Starting phenix.real_space_refine on Thu Mar 5 01:48:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7z22_14455/03_2026/7z22_14455.cif Found real_map, /net/cci-nas-00/data/ceres_data/7z22_14455/03_2026/7z22_14455.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7z22_14455/03_2026/7z22_14455.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7z22_14455/03_2026/7z22_14455.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7z22_14455/03_2026/7z22_14455.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7z22_14455/03_2026/7z22_14455.map" } resolution = 2.95 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= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 96 5.16 5 C 12396 2.51 5 N 2892 2.21 5 O 3108 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 96 residue(s): 0.02s 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: 18492 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 1541 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1541 Classifications: {'peptide': 189} Link IDs: {'PTRANS': 6, 'TRANS': 182} Chain breaks: 1 Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 2.06, per 1000 atoms: 0.11 Number of scatterers: 18492 At special positions: 0 Unit cell: (101.37, 98.754, 157.614, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 96 16.00 O 3108 8.00 N 2892 7.00 C 12396 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=36, symmetry=0 Simple disulfide: pdb=" SG CYS A 54 " - pdb=" SG CYS A 198 " distance=2.03 Simple disulfide: pdb=" SG CYS A 61 " - pdb=" SG CYS A 192 " distance=2.03 Simple disulfide: pdb=" SG CYS A 65 " - pdb=" SG CYS A 187 " distance=2.03 Simple disulfide: pdb=" SG CYS B 54 " - pdb=" SG CYS B 198 " distance=2.03 Simple disulfide: pdb=" SG CYS C 54 " - pdb=" SG CYS C 198 " distance=2.03 Simple disulfide: pdb=" SG CYS D 54 " - pdb=" SG CYS D 198 " distance=2.03 Simple disulfide: pdb=" SG CYS E 54 " - pdb=" SG CYS E 198 " distance=2.03 Simple disulfide: pdb=" SG CYS F 54 " - pdb=" SG CYS F 198 " distance=2.03 Simple disulfide: pdb=" SG CYS G 54 " - pdb=" SG CYS G 198 " distance=2.03 Simple disulfide: pdb=" SG CYS H 54 " - pdb=" SG CYS H 198 " distance=2.03 Simple disulfide: pdb=" SG CYS I 54 " - pdb=" SG CYS I 198 " distance=2.03 Simple disulfide: pdb=" SG CYS J 54 " - pdb=" SG CYS J 198 " distance=2.03 Simple disulfide: pdb=" SG CYS K 54 " - pdb=" SG CYS K 198 " distance=2.03 Simple disulfide: pdb=" SG CYS L 54 " - pdb=" SG CYS L 198 " distance=2.03 Simple disulfide: pdb=" SG CYS B 61 " - pdb=" SG CYS B 192 " distance=2.03 Simple disulfide: pdb=" SG CYS C 61 " - pdb=" SG CYS C 192 " distance=2.03 Simple disulfide: pdb=" SG CYS D 61 " - pdb=" SG CYS D 192 " distance=2.03 Simple disulfide: pdb=" SG CYS E 61 " - pdb=" SG CYS E 192 " distance=2.03 Simple disulfide: pdb=" SG CYS F 61 " - pdb=" SG CYS F 192 " distance=2.03 Simple disulfide: pdb=" SG CYS G 61 " - pdb=" SG CYS G 192 " distance=2.03 Simple disulfide: pdb=" SG CYS H 61 " - pdb=" SG CYS H 192 " distance=2.03 Simple disulfide: pdb=" SG CYS I 61 " - pdb=" SG CYS I 192 " distance=2.03 Simple disulfide: pdb=" SG CYS J 61 " - pdb=" SG CYS J 192 " distance=2.03 Simple disulfide: pdb=" SG CYS K 61 " - pdb=" SG CYS K 192 " distance=2.03 Simple disulfide: pdb=" SG CYS L 61 " - pdb=" SG CYS L 192 " distance=2.03 Simple disulfide: pdb=" SG CYS B 65 " - pdb=" SG CYS B 187 " distance=2.03 Simple disulfide: pdb=" SG CYS C 65 " - pdb=" SG CYS C 187 " distance=2.03 Simple disulfide: pdb=" SG CYS D 65 " - pdb=" SG CYS D 187 " distance=2.03 Simple disulfide: pdb=" SG CYS E 65 " - pdb=" SG CYS E 187 " distance=2.03 Simple disulfide: pdb=" SG CYS F 65 " - pdb=" SG CYS F 187 " distance=2.03 Simple disulfide: pdb=" SG CYS G 65 " - pdb=" SG CYS G 187 " distance=2.03 Simple disulfide: pdb=" SG CYS H 65 " - pdb=" SG CYS H 187 " distance=2.03 Simple disulfide: pdb=" SG CYS I 65 " - pdb=" SG CYS I 187 " distance=2.03 Simple disulfide: pdb=" SG CYS J 65 " - pdb=" SG CYS J 187 " distance=2.03 Simple disulfide: pdb=" SG CYS K 65 " - pdb=" SG CYS K 187 " distance=2.03 Simple disulfide: pdb=" SG CYS L 65 " - pdb=" SG CYS L 187 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.80 Conformation dependent library (CDL) restraints added in 898.9 milliseconds 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4320 Finding SS restraints... Secondary structure from input PDB file: 84 helices and 12 sheets defined 77.2% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'A' and resid 3 through 15 removed outlier: 3.896A pdb=" N LEU A 7 " --> pdb=" O ASP A 3 " (cutoff:3.500A) Processing helix chain 'A' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL A 24 " --> pdb=" O ALA A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) Processing helix chain 'A' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL A 64 " --> pdb=" O GLY A 60 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 105 Proline residue: A 88 - end of helix Processing helix chain 'A' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR A 177 " --> pdb=" O GLN A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 202 through 235 Processing helix chain 'B' and resid 3 through 15 removed outlier: 3.896A pdb=" N LEU B 7 " --> pdb=" O ASP B 3 " (cutoff:3.500A) Processing helix chain 'B' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL B 24 " --> pdb=" O ALA B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA B 44 " --> pdb=" O ALA B 40 " (cutoff:3.500A) Processing helix chain 'B' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL B 64 " --> pdb=" O GLY B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 73 through 105 Proline residue: B 88 - end of helix Processing helix chain 'B' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR B 177 " --> pdb=" O GLN B 173 " (cutoff:3.500A) Processing helix chain 'B' and resid 202 through 235 Processing helix chain 'C' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU C 7 " --> pdb=" O ASP C 3 " (cutoff:3.500A) Processing helix chain 'C' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL C 24 " --> pdb=" O ALA C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA C 44 " --> pdb=" O ALA C 40 " (cutoff:3.500A) Processing helix chain 'C' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL C 64 " --> pdb=" O GLY C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 105 Proline residue: C 88 - end of helix Processing helix chain 'C' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR C 177 " --> pdb=" O GLN C 173 " (cutoff:3.500A) Processing helix chain 'C' and resid 202 through 235 Processing helix chain 'D' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU D 7 " --> pdb=" O ASP D 3 " (cutoff:3.500A) Processing helix chain 'D' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL D 24 " --> pdb=" O ALA D 20 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA D 44 " --> pdb=" O ALA D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 60 through 70 removed outlier: 3.543A pdb=" N VAL D 64 " --> pdb=" O GLY D 60 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 105 Proline residue: D 88 - end of helix Processing helix chain 'D' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR D 177 " --> pdb=" O GLN D 173 " (cutoff:3.500A) Processing helix chain 'D' and resid 202 through 235 Processing helix chain 'E' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU E 7 " --> pdb=" O ASP E 3 " (cutoff:3.500A) Processing helix chain 'E' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL E 24 " --> pdb=" O ALA E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA E 44 " --> pdb=" O ALA E 40 " (cutoff:3.500A) Processing helix chain 'E' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL E 64 " --> pdb=" O GLY E 60 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 105 Proline residue: E 88 - end of helix Processing helix chain 'E' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR E 177 " --> pdb=" O GLN E 173 " (cutoff:3.500A) Processing helix chain 'E' and resid 202 through 235 Processing helix chain 'F' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU