Starting phenix.real_space_refine on Fri Mar 6 03:23:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7txi_26158/03_2026/7txi_26158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txi_26158/03_2026/7txi_26158.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7txi_26158/03_2026/7txi_26158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txi_26158/03_2026/7txi_26158.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7txi_26158/03_2026/7txi_26158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txi_26158/03_2026/7txi_26158.map" } resolution = 3.5 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 ------------------------------------------------------------------------------- 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= 0.005 sd= 0.034 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 120 5.16 5 C 18280 2.51 5 N 4580 2.21 5 O 5680 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 200 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 28660 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 1433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1433 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 8, 'TRANS': 187} Restraints were copied for chains: C, D, E, F, G, H, I, J, K, A, L, M, N, O, P, Q, R, S, T Time building chain proxies: 2.48, per 1000 atoms: 0.09 Number of scatterers: 28660 At special positions: 0 Unit cell: (111.24, 109.08, 219.24, 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 120 16.00 O 5680 8.00 N 4580 7.00 C 18280 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=20, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 132 " distance=2.03 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 132 " distance=2.03 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 132 " distance=2.03 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 132 " distance=2.03 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 132 " distance=2.03 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 132 " distance=2.03 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 132 " distance=2.03 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 132 " distance=2.03 Simple disulfide: pdb=" SG CYS J 110 " - pdb=" SG CYS J 132 " distance=2.03 Simple disulfide: pdb=" SG CYS K 110 " - pdb=" SG CYS K 132 " distance=2.03 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 132 " distance=2.03 Simple disulfide: pdb=" SG CYS L 110 " - pdb=" SG CYS L 132 " distance=2.03 Simple disulfide: pdb=" SG CYS M 110 " - pdb=" SG CYS M 132 " distance=2.03 Simple disulfide: pdb=" SG CYS N 110 " - pdb=" SG CYS N 132 " distance=2.03 Simple disulfide: pdb=" SG CYS O 110 " - pdb=" SG CYS O 132 " distance=2.03 Simple disulfide: pdb=" SG CYS P 110 " - pdb=" SG CYS P 132 " distance=2.03 Simple disulfide: pdb=" SG CYS Q 110 " - pdb=" SG CYS Q 132 " distance=2.03 Simple disulfide: pdb=" SG CYS R 110 " - pdb=" SG CYS R 132 " distance=2.03 Simple disulfide: pdb=" SG CYS S 110 " - pdb=" SG CYS S 132 " distance=2.03 Simple disulfide: pdb=" SG CYS T 110 " - pdb=" SG CYS T 132 " 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=30, symmetry=0 Number of additional bonds: simple=30, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.42 Conformation dependent library (CDL) restraints added in 1.3 seconds 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7120 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 80 sheets defined 28.1% alpha, 30.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.14 Creating SS restraints... Processing helix chain 'A' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA A 12 " --> pdb=" O VAL A 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR A 53 " --> pdb=" O LEU A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 130 Processing helix chain 'B' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA B 12 " --> pdb=" O VAL B 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 130 Processing helix chain 'C' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA C 12 " --> pdb=" O VAL C 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR C 53 " --> pdb=" O LEU C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 130 Processing helix chain 'D' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA D 12 " --> pdb=" O VAL D 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR D 53 " --> pdb=" O LEU D 49 " (cutoff:3.500A) Processing helix chain 'D' and resid 122 through 130 Processing helix chain 'E' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA E 12 " --> pdb=" O VAL E 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR E 53 " --> pdb=" O LEU E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 130 Processing helix chain 'F' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA F 12 " --> pdb=" O VAL F 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 