037 3.00e-02 1.11e+03 1.55e+00 ... (remaining 24875 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.79: 33075 1.79 - 3.58: 740 3.58 - 5.37: 98 5.37 - 7.16: 15 7.16 - 8.94: 6 Bond angle restraints: 33934 Sorted by residual: angle pdb=" C LYS C 236 " pdb=" N ASN C 237 " pdb=" CA ASN C 237 " ideal model delta sigma weight residual 122.46 126.45 -3.99 1.41e+00 5.03e-01 8.02e+00 angle pdb=" C LYS F 236 " pdb=" N ASN F 237 " pdb=" CA ASN F 237 " ideal model delta sigma weight residual 122.46 126.44 -3.98 1.41e+00 5.03e-01 7.96e+00 angle pdb=" CB LYS C 195 " pdb=" CG LYS C 195 " pdb=" CD LYS C 195 " ideal model delta sigma weight residual 111.30 117.56 -6.26 2.30e+00 1.89e-01 7.40e+00 angle pdb=" CB LYS F 195 " pdb=" CG LYS F 195 " pdb=" CD LYS F 195 " ideal model delta sigma weight residual 111.30 117.55 -6.25 2.30e+00 1.89e-01 7.39e+00 angle pdb=" CA LYS D 193 " pdb=" CB LYS D 193 " pdb=" CG LYS D 193 " ideal model delta sigma weight residual 114.10 119.50 -5.40 2.00e+00 2.50e-01 7.29e+00 ... (remaining 33929 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 13452 17.71 - 35.42: 944 35.42 - 53.13: 207 53.13 - 70.84: 34 70.84 - 88.55: 24 Dihedral angle restraints: 14661 sinusoidal: 5619 harmonic: 9042 Sorted by residual: dihedral pdb=" CA ARG D 179 " pdb=" C ARG D 179 " pdb=" N LYS D 180 " pdb=" CA LYS D 180 " ideal model delta harmonic sigma weight residual 180.00 153.32 26.68 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA ARG A 179 " pdb=" C ARG A 179 " pdb=" N LYS A 180 " pdb=" CA LYS A 180 " ideal model delta harmonic sigma weight residual 180.00 153.33 26.67 0 5.00e+00 4.00e-02 2.85e+01 dihedral pdb=" CA CYS B 254 " pdb=" C CYS B 254 " pdb=" N PHE B 255 " pdb=" CA PHE B 255 " ideal model delta harmonic sigma weight residual -180.00 -156.31 -23.69 0 5.00e+00 4.00e-02 2.24e+01 ... (remaining 14658 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2559 0.039 - 0.077: 852 0.077 - 0.116: 360 0.116 - 0.155: 69 0.155 - 0.193: 6 Chirality restraints: 3846 Sorted by residual: chirality pdb=" CB THR D 405 " pdb=" CA THR D 405 " pdb=" OG1 THR D 405 " pdb=" CG2 THR D 405 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.33e-01 chirality pdb=" CB THR A 405 " pdb=" CA THR A 405 " pdb=" OG1 THR A 405 " pdb=" CG2 THR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" CB ILE A 468 " pdb=" CA ILE A 468 " pdb=" CG1 ILE A 468 " pdb=" CG2 ILE A 468 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 8.03e-01 ... (remaining 3843 not shown) Planarity restraints: 4332 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 195 " 0.042 5.00e-02 4.00e+02 6.42e-02 6.60e+00 pdb=" N PRO D 196 " -0.111 5.00e-02 4.00e+02 pdb=" CA PRO D 196 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO D 196 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 195 " -0.042 5.00e-02 4.00e+02 6.42e-02 6.59e+00 pdb=" N PRO A 196 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO A 196 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 196 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN D 109 " -0.036 5.00e-02 4.00e+02 5.45e-02 4.76e+00 pdb=" N PRO D 110 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO D 110 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO D 110 " -0.030 5.00e-02 4.00e+02 ... (remaining 4329 not shown) Histogram of nonbonded interaction distances: 2.60 - 3.06: 14168 3.06 - 3.52: 24920 3.52 - 3.98: 40665 3.98 - 4.44: 45182 4.44 - 4.90: 73206 Nonbonded interactions: 198141 Sorted by model distance: nonbonded pdb=" N THR A 256 " pdb=" O THR A 256 " model vdw 2.597 2.496 nonbonded pdb=" N THR D 256 " pdb=" O THR D 256 " model vdw 2.598 2.496 nonbonded pdb=" N SER D 424 " pdb=" O SER D 424 " model vdw 2.613 2.496 nonbonded pdb=" N SER A 424 " pdb=" O SER A 424 " model vdw 2.613 2.496 nonbonded pdb=" N ASP A 620 " pdb=" O ASP A 620 " model vdw 2.614 2.496 ... (remaining 198136 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: 0.05 Found NCS groups: ncs_group { reference = chain 'G' selection = chain 'I' } ncs_group { reference = chain 'H' selection = chain 'J' } ncs_group { reference = chain 'A' selection = chain 'D' } ncs_group { reference = chain 'B' selection = chain 'E' } ncs_group { reference = chain 'C' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.960 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: 0.040 Extract box with map and model: 0.320 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 25.360 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.330 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5167 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 : 0.003 0.045 24893 Z= 0.125 Angle : 0.623 8.944 33960 Z= 0.315 Chirality : 0.046 0.193 3846 Planarity : 0.005 0.064 4332 Dihedral : 13.303 88.555 8810 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.48 (0.14), residues: 3112 helix: -0.59 (0.22), residues: 454 sheet: 0.52 (0.17), residues: 962 loop : -0.70 (0.14), residues: 1696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 179 TYR 0.018 0.001 TYR C 139 PHE 0.016 0.001 PHE F 297 TRP 0.021 0.001 TRP F 206 HIS 0.006 0.001 HIS C 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (24880) covalent geometry : angle 0.62302 / 0.32 (33934) SS BOND : bond 0.00117 / 0.07 ( 13) SS BOND : angle 1.01440 / 0.79 ( 26) hydrogen bonds : bond 0.25001 / 16.31 ( 881) hydrogen bonds : angle 9.79448 / 6.89 ( 2472) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 629 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 629 time to evaluate : 0.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 182 MET cc_start: 0.0690 (mmt) cc_final: -0.1669 (mmt) REVERT: A 321 ASP cc_start: 0.7201 (m-30) cc_final: 0.6934 (m-30) REVERT: B 147 MET cc_start: 0.4891 (tpt) cc_final: 0.4491 (tpt) REVERT: B 327 LEU cc_start: 0.7601 (mt) cc_final: 0.6552 (mt) REVERT: B 328 ASN cc_start: 0.7315 (t0) cc_final: 0.7053 (t0) REVERT: B 344 TRP cc_start: 0.6789 (p90) cc_final: 0.6401 (p90) REVERT: B 373 TYR cc_start: 0.7233 (t80) cc_final: 0.6977 (t80) REVERT: C 71 LYS cc_start: 0.8337 (pttp) cc_final: 0.7989 (pttp) REVERT: C 161 SER cc_start: 0.8508 (p) cc_final: 0.7880 (p) REVERT: C 169 SER cc_start: 0.8490 (p) cc_final: 0.8287 (m) REVERT: C 296 HIS cc_start: 0.8593 (t70) cc_final: 0.8348 (t70) REVERT: C 335 GLU cc_start: 0.7484 (tm-30) cc_final: 0.7167 (tm-30) REVERT: C 336 LEU cc_start: 0.8275 (mm) cc_final: 0.7039 (mm) REVERT: C 383 LEU cc_start: 0.8182 (mt) cc_final: 0.7963 (mt) REVERT: C 411 SER cc_start: 0.7956 (m) cc_final: 0.7429 (p) REVERT: D 66 ASN cc_start: 0.8295 (m-40) cc_final: 0.7561 (m-40) REVERT: E 137 LEU cc_start: 0.7060 (mt) cc_final: 0.6381 (mp) REVERT: E 147 MET cc_start: 0.4630 (tpt) cc_final: 0.4395 (tpt) REVERT: F 181 HIS cc_start: 0.7256 (p-80) cc_final: 0.7044 (p-80) REVERT: F 246 LEU cc_start: 0.7479 (tp) cc_final: 0.7229 (tp) REVERT: F 345 LEU cc_start: 0.8778 (tp) cc_final: 0.8572 (tp) REVERT: F 375 ASP cc_start: 0.7395 (m-30) cc_final: 0.6850 (m-30) REVERT: F 411 SER cc_start: 0.7722 (m) cc_final: 0.7280 (p) outliers start: 0 outliers final: 0 residues processed: 629 average time/residue: 0.1513 time to fit residues: 153.1591 Evaluate side-chains 504 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 504 time to evaluate : 0.822 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [197, 215, 20, 132, 261, 248, 207, 155, 244, 183, 298] chunk 197 optimal weight: 4.9990 chunk 215 optimal weight: 20.0000 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 40.0000 chunk 261 optimal weight: 50.0000 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 20.0000 chunk 155 optimal weight: 5.9990 chunk 244 optimal weight: 10.0000 chunk 183 optimal weight: 10.0000 chunk 298 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 209 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 2 GLN I 209 GLN I 249 HIS I 256 HIS J 2 GLN A 68 GLN A 239 GLN A 273 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 551 ASN A 584 GLN B 63 ASN B 68 GLN B 274 GLN ** C 181 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 237 ASN C 266 ASN C 296 HIS C 325 GLN C 374 GLN D 68 GLN D 121 GLN D 239 GLN D 273 ASN D 408 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 551 ASN D 584 GLN E 63 ASN E 68 GLN E 274 GLN ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 266 ASN F 325 GLN F 374 GLN Total number of N/Q/H flips: 32 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.150784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.098219 restraints weight = 74529.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.101773 restraints weight = 37678.354| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.104087 restraints weight = 24776.