F 7 " --> pdb=" O ASP F 3 " (cutoff:3.500A) Processing helix chain 'F' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL F 24 " --> pdb=" O ALA F 20 " (cutoff:3.500A) Processing helix chain 'F' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA F 44 " --> pdb=" O ALA F 40 " (cutoff:3.500A) Processing helix chain 'F' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL F 64 " --> pdb=" O GLY F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 73 through 105 Proline residue: F 88 - end of helix Processing helix chain 'F' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR F 177 " --> pdb=" O GLN F 173 " (cutoff:3.500A) Processing helix chain 'F' and resid 202 through 235 Processing helix chain 'G' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU G 7 " --> pdb=" O ASP G 3 " (cutoff:3.500A) Processing helix chain 'G' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL G 24 " --> pdb=" O ALA G 20 " (cutoff:3.500A) Processing helix chain 'G' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA G 44 " --> pdb=" O ALA G 40 " (cutoff:3.500A) Processing helix chain 'G' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL G 64 " --> pdb=" O GLY G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 73 through 105 Proline residue: G 88 - end of helix Processing helix chain 'G' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR G 177 " --> pdb=" O GLN G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 202 through 235 Processing helix chain 'H' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU H 7 " --> pdb=" O ASP H 3 " (cutoff:3.500A) Processing helix chain 'H' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL H 24 " --> pdb=" O ALA H 20 " (cutoff:3.500A) Processing helix chain 'H' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA H 44 " --> pdb=" O ALA H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL H 64 " --> pdb=" O GLY H 60 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 105 Proline residue: H 88 - end of helix Processing helix chain 'H' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR H 177 " --> pdb=" O GLN H 173 " (cutoff:3.500A) Processing helix chain 'H' and resid 202 through 235 Processing helix chain 'I' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU I 7 " --> pdb=" O ASP I 3 " (cutoff:3.500A) Processing helix chain 'I' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL I 24 " --> pdb=" O ALA I 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) Processing helix chain 'I' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL I 64 " --> pdb=" O GLY I 60 " (cutoff:3.500A) Processing helix chain 'I' and resid 73 through 105 Proline residue: I 88 - end of helix Processing helix chain 'I' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR I 177 " --> pdb=" O GLN I 173 " (cutoff:3.500A) Processing helix chain 'I' and resid 202 through 235 Processing helix chain 'J' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU J 7 " --> pdb=" O ASP J 3 " (cutoff:3.500A) Processing helix chain 'J' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL J 24 " --> pdb=" O ALA J 20 " (cutoff:3.500A) Processing helix chain 'J' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA J 44 " --> pdb=" O ALA J 40 " (cutoff:3.500A) Processing helix chain 'J' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL J 64 " --> pdb=" O GLY J 60 " (cutoff:3.500A) Processing helix chain 'J' and resid 73 through 105 Proline residue: J 88 - end of helix Processing helix chain 'J' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR J 177 " --> pdb=" O GLN J 173 " (cutoff:3.500A) Processing helix chain 'J' and resid 202 through 235 Processing helix chain 'K' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU K 7 " --> pdb=" O ASP K 3 " (cutoff:3.500A) Processing helix chain 'K' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL K 24 " --> pdb=" O ALA K 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA K 44 " --> pdb=" O ALA K 40 " (cutoff:3.500A) Processing helix chain 'K' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL K 64 " --> pdb=" O GLY K 60 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 105 Proline residue: K 88 - end of helix Processing helix chain 'K' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR K 177 " --> pdb=" O GLN K 173 " (cutoff:3.500A) Processing helix chain 'K' and resid 202 through 235 Processing helix chain 'L' and resid 3 through 15 removed outlier: 3.895A pdb=" N LEU L 7 " --> pdb=" O ASP L 3 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 40 removed outlier: 4.194A pdb=" N VAL L 24 " --> pdb=" O ALA L 20 " (cutoff:3.500A) Processing helix chain 'L' and resid 40 through 45 removed outlier: 3.669A pdb=" N ALA L 44 " --> pdb=" O ALA L 40 " (cutoff:3.500A) Processing helix chain 'L' and resid 60 through 70 removed outlier: 3.544A pdb=" N VAL L 64 " --> pdb=" O GLY L 60 " (cutoff:3.500A) Processing helix chain 'L' and resid 73 through 105 Proline residue: L 88 - end of helix Processing helix chain 'L' and resid 152 through 178 removed outlier: 3.885A pdb=" N TYR L 177 " --> pdb=" O GLN L 173 " (cutoff:3.500A) Processing helix chain 'L' and resid 202 through 235 Processing sheet with id=AA1, first strand: chain 'A' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG A 53 " --> pdb=" O PHE A 199 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG B 53 " --> pdb=" O PHE B 199 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG C 53 " --> pdb=" O PHE C 199 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG D 53 " --> pdb=" O PHE D 199 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG E 53 " --> pdb=" O PHE E 199 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG F 53 " --> pdb=" O PHE F 199 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG G 53 " --> pdb=" O PHE G 199 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG H 53 " --> pdb=" O PHE H 199 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'I' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG I 53 " --> pdb=" O PHE I 199 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'J' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG J 53 " --> pdb=" O PHE J 199 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG K 53 " --> pdb=" O PHE K 199 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.676A pdb=" N ARG L 53 " --> pdb=" O PHE L 199 " (cutoff:3.500A) 1380 hydrogen bonds defined for protein. 4104 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: 2.76 Time building geometry restraints manager: 2.39 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 5401 1.34 - 1.46: 4232 1.46 - 1.58: 9255 1.58 - 1.69: 0 1.69 - 1.81: 120 Bond restraints: 19008 Sorted by residual: bond pdb=" CB THR L 186 " pdb=" CG2 THR L 186 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR F 186 " pdb=" CG2 THR F 186 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.00e-01 bond pdb=" CB THR C 186 " pdb=" CG2 THR C 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB THR I 186 " pdb=" CG2 THR I 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.81e-01 bond pdb=" CB THR J 186 " pdb=" CG2 THR J 186 " ideal model delta sigma weight residual 1.521 1.494 0.027 3.30e-02 9.18e+02 6.78e-01 ... (remaining 19003 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.96: 24308 0.96 - 1.92: 1180 1.92 - 2.89: 216 2.89 - 3.85: 60 3.85 - 4.81: 36 Bond angle restraints: 25800 Sorted by residual: angle pdb=" C VAL J 87 " pdb=" CA VAL J 87 " pdb=" CB VAL J 87 " ideal model delta sigma weight residual 113.70 110.28 3.42 9.50e-01 1.11e+00 1.29e+01 angle pdb=" C VAL I 87 " pdb=" CA VAL I 87 " pdb=" CB VAL I 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL F 87 " pdb=" CA VAL F 87 " pdb=" CB VAL F 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL C 87 " pdb=" CA VAL C 87 " pdb=" CB VAL C 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 angle pdb=" C VAL L 87 " pdb=" CA VAL L 87 " pdb=" CB VAL L 87 " ideal model delta sigma weight residual 113.70 110.29 3.41 9.50e-01 1.11e+00 1.28e+01 ... (remaining 25795 