130 Processing helix chain 'G' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA G 12 " --> pdb=" O VAL G 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR G 53 " --> pdb=" O LEU G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 130 Processing helix chain 'H' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA H 12 " --> pdb=" O VAL H 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR H 53 " --> pdb=" O LEU H 49 " (cutoff:3.500A) Processing helix chain 'H' and resid 122 through 130 Processing helix chain 'I' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA I 12 " --> pdb=" O VAL I 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR I 53 " --> pdb=" O LEU I 49 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 130 Processing helix chain 'J' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA J 12 " --> pdb=" O VAL J 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR J 53 " --> pdb=" O LEU J 49 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 130 Processing helix chain 'K' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA K 12 " --> pdb=" O VAL K 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR K 53 " --> pdb=" O LEU K 49 " (cutoff:3.500A) Processing helix chain 'K' and resid 122 through 130 Processing helix chain 'L' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA L 12 " --> pdb=" O VAL L 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 122 through 130 Processing helix chain 'M' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA M 12 " --> pdb=" O VAL M 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR M 53 " --> pdb=" O LEU M 49 " (cutoff:3.500A) Processing helix chain 'M' and resid 122 through 130 Processing helix chain 'N' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA N 12 " --> pdb=" O VAL N 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR N 53 " --> pdb=" O LEU N 49 " (cutoff:3.500A) Processing helix chain 'N' and resid 122 through 130 Processing helix chain 'O' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA O 12 " --> pdb=" O VAL O 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR O 53 " --> pdb=" O LEU O 49 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 130 Processing helix chain 'P' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA P 12 " --> pdb=" O VAL P 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) Processing helix chain 'P' and resid 122 through 130 Processing helix chain 'Q' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA Q 12 " --> pdb=" O VAL Q 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR Q 53 " --> pdb=" O LEU Q 49 " (cutoff:3.500A) Processing helix chain 'Q' and resid 122 through 130 Processing helix chain 'R' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA R 12 " --> pdb=" O VAL R 8 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR R 53 " --> pdb=" O LEU R 49 " (cutoff:3.500A) Processing helix chain 'R' and resid 122 through 130 Processing helix chain 'S' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA S 12 " --> pdb=" O VAL S 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR S 53 " --> pdb=" O LEU S 49 " (cutoff:3.500A) Processing helix chain 'S' and resid 122 through 130 Processing helix chain 'T' and resid 8 through 53 removed outlier: 3.691A pdb=" N ALA T 12 " --> pdb=" O VAL T 8 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N THR T 53 " --> pdb=" O LEU T 49 " (cutoff:3.500A) Processing helix chain 'T' and resid 122 through 130 Processing sheet with id=1, first strand: chain 'A' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU A 139 " --> pdb=" O CYS A 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL A 112 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 141 " --> pdb=" O VAL A 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP A 114 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'A' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN A 65 " --> pdb=" O ASP A 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE A 74 " --> pdb=" O ILE A 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE A 63 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=4, first strand: chain 'A' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG A 188 " --> pdb=" O PHE A 172 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU B 139 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL B 112 " --> pdb=" O LEU B 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE B 141 " --> pdb=" O VAL B 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP B 114 " --> pdb=" O ILE B 141 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN B 65 " --> pdb=" O ASP B 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE B 74 " --> pdb=" O ILE B 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE B 63 " --> pdb=" O