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.105561 restraints weight = 18938.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.106342 restraints weight = 15951.259| |-----------------------------------------------------------------------------| r_work (final): 0.3687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7560 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 24893 Z= 0.283 Angle : 0.706 9.655 33960 Z= 0.363 Chirality : 0.045 0.163 3846 Planarity : 0.005 0.058 4332 Dihedral : 4.596 23.134 3340 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.26 % Allowed : 13.24 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.15 (0.15), residues: 3112 helix: 0.39 (0.25), residues: 450 sheet: 0.56 (0.17), residues: 948 loop : -0.59 (0.14), residues: 1714 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG J 81 TYR 0.019 0.002 TYR H 78 PHE 0.027 0.002 PHE F 404 TRP 0.028 0.002 TRP B 135 HIS 0.008 0.001 HIS D 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00591 / 0.28 (24880) covalent geometry : angle 0.70564 / 0.36 (33934) SS BOND : bond 0.00243 / 0.15 ( 13) SS BOND : angle 0.91235 / 0.63 ( 26) hydrogen bonds : bond 0.04465 / 2.95 ( 881) hydrogen bonds : angle 6.94628 / 4.87 ( 2472) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 567 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 507 time to evaluate : 0.928 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: G 118 MET cc_start: -0.0300 (ttt) cc_final: -0.0523 (tmt) REVERT: G 182 MET cc_start: 0.5990 (mmt) cc_final: 0.3484 (mmt) REVERT: A 134 MET cc_start: 0.9249 (mmm) cc_final: 0.8999 (mmm) REVERT: A 321 ASP cc_start: 0.8795 (m-30) cc_final: 0.8190 (m-30) REVERT: B 147 MET cc_start: 0.5258 (tpt) cc_final: 0.4878 (tpt) REVERT: B 158 LEU cc_start: 0.9384 (mt) cc_final: 0.9126 (mt) REVERT: B 325 GLN cc_start: 0.7789 (tm-30) cc_final: 0.7580 (tm-30) REVERT: C 72 GLN cc_start: 0.9117 (mm-40) cc_final: 0.8879 (mp10) REVERT: C 143 LYS cc_start: 0.9162 (tptt) cc_final: 0.8894 (tptt) REVERT: C 169 SER cc_start: 0.9134 (p) cc_final: 0.8917 (m) REVERT: C 223 ILE cc_start: 0.9293 (mp) cc_final: 0.9073 (mp) REVERT: C 335 GLU cc_start: 0.7823 (tm-30) cc_final: 0.7474 (tm-30) REVERT: C 336 LEU cc_start: 0.8338 (mm) cc_final: 0.7443 (mm) REVERT: C 375 ASP cc_start: 0.9180 (m-30) cc_final: 0.8542 (m-30) REVERT: C 380 LYS cc_start: 0.8886 (mtmm) cc_final: 0.8360 (mtmm) REVERT: C 383 LEU cc_start: 0.9128 (mt) cc_final: 0.8702 (mt) REVERT: C 411 SER cc_start: 0.8854 (m) cc_final: 0.8617 (p) REVERT: D 89 LEU cc_start: 0.9444 (mm) cc_final: 0.9220 (mm) REVERT: D 181 HIS cc_start: 0.8790 (p-80) cc_final: 0.8409 (p-80) REVERT: D 265 VAL cc_start: 0.9711 (m) cc_final: 0.9462 (t) REVERT: D 619 MET cc_start: 0.0577 (pmm) cc_final: 0.0224 (pmm) REVERT: E 158 LEU cc_start: 0.9358 (mt) cc_final: 0.9142 (mt) REVERT: E 217 ASP cc_start: 0.7887 (m-30) cc_final: 0.7676 (m-30) REVERT: E 325 GLN cc_start: 0.7731 (tm-30) cc_final: 0.7464 (tm-30) REVERT: E 327 LEU cc_start: 0.9276 (mt) cc_final: 0.9019 (mt) REVERT: F 106 ILE cc_start: 0.9357 (mm) cc_final: 0.8979 (tp) REVERT: F 132 TYR cc_start: 0.8815 (m-80) cc_final: 0.8397 (m-80) REVERT: F 143 LYS cc_start: 0.9223 (tptt) cc_final: 0.9023 (tptt) REVERT: F 181 HIS cc_start: 0.8887 (p-80) cc_final: 0.8038 (p90) REVERT: F 253 TRP cc_start: 0.8903 (m-90) cc_final: 0.8692 (m-90) REVERT: F 255 PHE cc_start: 0.8518 (m-10) cc_final: 0.8272 (m-10) REVERT: F 375 ASP cc_start: 0.9004 (m-30) cc_final: 0.8664 (m-30) REVERT: F 377 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.8871 (mm) REVERT: F 407 MET cc_start: 0.8669 (mmm) cc_final: 0.8443 (mmm) outliers start: 60 outliers final: 45 residues processed: 544 average time/residue: 0.1523 time to fit residues: 133.0039 Evaluate side-chains 515 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 469 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 249 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 366 SER Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 162 LEU Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 81 ILE Chi-restraints excluded: chain E residue 162 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 369 VAL Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 234 SER Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 414 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [271, 18, 86, 184, 283, 108, 248, 117, 78, 43, 176] chunk 271 optimal weight: 9.9990 chunk 18 optimal weight: 0.0050 chunk 86 optimal weight: 5.9990 chunk 184 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 chunk 108 optimal weight: 50.0000 chunk 248 optimal weight: 3.9990 chunk 117 optimal weight: 40.0000 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 40.0000 chunk 176 optimal weight: 30.0000 overall best weight: 3.4002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 181 HIS ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 274 GLN C 325 GLN D 374 GLN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 325 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.151642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.098755 restraints weight = 74158.829| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.102403 restraints weight = 37551.274| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.104738 restraints weight = 24728.212| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.106167 restraints weight = 18935.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.107157 restraints weight = 15988.434| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 24893 Z= 0.153 Angle : 0.619 13.571 33960 Z= 0.308 Chirality : 0.044 0.169 3846 Planarity : 0.004 0.052 4332 Dihedral : 4.479 23.324 3340 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.90 % Allowed : 15.61 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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 (0.15), residues: 3112 helix: 0.38 (0.25), residues: 448 sheet: 0.65 (0.17), residues: 936 loop : -0.61 (0.14), residues: 1728 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 62 TYR 0.022 0.001 TYR A 368 PHE 0.019 0.001 PHE F 404 TRP 0.022 0.001 TRP B 135 HIS 0.003 0.001 HIS C 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 (24880) covalent geometry : angle 0.61863 / 0.31 (33934) SS BOND : bond 0.00161 / 0.11 ( 13) SS BOND : angle 0.82458 / 0.60 ( 26) hydrogen bonds : bond 0.03626 / 2.40 ( 881) hydrogen bonds : angle 6.37649 / 4.47 ( 2472) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 508 time to evaluate : 0.976 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: G 182 MET cc_start: 0.6664 (mmt) cc_final: 0.4396 (mmt) REVERT: A 134 MET cc_start: 0.9173 (mmm) cc_final: 0.8851 (mmm) REVERT: A 136 LYS cc_start: 0.9461 (ptpt) cc_final: 0.9170 (ptpt) REVERT: A 189 ASN cc_start: 0.9531 (m-40) cc_final: 0.9245 (t0) REVERT: A 288 ILE cc_start: 0.9290 (mm) cc_final: 0.9007 (mm) REVERT: A 321 ASP cc_start: 0.8953 (m-30) cc_final: 0.8167 (m-30) REVERT: A 367 PHE cc_start: 0.9314 (m-10) cc_final: 0.9102 (m-10) REVERT: A 495 GLN cc_start: 0.9306 (mm-40) cc_final: 0.9057 (mp10) REVERT: A 640 MET cc_start: 0.3053 (mmm) cc_final: 0.2487 (mmm) REVERT: B 147 MET cc_start: 0.5050 (tpt) cc_final: 0.4747 (tpt) REVERT: B 213 ASP cc_start: 0.8873 (t70) cc_final: 0.8207 (t70) REVERT: B 232 MET cc_start: 0.9449 (mmm) cc_final: 0.9199 (mmm) REVERT: B 325 GLN cc_start: 0.7628 (tm-30) cc_final: 0.7411 (tm-30) REVERT: B 327 LEU cc_start: 0.9373 (mt) cc_final: 0.8459 (mp) REVERT: B 403 GLN cc_start: 0.9266 (tt0) cc_final: 0.9024 (tm-30) REVERT: C 60 ARG cc_start: 0.5645 (tpt170) cc_final: 0.4547 (mmp-170) REVERT: C 131 GLN cc_start: 0.8925 (tm-30) cc_final: 0.8434 (tm-30) REVERT: C 143 LYS cc_start: 0.9149 (tptt) cc_final: 0.8855 (tptt) REVERT: C 181 HIS cc_start: 0.8354 (p-80) cc_final: 0.8049 (p90) REVERT: C 203 ARG cc_start: 0.8394 (mmp-170) cc_final: 0.8146 (mmp-170) REVERT: C 224 GLU cc_start: 0.8084 (mp0) cc_final: 0.7631 (mp0) REVERT: C 335 GLU cc_start: 0.7917 (tm-30) cc_final: 0.7520 (tm-30) REVERT: C 336 LEU cc_start: 0.8388 (mm) cc_final: 0.7465 (mm) REVERT: C 375 ASP cc_start: 0.9197 (m-30) cc_final: 0.8525 (m-30) REVERT: C 380 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8364 (mtmm) REVERT: C 383 LEU cc_start: 0.9100 (mt) cc_final: 0.8672 (mt) REVERT: C 411 SER cc_start: 0.8873 (m) cc_final: 0.8548 (p) REVERT: D 134 MET cc_start: 0.9200 (mmm) cc_final: 0.8816 (mmm) REVERT: D 136 LYS cc_start: 0.9499 (ptpt) cc_final: 0.9204 (ptpt) REVERT: D 181 HIS cc_start: 0.8655 (p-80) cc_final: 