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.46: 9059 8.46 - 16.92: 1148 16.92 - 25.38: 389 25.38 - 33.84: 348 33.84 - 42.30: 120 Dihedral angle restraints: 11064 sinusoidal: 4392 harmonic: 6672 Sorted by residual: dihedral pdb=" CA GLN L 173 " pdb=" CB GLN L 173 " pdb=" CG GLN L 173 " pdb=" CD GLN L 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 dihedral pdb=" CA GLN I 173 " pdb=" CB GLN I 173 " pdb=" CG GLN I 173 " pdb=" CD GLN I 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 dihedral pdb=" CA GLN C 173 " pdb=" CB GLN C 173 " pdb=" CG GLN C 173 " pdb=" CD GLN C 173 " ideal model delta sinusoidal sigma weight residual -60.00 -99.97 39.97 3 1.50e+01 4.44e-03 7.10e+00 ... (remaining 11061 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1895 0.027 - 0.055: 725 0.055 - 0.082: 187 0.082 - 0.109: 108 0.109 - 0.137: 37 Chirality restraints: 2952 Sorted by residual: chirality pdb=" CA PRO B 203 " pdb=" N PRO B 203 " pdb=" C PRO B 203 " pdb=" CB PRO B 203 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.67e-01 chirality pdb=" CA PRO E 203 " pdb=" N PRO E 203 " pdb=" C PRO E 203 " pdb=" CB PRO E 203 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.62e-01 chirality pdb=" CA PRO D 203 " pdb=" N PRO D 203 " pdb=" C PRO D 203 " pdb=" CB PRO D 203 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 2949 not shown) Planarity restraints: 3096 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 76 " -0.082 9.50e-02 1.11e+02 3.68e-02 9.51e-01 pdb=" NE ARG H 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG H 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG H 76 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG H 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG D 76 " -0.081 9.50e-02 1.11e+02 3.65e-02 9.34e-01 pdb=" NE ARG D 76 " 0.007 2.00e-02 2.50e+03 pdb=" CZ ARG D 76 " -0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG D 76 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG D 76 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG J 76 " 0.081 9.50e-02 1.11e+02 3.65e-02 9.33e-01 pdb=" NE ARG J 76 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG J 76 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG J 76 " -0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG J 76 " 0.001 2.00e-02 2.50e+03 ... (remaining 3093 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1161 2.74 - 3.28: 18793 3.28 - 3.82: 32371 3.82 - 4.36: 33981 4.36 - 4.90: 62159 Nonbonded interactions: 148465 Sorted by model distance: nonbonded pdb=" OD1 ASN G 63 " pdb=" NH1 ARG L 53 " model vdw 2.198 3.120 nonbonded pdb=" NH1 ARG E 53 " pdb=" OD1 ASN F 63 " model vdw 2.198 3.120 nonbonded pdb=" NH1 ARG G 53 " pdb=" OD1 ASN H 63 " model vdw 2.199 3.120 nonbonded pdb=" NH1 ARG D 53 " pdb=" OD1 ASN E 63 " model vdw 2.199 3.120 nonbonded pdb=" OD1 ASN A 63 " pdb=" NH1 ARG F 53 " model vdw 2.199 3.120 ... (remaining 148460 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = chain '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: 5.270 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: 0.030 Extract box with map and model: 0.480 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 15.270 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 19044 Z= 0.126 Angle : 0.513 4.809 25872 Z= 0.298 Chirality : 0.036 0.137 2952 Planarity : 0.004 0.037 3096 Dihedral : 11.338 42.299 6636 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.18), residues: 2220 helix: 3.02 (0.11), residues: 1632 sheet: -1.64 (0.35), residues: 204 loop : -2.64 (0.31), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 76 TYR 0.011 0.002 TYR K 155 PHE 0.017 0.001 PHE B 212 TRP 0.005 0.001 TRP G 25 HIS 0.003 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00280 (19008) covalent geometry : angle 0.51354 (25800) SS BOND : bond 0.00143 ( 36) SS BOND : angle 0.44275 ( 72) hydrogen bonds : bond 0.10365 ( 1380) hydrogen bonds : angle 4.71540 ( 4104) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 754 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 754 time to evaluate : 0.551 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 18 residues processed: 754 average time/residue: 0.5138 time to fit residues: 439.3916 Evaluate side-chains 333 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 315 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 ILE Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain C residue 181 LEU Chi-restraints excluded: chain C residue 211 ILE Chi-restraints excluded: chain D residue 211 ILE Chi-restraints excluded: chain E residue 211 ILE Chi-restraints excluded: chain F residue 181 LEU Chi-restraints excluded: chain F residue 211 ILE Chi-restraints excluded: chain G residue 211 ILE Chi-restraints excluded: chain H residue 12 ASP Chi-restraints excluded: chain H residue 211 ILE Chi-restraints excluded: chain I residue 181 LEU Chi-restraints excluded: chain I residue 211 ILE Chi-restraints excluded: chain J residue 211 ILE Chi-restraints excluded: chain K residue 12 ASP Chi-restraints excluded: chain K residue 211 ILE Chi-restraints excluded: chain L residue 181 LEU Chi-restraints excluded: chain L residue 211 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 98 optimal weight: 7.9990 chunk 194 optimal weight: 7.9990 chunk 107 optimal weight: 5.9990 chunk 10 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 130 optimal weight: 0.5980 chunk 124 optimal weight: 0.9990 chunk 103 optimal weight: 7.9990 chunk 200 optimal weight: 0.8980 chunk 212 optimal weight: 2.9990 chunk 77 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- 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 = 0.4572 r_free = 0.4572 target = 0.166419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4270 r_free = 0.4270 target = 0.142628 restraints weight = 50516.076| |-----------------------------------------------------------------------------| r_work (start): 0.4217 rms_B_bonded: 4.08 r_work: 0.4125 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.4125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.5167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 19044 Z= 0.180 Angle : 0.875 12.314 25872 Z= 0.419 Chirality : 0.043 0.145 2952 Planarity : 0.004 0.024 3096 Dihedral : 4.424 25.324 2472 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 5.98 % Allowed : 15.05 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.71 (0.17), residues: 2220 helix: 2.20 (0.11), residues: 1632 sheet: -1.15 (0.37), residues: 204 loop : -2.34 (0.30), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG J 76 TYR 0.025 0.003 TYR J 98 PHE 0.026 0.003 PHE G 233 TRP 0.022 0.003 TRP F 78 HIS 0.004 0.001 HIS H 74 Details of bonding type rmsd covalent geometry : bond 0.00400 (19008) covalent geometry : angle 0.87613 (25800) SS BOND : bond 0.00032 ( 36) SS BOND : angle 0.45220 ( 72) hydrogen bonds : bond 0.03799 ( 1380) hydrogen bonds : angle 4.24251 ( 4104) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 514 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 122 poor density : 392 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 26 LEU cc_start: 0.7547 (pp) cc_final: 0.7240 (mt) REVERT: A 205 GLU cc_start: 0.8804 (tp30) cc_final: 0.8603 (tp30) REVERT: B 26 LEU cc_start: 0.7519 (pp) cc_final: 0.7180 (mt) REVERT: B 208 ILE cc_start: 0.7889 (OUTLIER) cc_final: 0.7597 (mm) REVERT: C 26 LEU cc_start: 0.7474 (pp) cc_final: 0.7173 (mt) REVERT: C 208 ILE cc_start: 0.7944 (OUTLIER) cc_final: 0.7636 (mt) REVERT: C 209 PHE cc_start: 0.7520 (m-10) cc_final: 0.7136 (m-80) REVERT: C 219 VAL cc_start: 0.7375 (t) cc_final: 0.7091 (p) REVERT: D 26 LEU cc_start: 0.7552 (pp) cc_final: 0.7245 (mt) REVERT: E 26 LEU cc_start: 0.7496 (pp) cc_final: 0.7155 (mt) REVERT: E 208 ILE cc_start: 0.7890 (OUTLIER) cc_final: 0.7603 (mm) REVERT: F 26 LEU cc_start: 0.7495 (pp) cc_final: 0.7193 (mt) REVERT: F 208 ILE cc_start: 0.7940 (OUTLIER) cc_final: 0.7632 (mt) REVERT: F 209 PHE cc_start: 0.7502 (m-10) cc_final: 0.7158 (m-80) REVERT: F 219 VAL cc_start: 0.7367 (t) cc_final: 0.7077 (p) REVERT: G 26 LEU cc_start: 0.7558 (pp) cc_final: 0.7251 (mt) REVERT: G 205 GLU cc_start: 0.8815 (tp30) cc_final: 0.8614 (tp30) REVERT: H 26 LEU cc_start: 0.7530 (pp) cc_final: 0.7195 (mt) REVERT: H 208 ILE cc_start: 0.7854 (OUTLIER) cc_final: 0.7557 (mm) REVERT: I 26 LEU cc_start: 0.7505 (pp) cc_final: 0.7205 (mt) REVERT: I 208 ILE cc_start: 0.7921 (OUTLIER) cc_final: 0.7606 (mt) REVERT: I 209 PHE cc_start: 0.7501 (m-10) cc_final: 0.7131 (m-80) REVERT: I 219 VAL cc_start: 0.7376 (t) cc_final: 0.7090 (p) REVERT: J 26 LEU cc_start: 0.7557 (pp) cc_final: 0.7248 (mt) REVERT: K 26 LEU cc_start: 0.7509 (pp) cc_final: 0.7167 (mt) REVERT: K 208 ILE cc_start: 0.7893 (OUTLIER) cc_final: 0.7603 (mm) REVERT: L 26 LEU cc_start: 0.7507 (pp) cc_final: 0.7202 (mt) REVERT: L 208 ILE cc_start: 0.7939 (OUTLIER) cc_final: 0.7624 (mt) REVERT: L 209 PHE cc_start: 0.7491 (m-10) cc_final: 0.7134 (m-80) REVERT: L 219 VAL cc_start: 0.7389 (t) cc_final: 0.7103 (p) outliers start: 122 outliers final: 16 residues processed: 454 average time/residue: 0.4570 time to fit residues: 239.9765 Evaluate side-chains 356 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 332 time to evaluate : 0.