ILE B 74 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'B' and resid 87 through 88 Processing sheet with id=8, first strand: chain 'B' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG B 188 " --> pdb=" O PHE B 172 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'C' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU C 139 " --> pdb=" O CYS C 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL C 112 " --> pdb=" O LEU C 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE C 141 " --> pdb=" O VAL C 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP C 114 " --> pdb=" O ILE C 141 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'C' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN C 65 " --> pdb=" O ASP C 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE C 74 " --> pdb=" O ILE C 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE C 63 " --> pdb=" O ILE C 74 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=12, first strand: chain 'C' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG C 188 " --> pdb=" O PHE C 172 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'D' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU D 139 " --> pdb=" O CYS D 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL D 112 " --> pdb=" O LEU D 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE D 141 " --> pdb=" O VAL D 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP D 114 " --> pdb=" O ILE D 141 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'D' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN D 65 " --> pdb=" O ASP D 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE D 74 " --> pdb=" O ILE D 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE D 63 " --> pdb=" O ILE D 74 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'D' and resid 87 through 88 Processing sheet with id=16, first strand: chain 'D' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG D 188 " --> pdb=" O PHE D 172 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'E' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU E 139 " --> pdb=" O CYS E 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL E 112 " --> pdb=" O LEU E 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE E 141 " --> pdb=" O VAL E 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP E 114 " --> pdb=" O ILE E 141 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'E' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN E 65 " --> pdb=" O ASP E 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE E 74 " --> pdb=" O ILE E 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE E 63 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'E' and resid 87 through 88 Processing sheet with id=20, first strand: chain 'E' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG E 188 " --> pdb=" O PHE E 172 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'F' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU F 139 " --> pdb=" O CYS F 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL F 112 " --> pdb=" O LEU F 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE F 141 " --> pdb=" O VAL F 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP F 114 " --> pdb=" O ILE F 141 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'F' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN F 65 " --> pdb=" O ASP F 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE F 74 " --> pdb=" O ILE F 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE F 63 " --> pdb=" O ILE F 74 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'F' and resid 87 through 88 Processing sheet with id=24, first strand: chain 'F' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG F 188 " --> pdb=" O PHE F 172 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'G' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU G 139 " --> pdb=" O CYS G 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL G 112 " --> pdb=" O LEU G 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE G 141 " --> pdb=" O VAL G 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP G 114 " --> pdb=" O ILE G 141 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'G' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN G 65 " --> pdb=" O ASP G 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE G 74 " --> pdb=" O ILE G 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE G 63 " --> pdb=" O ILE G 74 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'G' and resid 87 through 88 Processing sheet with id=28, first strand: chain 'G' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG G 188 " --> pdb=" O PHE G 172 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'H' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU H 139 " --> pdb=" O CYS H 