0.8169 (p90) REVERT: D 189 ASN cc_start: 0.9501 (m-40) cc_final: 0.8635 (t0) REVERT: D 636 MET cc_start: 0.7698 (mmm) cc_final: 0.7496 (mmp) REVERT: D 640 MET cc_start: 0.3412 (mmm) cc_final: 0.2745 (mmm) REVERT: E 72 GLN cc_start: 0.8306 (mm-40) cc_final: 0.7719 (mm110) REVERT: E 89 LEU cc_start: 0.8806 (mm) cc_final: 0.8524 (mm) REVERT: F 68 GLN cc_start: 0.9020 (OUTLIER) cc_final: 0.8744 (mp10) REVERT: F 70 ARG cc_start: 0.9065 (mtp180) cc_final: 0.8848 (mtp85) REVERT: F 106 ILE cc_start: 0.9414 (mm) cc_final: 0.9133 (tp) REVERT: F 109 ASN cc_start: 0.9098 (t0) cc_final: 0.8751 (m-40) REVERT: F 132 TYR cc_start: 0.8722 (m-80) cc_final: 0.8158 (m-80) REVERT: F 143 LYS cc_start: 0.9167 (tptt) cc_final: 0.8944 (tptt) REVERT: F 181 HIS cc_start: 0.8849 (p-80) cc_final: 0.8018 (p90) REVERT: F 208 LEU cc_start: 0.8917 (mt) cc_final: 0.8554 (mt) REVERT: F 246 LEU cc_start: 0.9500 (tp) cc_final: 0.9145 (tp) REVERT: F 253 TRP cc_start: 0.8970 (m-90) cc_final: 0.8718 (m-90) REVERT: F 255 PHE cc_start: 0.8404 (m-10) cc_final: 0.8084 (m-10) REVERT: F 375 ASP cc_start: 0.8976 (m-30) cc_final: 0.8701 (m-30) REVERT: F 407 MET cc_start: 0.8776 (mmm) cc_final: 0.8472 (mmm) outliers start: 77 outliers final: 64 residues processed: 554 average time/residue: 0.1512 time to fit residues: 134.7352 Evaluate side-chains 546 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 481 time to evaluate : 0.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 384 CYS Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 91 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 384 CYS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 414 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [290, 252, 25, 165, 304, 229, 132, 218, 81, 82, 228] chunk 290 optimal weight: 30.0000 chunk 252 optimal weight: 50.0000 chunk 25 optimal weight: 40.0000 chunk 165 optimal weight: 30.0000 chunk 304 optimal weight: 0.9980 chunk 229 optimal weight: 30.0000 chunk 132 optimal weight: 50.0000 chunk 218 optimal weight: 4.9990 chunk 81 optimal weight: 10.0000 chunk 82 optimal weight: 6.9990 chunk 228 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 374 GLN A 408 ASN ** A 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.150915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.098049 restraints weight = 75024.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.101432 restraints weight = 37786.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.103605 restraints weight = 24875.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.104977 restraints weight = 19112.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.105822 restraints weight = 16193.025| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.3340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24893 Z= 0.242 Angle : 0.673 10.966 33960 Z= 0.337 Chirality : 0.045 0.210 3846 Planarity : 0.005 0.108 4332 Dihedral : 4.690 22.398 3340 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 16.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.74 % Allowed : 15.95 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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 (0.15), residues: 3112 helix: 0.35 (0.25), residues: 462 sheet: 0.62 (0.17), residues: 970 loop : -0.51 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 70 TYR 0.028 0.002 TYR D 368 PHE 0.015 0.002 PHE F 342 TRP 0.019 0.002 TRP B 135 HIS 0.006 0.001 HIS F 296 Details of bonding type rmsd/Z covalent geometry : bond 0.00513 / 0.24 (24880) covalent geometry : angle 0.67250 / 0.34 (33934) SS BOND : bond 0.00390 / 0.22 ( 13) SS BOND : angle 1.04960 / 0.74 ( 26) hydrogen bonds : bond 0.03434 / 2.27 ( 881) hydrogen bonds : angle 5.96262 / 4.19 ( 2472) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 625 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 499 time to evaluate : 0.879 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: G 182 MET cc_start: 0.6160 (mmt) cc_final: 0.3590 (mmt) REVERT: A 83 GLN cc_start: 0.9268 (tp40) cc_final: 0.9013 (tp-100) REVERT: A 134 MET cc_start: 0.9199 (mmm) cc_final: 0.8749 (mmm) REVERT: A 136 LYS cc_start: 0.9525 (ptpt) cc_final: 0.9322 (ptmt) REVERT: A 640 MET cc_start: 0.3292 (mmm) cc_final: 0.2646 (mmm) REVERT: B 147 MET cc_start: 0.5166 (tpt) cc_final: 0.4839 (tpt) REVERT: B 327 LEU cc_start: 0.9418 (mt) cc_final: 0.8320 (mp) REVERT: B 403 GLN cc_start: 0.9285 (tt0) cc_final: 0.8941 (tm-30) REVERT: C 60 ARG cc_start: 0.5590 (tpt170) cc_final: 0.4446 (mmp-170) REVERT: C 115 ASP cc_start: 0.8751 (p0) cc_final: 0.8471 (p0) REVERT: C 131 GLN cc_start: 0.8837 (tm-30) cc_final: 0.8343 (tm-30) REVERT: C 134 MET cc_start: 0.8603 (ppp) cc_final: 0.8259 (ppp) REVERT: C 143 LYS cc_start: 0.9104 (tptt) cc_final: 0.8868 (tptt) REVERT: C 181 HIS cc_start: 0.8799 (p-80) cc_final: 0.8003 (p90) REVERT: C 203 ARG cc_start: 0.8505 (mmp-170) cc_final: 0.8206 (mmp-170) REVERT: C 375 ASP cc_start: 0.9285 (m-30) cc_final: 0.8672 (m-30) REVERT: C 380 LYS cc_start: 0.8952 (mtmm) cc_final: 0.8490 (mtmm) REVERT: C 411 SER cc_start: 0.8894 (m) cc_final: 0.8639 (p) REVERT: D 136 LYS cc_start: 0.9525 (ptpt) cc_final: 0.9303 (ptmt) REVERT: D 189 ASN cc_start: 0.9617 (m-40) cc_final: 0.8909 (t0) REVERT: D 288 ILE cc_start: 0.9391 (mm) cc_final: 0.9130 (mm) REVERT: D 640 MET cc_start: 0.3655 (mmm) cc_final: 0.2914 (mmm) REVERT: E 89 LEU cc_start: 0.9044 (mm) cc_final: 0.8686 (mm) REVERT: F 68 GLN cc_start: 0.9064 (OUTLIER) cc_final: 0.8800 (mp10) REVERT: F 115 ASP cc_start: 0.8779 (p0) cc_final: 0.8334 (p0) REVERT: F 132 TYR cc_start: 0.8773 (m-80) cc_final: 0.8320 (m-80) REVERT: F 143 LYS cc_start: 0.9080 (tptt) cc_final: 0.8850 (tptt) REVERT: F 181 HIS cc_start: 0.8897 (p-80) cc_final: 0.7991 (p-80) REVERT: F 203 ARG cc_start: 0.8536 (mmp-170) cc_final: 0.8198 (mmp-170) REVERT: F 253 TRP cc_start: 0.8987 (m-90) cc_final: 0.8650 (m-90) REVERT: F 375 ASP cc_start: 0.9153 (m-30) cc_final: 0.8902 (m-30) outliers start: 126 outliers final: 92 residues processed: 575 average time/residue: 0.1559 time to fit residues: 143.8157 Evaluate side-chains 570 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 477 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 92 VAL Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 185 THR Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 142 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 204 ASP Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 114 LYS Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain F residue 142 VAL Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 153 VAL Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 414 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [269, 0, 143, 97, 26, 204, 12, 134, 103, 112, 306] chunk 269 optimal weight: 6.9990 chunk 0 optimal weight: 40.0000 chunk 143 optimal weight: 6.9990 chunk 97 optimal weight: 0.8980 chunk 26 optimal weight: 30.0000 chunk 204 optimal weight: 10.0000 chunk 12 optimal weight: 50.0000 chunk 134 optimal weight: 20.0000 chunk 103 optimal weight: 0.0010 chunk 112 optimal weight: 30.0000 chunk 306 optimal weight: 0.9980 overall best weight: 3.1790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 142 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 83 ASN ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN A 409 GLN A 414 HIS ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN D 409 GLN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.153616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.100921 restraints weight = 73898.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104491 restraints weight = 36150.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.106768 restraints weight = 23376.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.108215 restraints weight = 17749.232| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.109107 restraints weight = 14932.969| |-----------------------------------------------------------------------------| r_work (final): 0.3654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.3412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 24893 Z= 0.150 Angle : 0.640 12.219 33960 Z= 0.314 Chirality : 0.044 0.167 3846 Planarity : 0.004 0.046 4332 Dihedral : 4.622 22.461 3340 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.69 % Allowed : 18.36 % Favored : 77.