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 104 GLU Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain B residue 208 ILE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain C residue 208 ILE Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 104 GLU Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain E residue 208 ILE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain F residue 208 ILE Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 104 GLU Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 208 ILE Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain I residue 208 ILE Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 104 GLU Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain K residue 208 ILE Chi-restraints excluded: chain L residue 190 ASP Chi-restraints excluded: chain L residue 208 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 197 optimal weight: 5.9990 chunk 142 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 211 optimal weight: 8.9990 chunk 13 optimal weight: 10.0000 chunk 6 optimal weight: 5.9990 chunk 215 optimal weight: 7.9990 chunk 76 optimal weight: 0.1980 chunk 141 optimal weight: 6.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 74 HIS A 195 GLN B 173 GLN B 195 GLN ** C 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN D 74 HIS D 195 GLN E 173 GLN E 195 GLN ** F 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 195 GLN G 74 HIS G 195 GLN H 173 GLN H 195 GLN ** I 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 195 GLN J 74 HIS J 195 GLN ** K 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 195 GLN ** L 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 195 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.122564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.095700 restraints weight = 45543.648| |-----------------------------------------------------------------------------| r_work (start): 0.3548 rms_B_bonded: 3.42 r_work: 0.3445 rms_B_bonded: 4.16 restraints_weight: 0.5000 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 1.0515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 19044 Z= 0.281 Angle : 0.941 12.178 25872 Z= 0.468 Chirality : 0.050 0.209 2952 Planarity : 0.005 0.024 3096 Dihedral : 4.581 15.292 2436 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 6.76 % Allowed : 18.73 % Favored : 74.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.80 (0.17), residues: 2220 helix: 1.48 (0.11), residues: 1632 sheet: -1.06 (0.37), residues: 204 loop : -2.66 (0.35), residues: 384 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.002 ARG D 76 TYR 0.018 0.003 TYR J 177 PHE 0.031 0.004 PHE D 233 TRP 0.013 0.002 TRP B 78 HIS 0.006 0.002 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00632 (19008) covalent geometry : angle 0.94103 (25800) SS BOND : bond 0.00126 ( 36) SS BOND : angle 0.81969 ( 72) hydrogen bonds : bond 0.06678 ( 1380) hydrogen bonds : angle 4.78945 ( 4104) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 529 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 138 poor density : 391 time to evaluate : 0.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8257 (OUTLIER) cc_final: 0.7967 (ptp90) REVERT: A 76 ARG cc_start: 0.9221 (OUTLIER) cc_final: 0.8671 (ttp-170) REVERT: A 98 TYR cc_start: 0.7413 (OUTLIER) cc_final: 0.6475 (m-80) REVERT: B 53 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7175 (ptp90) REVERT: B 84 PHE cc_start: 0.9068 (OUTLIER) cc_final: 0.8521 (t80) REVERT: C 53 ARG cc_start: 0.8262 (OUTLIER) cc_final: 0.7925 (ptp90) REVERT: C 84 PHE cc_start: 0.9145 (OUTLIER) cc_final: 0.8936 (t80) REVERT: C 205 GLU cc_start: 0.9151 (tp30) cc_final: 0.8938 (tt0) REVERT: D 53 ARG cc_start: 0.8230 (OUTLIER) cc_final: 0.7946 (ptp90) REVERT: E 53 ARG cc_start: 0.8210 (OUTLIER) cc_final: 0.7148 (ptp90) REVERT: E 84 PHE cc_start: 0.9080 (OUTLIER) cc_final: 0.8526 (t80) REVERT: E 205 GLU cc_start: 0.9123 (tp30) cc_final: 0.8915 (tt0) REVERT: F 53 ARG cc_start: 0.8336 (OUTLIER) cc_final: 0.8033 (ptp90) REVERT: F 84 PHE cc_start: 0.9128 (OUTLIER) cc_final: 0.8913 (t80) REVERT: F 205 GLU cc_start: 0.9162 (tp30) cc_final: 0.8888 (tt0) REVERT: G 53 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (ptp90) REVERT: G 76 ARG cc_start: 0.9226 (OUTLIER) cc_final: 0.8704 (ttp-170) REVERT: G 98 TYR cc_start: 0.7416 (OUTLIER) cc_final: 0.6482 (m-80) REVERT: H 53 ARG cc_start: 0.8251 (OUTLIER) cc_final: 0.7202 (ptp90) REVERT: H 84 PHE cc_start: 0.9073 (OUTLIER) cc_final: 0.8524 (t80) REVERT: I 84 PHE cc_start: 0.9132 (OUTLIER) cc_final: 0.8924 (t80) REVERT: J 53 ARG cc_start: 0.8245 (OUTLIER) cc_final: 0.7958 (ptp90) REVERT: K 53 ARG cc_start: 0.8226 (OUTLIER) cc_final: 0.7168 (ptp90) REVERT: K 84 PHE cc_start: 0.9072 (OUTLIER) cc_final: 0.8523 (t80) REVERT: L 53 ARG cc_start: 0.8351 (OUTLIER) cc_final: 0.8052 (ptp90) REVERT: L 84 PHE cc_start: 0.9142 (OUTLIER) cc_final: 0.8925 (t80) REVERT: L 205 GLU cc_start: 0.9154 (tp30) cc_final: 0.8870 (tt0) outliers start: 138 outliers final: 28 residues processed: 493 average time/residue: 0.5508 time to fit residues: 305.4893 Evaluate side-chains 317 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 266 time to evaluate : 0.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 ARG Chi-restraints excluded: chain A residue 76 ARG Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 100 MET Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 53 ARG Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 190 ASP Chi-restraints excluded: chain D residue 53 ARG Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 100 MET Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 210 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 53 ARG Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 53 ARG Chi-restraints excluded: chain G residue 76 ARG Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 100 MET Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 190 ASP Chi-restraints excluded: chain J residue 53 ARG Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 100 MET Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 210 ILE Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 53 ARG Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 190 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 183 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 177 optimal weight: 5.9990 chunk 87 optimal weight: 0.9980 chunk 119 optimal weight: 1.9990 chunk 178 optimal weight: 1.9990 chunk 129 optimal weight: 7.9990 chunk 19 optimal weight: 2.9990 chunk 158 optimal weight: 0.0470 chunk 64 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 74 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.117273 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.091108 restraints weight = 46649.773| |-----------------------------------------------------------------------------| r_work (start): 0.3480 rms_B_bonded: 3.38 r_work: 0.3381 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 1.