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL H 112 " --> pdb=" O LEU H 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE H 141 " --> pdb=" O VAL H 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP H 114 " --> pdb=" O ILE H 141 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'H' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN H 65 " --> pdb=" O ASP H 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE H 74 " --> pdb=" O ILE H 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE H 63 " --> pdb=" O ILE H 74 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'H' and resid 87 through 88 Processing sheet with id=32, first strand: chain 'H' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG H 188 " --> pdb=" O PHE H 172 " (cutoff:3.500A) Processing sheet with id=33, first strand: chain 'I' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU I 139 " --> pdb=" O CYS I 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL I 112 " --> pdb=" O LEU I 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE I 141 " --> pdb=" O VAL I 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP I 114 " --> pdb=" O ILE I 141 " (cutoff:3.500A) Processing sheet with id=34, first strand: chain 'I' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN I 65 " --> pdb=" O ASP I 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE I 74 " --> pdb=" O ILE I 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE I 63 " --> pdb=" O ILE I 74 " (cutoff:3.500A) Processing sheet with id=35, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=36, first strand: chain 'I' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG I 188 " --> pdb=" O PHE I 172 " (cutoff:3.500A) Processing sheet with id=37, first strand: chain 'J' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU J 139 " --> pdb=" O CYS J 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL J 112 " --> pdb=" O LEU J 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE J 141 " --> pdb=" O VAL J 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP J 114 " --> pdb=" O ILE J 141 " (cutoff:3.500A) Processing sheet with id=38, first strand: chain 'J' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN J 65 " --> pdb=" O ASP J 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE J 74 " --> pdb=" O ILE J 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE J 63 " --> pdb=" O ILE J 74 " (cutoff:3.500A) Processing sheet with id=39, first strand: chain 'J' and resid 87 through 88 Processing sheet with id=40, first strand: chain 'J' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG J 188 " --> pdb=" O PHE J 172 " (cutoff:3.500A) Processing sheet with id=41, first strand: chain 'K' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU K 139 " --> pdb=" O CYS K 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL K 112 " --> pdb=" O LEU K 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE K 141 " --> pdb=" O VAL K 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP K 114 " --> pdb=" O ILE K 141 " (cutoff:3.500A) Processing sheet with id=42, first strand: chain 'K' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN K 65 " --> pdb=" O ASP K 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE K 74 " --> pdb=" O ILE K 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE K 63 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing sheet with id=43, first strand: chain 'K' and resid 87 through 88 Processing sheet with id=44, first strand: chain 'K' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG K 188 " --> pdb=" O PHE K 172 " (cutoff:3.500A) Processing sheet with id=45, first strand: chain 'L' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU L 139 " --> pdb=" O CYS L 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL L 112 " --> pdb=" O LEU L 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE L 141 " --> pdb=" O VAL L 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP L 114 " --> pdb=" O ILE L 141 " (cutoff:3.500A) Processing sheet with id=46, first strand: chain 'L' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN L 65 " --> pdb=" O ASP L 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE L 74 " --> pdb=" O ILE L 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE L 63 " --> pdb=" O ILE L 74 " (cutoff:3.500A) Processing sheet with id=47, first strand: chain 'L' and resid 87 through 88 Processing sheet with id=48, first strand: chain 'L' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG L 188 " --> pdb=" O PHE L 172 " (cutoff:3.500A) Processing sheet with id=49, first strand: chain 'M' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU M 139 " --> pdb=" O CYS M 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL M 112 " --> pdb=" O LEU M 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE M 141 " --> pdb=" O