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.03 (0.15), residues: 3112 helix: 0.39 (0.25), residues: 458 sheet: 0.63 (0.17), residues: 956 loop : -0.47 (0.15), residues: 1698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 70 TYR 0.019 0.002 TYR A 368 PHE 0.015 0.001 PHE D 556 TRP 0.027 0.002 TRP C 253 HIS 0.014 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.15 (24880) covalent geometry : angle 0.63905 / 0.31 (33934) SS BOND : bond 0.00191 / 0.11 ( 13) SS BOND : angle 1.15863 / 0.84 ( 26) hydrogen bonds : bond 0.03273 / 2.17 ( 881) hydrogen bonds : angle 5.81608 / 4.09 ( 2472) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 500 time to evaluate : 0.819 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: G 182 MET cc_start: 0.5998 (mmt) cc_final: 0.3352 (mmt) REVERT: J 81 ARG cc_start: 0.8635 (ptt90) cc_final: 0.8405 (ttp80) REVERT: A 83 GLN cc_start: 0.9332 (tp40) cc_final: 0.9043 (tp-100) REVERT: A 134 MET cc_start: 0.9150 (mmm) cc_final: 0.8669 (mmm) REVERT: A 136 LYS cc_start: 0.9542 (ptpt) cc_final: 0.9317 (ptpt) REVERT: A 189 ASN cc_start: 0.9482 (t0) cc_final: 0.9159 (t0) REVERT: A 288 ILE cc_start: 0.9338 (mm) cc_final: 0.9078 (mm) REVERT: A 495 GLN cc_start: 0.9446 (mm-40) cc_final: 0.9142 (mp10) REVERT: A 640 MET cc_start: 0.3251 (mmm) cc_final: 0.2688 (mmm) REVERT: B 72 GLN cc_start: 0.8245 (mm-40) cc_final: 0.7974 (mm-40) REVERT: B 114 LYS cc_start: 0.9218 (ptmm) cc_final: 0.8705 (pttp) REVERT: B 140 LEU cc_start: 0.9721 (tp) cc_final: 0.9468 (tp) REVERT: B 147 MET cc_start: 0.5147 (tpt) cc_final: 0.4817 (tpt) REVERT: B 194 LEU cc_start: 0.9400 (OUTLIER) cc_final: 0.9164 (mm) REVERT: B 213 ASP cc_start: 0.8979 (t70) cc_final: 0.8251 (t70) REVERT: B 325 GLN cc_start: 0.7898 (tm-30) cc_final: 0.7453 (tm-30) REVERT: B 380 LYS cc_start: 0.9540 (mmmt) cc_final: 0.9244 (mmmm) REVERT: B 403 GLN cc_start: 0.9287 (tt0) cc_final: 0.8996 (tm-30) REVERT: C 115 ASP cc_start: 0.8815 (p0) cc_final: 0.8488 (p0) REVERT: C 131 GLN cc_start: 0.8936 (tm-30) cc_final: 0.8421 (tm-30) REVERT: C 143 LYS cc_start: 0.9164 (tptt) cc_final: 0.8917 (tptt) REVERT: C 181 HIS cc_start: 0.8817 (p-80) cc_final: 0.8001 (p90) REVERT: C 203 ARG cc_start: 0.8532 (mmp-170) cc_final: 0.8195 (mmp-170) REVERT: C 375 ASP cc_start: 0.9259 (m-30) cc_final: 0.8641 (m-30) REVERT: C 380 LYS cc_start: 0.9007 (mtmm) cc_final: 0.8558 (mtmm) REVERT: C 411 SER cc_start: 0.8822 (m) cc_final: 0.8487 (p) REVERT: D 66 ASN cc_start: 0.9512 (m-40) cc_final: 0.9126 (m110) REVERT: D 134 MET cc_start: 0.9165 (mmm) cc_final: 0.8344 (mmm) REVERT: D 136 LYS cc_start: 0.9551 (ptpt) cc_final: 0.9335 (ptmt) REVERT: D 181 HIS cc_start: 0.8789 (p-80) cc_final: 0.8159 (p-80) REVERT: D 189 ASN cc_start: 0.9588 (m-40) cc_final: 0.8874 (t0) REVERT: D 256 THR cc_start: 0.9248 (m) cc_final: 0.9015 (p) REVERT: D 288 ILE cc_start: 0.9364 (mm) cc_final: 0.9110 (mm) REVERT: D 640 MET cc_start: 0.3726 (mmm) cc_final: 0.2964 (mmm) REVERT: E 89 LEU cc_start: 0.8889 (mm) cc_final: 0.8491 (mm) REVERT: E 213 ASP cc_start: 0.9100 (t70) cc_final: 0.8415 (t70) REVERT: F 68 GLN cc_start: 0.9047 (OUTLIER) cc_final: 0.8747 (mp10) REVERT: F 115 ASP cc_start: 0.8819 (p0) cc_final: 0.8472 (p0) REVERT: F 132 TYR cc_start: 0.8617 (m-80) cc_final: 0.8234 (m-80) REVERT: F 143 LYS cc_start: 0.9125 (tptt) cc_final: 0.8874 (tptt) REVERT: F 181 HIS cc_start: 0.8852 (p-80) cc_final: 0.7825 (p-80) REVERT: F 203 ARG cc_start: 0.8524 (mmp-170) cc_final: 0.8169 (mmp-170) REVERT: F 246 LEU cc_start: 0.9500 (tp) cc_final: 0.9175 (tp) REVERT: F 253 TRP cc_start: 0.8997 (m-90) cc_final: 0.8758 (m-90) REVERT: F 347 LYS cc_start: 0.9583 (tptm) cc_final: 0.9309 (tptm) REVERT: F 375 ASP cc_start: 0.9110 (m-30) cc_final: 0.8844 (m-30) REVERT: F 377 LEU cc_start: 0.9262 (OUTLIER) cc_final: 0.8822 (mm) REVERT: F 407 MET cc_start: 0.8717 (mmm) cc_final: 0.8488 (mpp) outliers start: 98 outliers final: 75 residues processed: 564 average time/residue: 0.1513 time to fit residues: 136.6717 Evaluate side-chains 562 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 484 time to evaluate : 0.917 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 322 THR Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 122 PHE Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 414 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [143, 156, 128, 59, 80, 246, 11, 218, 85, 22, 188] chunk 143 optimal weight: 20.0000 chunk 156 optimal weight: 20.0000 chunk 128 optimal weight: 0.9980 chunk 59 optimal weight: 10.0000 chunk 80 optimal weight: 6.9990 chunk 246 optimal weight: 9.9990 chunk 11 optimal weight: 50.0000 chunk 218 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 22 optimal weight: 50.0000 chunk 188 optimal weight: 20.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.152002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.099400 restraints weight = 74946.005| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.102741 restraints weight = 38222.393| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.104932 restraints weight = 25269.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.106334 restraints weight = 19407.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.107201 restraints weight = 16397.942| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 24893 Z= 0.256 Angle : 0.692 11.275 33960 Z= 0.346 Chirality : 0.044 0.156 3846 Planarity : 0.005 0.054 4332 Dihedral : 4.782 24.295 3340 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 18.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 4.59 % Allowed : 18.10 % Favored : 77.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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 (0.15), residues: 3112 helix: 0.24 (0.24), residues: 478 sheet: 0.46 (0.16), residues: 966 loop : -0.53 (0.15), residues: 1668 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 70 TYR 0.021 0.002 TYR D 368 PHE 0.016 0.002 PHE F 342 TRP 0.040 0.002 TRP B 344 HIS 0.011 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.26 (24880) covalent geometry : angle 0.69170 / 0.35 (33934) SS BOND : bond 0.00211 / 0.12 ( 13) SS BOND : angle 1.22819 / 0.88 ( 26) hydrogen bonds : bond 0.03320 / 2.20 ( 881) hydrogen bonds : angle 5.86576 / 4.12 ( 2472) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 478 time to evaluate : 0.944 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: G 182 MET cc_start: 0.6040 (mmt) cc_final: 0.3275 (mmt) REVERT: A 83 GLN cc_start: 0.9363 (tp40) cc_final: 0.9034 (tp-100) REVERT: A 84 ARG cc_start: 0.8648 (mtm180) cc_final: 0.8399 (mtp180) REVERT: A 134 MET cc_start: 0.9196 (mmm) cc_final: 0.8770 (mmm) REVERT: A 136 LYS cc_start: 0.9538 (ptpt) cc_final: 0.9279 (ptpt) REVERT: A 189 ASN cc_start: 0.9505 (t0) cc_final: 0.9210 (t0) REVERT: A 193 LYS cc_start: 0.8907 (tptt) cc_final: 0.8696 (tptt) REVERT: A 195 LYS cc_start: 0.8943 (tptp) cc_final: 0.8111 (tptt) REVERT: A 232 MET cc_start: 0.7602 (tpp) cc_final: 0.7379 (tpp) REVERT: A 640 MET cc_start: 0.3918 (mmm) cc_final: 0.3313 (mmm) REVERT: B 114 LYS cc_start: 0.9328 (ptmm) cc_final: 0.8898 (pttp) REVERT: B 140 LEU cc_start: 0.9734 (tp) cc_final: 0.9498 (tp) REVERT: B 147 MET cc_start: 0.4965 (tpt) cc_final: 0.4629 (tpt) REVERT: B 194 LEU cc_start: 0.9389 (OUTLIER) cc_final: 0.9112 (mm) REVERT: B 213 ASP cc_start: 0.9091 (t70) cc_final: 0.8440 (t70) REVERT: B 218 THR cc_start: 0.9092 (t) cc_final: 0.8886 (t) REVERT: B 321 ASP cc_start: 0.9382 (t0) cc_final: 0.9173 (t0) REVERT: B 325 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7678 (tm-30) REVERT: B 403 GLN cc_start: 0.9327 (tt0) cc_final: 0.8945 (tm-30) REVERT: C 106 ILE cc_start: 0.9504 (OUTLIER) cc_final: 0.9131 (pt) REVERT: C 115 ASP cc_start: 0.8801 (p0) cc_final: 0.8512 (p0) REVERT: C 131 GLN cc_start: 0.8990 (tm-30) cc_final: 0.8468 (tm-30) REVERT: C 143 LYS cc_start: 0.9109 (tptt) cc_final: 0.8853 (tptt) REVERT: C 181 HIS cc_start: 0.8800 (p-80) cc_final: 0.7817 (p90) REVERT: C 224 GLU cc_start: 0.7882 (mp0) cc_final: 0.7477 (mp0) REVERT: C 253 TRP cc_start: 0.8971 (m-90) cc_final: 0.8350 (m-90) REVERT: C 375 ASP cc_start: 0.9324 (m-30) cc_final: 0.8762 (m-30) REVERT: C 380 LYS cc_start: 0.9031 (mtmm) cc_final: 0.8517 (mtmm) REVERT: C 411 SER cc_start: 0.8968 (m) cc_final: 0.8702 (p) REVERT: D 134 MET cc_start: 0.9203 (mmm) cc_final: 0.8760 (mmm) REVERT: D 136 LYS cc_start: 0.9573 (ptpt) cc_final: 0.9292 (ptpt) REVERT: D 189 ASN cc_start: 0.9578 (m-40) cc_final: 0.8754 (t0) REVERT: D 640 MET cc_start: 0.3918 (mmm) cc_final: 0.3197 (mmm) REVERT: E 89 LEU cc_start: 0.8982 (mm) cc_final: 0.8573 (mm) REVERT: E 213 ASP cc_start: 0.9118 (t70) cc_final: 0.8537 (t70) REVERT: E 218 THR cc_start: 0.9111 (t) cc_final: 0.8886 (t) REVERT: E 232 MET cc_start: 0.9486 (mmm) cc_final: 0.9166 (mmp) REVERT: F 68 GLN cc_start: 0.9071 (OUTLIER) cc_final: 0.8813 (mp10) REVERT: F 106 ILE cc_start: 0.9619 (mm) cc_final: 0.9207 (tt) REVERT: F 115 ASP cc_start: 0.8783 (p0) cc_final: 0.8435 (p0) REVERT: F 132 TYR cc_start: 0.8697 (m-80) cc_final: 0.8261 (m-80) REVERT: F 143 LYS cc_start: 0.9134 (tptt) cc_final: 0.8876 (tptt) REVERT: F 253 TRP cc_start: 0.9016 (m-90) cc_final: 0.8539 (m-90) REVERT: F 347 LYS cc_start: 0.9557 (tptm) cc_final: 0.9268 (tptm) REVERT: F 375 ASP cc_start: 0.9159 (m-30) cc_final: 0.8898 (m-30) REVERT: F 377 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8763 (mm) outliers start: 122 outliers final: 100 residues processed: 550 average time/residue: 0.1521 time to fit residues: 134.0265 Evaluate side-chains 565 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 461 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 121 ASP Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 204 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 89 LEU Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 204 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 375 ASP Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 106 ILE Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 109 ASN Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 380 LYS Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 414 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [247, 257, 63, 56, 171, 290, 97, 288, 213, 272, 90] chunk 247 optimal weight: 30.0000 chunk 257 optimal weight: 8.9990 chunk 63 optimal weight: 50.0000 chunk 56 optimal weight: 50.0000 chunk 171 optimal weight: 10.0000 chunk 290 optimal weight: 5.9990 chunk 97 optimal weight: 0.9990 chunk 288 optimal weight: 0.7980 chunk 213 optimal weight: 8.9990 chunk 272 optimal weight: 4.9990 chunk 90 optimal weight: 8.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 124 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.158159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3583 r_free = 0.3583 target = 0.103240 restraints weight = 72902.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.106598 restraints weight = 37912.929| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3660 r_free = 0.3660 target = 0.108705 restraints weight = 25543.112| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.109997 restraints weight = 19907.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.110910 restraints weight = 17034.103| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 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 0.041 24893 Z= 0.179 Angle : 0.659 13.973 33960 Z= 0.327 Chirality : 0.044 0.172 3846 Planarity : 0.004 0.054 4332 Dihedral : 4.703 24.156 3340 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 4.36 % Allowed : 18.77 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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 (0.15), residues: 3112 helix: 0.35 (0.25), residues: 458 sheet: 0.42 (0.16), residues: 968 loop : -0.46 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 299 TYR 0.019 0.002 TYR D 368 PHE 0.017 0.002 PHE A 367 TRP 0.028 0.002 TRP B 344 HIS 0.006 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00392 / 0.18 (24880) covalent geometry : angle 0.65865 / 0.33 (33934) SS BOND : bond 0.00390 / 0.20 ( 13) SS BOND : angle 1.26912 / 0.90 ( 26) hydrogen bonds : bond 0.03158 / 2.09 ( 881) hydrogen bonds : angle 5.73919 / 4.03 ( 2472) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 116 poor density : 489 time to evaluate : 0.842 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: G 182 MET cc_start: 0.7446 (mmt) cc_final: 0.5503 (mmt) REVERT: A 83 GLN cc_start: 0.9451 (tp40) cc_final: 0.9156 (tp-100) REVERT: A 84 ARG cc_start: 0.8686 (mtm180) cc_final: 0.8455 (mtp180) REVERT: A 134 MET cc_start: 0.9209 (mmm) cc_final: 0.8831 (mmm) REVERT: A 136 LYS cc_start: 0.9530 (ptpt) cc_final: 0.9184 (ptpt) REVERT: A 189 ASN cc_start: 0.9506 (t0) cc_final: 0.9210 (t0) REVERT: A 195 LYS cc_start: 0.8942 (tptp) cc_final: 0.8125 (tptt) REVERT: A 203 ARG cc_start: 0.8406 (mmp-170) cc_final: 0.8083 (mmp-170) REVERT: A 232 MET cc_start: 0.7707 (tpp) cc_final: 0.7474 (tpp) REVERT: A 288 ILE cc_start: 0.9344 (mm) cc_final: 0.9105 (mm) REVERT: A 347 LYS cc_start: 0.9012 (mttp) cc_final: 0.8802 (mttp) REVERT: A 378 SER cc_start: 0.9480 (m) cc_final: 0.9193 (p) REVERT: A 495 GLN cc_start: 0.9562 (mm-40) cc_final: 0.9251 (mm110) REVERT: B 114 LYS cc_start: 0.9296 (ptmm) cc_final: 0.8801 (pttp) REVERT: B 140 LEU cc_start: 0.9757 (tp) cc_final: 0.9525 (tp) REVERT: B 147 MET cc_start: 0.4975 (tpt) cc_final: 0.4564 (tpt) REVERT: B 194 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9038 (mm) REVERT: B 213 ASP cc_start: 0.9111 (t70) cc_final: 0.8425 (t70) REVERT: B 325 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7591 (tm-30) REVERT: B 347 LYS cc_start: 0.9393 (mppt) cc_final: 0.9034 (mmtt) REVERT: B 403 GLN cc_start: 0.9317 (tt0) cc_final: 0.8952 (tm-30) REVERT: C 115 ASP cc_start: 0.8872 (p0) cc_final: 0.8558 (p0) REVERT: C 131 GLN cc_start: 0.9018 (tm-30) cc_final: 0.8490 (tm-30) REVERT: C 143 LYS cc_start: 0.9153 (tptt) cc_final: 0.8881 (tptt) REVERT: C 181 HIS cc_start: 0.8803 (p-80) cc_final: 0.7856 (p90) REVERT: C 224 GLU cc_start: 0.7945 (mp0) cc_final: 0.7493 (mp0) REVERT: C 253 TRP cc_start: 0.8868 (m-90) cc_final: 0.8378 (m-90) REVERT: C 375 ASP cc_start: 0.9292 (m-30) cc_final: 0.8568 (m-30) REVERT: C 380 LYS cc_start: 0.9054 (mtmm) cc_final: 0.8452 (mtmm) REVERT: C 411 SER cc_start: 0.8942 (m) cc_final: 0.8670 (p) REVERT: D 83 GLN cc_start: 0.9479 (tp40) cc_final: 0.9241 (tp-100) REVERT: D 134 MET cc_start: 0.9190 (mmm) cc_final: 0.8674 (mmm) REVERT: D 136 LYS cc_start: 0.9571 (ptpt) cc_final: 0.9250 (ptpt) REVERT: D 189 ASN cc_start: 0.9591 (m-40) cc_final: 0.8807 (t0) REVERT: D 210 ASN cc_start: 0.9298 (t0) cc_final: 0.9061 (t0) REVERT: D 232 MET cc_start: 0.7919 (tpp) cc_final: 0.7661 (tpp) REVERT: D 256 THR cc_start: 0.9269 (m) cc_final: 0.9056 (p) REVERT: D 288 ILE cc_start: 0.9362 (mm) cc_final: 0.9115 (mm) REVERT: D 407 MET cc_start: 0.8933 (ptt) cc_final: 0.8585 (ptt) REVERT: D 640 MET cc_start: 0.3904 (mmm) cc_final: 0.3150 (mmm) REVERT: E 89 LEU cc_start: 0.8948 (mm) cc_final: 0.8523 (mm) REVERT: E 213 ASP cc_start: 0.9135 (t70) cc_final: 0.8533 (t70) REVERT: E 218 THR cc_start: 0.9097 (t) cc_final: 0.8846 (t) REVERT: F 68 GLN cc_start: 0.9048 (OUTLIER) cc_final: 0.8769 (mp10) REVERT: F 89 LEU cc_start: 0.9449 (tp) cc_final: 0.9034 (tp) REVERT: F 106 ILE cc_start: 0.9612 (mm) cc_final: 0.9196 (tt) REVERT: F 115 ASP cc_start: 0.8778 (p0) cc_final: 0.8381 (p0) REVERT: F 132 TYR cc_start: 0.8608 (m-80) cc_final: 0.8221 (m-80) REVERT: F 143 LYS cc_start: 0.9150 (tptt) cc_final: 0.8895 (tptt) REVERT: F 181 HIS cc_start: 0.9147 (p-80) cc_final: 0.8439 (p-80) REVERT: F 253 TRP cc_start: 0.9009 (m-90) cc_final: 0.8516 (m-90) REVERT: F 255 PHE cc_start: 0.8561 (m-10) cc_final: 0.8152 (m-10) REVERT: F 347 LYS cc_start: 0.9548 (tptm) cc_final: 0.9330 (tptm) REVERT: F 375 ASP cc_start: 0.9181 (m-30) cc_final: 0.8923 (m-30) REVERT: F 377 LEU cc_start: 0.9209 (OUTLIER) cc_final: 0.8717 (mm) outliers start: 116 outliers final: 96 residues processed: 561 average time/residue: 0.1507 time to fit residues: 135.8881 Evaluate side-chains 583 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 484 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 111 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 355 LEU Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 219 LEU Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 377 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 182 LEU Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 275 VAL Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 322 THR Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 380 LYS Chi-restraints excluded: chain F residue 400 THR Chi-restraints excluded: chain F residue 414 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [148, 52, 18, 121, 222, 198, 174, 87, 31, 181, 128] chunk 148 optimal weight: 20.0000 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 30.0000 chunk 121 optimal weight: 30.0000 chunk 222 optimal weight: 6.9990 chunk 198 optimal weight: 7.9990 chunk 174 optimal weight: 9.9990 chunk 87 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 chunk 181 optimal weight: 6.9990 chunk 128 optimal weight: 0.9980 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... G 124 GLN ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN C 109 ASN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 226 HIS ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.152593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.097639 restraints weight = 71415.