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 19044 Z= 0.136 Angle : 0.717 11.533 25872 Z= 0.347 Chirality : 0.039 0.140 2952 Planarity : 0.003 0.022 3096 Dihedral : 3.972 14.907 2436 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer: Outliers : 5.78 % Allowed : 21.52 % Favored : 72.70 % 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: 1.67 (0.17), residues: 2220 helix: 2.14 (0.11), residues: 1644 sheet: -0.68 (0.39), residues: 204 loop : -2.72 (0.34), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG G 76 TYR 0.020 0.003 TYR C 98 PHE 0.032 0.002 PHE D 32 TRP 0.005 0.001 TRP H 174 HIS 0.002 0.001 HIS B 74 Details of bonding type rmsd covalent geometry : bond 0.00318 (19008) covalent geometry : angle 0.71819 (25800) SS BOND : bond 0.00057 ( 36) SS BOND : angle 0.27194 ( 72) hydrogen bonds : bond 0.03896 ( 1380) hydrogen bonds : angle 4.09688 ( 4104) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 317 time to evaluate : 0.615 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 213 MET cc_start: 0.8977 (mmm) cc_final: 0.8734 (mmm) REVERT: B 84 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8504 (t80) REVERT: E 84 PHE cc_start: 0.9002 (OUTLIER) cc_final: 0.8503 (t80) REVERT: G 213 MET cc_start: 0.8985 (mmm) cc_final: 0.8738 (mmm) REVERT: H 84 PHE cc_start: 0.9025 (OUTLIER) cc_final: 0.8523 (t80) REVERT: K 84 PHE cc_start: 0.9006 (OUTLIER) cc_final: 0.8500 (t80) outliers start: 118 outliers final: 36 residues processed: 383 average time/residue: 0.4431 time to fit residues: 196.5615 Evaluate side-chains 317 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 277 time to evaluate : 0.512 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 190 ASP Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 190 ASP Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain F residue 190 ASP Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 190 ASP Chi-restraints excluded: chain H residue 228 LEU Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 190 ASP Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 93 optimal weight: 7.9990 chunk 12 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 191 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 192 optimal weight: 1.9990 chunk 104 optimal weight: 9.9990 chunk 139 optimal weight: 5.9990 chunk 208 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 74 HIS D 74 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 HIS J 74 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.096917 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.073793 restraints weight = 47996.772| |-----------------------------------------------------------------------------| r_work (start): 0.3183 rms_B_bonded: 3.19 r_work: 0.3078 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 1.3211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 19044 Z= 0.221 Angle : 0.813 13.666 25872 Z= 0.415 Chirality : 0.044 0.187 2952 Planarity : 0.005 0.039 3096 Dihedral : 4.429 31.857 2436 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 10.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 6.62 % Allowed : 22.30 % Favored : 71.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: 1.93 (0.17), residues: 2220 helix: 2.33 (0.11), residues: 1656 sheet: -0.62 (0.36), residues: 204 loop : -2.76 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 76 TYR 0.029 0.003 TYR D 98 PHE 0.026 0.002 PHE I 32 TRP 0.011 0.001 TRP A 174 HIS 0.004 0.002 HIS C 74 Details of bonding type rmsd covalent geometry : bond 0.00502 (19008) covalent geometry : angle 0.81330 (25800) SS BOND : bond 0.00121 ( 36) SS BOND : angle 0.55751 ( 72) hydrogen bonds : bond 0.06078 ( 1380) hydrogen bonds : angle 4.20284 ( 4104) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 352 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: B 84 PHE cc_start: 0.9213 (OUTLIER) cc_final: 0.8745 (t80) REVERT: B 226 ILE cc_start: 0.7967 (mt) cc_final: 0.7721 (mp) REVERT: E 84 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8736 (t80) REVERT: E 226 ILE cc_start: 0.7970 (mt) cc_final: 0.7725 (mp) REVERT: H 84 PHE cc_start: 0.9228 (OUTLIER) cc_final: 0.8759 (t80) REVERT: K 84 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8741 (t80) REVERT: K 226 ILE cc_start: 0.7994 (mt) cc_final: 0.7752 (mp) outliers start: 135 outliers final: 69 residues processed: 440 average time/residue: 0.4416 time to fit residues: 224.2354 Evaluate side-chains 329 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 256 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 39 THR Chi-restraints excluded: chain A residue 82 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 75 VAL Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 214 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 82 ILE Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 90 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain C residue 214 LEU Chi-restraints excluded: chain D residue 19 THR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 39 THR Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 75 VAL Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 214 LEU Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 82 ILE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 89 THR Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 39 THR Chi-restraints excluded: chain G residue 82 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 75 VAL Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 214 LEU Chi-restraints excluded: chain H residue 225 ILE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 82 ILE Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain I residue 214 LEU Chi-restraints excluded: chain J residue 19 THR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 39 THR Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 75 VAL Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 82 ILE Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 90 LEU Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 20 optimal weight: 1.9990 chunk 88 optimal weight: 0.5980 chunk 163 optimal weight: 8.9990 chunk 57 optimal weight: 0.4980 chunk 139 optimal weight: 9.9990 chunk 189 optimal weight: 0.9990 chunk 80 optimal weight: 0.0170 chunk 109 optimal weight: 9.9990 chunk 199 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 224 ASN ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 224 ASN ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.097094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.074675 restraints weight = 48727.643| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 3.27 r_work: 0.3099 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 1.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 19044 Z= 0.129 Angle : 0.726 12.769 25872 Z= 0.345 Chirality : 0.038 0.120 2952 Planarity : 0.003 0.022 3096 Dihedral : 3.995 21.180 2436 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 9.