VAL M 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP M 114 " --> pdb=" O ILE M 141 " (cutoff:3.500A) Processing sheet with id=50, first strand: chain 'M' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN M 65 " --> pdb=" O ASP M 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE M 74 " --> pdb=" O ILE M 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE M 63 " --> pdb=" O ILE M 74 " (cutoff:3.500A) Processing sheet with id=51, first strand: chain 'M' and resid 87 through 88 Processing sheet with id=52, first strand: chain 'M' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG M 188 " --> pdb=" O PHE M 172 " (cutoff:3.500A) Processing sheet with id=53, first strand: chain 'N' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU N 139 " --> pdb=" O CYS N 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL N 112 " --> pdb=" O LEU N 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE N 141 " --> pdb=" O VAL N 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP N 114 " --> pdb=" O ILE N 141 " (cutoff:3.500A) Processing sheet with id=54, first strand: chain 'N' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN N 65 " --> pdb=" O ASP N 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE N 74 " --> pdb=" O ILE N 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE N 63 " --> pdb=" O ILE N 74 " (cutoff:3.500A) Processing sheet with id=55, first strand: chain 'N' and resid 87 through 88 Processing sheet with id=56, first strand: chain 'N' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG N 188 " --> pdb=" O PHE N 172 " (cutoff:3.500A) Processing sheet with id=57, first strand: chain 'O' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU O 139 " --> pdb=" O CYS O 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL O 112 " --> pdb=" O LEU O 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE O 141 " --> pdb=" O VAL O 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP O 114 " --> pdb=" O ILE O 141 " (cutoff:3.500A) Processing sheet with id=58, first strand: chain 'O' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN O 65 " --> pdb=" O ASP O 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE O 74 " --> pdb=" O ILE O 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE O 63 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing sheet with id=59, first strand: chain 'O' and resid 87 through 88 Processing sheet with id=60, first strand: chain 'O' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG O 188 " --> pdb=" O PHE O 172 " (cutoff:3.500A) Processing sheet with id=61, first strand: chain 'P' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU P 139 " --> pdb=" O CYS P 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL P 112 " --> pdb=" O LEU P 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE P 141 " --> pdb=" O VAL P 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP P 114 " --> pdb=" O ILE P 141 " (cutoff:3.500A) Processing sheet with id=62, first strand: chain 'P' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN P 65 " --> pdb=" O ASP P 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE P 74 " --> pdb=" O ILE P 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE P 63 " --> pdb=" O ILE P 74 " (cutoff:3.500A) Processing sheet with id=63, first strand: chain 'P' and resid 87 through 88 Processing sheet with id=64, first strand: chain 'P' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG P 188 " --> pdb=" O PHE P 172 " (cutoff:3.500A) Processing sheet with id=65, first strand: chain 'Q' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU Q 139 " --> pdb=" O CYS Q 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL Q 112 " --> pdb=" O LEU Q 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE Q 141 " --> pdb=" O VAL Q 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP Q 114 " --> pdb=" O ILE Q 141 " (cutoff:3.500A) Processing sheet with id=66, first strand: chain 'Q' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN Q 65 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE Q 74 " --> pdb=" O ILE Q 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE Q 63 " --> pdb=" O ILE Q 74 " (cutoff:3.500A) Processing sheet with id=67, first strand: chain 'Q' and resid 87 through 88 Processing sheet with id=68, first strand: chain 'Q' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG Q 188 " --> pdb=" O PHE Q 172 " (cutoff:3.500A) Processing sheet with id=69, first strand: chain 'R' and resid 57 through 58 removed outlier: 7.696A pdb=" N LEU R 139 " --> pdb=" O CYS R 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL R 112 " --> pdb=" O LEU R 139 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N ILE R 141 " --> pdb=" O VAL R 112 " (cutoff:3.500A) removed outlier: 5.737A pdb=" N ASP R 114 " --> pdb=" O ILE R 