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.100818 restraints weight = 37089.272| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3652 r_free = 0.3652 target = 0.102870 restraints weight = 24965.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.104094 restraints weight = 19405.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3684 r_free = 0.3684 target = 0.104925 restraints weight = 16638.616| |-----------------------------------------------------------------------------| r_work (final): 0.3572 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7645 moved from start: 0.4165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 24893 Z= 0.204 Angle : 0.687 13.727 33960 Z= 0.340 Chirality : 0.044 0.262 3846 Planarity : 0.004 0.054 4332 Dihedral : 4.776 26.634 3340 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 17.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 4.29 % Allowed : 19.38 % Favored : 76.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.20 (0.15), residues: 3112 helix: 0.26 (0.24), residues: 474 sheet: 0.39 (0.16), residues: 958 loop : -0.50 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG C 299 TYR 0.021 0.002 TYR A 373 PHE 0.018 0.002 PHE A 367 TRP 0.025 0.002 TRP B 344 HIS 0.007 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00442 / 0.20 (24880) covalent geometry : angle 0.68687 / 0.34 (33934) SS BOND : bond 0.00249 / 0.12 ( 13) SS BOND : angle 1.25021 / 0.89 ( 26) hydrogen bonds : bond 0.03163 / 2.10 ( 881) hydrogen bonds : angle 5.69508 / 4.00 ( 2472) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 491 time to evaluate : 0.984 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: G 121 ASP cc_start: 0.8835 (m-30) cc_final: 0.8521 (p0) REVERT: G 182 MET cc_start: 0.7362 (mmt) cc_final: 0.5297 (mmt) REVERT: A 83 GLN cc_start: 0.9442 (tp40) cc_final: 0.9050 (tp-100) REVERT: A 84 ARG cc_start: 0.8695 (mtm180) cc_final: 0.8425 (mtp180) REVERT: A 134 MET cc_start: 0.9184 (mmm) cc_final: 0.8781 (mmm) REVERT: A 136 LYS cc_start: 0.9512 (ptpt) cc_final: 0.9217 (ptpt) REVERT: A 189 ASN cc_start: 0.9482 (t0) cc_final: 0.9180 (t0) REVERT: A 195 LYS cc_start: 0.8882 (tptp) cc_final: 0.8064 (tptt) REVERT: A 232 MET cc_start: 0.7782 (tpp) cc_final: 0.7503 (tpp) REVERT: A 288 ILE cc_start: 0.9351 (mm) cc_final: 0.9113 (mm) REVERT: A 378 SER cc_start: 0.9495 (m) cc_final: 0.9204 (p) REVERT: A 495 GLN cc_start: 0.9560 (mm-40) cc_final: 0.9287 (mm110) REVERT: B 140 LEU cc_start: 0.9749 (tp) cc_final: 0.9512 (tp) REVERT: B 147 MET cc_start: 0.5068 (tpt) cc_final: 0.4617 (tpt) REVERT: B 194 LEU cc_start: 0.9385 (OUTLIER) cc_final: 0.9083 (mm) REVERT: B 213 ASP cc_start: 0.9130 (t70) cc_final: 0.8451 (t70) REVERT: B 325 GLN cc_start: 0.7964 (tm-30) cc_final: 0.7659 (tm-30) REVERT: B 347 LYS cc_start: 0.9409 (mppt) cc_final: 0.8974 (mmtt) REVERT: B 403 GLN cc_start: 0.9336 (tt0) cc_final: 0.8932 (tm-30) REVERT: C 115 ASP cc_start: 0.8877 (p0) cc_final: 0.8561 (p0) REVERT: C 131 GLN cc_start: 0.9031 (tm-30) cc_final: 0.8501 (tm-30) REVERT: C 143 LYS cc_start: 0.9142 (tptt) cc_final: 0.8868 (tptt) REVERT: C 181 HIS cc_start: 0.8828 (p-80) cc_final: 0.7861 (p90) REVERT: C 224 GLU cc_start: 0.7944 (mp0) cc_final: 0.7515 (mp0) REVERT: C 253 TRP cc_start: 0.8937 (m-90) cc_final: 0.8592 (m-90) REVERT: C 375 ASP cc_start: 0.9294 (m-30) cc_final: 0.8575 (m-30) REVERT: C 380 LYS cc_start: 0.9065 (mtmm) cc_final: 0.8469 (mtmm) REVERT: C 411 SER cc_start: 0.8915 (m) cc_final: 0.8627 (p) REVERT: D 83 GLN cc_start: 0.9467 (tp40) cc_final: 0.9233 (tp-100) REVERT: D 134 MET cc_start: 0.9181 (mmm) cc_final: 0.8742 (mmm) REVERT: D 136 LYS cc_start: 0.9554 (ptpt) cc_final: 0.9285 (ptpt) REVERT: D 189 ASN cc_start: 0.9583 (m-40) cc_final: 0.8814 (t0) REVERT: D 256 THR cc_start: 0.9275 (m) cc_final: 0.9062 (p) REVERT: D 288 ILE cc_start: 0.9369 (mm) cc_final: 0.9122 (mm) REVERT: D 375 ASP cc_start: 0.8994 (m-30) cc_final: 0.8770 (t0) REVERT: D 378 SER cc_start: 0.9468 (m) cc_final: 0.9153 (p) REVERT: D 640 MET cc_start: 0.3889 (mmm) cc_final: 0.3102 (mmm) REVERT: E 89 LEU cc_start: 0.8997 (mm) cc_final: 0.8575 (mm) REVERT: E 213 ASP cc_start: 0.9178 (t70) cc_final: 0.8580 (t70) REVERT: F 68 GLN cc_start: 0.9057 (OUTLIER) cc_final: 0.8787 (mp10) REVERT: F 89 LEU cc_start: 0.9444 (tp) cc_final: 0.9002 (tp) REVERT: F 106 ILE cc_start: 0.9627 (mm) cc_final: 0.9227 (tt) REVERT: F 115 ASP cc_start: 0.8776 (p0) cc_final: 0.8458 (p0) REVERT: F 132 TYR cc_start: 0.8606 (m-80) cc_final: 0.8212 (m-80) REVERT: F 143 LYS cc_start: 0.9149 (tptt) cc_final: 0.8862 (tptt) REVERT: F 181 HIS cc_start: 0.9122 (p-80) cc_final: 0.8411 (p-80) REVERT: F 246 LEU cc_start: 0.9481 (tp) cc_final: 0.9180 (tp) REVERT: F 253 TRP cc_start: 0.9061 (m-90) cc_final: 0.8701 (m-90) REVERT: F 375 ASP cc_start: 0.9201 (m-30) cc_final: 0.8951 (m-30) REVERT: F 377 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8698 (mm) outliers start: 114 outliers final: 95 residues processed: 560 average time/residue: 0.1502 time to fit residues: 135.4986 Evaluate side-chains 575 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 477 time to evaluate : 0.827 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 228 LEU Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 319 THR Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 113 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 355 LEU Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 414 HIS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 204 ASP Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 337 VAL Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 380 LYS Chi-restraints excluded: chain F residue 400 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [111, 164, 229, 278, 282, 193, 10, 72, 298, 26, 62] chunk 111 optimal weight: 0.3980 chunk 164 optimal weight: 8.9990 chunk 229 optimal weight: 50.0000 chunk 278 optimal weight: 20.0000 chunk 282 optimal weight: 10.0000 chunk 193 optimal weight: 0.0980 chunk 10 optimal weight: 5.9990 chunk 72 optimal weight: 7.9990 chunk 298 optimal weight: 6.9990 chunk 26 optimal weight: 40.0000 chunk 62 optimal weight: 40.0000 overall best weight: 4.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 325 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 296 HIS ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.151770 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.097305 restraints weight = 71953.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.100605 restraints weight = 36975.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.102708 restraints weight = 24618.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.104004 restraints weight = 19037.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.104722 restraints weight = 16206.326| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7633 moved from start: 0.4261 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 24893 Z= 0.178 Angle : 0.691 14.440 33960 Z= 0.337 Chirality : 0.045 0.203 3846 Planarity : 0.004 0.054 4332 Dihedral : 4.787 25.279 3340 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 16.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 3.91 % Allowed : 19.98 % Favored : 76.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.21 (0.15), residues: 3112 helix: 0.23 (0.24), residues: 474 sheet: 0.39 (0.17), residues: 952 loop : -0.50 (0.15), residues: 1686 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 299 TYR 0.019 0.001 TYR D 368 PHE 0.020 0.001 PHE C 255 TRP 0.025 0.002 TRP E 253 HIS 0.005 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.18 (24880) covalent geometry : angle 0.69068 / 0.34 (33934) SS BOND : bond 0.00316 / 0.14 ( 13) SS BOND : angle 1.26759 / 0.90 ( 26) hydrogen bonds : bond 0.03095 / 2.06 ( 881) hydrogen bonds : angle 5.64284 / 3.95 ( 2472) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 496 time to evaluate : 0.973 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: G 121 ASP cc_start: 0.8886 (m-30) cc_final: 0.8582 (p0) REVERT: G 182 MET cc_start: 0.7188 (mmt) cc_final: 0.5007 (mmt) REVERT: A 83 GLN cc_start: 0.9451 (tp40) cc_final: 0.9025 (tp-100) REVERT: A 84 ARG cc_start: 0.8689 (mtm180) cc_final: 0.8417 (mtp180) REVERT: A 134 MET cc_start: 0.9165 (mmm) cc_final: 0.8769 (mmm) REVERT: A 136 LYS cc_start: 0.9506 (ptpt) cc_final: 0.9259 (ptmt) REVERT: A 189 ASN cc_start: 0.9464 (t0) cc_final: 0.8762 (t0) REVERT: A 195 LYS cc_start: 0.8799 (tptp) cc_final: 0.8143 (tptt) REVERT: A 232 MET cc_start: 0.7738 (tpp) cc_final: 