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.53 % Allowed : 29.85 % Favored : 66.62 % 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: 2.40 (0.18), residues: 2220 helix: 2.69 (0.12), residues: 1656 sheet: -0.47 (0.37), residues: 204 loop : -2.75 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 76 TYR 0.026 0.002 TYR A 98 PHE 0.031 0.002 PHE F 32 TRP 0.004 0.000 TRP E 174 HIS 0.002 0.001 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00278 (19008) covalent geometry : angle 0.72727 (25800) SS BOND : bond 0.00062 ( 36) SS BOND : angle 0.28136 ( 72) hydrogen bonds : bond 0.04050 ( 1380) hydrogen bonds : angle 3.96399 ( 4104) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 316 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 177 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7176 (p90) REVERT: A 226 ILE cc_start: 0.8123 (mm) cc_final: 0.7844 (mt) REVERT: B 53 ARG cc_start: 0.8094 (OUTLIER) cc_final: 0.7354 (ptp90) REVERT: B 84 PHE cc_start: 0.9206 (OUTLIER) cc_final: 0.8748 (t80) REVERT: B 212 PHE cc_start: 0.9239 (OUTLIER) cc_final: 0.8854 (t80) REVERT: B 226 ILE cc_start: 0.8030 (mt) cc_final: 0.7828 (mp) REVERT: B 229 PHE cc_start: 0.8280 (t80) cc_final: 0.7827 (t80) REVERT: C 229 PHE cc_start: 0.8301 (t80) cc_final: 0.7818 (t80) REVERT: D 177 TYR cc_start: 0.7903 (OUTLIER) cc_final: 0.7069 (p90) REVERT: E 53 ARG cc_start: 0.8092 (OUTLIER) cc_final: 0.7343 (ptp90) REVERT: E 84 PHE cc_start: 0.9192 (OUTLIER) cc_final: 0.8796 (t80) REVERT: E 226 ILE cc_start: 0.8021 (mt) cc_final: 0.7816 (mp) REVERT: E 229 PHE cc_start: 0.8270 (t80) cc_final: 0.7807 (t80) REVERT: F 229 PHE cc_start: 0.8289 (t80) cc_final: 0.7828 (t80) REVERT: G 177 TYR cc_start: 0.8001 (OUTLIER) cc_final: 0.7174 (p90) REVERT: G 226 ILE cc_start: 0.8133 (mm) cc_final: 0.7851 (mt) REVERT: H 53 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7358 (ptp90) REVERT: H 84 PHE cc_start: 0.9221 (OUTLIER) cc_final: 0.8763 (t80) REVERT: H 177 TYR cc_start: 0.8295 (OUTLIER) cc_final: 0.7757 (p90) REVERT: H 229 PHE cc_start: 0.8237 (t80) cc_final: 0.7759 (t80) REVERT: I 229 PHE cc_start: 0.8297 (t80) cc_final: 0.7813 (t80) REVERT: J 177 TYR cc_start: 0.7921 (OUTLIER) cc_final: 0.7090 (p90) REVERT: K 53 ARG cc_start: 0.8103 (OUTLIER) cc_final: 0.7361 (ptp90) REVERT: K 84 PHE cc_start: 0.9195 (OUTLIER) cc_final: 0.8789 (t80) REVERT: K 226 ILE cc_start: 0.8022 (mt) cc_final: 0.7819 (mp) REVERT: K 229 PHE cc_start: 0.8267 (t80) cc_final: 0.7799 (t80) REVERT: L 229 PHE cc_start: 0.8297 (t80) cc_final: 0.7835 (t80) outliers start: 72 outliers final: 41 residues processed: 356 average time/residue: 0.5405 time to fit residues: 216.7850 Evaluate side-chains 331 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 276 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 83 ILE Chi-restraints excluded: chain D residue 84 PHE Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 19 THR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 84 PHE Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 140 optimal weight: 7.9990 chunk 149 optimal weight: 8.9990 chunk 155 optimal weight: 3.9990 chunk 26 optimal weight: 6.9990 chunk 166 optimal weight: 0.3980 chunk 190 optimal weight: 0.9990 chunk 184 optimal weight: 6.9990 chunk 79 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 199 optimal weight: 3.9990 chunk 209 optimal weight: 3.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN ** L 224 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.092011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.070368 restraints weight = 49574.021| |-----------------------------------------------------------------------------| r_work (start): 0.3133 rms_B_bonded: 3.18 r_work: 0.3024 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 1.3971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 19044 Z= 0.161 Angle : 0.763 13.429 25872 Z= 0.361 Chirality : 0.039 0.170 2952 Planarity : 0.003 0.023 3096 Dihedral : 3.911 24.743 2436 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 5.25 % Allowed : 28.19 % Favored : 66.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.59 (0.18), residues: 2220 helix: 2.84 (0.12), residues: 1656 sheet: -0.36 (0.38), residues: 204 loop : -2.78 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG I 101 TYR 0.029 0.003 TYR C 98 PHE 0.027 0.002 PHE F 32 TRP 0.005 0.001 TRP I 174 HIS 0.004 0.001 HIS I 95 Details of bonding type rmsd covalent geometry : bond 0.00372 (19008) covalent geometry : angle 0.76437 (25800) SS BOND : bond 0.00061 ( 36) SS BOND : angle 0.28961 ( 72) hydrogen bonds : bond 0.04579 ( 1380) hydrogen bonds : angle 3.96320 ( 4104) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 311 time to evaluate : 0.516 Fit side-chains REVERT: A 173 GLN cc_start: 0.9500 (OUTLIER) cc_final: 0.9266 (tm-30) REVERT: A 177 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.7188 (p90) REVERT: B 53 ARG cc_start: 0.8176 (OUTLIER) cc_final: 0.7510 (ptp90) REVERT: B 84 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8806 (t80) REVERT: B 177 TYR cc_start: 0.8417 (OUTLIER) cc_final: 0.7892 (p90) REVERT: B 212 PHE cc_start: 0.9281 (OUTLIER) cc_final: 0.8939 (t80) REVERT: D 173 GLN cc_start: 0.9538 (OUTLIER) cc_final: 0.9220 (tm-30) REVERT: D 177 TYR cc_start: 0.8141 (OUTLIER) cc_final: 0.7106 (p90) REVERT: E 53 ARG cc_start: 0.8171 (OUTLIER) cc_final: 0.7475 (ptp90) REVERT: E 84 PHE cc_start: 0.9216 (OUTLIER) cc_final: 0.8809 (t80) REVERT: E 100 MET cc_start: 0.8722 (tpt) cc_final: 0.8512 (tpt) REVERT: E 177 TYR cc_start: 0.8418 (OUTLIER) cc_final: 0.7890 (p90) REVERT: E 212 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8935 (t80) REVERT: G 173 GLN cc_start: 0.9493 (OUTLIER) cc_final: 0.9256 (tm-30) REVERT: G 177 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.7228 (p90) REVERT: H 15 GLN cc_start: 0.8006 (mt0) cc_final: 0.7763 (pp30) REVERT: H 53 ARG cc_start: 0.8165 (OUTLIER) cc_final: 0.7502 (ptp90) REVERT: H 84 PHE cc_start: 0.9240 (OUTLIER) cc_final: 0.8825 (t80) REVERT: H 177 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7900 (p90) REVERT: H 212 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8949 (t80) REVERT: I 98 TYR cc_start: 0.7879 (OUTLIER) cc_final: 0.7452 (m-80) REVERT: J 173 GLN cc_start: 0.9531 (OUTLIER) cc_final: 0.9218 (tm-30) REVERT: J 177 TYR cc_start: 0.8160 (OUTLIER) cc_final: 0.7136 (p90) REVERT: K 53 ARG cc_start: 0.8194 (OUTLIER) cc_final: 0.7537 (ptp90) REVERT: K 84 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8816 (t80) REVERT: K 177 TYR cc_start: 0.8421 (OUTLIER) cc_final: 0.7894 (p90) REVERT: K 212 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8939 (t80) outliers start: 107 outliers final: 40 residues processed: 366 average time/residue: 0.5362 time to fit residues: 221.2725 Evaluate side-chains 345 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 280 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 90 LEU Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 225 ILE Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 98 TYR Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 90 LEU Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 173 GLN Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 225 ILE Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 7 optimal weight: 0.9990 chunk 131 optimal weight: 1.9990 chunk 171 optimal weight: 0.9980 chunk 212 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 129 optimal weight: 8.9990 chunk 180 optimal weight: 20.0000 chunk 139 optimal weight: 8.9990 chunk 50 optimal weight: 6.9990 chunk 77 optimal weight: 0.9980 chunk 167 optimal weight: 2.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN C 224 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN F 224 ASN I 224 ASN K 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.090282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.069321 restraints weight = 49363.026| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.15 r_work: 0.3012 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 1.