141 " (cutoff:3.500A) Processing sheet with id=70, first strand: chain 'R' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN R 65 " --> pdb=" O ASP R 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE R 74 " --> pdb=" O ILE R 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE R 63 " --> pdb=" O ILE R 74 " (cutoff:3.500A) Processing sheet with id=71, first strand: chain 'R' and resid 87 through 88 Processing sheet with id=72, first strand: chain 'R' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG R 188 " --> pdb=" O PHE R 172 " (cutoff:3.500A) Processing sheet with id=73, first strand: chain 'S' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU S 139 " --> pdb=" O CYS S 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL S 112 " --> pdb=" O LEU S 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE S 141 " --> pdb=" O VAL S 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP S 114 " --> pdb=" O ILE S 141 " (cutoff:3.500A) Processing sheet with id=74, first strand: chain 'S' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN S 65 " --> pdb=" O ASP S 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE S 74 " --> pdb=" O ILE S 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE S 63 " --> pdb=" O ILE S 74 " (cutoff:3.500A) Processing sheet with id=75, first strand: chain 'S' and resid 87 through 88 Processing sheet with id=76, first strand: chain 'S' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG S 188 " --> pdb=" O PHE S 172 " (cutoff:3.500A) Processing sheet with id=77, first strand: chain 'T' and resid 57 through 58 removed outlier: 7.697A pdb=" N LEU T 139 " --> pdb=" O CYS T 110 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N VAL T 112 " --> pdb=" O LEU T 139 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE T 141 " --> pdb=" O VAL T 112 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N ASP T 114 " --> pdb=" O ILE T 141 " (cutoff:3.500A) Processing sheet with id=78, first strand: chain 'T' and resid 57 through 58 removed outlier: 6.306A pdb=" N ASN T 65 " --> pdb=" O ASP T 72 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N ILE T 74 " --> pdb=" O ILE T 63 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ILE T 63 " --> pdb=" O ILE T 74 " (cutoff:3.500A) Processing sheet with id=79, first strand: chain 'T' and resid 87 through 88 Processing sheet with id=80, first strand: chain 'T' and resid 104 through 105 removed outlier: 3.535A pdb=" N ARG T 188 " --> pdb=" O PHE T 172 " (cutoff:3.500A) 1640 hydrogen bonds defined for protein. 4500 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: 6.77 Time building geometry restraints manager: 3.29 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: 9380 1.34 - 1.46: 5788 1.46 - 1.58: 13672 1.58 - 1.70: 20 1.70 - 1.81: 200 Bond restraints: 29060 Sorted by residual: bond pdb=" CG PRO T 165 " pdb=" CD PRO T 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO F 165 " pdb=" CD PRO F 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO K 165 " pdb=" CD PRO K 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO O 165 " pdb=" CD PRO O 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.57e+01 bond pdb=" CG PRO R 165 " pdb=" CD PRO R 165 " ideal model delta sigma weight residual 1.503 1.273 0.230 3.40e-02 8.65e+02 4.56e+01 ... (remaining 29055 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.41: 39100 3.41 - 6.82: 360 6.82 - 10.22: 40 10.22 - 13.63: 20 13.63 - 17.04: 40 Bond angle restraints: 39560 Sorted by residual: angle pdb=" CA PRO L 165 " pdb=" N PRO L 165 " pdb=" CD PRO L 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO Q 165 " pdb=" N PRO Q 165 " pdb=" CD PRO Q 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO H 165 " pdb=" N PRO H 165 " pdb=" CD PRO H 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO C 165 " pdb=" N PRO C 165 " pdb=" CD PRO C 165 " ideal model delta sigma weight residual 112.00 98.22 13.78 1.40e+00 5.10e-01 9.69e+01 angle pdb=" CA PRO R 165 " pdb=" N PRO R 165 " pdb=" CD PRO R 165 " ideal model delta sigma weight residual 112.00 98.23 13.77 1.40e+00 5.10e-01 9.68e+01 ... (remaining 39555 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 10.94: 15220 10.94 - 21.89: 1280 21.89 - 32.83: 620 32.83 - 43.78: 280 43.78 - 54.72: 120 Dihedral angle restraints: 17520 sinusoidal: 6420 harmonic: 11100 Sorted by residual: dihedral pdb=" CB CYS M 110 " pdb=" SG CYS M 110 " pdb=" SG CYS M 132 " pdb=" CB CYS M 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.28 54.72 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CB CYS D 110 " pdb=" SG CYS D 110 " pdb=" SG CYS D 132 " pdb=" CB CYS D 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.28 54.72 1 1.00e+01 1.00e-02 4.06e+01 dihedral pdb=" CB CYS R 110 " pdb=" SG CYS R 110 " pdb=" SG CYS R 132 " pdb=" CB CYS