0.7450 (tpp) REVERT: A 288 ILE cc_start: 0.9365 (mm) cc_final: 0.9139 (mm) REVERT: A 378 SER cc_start: 0.9383 (m) cc_final: 0.9116 (p) REVERT: A 495 GLN cc_start: 0.9578 (mm-40) cc_final: 0.9298 (mm110) REVERT: A 640 MET cc_start: 0.4487 (mmm) cc_final: 0.3882 (mmm) REVERT: B 140 LEU cc_start: 0.9751 (tp) cc_final: 0.9519 (tp) REVERT: B 147 MET cc_start: 0.5030 (tpt) cc_final: 0.4578 (tpt) REVERT: B 194 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9046 (mm) REVERT: B 213 ASP cc_start: 0.9134 (t70) cc_final: 0.8490 (t70) REVERT: B 218 THR cc_start: 0.9089 (t) cc_final: 0.8856 (t) REVERT: B 325 GLN cc_start: 0.7919 (tm-30) cc_final: 0.7504 (tm-30) REVERT: B 327 LEU cc_start: 0.9466 (mp) cc_final: 0.8268 (mp) REVERT: B 347 LYS cc_start: 0.9293 (mppt) cc_final: 0.8933 (mmtt) REVERT: B 403 GLN cc_start: 0.9362 (tt0) cc_final: 0.8819 (tm-30) REVERT: C 115 ASP cc_start: 0.8937 (p0) cc_final: 0.8650 (p0) REVERT: C 131 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8495 (tm-30) REVERT: C 143 LYS cc_start: 0.9125 (tptt) cc_final: 0.8866 (tptt) REVERT: C 181 HIS cc_start: 0.8793 (p-80) cc_final: 0.7839 (p90) REVERT: C 224 GLU cc_start: 0.7958 (mp0) cc_final: 0.7552 (mp0) REVERT: C 253 TRP cc_start: 0.8904 (m-90) cc_final: 0.8522 (m-90) REVERT: C 375 ASP cc_start: 0.9287 (m-30) cc_final: 0.8485 (m-30) REVERT: C 380 LYS cc_start: 0.9072 (mtmm) cc_final: 0.8431 (mtmm) REVERT: C 411 SER cc_start: 0.8921 (m) cc_final: 0.8597 (p) REVERT: D 115 ASP cc_start: 0.9052 (OUTLIER) cc_final: 0.8848 (t70) REVERT: D 134 MET cc_start: 0.9169 (mmm) cc_final: 0.8749 (mmm) REVERT: D 136 LYS cc_start: 0.9560 (ptpt) cc_final: 0.9288 (ptpt) REVERT: D 189 ASN cc_start: 0.9576 (m-40) cc_final: 0.8839 (t0) REVERT: D 210 ASN cc_start: 0.9327 (t0) cc_final: 0.9082 (t0) REVERT: D 232 MET cc_start: 0.7736 (tpp) cc_final: 0.7378 (tpp) REVERT: D 256 THR cc_start: 0.9265 (m) cc_final: 0.9053 (p) REVERT: D 288 ILE cc_start: 0.9365 (mm) cc_final: 0.9119 (mm) REVERT: D 378 SER cc_start: 0.9454 (m) cc_final: 0.9151 (p) REVERT: D 640 MET cc_start: 0.3984 (mmm) cc_final: 0.3228 (mmm) REVERT: E 89 LEU cc_start: 0.8961 (mm) cc_final: 0.8537 (mm) REVERT: E 213 ASP cc_start: 0.9143 (t70) cc_final: 0.8448 (t70) REVERT: E 232 MET cc_start: 0.9413 (mmm) cc_final: 0.9034 (mmp) REVERT: E 235 TYR cc_start: 0.8019 (OUTLIER) cc_final: 0.7640 (m-10) REVERT: F 68 GLN cc_start: 0.9051 (OUTLIER) cc_final: 0.8797 (mp10) REVERT: F 106 ILE cc_start: 0.9624 (mm) cc_final: 0.9242 (tt) REVERT: F 115 ASP cc_start: 0.8811 (p0) cc_final: 0.8452 (p0) REVERT: F 132 TYR cc_start: 0.8589 (m-80) cc_final: 0.8195 (m-80) REVERT: F 143 LYS cc_start: 0.9141 (tptt) cc_final: 0.8880 (tptt) REVERT: F 181 HIS cc_start: 0.9071 (p-80) cc_final: 0.8350 (p-80) REVERT: F 246 LEU cc_start: 0.9481 (tp) cc_final: 0.9195 (tp) REVERT: F 253 TRP cc_start: 0.9070 (m-90) cc_final: 0.8773 (m-90) REVERT: F 375 ASP cc_start: 0.9195 (m-30) cc_final: 0.8953 (m-30) REVERT: F 412 LEU cc_start: 0.9119 (mp) cc_final: 0.8912 (mt) outliers start: 104 outliers final: 92 residues processed: 561 average time/residue: 0.1487 time to fit residues: 133.9494 Evaluate side-chains 587 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 491 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 198 ASP Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 337 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain C residue 377 LEU Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 115 ASP Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 414 HIS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 353 VAL Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 380 LYS Chi-restraints excluded: chain F residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [258, 60, 217, 81, 282, 22, 54, 306, 108, 263, 178] chunk 258 optimal weight: 0.7980 chunk 60 optimal weight: 50.0000 chunk 217 optimal weight: 0.6980 chunk 81 optimal weight: 8.9990 chunk 282 optimal weight: 9.9990 chunk 22 optimal weight: 50.0000 chunk 54 optimal weight: 40.0000 chunk 306 optimal weight: 8.9990 chunk 108 optimal weight: 40.0000 chunk 263 optimal weight: 20.0000 chunk 178 optimal weight: 2.9990 overall best weight: 4.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 266 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 408 ASN ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 226 HIS ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 261 ASN ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 290 ASN ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.153184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.101515 restraints weight = 74344.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.104903 restraints weight = 37367.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3675 r_free = 0.3675 target = 0.107093 restraints weight = 24508.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.108494 restraints weight = 18722.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.109312 restraints weight = 15733.496| |-----------------------------------------------------------------------------| r_work (final): 0.3616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.4404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 24893 Z= 0.186 Angle : 0.705 13.997 33960 Z= 0.345 Chirality : 0.045 0.253 3846 Planarity : 0.004 0.053 4332 Dihedral : 4.817 28.500 3340 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 17.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 3.72 % Allowed : 20.47 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.25 (0.15), residues: 3112 helix: 0.18 (0.24), residues: 474 sheet: 0.31 (0.17), residues: 958 loop : -0.49 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 299 TYR 0.021 0.002 TYR D 368 PHE 0.028 0.002 PHE F 240 TRP 0.024 0.002 TRP E 253 HIS 0.005 0.001 HIS A 414 Details of bonding type rmsd/Z covalent geometry : bond 0.00411 / 0.19 (24880) covalent geometry : angle 0.70407 / 0.34 (33934) SS BOND : bond 0.00307 / 0.15 ( 13) SS BOND : angle 1.25733 / 0.89 ( 26) hydrogen bonds : bond 0.03129 / 2.08 ( 881) hydrogen bonds : angle 5.65172 / 3.95 ( 2472) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6224 Ramachandran restraints generated. 3112 Oldfield, 0 Emsley, 3112 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 592 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 493 time to evaluate : 0.765 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: G 121 ASP cc_start: 0.8970 (m-30) cc_final: 0.8617 (p0) REVERT: G 182 MET cc_start: 0.6082 (mmt) cc_final: 0.3303 (mmt) REVERT: A 83 GLN cc_start: 0.9456 (tp40) cc_final: 0.9030 (tp-100) REVERT: A 84 ARG cc_start: 0.8684 (mtm180) cc_final: 0.8414 (mtp180) REVERT: A 134 MET cc_start: 0.9142 (mmm) cc_final: 0.8770 (mmm) REVERT: A 136 LYS cc_start: 0.9517 (ptpt) cc_final: 0.9290 (ptmt) REVERT: A 189 ASN cc_start: 0.9464 (t0) cc_final: 0.8825 (t0) REVERT: A 195 LYS cc_start: 0.8819 (tptp) cc_final: 0.8205 (tptt) REVERT: A 232 MET cc_start: 0.7611 (tpp) cc_final: 0.7262 (tpp) REVERT: A 378 SER cc_start: 0.9360 (m) cc_final: 0.9115 (p) REVERT: A 407 MET cc_start: 0.9085 (tmm) cc_final: 0.8408 (ppp) REVERT: A 495 GLN cc_start: 0.9645 (mm-40) cc_final: 0.9331 (mm110) REVERT: A 640 MET cc_start: 0.4509 (mmm) cc_final: 0.3929 (mmm) REVERT: B 140 LEU cc_start: 0.9763 (tp) cc_final: 0.9535 (tp) REVERT: B 147 MET cc_start: 0.5319 (tpt) cc_final: 0.4838 (tpt) REVERT: B 194 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9047 (mm) REVERT: B 213 ASP cc_start: 0.9161 (t70) cc_final: 0.8532 (t70) REVERT: B 218 THR cc_start: 0.9070 (t) cc_final: 0.8836 (t) REVERT: B 325 GLN cc_start: 0.7808 (tm-30) cc_final: 0.7431 (tm-30) REVERT: B 327 LEU cc_start: 0.9427 (mp) cc_final: 0.8347 (mp) REVERT: B 347 LYS cc_start: 0.9285 (mppt) cc_final: 0.8947 (mmtt) REVERT: B 403 GLN cc_start: 0.9318 (tt0) cc_final: 0.8860 (tm-30) REVERT: C 115 ASP cc_start: 0.8967 (p0) cc_final: 0.8665 (p0) REVERT: C 131 GLN cc_start: 0.9028 (tm-30) cc_final: 0.8500 (tm-30) REVERT: C 143 LYS cc_start: 0.9116 (tptt) cc_final: 0.8861 (tptt) REVERT: C 181 HIS cc_start: 0.8797 (p-80) cc_final: 0.7903 (p90) REVERT: C 224 GLU cc_start: 0.8025 (mp0) cc_final: 0.7542 (mp0) REVERT: C 253 TRP cc_start: 0.8847 (m-90) cc_final: 0.8459 (m-90) REVERT: C 299 ARG cc_start: 0.8632 (mpp80) cc_final: 0.8413 (ptp90) REVERT: C 375 ASP cc_start: 0.9295 (m-30) cc_final: 0.8506 (m-30) REVERT: C 380 LYS cc_start: 0.9083 (mtmm) cc_final: 0.8458 (mtmm) REVERT: C 411 SER cc_start: 0.8928 (m) cc_final: 0.8605 (p) REVERT: D 83 GLN cc_start: 0.9137 (tp-100) cc_final: 0.8735 (tp-100) REVERT: D 134 