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19044 Z= 0.136 Angle : 0.760 13.807 25872 Z= 0.354 Chirality : 0.039 0.144 2952 Planarity : 0.003 0.026 3096 Dihedral : 3.760 19.378 2436 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 5.34 % Allowed : 28.63 % Favored : 66.03 % 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: 2.62 (0.18), residues: 2220 helix: 2.85 (0.12), residues: 1656 sheet: -0.25 (0.38), residues: 204 loop : -2.76 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG J 153 TYR 0.023 0.002 TYR L 98 PHE 0.028 0.002 PHE F 32 TRP 0.005 0.000 TRP C 25 HIS 0.002 0.001 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00317 (19008) covalent geometry : angle 0.76047 (25800) SS BOND : bond 0.00064 ( 36) SS BOND : angle 0.28367 ( 72) hydrogen bonds : bond 0.04319 ( 1380) hydrogen bonds : angle 3.90872 ( 4104) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 415 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 306 time to evaluate : 0.542 Fit side-chains REVERT: A 100 MET cc_start: 0.8479 (tpt) cc_final: 0.7998 (tpt) REVERT: A 173 GLN cc_start: 0.9510 (OUTLIER) cc_final: 0.9208 (tm-30) REVERT: A 177 TYR cc_start: 0.8257 (OUTLIER) cc_final: 0.7214 (p90) REVERT: B 53 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7256 (ptp90) REVERT: B 84 PHE cc_start: 0.9231 (OUTLIER) cc_final: 0.8849 (t80) REVERT: B 177 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8041 (p90) REVERT: B 212 PHE cc_start: 0.9284 (OUTLIER) cc_final: 0.9007 (t80) REVERT: D 100 MET cc_start: 0.8502 (tpt) cc_final: 0.7990 (tpt) REVERT: D 173 GLN cc_start: 0.9557 (OUTLIER) cc_final: 0.9273 (tm-30) REVERT: D 177 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.7247 (p90) REVERT: E 53 ARG cc_start: 0.8102 (OUTLIER) cc_final: 0.7255 (ptp90) REVERT: E 84 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8853 (t80) REVERT: E 177 TYR cc_start: 0.8455 (OUTLIER) cc_final: 0.8026 (p90) REVERT: E 212 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8999 (t80) REVERT: G 100 MET cc_start: 0.8503 (tpt) cc_final: 0.8010 (tpt) REVERT: G 173 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9214 (tm-30) REVERT: G 177 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.7246 (p90) REVERT: H 15 GLN cc_start: 0.8235 (mt0) cc_final: 0.7811 (pp30) REVERT: H 53 ARG cc_start: 0.8107 (OUTLIER) cc_final: 0.7265 (ptp90) REVERT: H 84 PHE cc_start: 0.9247 (OUTLIER) cc_final: 0.8873 (t80) REVERT: H 177 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8030 (p90) REVERT: H 212 PHE cc_start: 0.9290 (OUTLIER) cc_final: 0.8998 (t80) REVERT: J 100 MET cc_start: 0.8492 (tpt) cc_final: 0.8015 (tpt) REVERT: J 173 GLN cc_start: 0.9548 (OUTLIER) cc_final: 0.9269 (tm-30) REVERT: J 177 TYR cc_start: 0.8236 (OUTLIER) cc_final: 0.7256 (p90) REVERT: K 53 ARG cc_start: 0.8112 (OUTLIER) cc_final: 0.7262 (ptp90) REVERT: K 84 PHE cc_start: 0.9227 (OUTLIER) cc_final: 0.8853 (t80) REVERT: K 177 TYR cc_start: 0.8466 (OUTLIER) cc_final: 0.8038 (p90) REVERT: K 212 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8999 (t80) outliers start: 109 outliers final: 43 residues processed: 368 average time/residue: 0.4986 time to fit residues: 209.0943 Evaluate side-chains 357 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 290 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 98 TYR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 98 TYR Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 64 VAL Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 90 LEU Chi-restraints excluded: chain G residue 98 TYR Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 90 LEU Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 98 TYR Chi-restraints excluded: chain J residue 173 GLN Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 34 ILE Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 118 optimal weight: 7.9990 chunk 210 optimal weight: 8.9990 chunk 153 optimal weight: 1.9990 chunk 137 optimal weight: 0.9990 chunk 39 optimal weight: 6.9990 chunk 173 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 203 optimal weight: 3.9990 chunk 104 optimal weight: 0.1980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 224 ASN C 15 GLN C 224 ASN ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 224 ASN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN L 15 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.089772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.069018 restraints weight = 49833.611| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 3.13 r_work: 0.3008 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 1.4506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 19044 Z= 0.123 Angle : 0.743 13.629 25872 Z= 0.341 Chirality : 0.038 0.195 2952 Planarity : 0.003 0.034 3096 Dihedral : 3.630 22.291 2436 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 4.22 % Allowed : 29.85 % Favored : 65.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.77 (0.18), residues: 2220 helix: 2.95 (0.12), residues: 1656 sheet: -0.14 (0.38), residues: 204 loop : -2.68 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG I 101 TYR 0.021 0.002 TYR F 98 PHE 0.027 0.001 PHE L 32 TRP 0.005 0.000 TRP C 174 HIS 0.002 0.000 HIS B 95 Details of bonding type rmsd covalent geometry : bond 0.00281 (19008) covalent geometry : angle 0.74425 (25800) SS BOND : bond 0.00041 ( 36) SS BOND : angle 0.25669 ( 72) hydrogen bonds : bond 0.03988 ( 1380) hydrogen bonds : angle 3.85760 ( 4104) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 328 time to evaluate : 0.686 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 173 GLN cc_start: 0.9514 (OUTLIER) cc_final: 0.9251 (tm-30) REVERT: A 177 TYR cc_start: 0.8275 (OUTLIER) cc_final: 0.7270 (p90) REVERT: B 84 PHE cc_start: 0.9219 (OUTLIER) cc_final: 0.8856 (t80) REVERT: B 177 TYR cc_start: 0.8453 (OUTLIER) cc_final: 0.8027 (p90) REVERT: B 212 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.9025 (t80) REVERT: D 177 TYR cc_start: 0.8234 (OUTLIER) cc_final: 0.7265 (p90) REVERT: E 53 ARG cc_start: 0.8089 (OUTLIER) cc_final: 0.7229 (ptp90) REVERT: E 84 PHE cc_start: 0.9214 (OUTLIER) cc_final: 0.8860 (t80) REVERT: E 101 ARG cc_start: 0.8394 (tpp-160) cc_final: 0.8170 (tpp80) REVERT: E 177 TYR cc_start: 0.8449 (OUTLIER) cc_final: 0.8026 (p90) REVERT: E 212 PHE cc_start: 0.9271 (OUTLIER) cc_final: 0.9021 (t80) REVERT: G 173 GLN cc_start: 0.9511 (OUTLIER) cc_final: 0.9252 (tm-30) REVERT: G 177 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7295 (p90) REVERT: H 15 GLN cc_start: 0.8356 (mt0) cc_final: 0.7849 (pp30) REVERT: H 84 PHE cc_start: 0.9222 (OUTLIER) cc_final: 0.8866 (t80) REVERT: H 177 TYR cc_start: 0.8446 (OUTLIER) cc_final: 0.8021 (p90) REVERT: H 212 PHE cc_start: 0.9285 (OUTLIER) cc_final: 0.9049 (t80) REVERT: J 173 GLN cc_start: 0.9565 (OUTLIER) cc_final: 0.9323 (tm-30) REVERT: J 177 TYR cc_start: 0.8256 (OUTLIER) cc_final: 0.7196 (p90) REVERT: K 84 PHE cc_start: 0.9215 (OUTLIER) cc_final: 0.8861 (t80) REVERT: K 177 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8032 (p90) REVERT: K 212 PHE cc_start: 0.9273 (OUTLIER) cc_final: 0.9024 (t80) outliers start: 86 outliers final: 36 residues processed: 373 average time/residue: 0.5042 time to fit residues: 213.4758 Evaluate side-chains 363 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 307 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 84 PHE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain A residue 190 ASP Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 87 VAL Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain C residue 84 PHE Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 53 ARG Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 84 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 10 LEU Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 84 PHE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 84 PHE Chi-restraints excluded: chain I residue 98 TYR Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 10 LEU Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 173 GLN Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 190 ASP Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 84 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 182 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 148 optimal weight: 0.5980 chunk 88 optimal weight: 4.9990 chunk 210 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 143 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 206 optimal weight: 0.2980 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 224 ASN B 224 ASN E 224 ASN J 15 GLN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 224 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.088715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.068376 restraints weight = 48958.957| |-----------------------------------------------------------------------------| r_work (start): 0.3122 rms_B_bonded: 3.14 r_work: 0.3007 rms_B_bonded: 3.70 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 1.