R 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.28 54.72 1 1.00e+01 1.00e-02 4.06e+01 ... (remaining 17517 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 2756 0.029 - 0.059: 1240 0.059 - 0.088: 564 0.088 - 0.118: 348 0.118 - 0.147: 52 Chirality restraints: 4960 Sorted by residual: chirality pdb=" CA TYR G 169 " pdb=" N TYR G 169 " pdb=" C TYR G 169 " pdb=" CB TYR G 169 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA TYR A 169 " pdb=" N TYR A 169 " pdb=" C TYR A 169 " pdb=" CB TYR A 169 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 chirality pdb=" CA TYR B 169 " pdb=" N TYR B 169 " pdb=" C TYR B 169 " pdb=" CB TYR B 169 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.44e-01 ... (remaining 4957 not shown) Planarity restraints: 5020 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR I 164 " -0.146 5.00e-02 4.00e+02 2.07e-01 6.82e+01 pdb=" N PRO I 165 " 0.356 5.00e-02 4.00e+02 pdb=" CA PRO I 165 " -0.120 5.00e-02 4.00e+02 pdb=" CD PRO I 165 " -0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR M 164 " 0.146 5.00e-02 4.00e+02 2.07e-01 6.82e+01 pdb=" N PRO M 165 " -0.356 5.00e-02 4.00e+02 pdb=" CA PRO M 165 " 0.120 5.00e-02 4.00e+02 pdb=" CD PRO M 165 " 0.090 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR R 164 " -0.146 5.00e-02 4.00e+02 2.07e-01 6.82e+01 pdb=" N PRO R 165 " 0.356 5.00e-02 4.00e+02 pdb=" CA PRO R 165 " -0.120 5.00e-02 4.00e+02 pdb=" CD PRO R 165 " -0.090 5.00e-02 4.00e+02 ... (remaining 5017 not shown) Histogram of nonbonded interaction distances: 1.27 - 2.00: 98 2.00 - 2.72: 1464 2.72 - 3.45: 42187 3.45 - 4.17: 63553 4.17 - 4.90: 115335 Nonbonded interactions: 222637 Sorted by model distance: nonbonded pdb=" CZ ARG P 84 " pdb=" NH2 ARG S 47 " model vdw 1.269 2.680 nonbonded pdb=" CZ ARG A 84 " pdb=" NH2 ARG N 47 " model vdw 1.269 2.680 nonbonded pdb=" CZ ARG B 84 " pdb=" NH2 ARG E 47 " model vdw 1.269 2.680 nonbonded pdb=" CZ ARG G 84 " pdb=" NH2 ARG J 47 " model vdw 1.269 2.680 nonbonded pdb=" CZ ARG O 84 " pdb=" NH2 ARG R 47 " model vdw 1.269 2.680 ... (remaining 222632 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.08 Found NCS groups: ncs_group { reference = chain '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 'A' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.380 Check model and map are aligned: 0.080 Set scattering table: 0.090 Process input model: 23.790 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8104 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 : 0.026 1.021 29110 Z= 2.489 Angle : 0.991 17.041 39600 Z= 0.536 Chirality : 0.047 0.147 4960 Planarity : 0.014 0.207 5020 Dihedral : 12.090 50.273 10340 Min Nonbonded Distance : 1.269 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.52 % Allowed : 5.67 % Favored : 93.81 % 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: 1.39 (0.14), residues: 3880 helix: 3.50 (0.15), residues: 1040 sheet: 1.98 (0.18), residues: 900 loop : -1.18 (0.13), residues: 1940 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG T 84 TYR 0.010 0.002 TYR I 138 PHE 0.021 0.002 PHE T 28 TRP 0.012 0.003 TRP T 136 Details of bonding type rmsd covalent geometry : bond 0.00756 (29060) covalent geometry : angle 0.99087 (39560) SS BOND : bond 0.00041 ( 20) SS BOND : angle 0.87436 ( 40) hydrogen bonds : bond 0.16371 ( 1600) hydrogen bonds : angle 6.63837 ( 4500) Misc. bond : bond 0.77074 ( 30) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1079 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1079 time to evaluate : 0.894 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LYS cc_start: 0.6243 (mttt) cc_final: 0.5711 (mmtp) REVERT: B 187 GLU cc_start: 0.7824 (tt0) cc_final: 0.7522 (tt0) REVERT: C 43 GLU cc_start: 0.8018 (tm-30) cc_final: 0.7658 (tm-30) REVERT: C 93 LYS cc_start: 0.6947 (mttt) cc_final: 0.6140 (mmtm) REVERT: C 121 SER cc_start: 0.8160 (m) cc_final: 0.7081 (t) REVERT: D 95 THR cc_start: 0.9334 (m) cc_final: 0.9036 (p) REVERT: D 121 SER cc_start: 0.8701 (m) cc_final: 0.8424 (m) REVERT: D 138 TYR cc_start: 0.8580 (p90) cc_final: 0.7979 (p90) REVERT: E 46 GLN cc_start: 0.8925 (tt0) cc_final: 0.8549 (tm-30) REVERT: E 121 SER cc_start: 0.8904 (m) cc_final: 0.7911 (p) REVERT: E 138 TYR cc_start: 0.8916 (p90) cc_final: 0.8490 (p90) REVERT: F 43 GLU cc_start: 0.8213 (tm-30) cc_final: 0.7962 (tm-30) REVERT: F 170 GLU cc_start: 0.8451 (pm20) cc_final: 0.8091 (pm20) REVERT: F 187 GLU cc_start: 0.7519 (tt0) cc_final: 0.6932 (tt0) REVERT: G 46 GLN cc_start: 0.9040 (tt0) cc_final: 0.8612 (tm-30) REVERT: G 92 ASP cc_start: 0.8611 (m-30) cc_final: 0.8410 (p0) REVERT: G 103 LYS cc_start: 0.7528 (mppt) cc_final: 0.7214 (mtmt) REVERT: H 19 PHE cc_start: 0.8434 (m-80) cc_final: 0.8215 (m-80) REVERT: H 93 LYS cc_start: 0.7076 (mttt) cc_final: 0.6049 (mmtp) REVERT: H 138 TYR cc_start: 