MET cc_start: 0.9149 (mmm) cc_final: 0.8822 (mmm) REVERT: D 189 ASN cc_start: 0.9559 (m-40) cc_final: 0.8831 (t0) REVERT: D 232 MET cc_start: 0.7618 (tpp) cc_final: 0.7268 (tpp) REVERT: D 256 THR cc_start: 0.9257 (m) cc_final: 0.9050 (p) REVERT: D 288 ILE cc_start: 0.9385 (mm) cc_final: 0.9158 (mm) REVERT: D 375 ASP cc_start: 0.8997 (m-30) cc_final: 0.8746 (t0) REVERT: D 378 SER cc_start: 0.9448 (m) cc_final: 0.9158 (p) REVERT: D 640 MET cc_start: 0.4090 (mmm) cc_final: 0.3287 (mmm) REVERT: E 89 LEU cc_start: 0.8943 (mm) cc_final: 0.8504 (mm) REVERT: E 213 ASP cc_start: 0.9157 (t70) cc_final: 0.8485 (t70) REVERT: E 219 LEU cc_start: 0.9193 (OUTLIER) cc_final: 0.8930 (mm) REVERT: E 232 MET cc_start: 0.9435 (mmm) cc_final: 0.9105 (mmp) REVERT: E 235 TYR cc_start: 0.8014 (OUTLIER) cc_final: 0.7656 (m-10) REVERT: E 335 GLU cc_start: 0.8701 (pm20) cc_final: 0.8240 (pp20) REVERT: F 68 GLN cc_start: 0.9060 (OUTLIER) cc_final: 0.8800 (mp10) REVERT: F 106 ILE cc_start: 0.9612 (mm) cc_final: 0.9262 (tt) REVERT: F 115 ASP cc_start: 0.8865 (p0) cc_final: 0.8527 (p0) REVERT: F 132 TYR cc_start: 0.8580 (m-80) cc_final: 0.8188 (m-80) REVERT: F 143 LYS cc_start: 0.9137 (tptt) cc_final: 0.8857 (tptt) REVERT: F 181 HIS cc_start: 0.9050 (p-80) cc_final: 0.8334 (p-80) REVERT: F 246 LEU cc_start: 0.9512 (tp) cc_final: 0.9241 (tp) REVERT: F 253 TRP cc_start: 0.9052 (m-90) cc_final: 0.8718 (m-90) REVERT: F 375 ASP cc_start: 0.9218 (m-30) cc_final: 0.8983 (m-30) REVERT: F 377 LEU cc_start: 0.9178 (OUTLIER) cc_final: 0.8765 (mm) outliers start: 99 outliers final: 91 residues processed: 557 average time/residue: 0.1518 time to fit residues: 137.2609 Evaluate side-chains 577 residues out of total 2682 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 481 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain I residue 142 GLN Chi-restraints excluded: chain J residue 13 HIS Chi-restraints excluded: chain A residue 81 ILE Chi-restraints excluded: chain A residue 113 VAL Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 191 THR Chi-restraints excluded: chain A residue 218 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 247 VAL Chi-restraints excluded: chain A residue 264 LEU Chi-restraints excluded: chain A residue 321 ASP Chi-restraints excluded: chain A residue 343 ASN Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 408 ASN Chi-restraints excluded: chain A residue 567 THR Chi-restraints excluded: chain A residue 628 MET Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 99 THR Chi-restraints excluded: chain B residue 111 VAL Chi-restraints excluded: chain B residue 158 LEU Chi-restraints excluded: chain B residue 160 VAL Chi-restraints excluded: chain B residue 194 LEU Chi-restraints excluded: chain B residue 198 ASP Chi-restraints excluded: chain B residue 275 VAL Chi-restraints excluded: chain B residue 338 THR Chi-restraints excluded: chain B residue 372 SER Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 384 CYS Chi-restraints excluded: chain B residue 411 SER Chi-restraints excluded: chain C residue 61 VAL Chi-restraints excluded: chain C residue 68 GLN Chi-restraints excluded: chain C residue 113 VAL Chi-restraints excluded: chain C residue 117 THR Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 138 LYS Chi-restraints excluded: chain C residue 142 VAL Chi-restraints excluded: chain C residue 145 THR Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 169 SER Chi-restraints excluded: chain C residue 212 ASN Chi-restraints excluded: chain C residue 218 THR Chi-restraints excluded: chain C residue 256 THR Chi-restraints excluded: chain C residue 272 ASP Chi-restraints excluded: chain C residue 275 VAL Chi-restraints excluded: chain C residue 297 PHE Chi-restraints excluded: chain D residue 88 THR Chi-restraints excluded: chain D residue 92 VAL Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain D residue 186 VAL Chi-restraints excluded: chain D residue 191 THR Chi-restraints excluded: chain D residue 218 THR Chi-restraints excluded: chain D residue 227 THR Chi-restraints excluded: chain D residue 228 LEU Chi-restraints excluded: chain D residue 247 VAL Chi-restraints excluded: chain D residue 264 LEU Chi-restraints excluded: chain D residue 343 ASN Chi-restraints excluded: chain D residue 408 ASN Chi-restraints excluded: chain D residue 414 HIS Chi-restraints excluded: chain D residue 567 THR Chi-restraints excluded: chain D residue 628 MET Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 99 THR Chi-restraints excluded: chain E residue 111 VAL Chi-restraints excluded: chain E residue 160 VAL Chi-restraints excluded: chain E residue 219 LEU Chi-restraints excluded: chain E residue 235 TYR Chi-restraints excluded: chain E residue 246 LEU Chi-restraints excluded: chain E residue 275 VAL Chi-restraints excluded: chain E residue 277 VAL Chi-restraints excluded: chain E residue 319 THR Chi-restraints excluded: chain E residue 323 VAL Chi-restraints excluded: chain E residue 327 LEU Chi-restraints excluded: chain E residue 338 THR Chi-restraints excluded: chain E residue 372 SER Chi-restraints excluded: chain E residue 384 CYS Chi-restraints excluded: chain E residue 411 SER Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 68 GLN Chi-restraints excluded: chain F residue 102 ILE Chi-restraints excluded: chain F residue 113 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 145 THR Chi-restraints excluded: chain F residue 161 SER Chi-restraints excluded: chain F residue 185 THR Chi-restraints excluded: chain F residue 212 ASN Chi-restraints excluded: chain F residue 223 ILE Chi-restraints excluded: chain F residue 256 THR Chi-restraints excluded: chain F residue 297 PHE Chi-restraints excluded: chain F residue 372 SER Chi-restraints excluded: chain F residue 377 LEU Chi-restraints excluded: chain F residue 380 LYS Chi-restraints excluded: chain F residue 400 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 310 random chunks: [70, 170, 94, 184, 57, 21, 89, 226, 209, 137, 199] chunk 70 optimal weight: 0.8980 chunk 170 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 184 optimal weight: 3.9990 chunk 57 optimal weight: 50.0000 chunk 21 optimal weight: 50.0000 chunk 89 optimal weight: 2.9990 chunk 226 optimal weight: 0.0970 chunk 209 optimal weight: 0.9980 chunk 137 optimal weight: 7.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 256 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 239 GLN A 266 ASN ** A 408 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 72 GLN ** C 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 66 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 239 GLN D 408 ASN ** D 414 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 379 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 403 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.152827 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.099519 restraints weight = 71778.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.102926 restraints weight = 36138.802| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.105084 restraints weight = 23688.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.106473 restraints weight = 18066.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.3751 r_free = 0.3751 target = 0.107317 restraints weight = 15225.086| |-----------------------------------------------------------------------------| r_work (final): 0.3637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.4353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 24893 Z= 0.127 Angle : 0.699 13.933 33960 Z= 0.336 Chirality : 0.045 0.242 3846 Planarity : 0.004 0.055 4332 Dihedral : 4.735 29.355 3340 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 2.75 % Allowed : 21.86 % Favored : 75.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.45 % 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: -0.18 (0.15), residues: 3112 helix: 0.32 (0.25), residues: 460 sheet: 0.21 (0.16), residues: 1014 loop : -0.37 (0.15), residues: 1638 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 70 TYR 0.022 0.001 TYR D 368 PHE 0.024 0.002 PHE C 255 TRP 0.023 0.002 TRP E 253 HIS 0.004 0.001 HIS F 181 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (24880) covalent geometry : angle 0.69864 / 0.34 (33934) SS BOND : bond 0.00159 / 0.08 ( 13) SS BOND : angle 1.17498 / 0.83 ( 26) hydrogen bonds : bond 0.03036 / 2.02 ( 881) hydrogen bonds : angle 5.52989 / 3.87 ( 2472) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5610.33 seconds wall clock time: 97 minutes 22.14 seconds (5842.14 seconds total)