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 19044 Z= 0.126 Angle : 0.763 13.451 25872 Z= 0.349 Chirality : 0.038 0.139 2952 Planarity : 0.003 0.029 3096 Dihedral : 3.553 18.630 2436 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.87 % Allowed : 30.39 % Favored : 65.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.89 (0.18), residues: 2220 helix: 3.04 (0.12), residues: 1656 sheet: -0.19 (0.38), residues: 204 loop : -2.61 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG I 101 TYR 0.020 0.002 TYR E 177 PHE 0.027 0.001 PHE F 32 TRP 0.005 0.000 TRP I 174 HIS 0.001 0.000 HIS D 74 Details of bonding type rmsd covalent geometry : bond 0.00293 (19008) covalent geometry : angle 0.76416 (25800) SS BOND : bond 0.00040 ( 36) SS BOND : angle 0.24781 ( 72) hydrogen bonds : bond 0.03946 ( 1380) hydrogen bonds : angle 3.82487 ( 4104) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4440 Ramachandran restraints generated. 2220 Oldfield, 0 Emsley, 2220 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 421 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 342 time to evaluate : 0.738 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 GLU cc_start: 0.8362 (tp30) cc_final: 0.7850 (pt0) REVERT: A 173 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9168 (tm-30) REVERT: A 177 TYR cc_start: 0.8314 (OUTLIER) cc_final: 0.7210 (p90) REVERT: B 42 GLU cc_start: 0.7865 (pm20) cc_final: 0.7659 (pm20) REVERT: B 53 ARG cc_start: 0.8065 (OUTLIER) cc_final: 0.7125 (ptp90) REVERT: B 84 PHE cc_start: 0.9205 (OUTLIER) cc_final: 0.8887 (t80) REVERT: B 101 ARG cc_start: 0.8392 (tpp-160) cc_final: 0.8158 (tpp80) REVERT: B 177 TYR cc_start: 0.8445 (OUTLIER) cc_final: 0.8028 (p90) REVERT: B 212 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8943 (t80) REVERT: C 15 GLN cc_start: 0.8598 (mt0) cc_final: 0.8213 (pp30) REVERT: D 103 GLU cc_start: 0.8335 (tp30) cc_final: 0.7870 (pt0) REVERT: D 173 GLN cc_start: 0.9574 (OUTLIER) cc_final: 0.9268 (tm-30) REVERT: D 177 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7248 (p90) REVERT: E 42 GLU cc_start: 0.7886 (pm20) cc_final: 0.7684 (pm20) REVERT: E 84 PHE cc_start: 0.9199 (OUTLIER) cc_final: 0.8895 (t80) REVERT: E 100 MET cc_start: 0.8704 (tpp) cc_final: 0.8475 (ttm) REVERT: E 177 TYR cc_start: 0.8458 (OUTLIER) cc_final: 0.8039 (p90) REVERT: E 212 PHE cc_start: 0.9272 (OUTLIER) cc_final: 0.8928 (t80) REVERT: F 15 GLN cc_start: 0.8627 (mt0) cc_final: 0.8232 (pp30) REVERT: G 103 GLU cc_start: 0.8338 (tp30) cc_final: 0.7865 (pt0) REVERT: G 173 GLN cc_start: 0.9507 (OUTLIER) cc_final: 0.9174 (tm-30) REVERT: G 177 TYR cc_start: 0.8345 (OUTLIER) cc_final: 0.7256 (p90) REVERT: H 42 GLU cc_start: 0.7852 (pm20) cc_final: 0.7651 (pm20) REVERT: H 53 ARG cc_start: 0.8059 (OUTLIER) cc_final: 0.7118 (ptp90) REVERT: H 84 PHE cc_start: 0.9224 (OUTLIER) cc_final: 0.8914 (t80) REVERT: H 177 TYR cc_start: 0.8460 (OUTLIER) cc_final: 0.8048 (p90) REVERT: H 212 PHE cc_start: 0.9280 (OUTLIER) cc_final: 0.8941 (t80) REVERT: I 15 GLN cc_start: 0.8603 (mt0) cc_final: 0.8208 (pp30) REVERT: J 103 GLU cc_start: 0.8349 (tp30) cc_final: 0.7856 (pt0) REVERT: J 173 GLN cc_start: 0.9572 (OUTLIER) cc_final: 0.9353 (tm-30) REVERT: J 177 TYR cc_start: 0.8307 (OUTLIER) cc_final: 0.7284 (p90) REVERT: J 212 PHE cc_start: 0.9252 (OUTLIER) cc_final: 0.9051 (t80) REVERT: K 42 GLU cc_start: 0.7872 (pm20) cc_final: 0.7667 (pm20) REVERT: K 53 ARG cc_start: 0.8071 (OUTLIER) cc_final: 0.7126 (ptp90) REVERT: K 84 PHE cc_start: 0.9209 (OUTLIER) cc_final: 0.8903 (t80) REVERT: K 177 TYR cc_start: 0.8463 (OUTLIER) cc_final: 0.8046 (p90) REVERT: K 212 PHE cc_start: 0.9278 (OUTLIER) cc_final: 0.8941 (t80) REVERT: L 15 GLN cc_start: 0.8615 (mt0) cc_final: 0.8231 (pp30) outliers start: 79 outliers final: 25 residues processed: 382 average time/residue: 0.5361 time to fit residues: 231.5693 Evaluate side-chains 367 residues out of total 2040 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 318 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ILE Chi-restraints excluded: chain A residue 87 VAL Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 177 TYR Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 53 ARG Chi-restraints excluded: chain B residue 84 PHE Chi-restraints excluded: chain B residue 98 TYR Chi-restraints excluded: chain B residue 177 TYR Chi-restraints excluded: chain B residue 212 PHE Chi-restraints excluded: chain B residue 223 LEU Chi-restraints excluded: chain C residue 177 TYR Chi-restraints excluded: chain D residue 34 ILE Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 173 GLN Chi-restraints excluded: chain D residue 177 TYR Chi-restraints excluded: chain D residue 190 ASP Chi-restraints excluded: chain E residue 34 ILE Chi-restraints excluded: chain E residue 84 PHE Chi-restraints excluded: chain E residue 87 VAL Chi-restraints excluded: chain E residue 98 TYR Chi-restraints excluded: chain E residue 177 TYR Chi-restraints excluded: chain E residue 212 PHE Chi-restraints excluded: chain F residue 177 TYR Chi-restraints excluded: chain G residue 34 ILE Chi-restraints excluded: chain G residue 87 VAL Chi-restraints excluded: chain G residue 173 GLN Chi-restraints excluded: chain G residue 177 TYR Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 84 PHE Chi-restraints excluded: chain H residue 87 VAL Chi-restraints excluded: chain H residue 98 TYR Chi-restraints excluded: chain H residue 177 TYR Chi-restraints excluded: chain H residue 212 PHE Chi-restraints excluded: chain I residue 98 TYR Chi-restraints excluded: chain I residue 177 TYR Chi-restraints excluded: chain J residue 34 ILE Chi-restraints excluded: chain J residue 87 VAL Chi-restraints excluded: chain J residue 173 GLN Chi-restraints excluded: chain J residue 177 TYR Chi-restraints excluded: chain J residue 212 PHE Chi-restraints excluded: chain K residue 53 ARG Chi-restraints excluded: chain K residue 84 PHE Chi-restraints excluded: chain K residue 87 VAL Chi-restraints excluded: chain K residue 98 TYR Chi-restraints excluded: chain K residue 177 TYR Chi-restraints excluded: chain K residue 212 PHE Chi-restraints excluded: chain L residue 177 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 216 random chunks: chunk 72 optimal weight: 30.0000 chunk 94 optimal weight: 3.9990 chunk 163 optimal weight: 0.7980 chunk 88 optimal weight: 3.9990 chunk 202 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 chunk 37 optimal weight: 7.9990 chunk 99 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 206 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 GLN A 224 ASN B 224 ASN D 15 GLN D 224 ASN E 15 GLN E 224 ASN F 224 ASN G 15 GLN G 224 ASN H 224 ASN I 224 ASN J 15 GLN J 224 ASN K 224 ASN L 224 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.080999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.061200 restraints weight = 50120.877| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 2.98 r_work: 0.2873 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 moved from start: 1.5448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 19044 Z= 0.177 Angle : 0.813 13.484 25872 Z= 0.384 Chirality : 0.041 0.217 2952 Planarity : 0.004 0.043 3096 Dihedral : 3.797 16.398 2436 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 3.33 % Allowed : 32.06 % Favored : 64.61 % 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: 2.78 (0.18), residues: 2220 helix: 2.92 (0.12), residues: 1656 sheet: 0.02 (0.39), residues: 204 loop : -2.64 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 153 TYR 0.026 0.002 TYR H 177 PHE 0.024 0.002 PHE L 32 TRP 0.006 0.001 TRP C 25 HIS 0.003 0.001 HIS J 74 Details of bonding type rmsd covalent geometry : bond 0.00428 (19008) covalent geometry : angle 0.81390 (25800) SS BOND : bond 0.00106 ( 36) SS BOND : angle 0.39831 ( 72) hydrogen bonds : bond 0.05868 ( 1380) hydrogen bonds : angle 3.95476 ( 4104) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5992.15 seconds wall clock time: 103 minutes 35.22 seconds (6215.22 seconds total)