Starting phenix.real_space_refine on Thu Mar 5 17:18:48 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7pv4_13665/03_2026/7pv4_13665.cif Found real_map, /net/cci-nas-00/data/ceres_data/7pv4_13665/03_2026/7pv4_13665.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7pv4_13665/03_2026/7pv4_13665.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7pv4_13665/03_2026/7pv4_13665.map" model { file = "/net/cci-nas-00/data/ceres_data/7pv4_13665/03_2026/7pv4_13665.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7pv4_13665/03_2026/7pv4_13665.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 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 144 5.16 5 C 15588 2.51 5 N 4020 2.21 5 O 4584 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 264 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 24336 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2028 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 12, 'TRANS': 243} Chain breaks: 1 Unresolved non-hydrogen bonds: 42 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 33 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'ASN:plan1': 3, 'ASP:plan': 1, 'PHE:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 22 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.40, per 1000 atoms: 0.10 Number of scatterers: 24336 At special positions: 0 Unit cell: (172.27, 172.27, 96.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 144 16.00 O 4584 8.00 N 4020 7.00 C 15588 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 925.2 milliseconds 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5808 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 36 sheets defined 47.3% alpha, 14.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.78 Creating SS restraints... Processing helix chain 'A' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG A 39 " --> pdb=" O PHE A 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR A 40 " --> pdb=" O MET A 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR A 43 " --> pdb=" O ARG A 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET A 47 " --> pdb=" O TYR A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE A 66 " --> pdb=" O GLU A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE A 143 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS A 186 " --> pdb=" O ASN A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 197 through 203 Processing helix chain 'A' and resid 220 through 239 Processing helix chain 'A' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG A 275 " --> pdb=" O ALA A 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG A 281 " --> pdb=" O ASP A 277 " (cutoff:3.500A) Processing helix chain 'B' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG B 39 " --> pdb=" O PHE B 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR B 40 " --> pdb=" O MET B 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR B 43 " --> pdb=" O ARG B 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET B 47 " --> pdb=" O TYR B 43 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE B 66 " --> pdb=" O GLU B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) Processing helix chain 'B' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS B 186 " --> pdb=" O ASN B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 197 through 203 Processing helix chain 'B' and resid 220 through 239 Processing helix chain 'B' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG B 275 " --> pdb=" O ALA B 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG B 281 " --> pdb=" O ASP B 277 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG C 39 " --> pdb=" O PHE C 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR C 40 " --> pdb=" O MET C 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR C 43 " --> pdb=" O ARG C 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET C 47 " --> pdb=" O TYR C 43 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE C 66 " --> pdb=" O GLU C 62 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 145 " --> pdb=" O ARG C 141 " (cutoff:3.500A) Processing helix chain 'C' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS C 186 " --> pdb=" O ASN C 182 " (cutoff:3.500A) Processing helix chain 'C' and resid 197 through 203 Processing helix chain 'C' and resid 220 through 239 Processing helix chain 'C' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG C 275 " --> pdb=" O ALA C 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG C 281 " --> pdb=" O ASP C 277 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG D 39 " --> pdb=" O PHE D 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR D 40 " --> pdb=" O MET D 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR D 43 " --> pdb=" O ARG D 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET D 47 " --> pdb=" O TYR D 43 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE D 66 " --> pdb=" O GLU D 62 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE D 143 " --> pdb=" O PRO D 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS D 186 " --> pdb=" O ASN D 182 " (cutoff:3.500A) Processing helix chain 'D' and resid 197 through 203 Processing helix chain 'D' and resid 220 through 239 Processing helix chain 'D' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG D 275 " --> pdb=" O ALA D 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG D 281 " --> pdb=" O ASP D 277 " (cutoff:3.500A) Processing helix chain 'E' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG E 39 " --> pdb=" O PHE E 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR E 40 " --> pdb=" O MET E 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR E 43 " --> pdb=" O ARG E 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET E 47 " --> pdb=" O TYR E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE E 66 " --> pdb=" O GLU E 62 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE E 143 " --> pdb=" O PRO E 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR E 145 " --> pdb=" O ARG E 141 " (cutoff:3.500A) Processing helix chain 'E' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS E 186 " --> pdb=" O ASN E 182 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 203 Processing helix chain 'E' and resid 220 through 239 Processing helix chain 'E' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG E 275 " --> pdb=" O ALA E 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG E 281 " --> pdb=" O ASP E 277 " (cutoff:3.500A) Processing helix chain 'F' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG F 39 " --> pdb=" O PHE F 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR F 40 " --> pdb=" O MET F 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR F 43 " --> pdb=" O ARG F 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET F 47 " --> pdb=" O TYR F 43 " (cutoff:3.500A) Processing helix chain 'F' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE F 66 " --> pdb=" O GLU F 62 " (cutoff:3.500A) Processing helix chain 'F' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE F 143 " --> pdb=" O PRO F 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS F 186 " --> pdb=" O ASN F 182 " (cutoff:3.500A) Processing helix chain 'F' and resid 197 through 203 Processing helix chain 'F' and resid 220 through 239 Processing helix chain 'F' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG F 275 " --> pdb=" O ALA F 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG F 281 " --> pdb=" O ASP F 277 " (cutoff:3.500A) Processing helix chain 'G' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG G 39 " --> pdb=" O PHE G 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR G 40 " --> pdb=" O MET G 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR G 43 " --> pdb=" O ARG G 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET G 47 " --> pdb=" O TYR G 43 " (cutoff:3.500A) Processing helix chain 'G' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE G 66 " --> pdb=" O GLU G 62 " (cutoff:3.500A) Processing helix chain 'G' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE G 143 " --> pdb=" O PRO G 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR G 145 " --> pdb=" O ARG G 141 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 197 through 203 Processing helix chain 'G' and resid 220 through 239 Processing helix chain 'G' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG G 275 " --> pdb=" O ALA G 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG G 281 " --> pdb=" O ASP G 277 " (cutoff:3.500A) Processing helix chain 'H' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG H 39 " --> pdb=" O PHE H 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR H 40 " --> pdb=" O MET H 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR H 43 " --> pdb=" O ARG H 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET H 47 " --> pdb=" O TYR H 43 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE H 66 " --> pdb=" O GLU H 62 " (cutoff:3.500A) Processing helix chain 'H' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE H 143 " --> pdb=" O PRO H 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR H 145 " --> pdb=" O ARG H 141 " (cutoff:3.500A) Processing helix chain 'H' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS H 186 " --> pdb=" O ASN H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 197 through 203 Processing helix chain 'H' and resid 220 through 239 Processing helix chain 'H' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG H 275 " --> pdb=" O ALA H 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG H 281 " --> pdb=" O ASP H 277 " (cutoff:3.500A) Processing helix chain 'I' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG I 39 " --> pdb=" O PHE I 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR I 40 " --> pdb=" O MET I 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR I 43 " --> pdb=" O ARG I 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET I 47 " --> pdb=" O TYR I 43 " (cutoff:3.500A) Processing helix chain 'I' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE I 66 " --> pdb=" O GLU I 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE I 143 " --> pdb=" O PRO I 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR I 145 " --> pdb=" O ARG I 141 " (cutoff:3.500A) Processing helix chain 'I' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS I 186 " --> pdb=" O ASN I 182 " (cutoff:3.500A) Processing helix chain 'I' and resid 197 through 203 Processing helix chain 'I' and resid 220 through 239 Processing helix chain 'I' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG I 275 " --> pdb=" O ALA I 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG I 281 " --> pdb=" O ASP I 277 " (cutoff:3.500A) Processing helix chain 'J' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG J 39 " --> pdb=" O PHE J 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR J 40 " --> pdb=" O MET J 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR J 43 " --> pdb=" O ARG J 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET J 47 " --> pdb=" O TYR J 43 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE J 66 " --> pdb=" O GLU J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE J 143 " --> pdb=" O PRO J 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR J 145 " --> pdb=" O ARG J 141 " (cutoff:3.500A) Processing helix chain 'J' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS J 186 " --> pdb=" O ASN J 182 " (cutoff:3.500A) Processing helix chain 'J' and resid 197 through 203 Processing helix chain 'J' and resid 220 through 239 Processing helix chain 'J' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG J 275 " --> pdb=" O ALA J 271 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ARG J 281 " --> pdb=" O ASP J 277 " (cutoff:3.500A) Processing helix chain 'K' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG K 39 " --> pdb=" O PHE K 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR K 40 " --> pdb=" O MET K 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR K 43 " --> pdb=" O ARG K 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET K 47 " --> pdb=" O TYR K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 74 removed outlier: 3.924A pdb=" N ILE K 66 " --> pdb=" O GLU K 62 " (cutoff:3.500A) Processing helix chain 'K' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE K 143 " --> pdb=" O PRO K 139 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR K 145 " --> pdb=" O ARG K 141 " (cutoff:3.500A) Processing helix chain 'K' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS K 186 " --> pdb=" O ASN K 182 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 203 Processing helix chain 'K' and resid 220 through 239 Processing helix chain 'K' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG K 275 " --> pdb=" O ALA K 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG K 281 " --> pdb=" O ASP K 277 " (cutoff:3.500A) Processing helix chain 'L' and resid 35 through 49 removed outlier: 4.370A pdb=" N ARG L 39 " --> pdb=" O PHE L 35 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N TYR L 40 " --> pdb=" O MET L 36 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N TYR L 43 " --> pdb=" O ARG L 39 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N MET L 47 " --> pdb=" O TYR L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 62 through 74 removed outlier: 3.925A pdb=" N ILE L 66 " --> pdb=" O GLU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 139 through 164 removed outlier: 3.630A pdb=" N ILE L 143 " --> pdb=" O PRO L 139 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR L 145 " --> pdb=" O ARG L 141 " (cutoff:3.500A) Processing helix chain 'L' and resid 173 through 186 removed outlier: 3.714A pdb=" N LYS L 186 " --> pdb=" O ASN L 182 " (cutoff:3.500A) Processing helix chain 'L' and resid 197 through 203 Processing helix chain 'L' and resid 220 through 239 Processing helix chain 'L' and resid 262 through 287 removed outlier: 3.736A pdb=" N ARG L 275 " --> pdb=" O ALA L 271 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ARG L 281 " --> pdb=" O ASP L 277 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 52 through 54 Processing sheet with id=AA2, first strand: chain 'A' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR A 118 " --> pdb=" O GLY A 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY A 114 " --> pdb=" O TYR A 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR A 120 " --> pdb=" O GLY A 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY A 112 " --> pdb=" O THR A 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN A 75 " --> pdb=" O CYS A 95 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU A 195 " --> pdb=" O ILE A 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE A 170 " --> pdb=" O LEU A 195 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 52 through 54 Processing sheet with id=AA5, first strand: chain 'B' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR B 118 " --> pdb=" O GLY B 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY B 114 " --> pdb=" O TYR B 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR B 120 " --> pdb=" O GLY B 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY B 112 " --> pdb=" O THR B 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN B 75 " --> pdb=" O CYS B 95 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU B 195 " --> pdb=" O ILE B 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE B 170 " --> pdb=" O LEU B 195 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 52 through 54 Processing sheet with id=AA8, first strand: chain 'C' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR C 118 " --> pdb=" O GLY C 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY C 114 " --> pdb=" O TYR C 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR C 120 " --> pdb=" O GLY C 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY C 112 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN C 75 " --> pdb=" O CYS C 95 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU C 195 " --> pdb=" O ILE C 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE C 170 " --> pdb=" O LEU C 195 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 52 through 54 Processing sheet with id=AB2, first strand: chain 'D' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR D 118 " --> pdb=" O GLY D 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY D 114 " --> pdb=" O TYR D 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR D 120 " --> pdb=" O GLY D 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY D 112 " --> pdb=" O THR D 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN D 75 " --> pdb=" O CYS D 95 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU D 195 " --> pdb=" O ILE D 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE D 170 " --> pdb=" O LEU D 195 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 52 through 54 Processing sheet with id=AB5, first strand: chain 'E' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR E 118 " --> pdb=" O GLY E 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY E 114 " --> pdb=" O TYR E 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR E 120 " --> pdb=" O GLY E 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY E 112 " --> pdb=" O THR E 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN E 75 " --> pdb=" O CYS E 95 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU E 195 " --> pdb=" O ILE E 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE E 170 " --> pdb=" O LEU E 195 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'F' and resid 52 through 54 Processing sheet with id=AB8, first strand: chain 'F' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR F 118 " --> pdb=" O GLY F 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY F 114 " --> pdb=" O TYR F 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR F 120 " --> pdb=" O GLY F 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY F 112 " --> pdb=" O THR F 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN F 75 " --> pdb=" O CYS F 95 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'F' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU F 195 " --> pdb=" O ILE F 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE F 170 " --> pdb=" O LEU F 195 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'G' and resid 52 through 54 Processing sheet with id=AC2, first strand: chain 'G' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR G 118 " --> pdb=" O GLY G 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY G 114 " --> pdb=" O TYR G 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR G 120 " --> pdb=" O GLY G 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY G 112 " --> pdb=" O THR G 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN G 75 " --> pdb=" O CYS G 95 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'G' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU G 195 " --> pdb=" O ILE G 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE G 170 " --> pdb=" O LEU G 195 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'H' and resid 52 through 54 Processing sheet with id=AC5, first strand: chain 'H' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR H 118 " --> pdb=" O GLY H 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY H 114 " --> pdb=" O TYR H 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR H 120 " --> pdb=" O GLY H 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY H 112 " --> pdb=" O THR H 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN H 75 " --> pdb=" O CYS H 95 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'H' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU H 195 " --> pdb=" O ILE H 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE H 170 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'I' and resid 52 through 54 Processing sheet with id=AC8, first strand: chain 'I' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR I 118 " --> pdb=" O GLY I 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY I 114 " --> pdb=" O TYR I 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR I 120 " --> pdb=" O GLY I 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY I 112 " --> pdb=" O THR I 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN I 75 " --> pdb=" O CYS I 95 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'I' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU I 195 " --> pdb=" O ILE I 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE I 170 " --> pdb=" O LEU I 195 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'J' and resid 52 through 54 Processing sheet with id=AD2, first strand: chain 'J' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR J 118 " --> pdb=" O GLY J 114 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N GLY J 114 " --> pdb=" O TYR J 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR J 120 " --> pdb=" O GLY J 112 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N GLY J 112 " --> pdb=" O THR J 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN J 75 " --> pdb=" O CYS J 95 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'J' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU J 195 " --> pdb=" O ILE J 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE J 170 " --> pdb=" O LEU J 195 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'K' and resid 52 through 54 Processing sheet with id=AD5, first strand: chain 'K' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR K 118 " --> pdb=" O GLY K 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY K 114 " --> pdb=" O TYR K 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR K 120 " --> pdb=" O GLY K 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY K 112 " --> pdb=" O THR K 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN K 75 " --> pdb=" O CYS K 95 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'K' and resid 194 through 196 removed outlier: 8.710A pdb=" N LEU K 195 " --> pdb=" O ILE K 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE K 170 " --> pdb=" O LEU K 195 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'L' and resid 52 through 54 Processing sheet with id=AD8, first strand: chain 'L' and resid 117 through 122 removed outlier: 5.088A pdb=" N TYR L 118 " --> pdb=" O GLY L 114 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N GLY L 114 " --> pdb=" O TYR L 118 " (cutoff:3.500A) removed outlier: 5.579A pdb=" N THR L 120 " --> pdb=" O GLY L 112 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N GLY L 112 " --> pdb=" O THR L 120 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N GLN L 75 " --> pdb=" O CYS L 95 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'L' and resid 194 through 196 removed outlier: 8.709A pdb=" N LEU L 195 " --> pdb=" O ILE L 168 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ILE L 170 " --> pdb=" O LEU L 195 " (cutoff:3.500A) 1236 hydrogen bonds defined for protein. 3636 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: 4.31 Time building geometry restraints manager: 2.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 4896 1.32 - 1.45: 5700 1.45 - 1.57: 14004 1.57 - 1.70: 0 1.70 - 1.82: 240 Bond restraints: 24840 Sorted by residual: bond pdb=" CZ ARG J 275 " pdb=" NH2 ARG J 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG A 275 " pdb=" NH2 ARG A 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG G 275 " pdb=" NH2 ARG G 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG D 275 " pdb=" NH2 ARG D 275 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.17e+01 bond pdb=" CZ ARG D 64 " pdb=" NH2 ARG D 64 " ideal model delta sigma weight residual 1.330 1.286 0.044 1.30e-02 5.92e+03 1.15e+01 ... (remaining 24835 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.02: 33348 5.02 - 10.04: 288 10.04 - 15.06: 0 15.06 - 20.08: 0 20.08 - 25.10: 12 Bond angle restraints: 33648 Sorted by residual: angle pdb=" CB LEU K 204 " pdb=" CG LEU K 204 " pdb=" CD1 LEU K 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU B 204 " pdb=" CG LEU B 204 " pdb=" CD1 LEU B 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU E 204 " pdb=" CG LEU E 204 " pdb=" CD1 LEU E 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU H 204 " pdb=" CG LEU H 204 " pdb=" CD1 LEU H 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 angle pdb=" CB LEU L 204 " pdb=" CG LEU L 204 " pdb=" CD1 LEU L 204 " ideal model delta sigma weight residual 110.70 135.80 -25.10 3.00e+00 1.11e-01 7.00e+01 ... (remaining 33643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.64: 13776 17.64 - 35.27: 1020 35.27 - 52.91: 144 52.91 - 70.54: 48 70.54 - 88.18: 12 Dihedral angle restraints: 15000 sinusoidal: 5976 harmonic: 9024 Sorted by residual: dihedral pdb=" C ASN L 289 " pdb=" N ASN L 289 " pdb=" CA ASN L 289 " pdb=" CB ASN L 289 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" C ASN I 289 " pdb=" N ASN I 289 " pdb=" CA ASN I 289 " pdb=" CB ASN I 289 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.89e+01 dihedral pdb=" C ASN C 289 " pdb=" N ASN C 289 " pdb=" CA ASN C 289 " pdb=" CB ASN C 289 " ideal model delta harmonic sigma weight residual -122.60 -136.03 13.43 0 2.50e+00 1.60e-01 2.89e+01 ... (remaining 14997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.208: 3540 0.208 - 0.415: 96 0.415 - 0.623: 24 0.623 - 0.831: 0 0.831 - 1.038: 12 Chirality restraints: 3672 Sorted by residual: chirality pdb=" CG LEU E 204 " pdb=" CB LEU E 204 " pdb=" CD1 LEU E 204 " pdb=" CD2 LEU E 204 " both_signs ideal model delta sigma weight residual False -2.59 -1.55 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CG LEU H 204 " pdb=" CB LEU H 204 " pdb=" CD1 LEU H 204 " pdb=" CD2 LEU H 204 " both_signs ideal model delta sigma weight residual False -2.59 -1.55 -1.04 2.00e-01 2.50e+01 2.70e+01 chirality pdb=" CG LEU K 204 " pdb=" CB LEU K 204 " pdb=" CD1 LEU K 204 " pdb=" CD2 LEU K 204 " both_signs ideal model delta sigma weight residual False -2.59 -1.55 -1.04 2.00e-01 2.50e+01 2.70e+01 ... (remaining 3669 not shown) Planarity restraints: 4440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR E 145 " 0.119 2.00e-02 2.50e+03 6.12e-02 7.50e+01 pdb=" CG TYR E 145 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR E 145 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR E 145 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR E 145 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR E 145 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR E 145 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR E 145 " 0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 145 " -0.119 2.00e-02 2.50e+03 6.12e-02 7.50e+01 pdb=" CG TYR K 145 " 0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR K 145 " 0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR K 145 " 0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR K 145 " 0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR K 145 " 0.024 2.00e-02 2.50e+03 pdb=" CZ TYR K 145 " -0.019 2.00e-02 2.50e+03 pdb=" OH TYR K 145 " -0.072 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 145 " 0.119 2.00e-02 2.50e+03 6.12e-02 7.50e+01 pdb=" CG TYR B 145 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TYR B 145 " -0.063 2.00e-02 2.50e+03 pdb=" CD2 TYR B 145 " -0.054 2.00e-02 2.50e+03 pdb=" CE1 TYR B 145 " -0.019 2.00e-02 2.50e+03 pdb=" CE2 TYR B 145 " -0.024 2.00e-02 2.50e+03 pdb=" CZ TYR B 145 " 0.019 2.00e-02 2.50e+03 pdb=" OH TYR B 145 " 0.072 2.00e-02 2.50e+03 ... (remaining 4437 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 96 2.62 - 3.19: 19000 3.19 - 3.76: 36332 3.76 - 4.33: 51904 4.33 - 4.90: 83524 Nonbonded interactions: 190856 Sorted by model distance: nonbonded pdb=" OG1 THR A 173 " pdb=" OE2 GLU B 198 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR D 173 " pdb=" OE2 GLU E 198 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR J 173 " pdb=" OE2 GLU K 198 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR G 173 " pdb=" OE2 GLU H 198 " model vdw 2.051 3.040 nonbonded pdb=" OG1 THR B 173 " pdb=" OE2 GLU C 198 " model vdw 2.051 3.040 ... (remaining 190851 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: 0.07 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.360 Check model and map are aligned: 0.080 Set scattering table: 0.060 Process input model: 17.930 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.180 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5855 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 : 0.013 0.044 24840 Z= 0.771 Angle : 1.959 25.099 33648 Z= 1.325 Chirality : 0.119 1.038 3672 Planarity : 0.016 0.158 4440 Dihedral : 13.223 88.176 9192 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.40 % Allowed : 1.19 % Favored : 98.41 % Rotamer: Outliers : 1.40 % Allowed : 2.33 % Favored : 96.28 % Cbeta Deviations : 0.41 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.63 (0.13), residues: 3024 helix: -0.30 (0.12), residues: 1344 sheet: 1.99 (0.23), residues: 348 loop : -1.14 (0.15), residues: 1332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.002 ARG A 64 TYR 0.119 0.024 TYR H 148 PHE 0.059 0.013 PHE E 190 TRP 0.045 0.021 TRP A 54 HIS 0.013 0.006 HIS J 65 Details of bonding type rmsd covalent geometry : bond 0.01284 (24840) covalent geometry : angle 1.95887 (33648) hydrogen bonds : bond 0.22454 ( 1236) hydrogen bonds : angle 7.48943 ( 3636) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 560 time to evaluate : 0.919 Fit side-chains REVERT: A 148 TYR cc_start: 0.6831 (t80) cc_final: 0.6578 (t80) REVERT: A 285 MET cc_start: 0.7168 (ttm) cc_final: 0.6939 (ttp) REVERT: B 148 TYR cc_start: 0.6711 (t80) cc_final: 0.6420 (t80) REVERT: C 148 TYR cc_start: 0.6783 (t80) cc_final: 0.6512 (t80) REVERT: D 148 TYR cc_start: 0.6839 (t80) cc_final: 0.6587 (t80) REVERT: D 285 MET cc_start: 0.7168 (ttm) cc_final: 0.6939 (ttp) REVERT: E 148 TYR cc_start: 0.6710 (t80) cc_final: 0.6422 (t80) REVERT: F 148 TYR cc_start: 0.6782 (t80) cc_final: 0.6511 (t80) REVERT: G 148 TYR cc_start: 0.6847 (t80) cc_final: 0.6594 (t80) REVERT: G 285 MET cc_start: 0.7165 (ttm) cc_final: 0.6936 (ttp) REVERT: H 148 TYR cc_start: 0.6709 (t80) cc_final: 0.6420 (t80) REVERT: I 148 TYR cc_start: 0.6779 (t80) cc_final: 0.6505 (t80) REVERT: J 148 TYR cc_start: 0.6843 (t80) cc_final: 0.6589 (t80) REVERT: J 285 MET cc_start: 0.7167 (ttm) cc_final: 0.6940 (ttp) REVERT: K 148 TYR cc_start: 0.6714 (t80) cc_final: 0.6422 (t80) REVERT: L 148 TYR cc_start: 0.6779 (t80) cc_final: 0.6505 (t80) outliers start: 36 outliers final: 0 residues processed: 596 average time/residue: 0.6525 time to fit residues: 445.8286 Evaluate side-chains 360 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 360 time to evaluate : 0.886 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 197 optimal weight: 2.9990 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 132 optimal weight: 0.0000 chunk 261 optimal weight: 0.8980 chunk 248 optimal weight: 0.5980 chunk 207 optimal weight: 0.0000 chunk 155 optimal weight: 0.9990 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.9980 chunk 298 optimal weight: 2.9990 overall best weight: 0.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 GLN A 121 ASN B 65 HIS B 101 GLN B 121 ASN C 65 HIS C 75 GLN C 85 ASN C 99 ASN C 121 ASN D 65 HIS D 101 GLN D 121 ASN E 65 HIS E 101 GLN E 121 ASN F 65 HIS F 75 GLN F 85 ASN F 99 ASN F 121 ASN G 65 HIS G 101 GLN G 121 ASN H 65 HIS H 85 ASN H 101 GLN H 121 ASN I 65 HIS I 75 GLN I 99 ASN I 121 ASN J 65 HIS J 101 GLN J 121 ASN K 65 HIS K 85 ASN K 101 GLN K 121 ASN L 65 HIS L 75 GLN L 85 ASN L 99 ASN L 121 ASN Total number of N/Q/H flips: 44 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.163457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.122470 restraints weight = 28496.397| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.07 r_work: 0.3154 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 24840 Z= 0.149 Angle : 0.632 6.396 33648 Z= 0.338 Chirality : 0.044 0.118 3672 Planarity : 0.004 0.030 4440 Dihedral : 4.998 25.713 3312 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 2.52 % Allowed : 11.01 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.14), residues: 3024 helix: 2.06 (0.13), residues: 1404 sheet: 1.97 (0.23), residues: 336 loop : -0.78 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 141 TYR 0.011 0.001 TYR L 43 PHE 0.014 0.002 PHE J 119 TRP 0.007 0.002 TRP L 54 HIS 0.004 0.001 HIS E 65 Details of bonding type rmsd covalent geometry : bond 0.00315 (24840) covalent geometry : angle 0.63236 (33648) hydrogen bonds : bond 0.04371 ( 1236) hydrogen bonds : angle 4.82641 ( 3636) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 481 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 416 time to evaluate : 1.130 Fit side-chains REVERT: A 208 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5815 (mppt) REVERT: A 291 GLU cc_start: 0.6459 (tt0) cc_final: 0.6229 (pt0) REVERT: C 150 MET cc_start: 0.8588 (OUTLIER) cc_final: 0.7522 (mpp) REVERT: D 208 LYS cc_start: 0.6078 (OUTLIER) cc_final: 0.5807 (mppt) REVERT: D 291 GLU cc_start: 0.6469 (tt0) cc_final: 0.6240 (pt0) REVERT: F 150 MET cc_start: 0.8594 (OUTLIER) cc_final: 0.7532 (mpp) REVERT: G 208 LYS cc_start: 0.6086 (OUTLIER) cc_final: 0.5814 (mppt) REVERT: G 291 GLU cc_start: 0.6463 (tt0) cc_final: 0.6232 (pt0) REVERT: I 150 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7524 (mpp) REVERT: I 291 GLU cc_start: 0.6512 (tt0) cc_final: 0.6310 (pt0) REVERT: J 208 LYS cc_start: 0.6087 (OUTLIER) cc_final: 0.5813 (mppt) REVERT: J 291 GLU cc_start: 0.6460 (tt0) cc_final: 0.6234 (pt0) REVERT: L 150 MET cc_start: 0.8593 (OUTLIER) cc_final: 0.7528 (mpp) outliers start: 65 outliers final: 12 residues processed: 453 average time/residue: 0.6319 time to fit residues: 331.5559 Evaluate side-chains 292 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 272 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 208 LYS Chi-restraints excluded: chain B residue 95 CYS Chi-restraints excluded: chain B residue 170 ILE Chi-restraints excluded: chain C residue 72 ASN Chi-restraints excluded: chain C residue 150 MET Chi-restraints excluded: chain D residue 208 LYS Chi-restraints excluded: chain E residue 95 CYS Chi-restraints excluded: chain E residue 170 ILE Chi-restraints excluded: chain F residue 72 ASN Chi-restraints excluded: chain F residue 150 MET Chi-restraints excluded: chain G residue 208 LYS Chi-restraints excluded: chain H residue 95 CYS Chi-restraints excluded: chain H residue 170 ILE Chi-restraints excluded: chain I residue 72 ASN Chi-restraints excluded: chain I residue 150 MET Chi-restraints excluded: chain J residue 208 LYS Chi-restraints excluded: chain K residue 95 CYS Chi-restraints excluded: chain K residue 170 ILE Chi-restraints excluded: chain L residue 72 ASN Chi-restraints excluded: chain L residue 150 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 199 optimal weight: 0.6980 chunk 88 optimal weight: 2.9990 chunk 282 optimal weight: 4.9990 chunk 186 optimal weight: 0.9990 chunk 183 optimal weight: 0.0010 chunk 260 optimal weight: 0.0060 chunk 257 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 297 optimal weight: 0.9990 chunk 274 optimal weight: 0.0000 chunk 211 optimal weight: 3.9990 overall best weight: 0.3006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 182 ASN B 68 GLN B 182 ASN C 65 HIS C 182 ASN D 75 GLN D 182 ASN E 68 GLN E 182 ASN F 65 HIS F 182 ASN G 75 GLN G 182 ASN H 68 GLN H 182 ASN I 65 HIS I 182 ASN J 75 GLN J 182 ASN K 68 GLN K 182 ASN L 65 HIS L 182 ASN Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3851 r_free = 0.3851 target = 0.165388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.123523 restraints weight = 28426.988| |-----------------------------------------------------------------------------| r_work (start): 0.3333 rms_B_bonded: 2.09 r_work: 0.3189 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3048 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.3048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 24840 Z= 0.118 Angle : 0.521 6.952 33648 Z= 0.277 Chirality : 0.042 0.203 3672 Planarity : 0.003 0.031 4440 Dihedral : 4.114 17.017 3312 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.03 % Allowed : 12.75 % Favored : 83.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.88 (0.15), residues: 3024 helix: 2.70 (0.13), residues: 1416 sheet: 1.75 (0.23), residues: 336 loop : -0.64 (0.16), residues: 1272 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 141 TYR 0.009 0.001 TYR I 44 PHE 0.014 0.001 PHE B 286 TRP 0.007 0.001 TRP E 54 HIS 0.003 0.001 HIS I 65 Details of bonding type rmsd covalent geometry : bond 0.00226 (24840) covalent geometry : angle 0.52119 (33648) hydrogen bonds : bond 0.04193 ( 1236) hydrogen bonds : angle 4.30428 ( 3636) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 547 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 443 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 150 MET cc_start: 0.9023 (OUTLIER) cc_final: 0.8751 (mtt) REVERT: A 229 LYS cc_start: 0.8718 (tptt) cc_final: 0.8269 (mttp) REVERT: A 232 GLU cc_start: 0.8336 (tt0) cc_final: 0.7955 (tt0) REVERT: D 150 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8739 (mtt) REVERT: D 229 LYS cc_start: 0.8722 (tptt) cc_final: 0.8275 (mttp) REVERT: D 232 GLU cc_start: 0.8347 (tt0) cc_final: 0.7967 (tt0) REVERT: G 150 MET cc_start: 0.9013 (OUTLIER) cc_final: 0.8739 (mtt) REVERT: G 229 LYS cc_start: 0.8727 (tptt) cc_final: 0.8276 (mttp) REVERT: G 232 GLU cc_start: 0.8353 (tt0) cc_final: 0.7970 (tt0) REVERT: J 150 MET cc_start: 0.9016 (OUTLIER) cc_final: 0.8743 (mtt) REVERT: J 229 LYS cc_start: 0.8720 (tptt) cc_final: 0.8272 (mttp) REVERT: J 232 GLU cc_start: 0.8337 (tt0) cc_final: 0.7959 (tt0) outliers start: 104 outliers final: 16 residues processed: 479 average time/residue: 0.7908 time to fit residues: 424.6846 Evaluate side-chains 340 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 320 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 150 MET Chi-restraints excluded: chain B residue 122 LEU Chi-restraints excluded: chain B residue 180 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 168 ILE Chi-restraints excluded: chain D residue 150 MET Chi-restraints excluded: chain E residue 122 LEU Chi-restraints excluded: chain E residue 180 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 168 ILE Chi-restraints excluded: chain G residue 150 MET Chi-restraints excluded: chain H residue 122 LEU Chi-restraints excluded: chain H residue 180 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 168 ILE Chi-restraints excluded: chain J residue 150 MET Chi-restraints excluded: chain K residue 122 LEU Chi-restraints excluded: chain K residue 180 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 168 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 273 optimal weight: 4.9990 chunk 257 optimal weight: 0.0270 chunk 135 optimal weight: 0.4980 chunk 8 optimal weight: 6.9990 chunk 162 optimal weight: 1.9990 chunk 247 optimal weight: 5.9990 chunk 177 optimal weight: 4.9990 chunk 98 optimal weight: 0.9990 chunk 173 optimal weight: 0.9980 chunk 267 optimal weight: 3.9990 chunk 255 optimal weight: 0.0670 overall best weight: 0.5178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 81 ASN A 283 ASN B 99 ASN B 283 ASN D 81 ASN D 283 ASN E 99 ASN E 283 ASN G 81 ASN G 283 ASN H 99 ASN H 283 ASN J 81 ASN J 283 ASN K 99 ASN K 283 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.162219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.119337 restraints weight = 28136.885| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 2.09 r_work: 0.3117 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2971 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 24840 Z= 0.124 Angle : 0.518 7.314 33648 Z= 0.273 Chirality : 0.042 0.204 3672 Planarity : 0.003 0.027 4440 Dihedral : 4.011 20.727 3312 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.37 % Allowed : 17.02 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.95 (0.15), residues: 3024 helix: 2.69 (0.14), residues: 1404 sheet: 1.73 (0.25), residues: 336 loop : -0.45 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG K 141 TYR 0.009 0.001 TYR I 44 PHE 0.011 0.001 PHE J 90 TRP 0.009 0.001 TRP E 54 HIS 0.002 0.001 HIS J 65 Details of bonding type rmsd covalent geometry : bond 0.00252 (24840) covalent geometry : angle 0.51804 (33648) hydrogen bonds : bond 0.04135 ( 1236) hydrogen bonds : angle 4.27567 ( 3636) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 503 time to evaluate : 0.970 Fit side-chains revert: symmetry clash REVERT: A 132 ASP cc_start: 0.8073 (t70) cc_final: 0.7854 (t70) REVERT: A 232 GLU cc_start: 0.8681 (tt0) cc_final: 0.8327 (tt0) REVERT: A 270 MET cc_start: 0.6816 (ttm) cc_final: 0.6182 (mtm) REVERT: C 55 LYS cc_start: 0.7465 (mmmt) cc_final: 0.7250 (mmmt) REVERT: C 90 PHE cc_start: 0.8467 (m-80) cc_final: 0.8247 (m-80) REVERT: C 178 LEU cc_start: 0.7970 (tp) cc_final: 0.7702 (mt) REVERT: C 213 LEU cc_start: 0.7732 (OUTLIER) cc_final: 0.7342 (pp) REVERT: C 270 MET cc_start: 0.6502 (ttm) cc_final: 0.6033 (mtm) REVERT: D 132 ASP cc_start: 0.8068 (t70) cc_final: 0.7847 (t70) REVERT: D 232 GLU cc_start: 0.8673 (tt0) cc_final: 0.8319 (tt0) REVERT: D 270 MET cc_start: 0.6780 (ttm) cc_final: 0.6231 (mtm) REVERT: F 55 LYS cc_start: 0.7469 (mmmt) cc_final: 0.7252 (mmmt) REVERT: F 90 PHE cc_start: 0.8466 (m-80) cc_final: 0.8241 (m-80) REVERT: F 178 LEU cc_start: 0.7966 (tp) cc_final: 0.7703 (mt) REVERT: F 213 LEU cc_start: 0.7736 (OUTLIER) cc_final: 0.7360 (pp) REVERT: F 270 MET cc_start: 0.6478 (ttm) cc_final: 0.6016 (mtm) REVERT: G 132 ASP cc_start: 0.8072 (t70) cc_final: 0.7857 (t70) REVERT: G 232 GLU cc_start: 0.8690 (tt0) cc_final: 0.8332 (tt0) REVERT: G 270 MET cc_start: 0.6827 (ttm) cc_final: 0.6195 (mtm) REVERT: I 90 PHE cc_start: 0.8479 (m-80) cc_final: 0.8250 (m-80) REVERT: I 178 LEU cc_start: 0.7972 (tp) cc_final: 0.7705 (mt) REVERT: I 213 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7356 (pp) REVERT: I 270 MET cc_start: 0.6501 (ttm) cc_final: 0.6039 (mtm) REVERT: J 132 ASP cc_start: 0.8078 (t70) cc_final: 0.7857 (t70) REVERT: J 232 GLU cc_start: 0.8681 (tt0) cc_final: 0.8328 (tt0) REVERT: J 270 MET cc_start: 0.6824 (ttm) cc_final: 0.6189 (mtm) REVERT: L 55 LYS cc_start: 0.7471 (mmmt) cc_final: 0.7254 (mmmt) REVERT: L 90 PHE cc_start: 0.8462 (m-80) cc_final: 0.8241 (m-80) REVERT: L 178 LEU cc_start: 0.7970 (tp) cc_final: 0.7703 (mt) REVERT: L 213 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7352 (pp) REVERT: L 270 MET cc_start: 0.6513 (ttm) cc_final: 0.6037 (mtm) outliers start: 87 outliers final: 20 residues processed: 534 average time/residue: 0.7225 time to fit residues: 437.9219 Evaluate side-chains 432 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 408 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 213 LEU Chi-restraints excluded: chain E residue 77 VAL Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 213 LEU Chi-restraints excluded: chain H residue 77 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 213 LEU Chi-restraints excluded: chain K residue 77 VAL Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 213 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 27 optimal weight: 4.9990 chunk 41 optimal weight: 1.9990 chunk 208 optimal weight: 0.9980 chunk 256 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 189 optimal weight: 0.9990 chunk 192 optimal weight: 0.0470 chunk 216 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 163 optimal weight: 2.9990 chunk 265 optimal weight: 3.9990 overall best weight: 1.2084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 HIS A 99 ASN A 160 ASN A 283 ASN B 65 HIS B 81 ASN B 99 ASN B 160 ASN B 214 ASN C 160 ASN D 99 ASN D 160 ASN D 283 ASN E 65 HIS E 81 ASN E 99 ASN E 160 ASN E 214 ASN F 160 ASN G 99 ASN G 160 ASN G 283 ASN H 65 HIS H 99 ASN H 160 ASN I 160 ASN J 99 ASN J 160 ASN J 283 ASN K 65 HIS K 99 ASN K 160 ASN L 160 ASN Total number of N/Q/H flips: 33 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.151270 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.106570 restraints weight = 27253.603| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 2.02 r_work: 0.2859 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2706 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2706 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 1.0047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 24840 Z= 0.161 Angle : 0.601 5.824 33648 Z= 0.319 Chirality : 0.045 0.154 3672 Planarity : 0.004 0.029 4440 Dihedral : 4.442 19.906 3312 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.53 % Allowed : 19.53 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.86 (0.15), residues: 3024 helix: 2.51 (0.14), residues: 1380 sheet: 0.95 (0.23), residues: 480 loop : -0.20 (0.17), residues: 1164 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG G 39 TYR 0.015 0.002 TYR H 44 PHE 0.014 0.002 PHE D 266 TRP 0.013 0.002 TRP A 54 HIS 0.002 0.001 HIS L 142 Details of bonding type rmsd covalent geometry : bond 0.00355 (24840) covalent geometry : angle 0.60081 (33648) hydrogen bonds : bond 0.06414 ( 1236) hydrogen bonds : angle 4.60548 ( 3636) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 609 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 518 time to evaluate : 0.852 Fit side-chains REVERT: A 162 ASP cc_start: 0.9113 (t70) cc_final: 0.8848 (t0) REVERT: A 178 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8583 (mt) REVERT: A 232 GLU cc_start: 0.8672 (tt0) cc_final: 0.8453 (tt0) REVERT: A 269 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8144 (mm-30) REVERT: C 178 LEU cc_start: 0.8630 (tp) cc_final: 0.8281 (mt) REVERT: C 213 LEU cc_start: 0.8277 (pt) cc_final: 0.7986 (pp) REVERT: C 266 PHE cc_start: 0.8537 (t80) cc_final: 0.8265 (t80) REVERT: C 291 GLU cc_start: 0.8433 (pt0) cc_final: 0.8066 (pt0) REVERT: D 162 ASP cc_start: 0.9116 (t70) cc_final: 0.8852 (t0) REVERT: D 178 LEU cc_start: 0.8787 (OUTLIER) cc_final: 0.8585 (mt) REVERT: D 232 GLU cc_start: 0.8675 (tt0) cc_final: 0.8455 (tt0) REVERT: D 269 GLU cc_start: 0.8358 (mm-30) cc_final: 0.8150 (mm-30) REVERT: E 291 GLU cc_start: 0.8136 (pt0) cc_final: 0.7936 (pt0) REVERT: F 178 LEU cc_start: 0.8633 (tp) cc_final: 0.8282 (mt) REVERT: F 213 LEU cc_start: 0.8274 (pt) cc_final: 0.7993 (pp) REVERT: F 266 PHE cc_start: 0.8537 (t80) cc_final: 0.8262 (t80) REVERT: F 291 GLU cc_start: 0.8438 (pt0) cc_final: 0.8073 (pt0) REVERT: G 162 ASP cc_start: 0.9113 (t70) cc_final: 0.8850 (t0) REVERT: G 178 LEU cc_start: 0.8784 (OUTLIER) cc_final: 0.8582 (mt) REVERT: G 232 GLU cc_start: 0.8673 (tt0) cc_final: 0.8453 (tt0) REVERT: G 269 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8158 (mm-30) REVERT: I 178 LEU cc_start: 0.8631 (tp) cc_final: 0.8279 (mt) REVERT: I 213 LEU cc_start: 0.8278 (pt) cc_final: 0.7990 (pp) REVERT: I 266 PHE cc_start: 0.8545 (t80) cc_final: 0.8269 (t80) REVERT: J 162 ASP cc_start: 0.9113 (t70) cc_final: 0.8850 (t0) REVERT: J 178 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8583 (mt) REVERT: J 232 GLU cc_start: 0.8669 (tt0) cc_final: 0.8451 (tt0) REVERT: J 269 GLU cc_start: 0.8368 (mm-30) cc_final: 0.8160 (mm-30) REVERT: L 178 LEU cc_start: 0.8634 (tp) cc_final: 0.8284 (mt) REVERT: L 213 LEU cc_start: 0.8275 (pt) cc_final: 0.7991 (pp) REVERT: L 266 PHE cc_start: 0.8543 (t80) cc_final: 0.8262 (t80) REVERT: L 291 GLU cc_start: 0.8426 (pt0) cc_final: 0.8060 (pt0) outliers start: 91 outliers final: 16 residues processed: 573 average time/residue: 0.6286 time to fit residues: 416.1382 Evaluate side-chains 431 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 411 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 159 MET Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 159 MET Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 159 MET Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 219 optimal weight: 0.0000 chunk 139 optimal weight: 0.9990 chunk 64 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 95 optimal weight: 0.9980 chunk 97 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 102 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 290 optimal weight: 0.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 GLN B 202 GLN C 202 GLN D 202 GLN E 202 GLN F 202 GLN G 202 GLN H 202 GLN I 202 GLN J 202 GLN K 202 GLN L 202 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.151538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.108378 restraints weight = 27844.663| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 1.97 r_work: 0.2883 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.2736 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 1.0195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24840 Z= 0.117 Angle : 0.524 6.649 33648 Z= 0.273 Chirality : 0.042 0.140 3672 Planarity : 0.004 0.030 4440 Dihedral : 4.107 17.271 3312 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 2.33 % Allowed : 22.75 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.79 (0.15), residues: 3024 helix: 2.67 (0.14), residues: 1404 sheet: 1.34 (0.26), residues: 336 loop : -0.58 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 64 TYR 0.011 0.001 TYR A 146 PHE 0.010 0.001 PHE I 78 TRP 0.007 0.001 TRP A 54 HIS 0.002 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00253 (24840) covalent geometry : angle 0.52430 (33648) hydrogen bonds : bond 0.04728 ( 1236) hydrogen bonds : angle 4.23109 ( 3636) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 486 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 426 time to evaluate : 0.899 Fit side-chains REVERT: A 38 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7809 (m-30) REVERT: A 213 LEU cc_start: 0.8642 (pt) cc_final: 0.8365 (pp) REVERT: A 232 GLU cc_start: 0.8655 (tt0) cc_final: 0.8410 (tt0) REVERT: A 269 GLU cc_start: 0.8350 (mm-30) cc_final: 0.8102 (mm-30) REVERT: B 62 GLU cc_start: 0.8004 (mt-10) cc_final: 0.7711 (mt-10) REVERT: C 178 LEU cc_start: 0.8610 (tp) cc_final: 0.8254 (mt) REVERT: C 213 LEU cc_start: 0.8203 (pt) cc_final: 0.7846 (pp) REVERT: C 291 GLU cc_start: 0.8316 (pt0) cc_final: 0.8090 (pt0) REVERT: D 38 ASP cc_start: 0.8156 (OUTLIER) cc_final: 0.7822 (m-30) REVERT: D 213 LEU cc_start: 0.8644 (pt) cc_final: 0.8366 (pp) REVERT: D 232 GLU cc_start: 0.8662 (tt0) cc_final: 0.8418 (tt0) REVERT: D 269 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8106 (mm-30) REVERT: E 62 GLU cc_start: 0.8006 (mt-10) cc_final: 0.7705 (mt-10) REVERT: F 178 LEU cc_start: 0.8617 (tp) cc_final: 0.8262 (mt) REVERT: F 213 LEU cc_start: 0.8201 (pt) cc_final: 0.7843 (pp) REVERT: F 291 GLU cc_start: 0.8338 (pt0) cc_final: 0.8113 (pt0) REVERT: G 38 ASP cc_start: 0.8150 (OUTLIER) cc_final: 0.7813 (m-30) REVERT: G 213 LEU cc_start: 0.8636 (pt) cc_final: 0.8358 (pp) REVERT: G 232 GLU cc_start: 0.8658 (tt0) cc_final: 0.8413 (tt0) REVERT: G 269 GLU cc_start: 0.8353 (mm-30) cc_final: 0.8105 (mm-30) REVERT: H 62 GLU cc_start: 0.7998 (mt-10) cc_final: 0.7703 (mt-10) REVERT: I 53 ARG cc_start: 0.8379 (ttp-170) cc_final: 0.8090 (ttm110) REVERT: I 178 LEU cc_start: 0.8614 (tp) cc_final: 0.8259 (mt) REVERT: I 213 LEU cc_start: 0.8197 (pt) cc_final: 0.7839 (pp) REVERT: J 38 ASP cc_start: 0.8142 (OUTLIER) cc_final: 0.7805 (m-30) REVERT: J 213 LEU cc_start: 0.8638 (pt) cc_final: 0.8356 (pp) REVERT: J 232 GLU cc_start: 0.8661 (tt0) cc_final: 0.8417 (tt0) REVERT: J 269 GLU cc_start: 0.8352 (mm-30) cc_final: 0.8101 (mm-30) REVERT: K 62 GLU cc_start: 0.7994 (mt-10) cc_final: 0.7701 (mt-10) REVERT: L 178 LEU cc_start: 0.8605 (tp) cc_final: 0.8249 (mt) REVERT: L 213 LEU cc_start: 0.8200 (pt) cc_final: 0.7843 (pp) REVERT: L 291 GLU cc_start: 0.8334 (pt0) cc_final: 0.8107 (pt0) outliers start: 60 outliers final: 16 residues processed: 458 average time/residue: 0.6340 time to fit residues: 335.9661 Evaluate side-chains 419 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 399 time to evaluate : 1.012 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 177 optimal weight: 1.9990 chunk 254 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 121 optimal weight: 3.9990 chunk 206 optimal weight: 3.9990 chunk 125 optimal weight: 7.9990 chunk 193 optimal weight: 6.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3622 r_free = 0.3622 target = 0.144557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.099413 restraints weight = 27395.063| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 2.02 r_work: 0.2769 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2617 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 1.0541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 24840 Z= 0.249 Angle : 0.660 7.915 33648 Z= 0.342 Chirality : 0.048 0.154 3672 Planarity : 0.005 0.036 4440 Dihedral : 4.661 19.145 3312 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.60 % Allowed : 23.02 % Favored : 74.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.21 (0.15), residues: 3024 helix: 2.28 (0.14), residues: 1404 sheet: 0.38 (0.25), residues: 408 loop : -0.86 (0.16), residues: 1212 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 39 TYR 0.018 0.002 TYR J 146 PHE 0.020 0.002 PHE E 266 TRP 0.011 0.002 TRP D 54 HIS 0.004 0.002 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00616 (24840) covalent geometry : angle 0.66025 (33648) hydrogen bonds : bond 0.07391 ( 1236) hydrogen bonds : angle 4.58707 ( 3636) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 492 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 425 time to evaluate : 1.048 Fit side-chains REVERT: A 38 ASP cc_start: 0.8254 (OUTLIER) cc_final: 0.7916 (m-30) REVERT: A 178 LEU cc_start: 0.8822 (OUTLIER) cc_final: 0.8342 (mp) REVERT: A 232 GLU cc_start: 0.8698 (tt0) cc_final: 0.8452 (tt0) REVERT: A 266 PHE cc_start: 0.8651 (t80) cc_final: 0.8450 (t80) REVERT: B 62 GLU cc_start: 0.8309 (mt-10) cc_final: 0.8004 (mt-10) REVERT: B 141 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8788 (mmm160) REVERT: B 150 MET cc_start: 0.9268 (OUTLIER) cc_final: 0.9038 (mpp) REVERT: C 106 ASP cc_start: 0.8672 (m-30) cc_final: 0.8427 (m-30) REVERT: C 178 LEU cc_start: 0.8779 (tp) cc_final: 0.8359 (mt) REVERT: C 291 GLU cc_start: 0.8352 (pt0) cc_final: 0.8092 (pt0) REVERT: D 38 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7912 (m-30) REVERT: D 178 LEU cc_start: 0.8796 (OUTLIER) cc_final: 0.8302 (mp) REVERT: D 232 GLU cc_start: 0.8705 (tt0) cc_final: 0.8459 (tt0) REVERT: E 62 GLU cc_start: 0.8314 (mt-10) cc_final: 0.8006 (mt-10) REVERT: E 141 ARG cc_start: 0.9103 (mmm-85) cc_final: 0.8781 (mmm160) REVERT: E 150 MET cc_start: 0.9271 (OUTLIER) cc_final: 0.9042 (mpp) REVERT: F 106 ASP cc_start: 0.8669 (m-30) cc_final: 0.8425 (m-30) REVERT: F 178 LEU cc_start: 0.8779 (tp) cc_final: 0.8359 (mt) REVERT: F 291 GLU cc_start: 0.8350 (pt0) cc_final: 0.8088 (pt0) REVERT: G 38 ASP cc_start: 0.8249 (OUTLIER) cc_final: 0.7904 (m-30) REVERT: G 178 LEU cc_start: 0.8792 (OUTLIER) cc_final: 0.8295 (mp) REVERT: G 232 GLU cc_start: 0.8708 (tt0) cc_final: 0.8461 (tt0) REVERT: H 62 GLU cc_start: 0.8308 (mt-10) cc_final: 0.8003 (mt-10) REVERT: H 141 ARG cc_start: 0.9098 (mmm-85) cc_final: 0.8778 (mmm160) REVERT: H 150 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.9044 (mpp) REVERT: I 106 ASP cc_start: 0.8679 (m-30) cc_final: 0.8434 (m-30) REVERT: I 178 LEU cc_start: 0.8781 (tp) cc_final: 0.8360 (mt) REVERT: J 38 ASP cc_start: 0.8255 (OUTLIER) cc_final: 0.7914 (m-30) REVERT: J 178 LEU cc_start: 0.8788 (OUTLIER) cc_final: 0.8289 (mp) REVERT: J 232 GLU cc_start: 0.8709 (tt0) cc_final: 0.8462 (tt0) REVERT: J 266 PHE cc_start: 0.8637 (t80) cc_final: 0.8437 (t80) REVERT: K 62 GLU cc_start: 0.8320 (mt-10) cc_final: 0.8014 (mt-10) REVERT: K 141 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8790 (mmm160) REVERT: K 150 MET cc_start: 0.9270 (OUTLIER) cc_final: 0.9042 (mpp) REVERT: L 106 ASP cc_start: 0.8679 (m-30) cc_final: 0.8433 (m-30) REVERT: L 178 LEU cc_start: 0.8783 (tp) cc_final: 0.8362 (mt) REVERT: L 291 GLU cc_start: 0.8346 (pt0) cc_final: 0.8088 (pt0) outliers start: 67 outliers final: 20 residues processed: 460 average time/residue: 0.6703 time to fit residues: 355.2090 Evaluate side-chains 399 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 367 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 178 LEU Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 120 THR Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 282 ILE Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 178 LEU Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 120 THR Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 282 ILE Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 178 LEU Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 120 THR Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 282 ILE Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 178 LEU Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 120 THR Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 282 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 193 optimal weight: 5.9990 chunk 207 optimal weight: 5.9990 chunk 95 optimal weight: 0.6980 chunk 12 optimal weight: 0.9990 chunk 75 optimal weight: 0.5980 chunk 93 optimal weight: 4.9990 chunk 178 optimal weight: 0.7980 chunk 117 optimal weight: 1.9990 chunk 165 optimal weight: 0.9980 chunk 198 optimal weight: 0.6980 chunk 46 optimal weight: 2.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.149053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.105291 restraints weight = 27668.136| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.00 r_work: 0.2982 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 1.0663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 24840 Z= 0.113 Angle : 0.511 6.510 33648 Z= 0.267 Chirality : 0.042 0.131 3672 Planarity : 0.004 0.033 4440 Dihedral : 4.166 17.814 3312 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 1.86 % Allowed : 24.50 % Favored : 73.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.60 (0.15), residues: 3024 helix: 2.59 (0.14), residues: 1404 sheet: 0.90 (0.26), residues: 336 loop : -0.68 (0.16), residues: 1284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 64 TYR 0.012 0.001 TYR D 146 PHE 0.017 0.001 PHE H 266 TRP 0.008 0.001 TRP H 54 HIS 0.002 0.001 HIS C 142 Details of bonding type rmsd covalent geometry : bond 0.00245 (24840) covalent geometry : angle 0.51106 (33648) hydrogen bonds : bond 0.04677 ( 1236) hydrogen bonds : angle 4.26131 ( 3636) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 455 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 407 time to evaluate : 0.952 Fit side-chains REVERT: A 38 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7870 (m-30) REVERT: A 62 GLU cc_start: 0.8382 (mt-10) cc_final: 0.7867 (mt-10) REVERT: A 68 GLN cc_start: 0.8800 (pt0) cc_final: 0.8495 (pt0) REVERT: A 232 GLU cc_start: 0.8646 (tt0) cc_final: 0.8421 (tt0) REVERT: B 62 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7849 (mt-10) REVERT: B 117 LYS cc_start: 0.8206 (OUTLIER) cc_final: 0.7965 (mmtm) REVERT: B 141 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8629 (mmm160) REVERT: C 178 LEU cc_start: 0.8738 (tp) cc_final: 0.8340 (mt) REVERT: D 38 ASP cc_start: 0.8224 (OUTLIER) cc_final: 0.7876 (m-30) REVERT: D 62 GLU cc_start: 0.8387 (mt-10) cc_final: 0.7868 (mt-10) REVERT: D 68 GLN cc_start: 0.8799 (pt0) cc_final: 0.8494 (pt0) REVERT: D 232 GLU cc_start: 0.8648 (tt0) cc_final: 0.8423 (tt0) REVERT: E 62 GLU cc_start: 0.8091 (mt-10) cc_final: 0.7841 (mt-10) REVERT: E 117 LYS cc_start: 0.8200 (OUTLIER) cc_final: 0.7956 (mmtm) REVERT: E 141 ARG cc_start: 0.8912 (mmm-85) cc_final: 0.8628 (mmm160) REVERT: F 178 LEU cc_start: 0.8733 (tp) cc_final: 0.8339 (mt) REVERT: G 38 ASP cc_start: 0.8208 (OUTLIER) cc_final: 0.7861 (m-30) REVERT: G 62 GLU cc_start: 0.8390 (mt-10) cc_final: 0.7875 (mt-10) REVERT: G 68 GLN cc_start: 0.8795 (pt0) cc_final: 0.8490 (pt0) REVERT: G 232 GLU cc_start: 0.8644 (tt0) cc_final: 0.8415 (tt0) REVERT: H 62 GLU cc_start: 0.8089 (mt-10) cc_final: 0.7841 (mt-10) REVERT: H 117 LYS cc_start: 0.8203 (OUTLIER) cc_final: 0.7961 (mmtm) REVERT: H 141 ARG cc_start: 0.8909 (mmm-85) cc_final: 0.8627 (mmm160) REVERT: I 178 LEU cc_start: 0.8735 (tp) cc_final: 0.8343 (mt) REVERT: J 38 ASP cc_start: 0.8212 (OUTLIER) cc_final: 0.7864 (m-30) REVERT: J 62 GLU cc_start: 0.8379 (mt-10) cc_final: 0.7866 (mt-10) REVERT: J 68 GLN cc_start: 0.8797 (pt0) cc_final: 0.8487 (pt0) REVERT: J 232 GLU cc_start: 0.8647 (tt0) cc_final: 0.8418 (tt0) REVERT: K 62 GLU cc_start: 0.8097 (mt-10) cc_final: 0.7850 (mt-10) REVERT: K 117 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7973 (mmtm) REVERT: K 141 ARG cc_start: 0.8910 (mmm-85) cc_final: 0.8629 (mmm160) REVERT: L 178 LEU cc_start: 0.8731 (tp) cc_final: 0.8335 (mt) outliers start: 48 outliers final: 20 residues processed: 433 average time/residue: 0.6789 time to fit residues: 336.5420 Evaluate side-chains 409 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 381 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 117 LYS Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 118 optimal weight: 2.9990 chunk 236 optimal weight: 2.9990 chunk 137 optimal weight: 2.9990 chunk 207 optimal weight: 4.9990 chunk 89 optimal weight: 0.7980 chunk 224 optimal weight: 7.9990 chunk 246 optimal weight: 0.6980 chunk 278 optimal weight: 0.4980 chunk 205 optimal weight: 7.9990 chunk 243 optimal weight: 0.1980 chunk 175 optimal weight: 20.0000 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.147686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.103538 restraints weight = 27643.409| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 2.02 r_work: 0.2860 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 1.0746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 24840 Z= 0.131 Angle : 0.539 10.005 33648 Z= 0.278 Chirality : 0.042 0.136 3672 Planarity : 0.004 0.032 4440 Dihedral : 4.143 17.434 3312 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.63 % Allowed : 25.66 % Favored : 72.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.72 (0.15), residues: 3024 helix: 2.60 (0.14), residues: 1404 sheet: 0.47 (0.23), residues: 480 loop : -0.42 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.013 0.002 TYR F 146 PHE 0.013 0.002 PHE C 210 TRP 0.008 0.001 TRP E 54 HIS 0.003 0.001 HIS E 142 Details of bonding type rmsd covalent geometry : bond 0.00299 (24840) covalent geometry : angle 0.53908 (33648) hydrogen bonds : bond 0.05314 ( 1236) hydrogen bonds : angle 4.31198 ( 3636) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 441 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 399 time to evaluate : 1.166 Fit side-chains REVERT: A 38 ASP cc_start: 0.8220 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: A 62 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7884 (mt-10) REVERT: A 68 GLN cc_start: 0.8848 (pt0) cc_final: 0.8563 (pt0) REVERT: B 62 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7884 (mt-10) REVERT: B 117 LYS cc_start: 0.8210 (OUTLIER) cc_final: 0.7963 (mmtm) REVERT: B 141 ARG cc_start: 0.8969 (mmm-85) cc_final: 0.8721 (mmm160) REVERT: B 150 MET cc_start: 0.9258 (OUTLIER) cc_final: 0.9041 (mpp) REVERT: C 178 LEU cc_start: 0.8771 (tp) cc_final: 0.8364 (mt) REVERT: D 38 ASP cc_start: 0.8225 (OUTLIER) cc_final: 0.7873 (m-30) REVERT: D 62 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 68 GLN cc_start: 0.8813 (pt0) cc_final: 0.8512 (pt0) REVERT: E 62 GLU cc_start: 0.8105 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 117 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7962 (mmtm) REVERT: E 141 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8726 (mmm160) REVERT: E 150 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9038 (mpp) REVERT: F 178 LEU cc_start: 0.8764 (tp) cc_final: 0.8355 (mt) REVERT: G 38 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7869 (m-30) REVERT: G 62 GLU cc_start: 0.8367 (mt-10) cc_final: 0.7865 (mt-10) REVERT: G 68 GLN cc_start: 0.8815 (pt0) cc_final: 0.8516 (pt0) REVERT: H 62 GLU cc_start: 0.8096 (mt-10) cc_final: 0.7878 (mt-10) REVERT: H 117 LYS cc_start: 0.8201 (OUTLIER) cc_final: 0.7960 (mmtm) REVERT: H 141 ARG cc_start: 0.8970 (mmm-85) cc_final: 0.8725 (mmm160) REVERT: H 150 MET cc_start: 0.9249 (OUTLIER) cc_final: 0.9033 (mpp) REVERT: I 178 LEU cc_start: 0.8770 (tp) cc_final: 0.8364 (mt) REVERT: J 38 ASP cc_start: 0.8217 (OUTLIER) cc_final: 0.7866 (m-30) REVERT: J 62 GLU cc_start: 0.8356 (mt-10) cc_final: 0.7870 (mt-10) REVERT: J 68 GLN cc_start: 0.8849 (pt0) cc_final: 0.8561 (pt0) REVERT: K 62 GLU cc_start: 0.8100 (mt-10) cc_final: 0.7879 (mt-10) REVERT: K 117 LYS cc_start: 0.8202 (OUTLIER) cc_final: 0.7963 (mmtm) REVERT: K 141 ARG cc_start: 0.8973 (mmm-85) cc_final: 0.8728 (mmm160) REVERT: K 150 MET cc_start: 0.9255 (OUTLIER) cc_final: 0.9037 (mpp) REVERT: L 178 LEU cc_start: 0.8770 (tp) cc_final: 0.8362 (mt) outliers start: 42 outliers final: 24 residues processed: 425 average time/residue: 0.7018 time to fit residues: 341.8665 Evaluate side-chains 413 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 377 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 277 ASP Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 117 LYS Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 185 optimal weight: 5.9990 chunk 276 optimal weight: 1.9990 chunk 143 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 109 optimal weight: 2.9990 chunk 272 optimal weight: 5.9990 chunk 4 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.144984 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.100479 restraints weight = 27540.043| |-----------------------------------------------------------------------------| r_work (start): 0.3002 rms_B_bonded: 1.99 r_work: 0.2848 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.2697 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 1.0855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 24840 Z= 0.185 Angle : 0.599 8.769 33648 Z= 0.311 Chirality : 0.045 0.135 3672 Planarity : 0.004 0.032 4440 Dihedral : 4.415 17.842 3312 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.67 % Allowed : 26.12 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.41 (0.15), residues: 3024 helix: 2.48 (0.14), residues: 1404 sheet: 0.02 (0.22), residues: 552 loop : -0.66 (0.17), residues: 1068 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 39 TYR 0.016 0.002 TYR F 146 PHE 0.015 0.002 PHE C 78 TRP 0.009 0.001 TRP H 54 HIS 0.004 0.001 HIS F 142 Details of bonding type rmsd covalent geometry : bond 0.00446 (24840) covalent geometry : angle 0.59911 (33648) hydrogen bonds : bond 0.06406 ( 1236) hydrogen bonds : angle 4.44975 ( 3636) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6048 Ramachandran restraints generated. 3024 Oldfield, 0 Emsley, 3024 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 420 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 377 time to evaluate : 1.142 Fit side-chains REVERT: A 38 ASP cc_start: 0.8277 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: A 62 GLU cc_start: 0.8342 (mt-10) cc_final: 0.7852 (mt-10) REVERT: A 68 GLN cc_start: 0.8915 (pt0) cc_final: 0.8564 (pt0) REVERT: B 62 GLU cc_start: 0.8241 (mt-10) cc_final: 0.8035 (mt-10) REVERT: B 117 LYS cc_start: 0.8257 (OUTLIER) cc_final: 0.8008 (mmtm) REVERT: B 141 ARG cc_start: 0.9079 (mmm-85) cc_final: 0.8775 (mmm160) REVERT: B 150 MET cc_start: 0.9262 (OUTLIER) cc_final: 0.9036 (mpp) REVERT: C 178 LEU cc_start: 0.8783 (tp) cc_final: 0.8369 (mt) REVERT: D 38 ASP cc_start: 0.8278 (OUTLIER) cc_final: 0.7947 (m-30) REVERT: D 62 GLU cc_start: 0.8345 (mt-10) cc_final: 0.7859 (mt-10) REVERT: D 68 GLN cc_start: 0.8910 (pt0) cc_final: 0.8561 (pt0) REVERT: E 62 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8013 (mt-10) REVERT: E 117 LYS cc_start: 0.8261 (OUTLIER) cc_final: 0.8013 (mmtm) REVERT: E 141 ARG cc_start: 0.9082 (mmm-85) cc_final: 0.8775 (mmm160) REVERT: E 150 MET cc_start: 0.9257 (OUTLIER) cc_final: 0.9029 (mpp) REVERT: F 178 LEU cc_start: 0.8781 (tp) cc_final: 0.8366 (mt) REVERT: G 38 ASP cc_start: 0.8275 (OUTLIER) cc_final: 0.7944 (m-30) REVERT: G 62 GLU cc_start: 0.8349 (mt-10) cc_final: 0.7863 (mt-10) REVERT: G 68 GLN cc_start: 0.8909 (pt0) cc_final: 0.8559 (pt0) REVERT: H 62 GLU cc_start: 0.8162 (mt-10) cc_final: 0.7930 (mt-10) REVERT: H 117 LYS cc_start: 0.8256 (OUTLIER) cc_final: 0.8013 (mmtm) REVERT: H 141 ARG cc_start: 0.9072 (mmm-85) cc_final: 0.8769 (mmm160) REVERT: H 150 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.9033 (mpp) REVERT: I 178 LEU cc_start: 0.8787 (tp) cc_final: 0.8374 (mt) REVERT: J 38 ASP cc_start: 0.8280 (OUTLIER) cc_final: 0.7954 (m-30) REVERT: J 62 GLU cc_start: 0.8341 (mt-10) cc_final: 0.7858 (mt-10) REVERT: J 68 GLN cc_start: 0.8909 (pt0) cc_final: 0.8558 (pt0) REVERT: K 62 GLU cc_start: 0.8240 (mt-10) cc_final: 0.8032 (mt-10) REVERT: K 117 LYS cc_start: 0.8260 (OUTLIER) cc_final: 0.8015 (mmtm) REVERT: K 141 ARG cc_start: 0.9076 (mmm-85) cc_final: 0.8774 (mmm160) REVERT: K 150 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9037 (mpp) REVERT: L 178 LEU cc_start: 0.8787 (tp) cc_final: 0.8374 (mt) outliers start: 43 outliers final: 27 residues processed: 401 average time/residue: 0.7006 time to fit residues: 321.0309 Evaluate side-chains 408 residues out of total 2736 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 369 time to evaluate : 1.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 213 LEU Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain B residue 117 LYS Chi-restraints excluded: chain B residue 120 THR Chi-restraints excluded: chain B residue 150 MET Chi-restraints excluded: chain B residue 277 ASP Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain C residue 159 MET Chi-restraints excluded: chain C residue 299 LEU Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 213 LEU Chi-restraints excluded: chain D residue 299 LEU Chi-restraints excluded: chain E residue 117 LYS Chi-restraints excluded: chain E residue 120 THR Chi-restraints excluded: chain E residue 150 MET Chi-restraints excluded: chain E residue 277 ASP Chi-restraints excluded: chain E residue 299 LEU Chi-restraints excluded: chain F residue 159 MET Chi-restraints excluded: chain F residue 299 LEU Chi-restraints excluded: chain G residue 38 ASP Chi-restraints excluded: chain G residue 213 LEU Chi-restraints excluded: chain G residue 299 LEU Chi-restraints excluded: chain H residue 117 LYS Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain H residue 150 MET Chi-restraints excluded: chain H residue 299 LEU Chi-restraints excluded: chain I residue 159 MET Chi-restraints excluded: chain I residue 299 LEU Chi-restraints excluded: chain J residue 38 ASP Chi-restraints excluded: chain J residue 213 LEU Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 117 LYS Chi-restraints excluded: chain K residue 120 THR Chi-restraints excluded: chain K residue 150 MET Chi-restraints excluded: chain K residue 277 ASP Chi-restraints excluded: chain K residue 299 LEU Chi-restraints excluded: chain L residue 159 MET Chi-restraints excluded: chain L residue 299 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 300 random chunks: chunk 191 optimal weight: 0.9980 chunk 152 optimal weight: 0.9990 chunk 204 optimal weight: 0.9990 chunk 123 optimal weight: 1.9990 chunk 178 optimal weight: 0.8980 chunk 179 optimal weight: 1.9990 chunk 5 optimal weight: 5.9990 chunk 274 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 102 optimal weight: 0.8980 chunk 222 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3654 r_free = 0.3654 target = 0.147457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.103446 restraints weight = 27784.346| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.99 r_work: 0.2854 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.2707 rms_B_bonded: 3.96 restraints_weight: 0.2500 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 1.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 24840 Z= 0.124 Angle : 0.533 7.693 33648 Z= 0.277 Chirality : 0.042 0.132 3672 Planarity : 0.004 0.032 4440 Dihedral : 4.194 17.264 3312 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 3.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 1.32 % Allowed : 26.59 % Favored : 72.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.64 (0.15), residues: 3024 helix: 2.59 (0.14), residues: 1404 sheet: 0.31 (0.23), residues: 480 loop : -0.49 (0.17), residues: 1140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG J 39 TYR 0.014 0.001 TYR K 118 PHE 0.013 0.001 PHE J 210 TRP 0.008 0.001 TRP E 54 HIS 0.002 0.001 HIS H 142 Details of bonding type rmsd covalent geometry : bond 0.00280 (24840) covalent geometry : angle 0.53267 (33648) hydrogen bonds : bond 0.05059 ( 1236) hydrogen bonds : angle 4.31444 ( 3636) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10355.93 seconds wall clock time: 176 minutes 20.07 seconds (10580.07 seconds total)