0.8989 (p90) cc_final: 0.8759 (p90) REVERT: I 19 PHE cc_start: 0.8885 (m-80) cc_final: 0.8638 (m-80) REVERT: I 85 GLU cc_start: 0.7776 (tp30) cc_final: 0.7458 (tp30) REVERT: J 19 PHE cc_start: 0.8650 (m-80) cc_final: 0.8321 (m-80) REVERT: J 32 ASN cc_start: 0.9382 (t0) cc_final: 0.9173 (t0) REVERT: J 85 GLU cc_start: 0.7363 (tp30) cc_final: 0.6909 (tp30) REVERT: J 138 TYR cc_start: 0.8842 (p90) cc_final: 0.8263 (p90) REVERT: J 170 GLU cc_start: 0.8809 (pm20) cc_final: 0.8356 (pm20) REVERT: K 95 THR cc_start: 0.9479 (m) cc_final: 0.9241 (p) REVERT: K 105 TYR cc_start: 0.8956 (m-80) cc_final: 0.8649 (m-80) REVERT: K 138 TYR cc_start: 0.8470 (p90) cc_final: 0.8205 (p90) REVERT: K 173 LYS cc_start: 0.8658 (tttt) cc_final: 0.8359 (tttm) REVERT: L 11 GLU cc_start: 0.7944 (pm20) cc_final: 0.7709 (pm20) REVERT: M 85 GLU cc_start: 0.7897 (tp30) cc_final: 0.7537 (tp30) REVERT: M 171 GLU cc_start: 0.8197 (mt-10) cc_final: 0.7989 (mt-10) REVERT: N 17 ILE cc_start: 0.9276 (mt) cc_final: 0.8960 (mt) REVERT: N 19 PHE cc_start: 0.8225 (m-80) cc_final: 0.7856 (m-80) REVERT: N 46 GLN cc_start: 0.9043 (tt0) cc_final: 0.8513 (tm-30) REVERT: N 85 GLU cc_start: 0.7974 (tp30) cc_final: 0.7467 (tp30) REVERT: N 173 LYS cc_start: 0.8749 (tttt) cc_final: 0.8442 (tttm) REVERT: O 173 LYS cc_start: 0.8462 (tttt) cc_final: 0.8209 (ttpt) REVERT: O 187 GLU cc_start: 0.7894 (tt0) cc_final: 0.7608 (tt0) REVERT: P 11 GLU cc_start: 0.7757 (pm20) cc_final: 0.7475 (pm20) REVERT: P 136 TRP cc_start: 0.7582 (m-90) cc_final: 0.7266 (m-10) REVERT: P 173 LYS cc_start: 0.8651 (tttt) cc_final: 0.8317 (tttm) REVERT: Q 28 PHE cc_start: 0.8929 (t80) cc_final: 0.8728 (t80) REVERT: Q 95 THR cc_start: 0.9186 (m) cc_final: 0.8898 (p) REVERT: Q 175 GLU cc_start: 0.8120 (tt0) cc_final: 0.7839 (tt0) REVERT: R 11 GLU cc_start: 0.8329 (pm20) cc_final: 0.8080 (pm20) REVERT: R 84 ARG cc_start: 0.7845 (mpt180) cc_final: 0.7041 (mpt180) REVERT: R 122 LYS cc_start: 0.7544 (mmmm) cc_final: 0.7199 (mmtt) REVERT: R 155 LYS cc_start: 0.8239 (mmtm) cc_final: 0.6975 (mmmt) REVERT: S 11 GLU cc_start: 0.7980 (pm20) cc_final: 0.7574 (pm20) REVERT: S 17 ILE cc_start: 0.9371 (mt) cc_final: 0.9169 (mt) REVERT: S 19 PHE cc_start: 0.8596 (m-80) cc_final: 0.8015 (m-80) REVERT: S 42 LYS cc_start: 0.9273 (tttt) cc_final: 0.8716 (tptt) REVERT: S 51 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8214 (tp30) REVERT: S 122 LYS cc_start: 0.8422 (mmmm) cc_final: 0.7373 (mmtt) REVERT: S 170 GLU cc_start: 0.8614 (pm20) cc_final: 0.8360 (pm20) REVERT: T 85 GLU cc_start: 0.8118 (tp30) cc_final: 0.7540 (tp30) REVERT: T 121 SER cc_start: 0.8597 (m) cc_final: 0.7858 (t) REVERT: T 122 LYS cc_start: 0.8486 (mmmm) cc_final: 0.8037 (mmtt) REVERT: T 138 TYR cc_start: 0.8616 (p90) cc_final: 0.8216 (p90) REVERT: T 187 GLU cc_start: 0.7622 (tt0) cc_final: 0.7118 (tt0) outliers start: 0 outliers final: 0 residues processed: 1079 average time/residue: 0.1773 time to fit residues: 300.0312 Evaluate side-chains 723 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 723 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 197 optimal weight: 0.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 6.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 6.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 6.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 0.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN D 143 ASN F 143 ASN I 143 ASN I 180 GLN J 143 ASN P 180 GLN S 46 GLN T 180 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.112740 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.098940 restraints weight = 57746.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102424 restraints weight = 28673.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104706 restraints weight = 17431.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106251 restraints weight = 11888.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.107305 restraints weight = 8755.566| |-----------------------------------------------------------------------------| r_work (final): 0.3620 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8129 moved from start: 0.2327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 29110 Z= 0.147 Angle : 0.708 8.874 39600 Z= 0.361 Chirality : 0.047 0.159 4960 Planarity : 0.011 0.216 5020 Dihedral : 6.148 177.970 4080 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 9.69 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.64 % Favored : 93.32 % Rotamer: Outliers : 1.96 % Allowed : 8.99 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % 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: 1.33 (0.14), residues: 3880 helix: 3.47 (0.15), residues: 1040 sheet: 1.46 (0.16), residues: 1160 loop : -1.37 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.029 0.002 ARG P 47 TYR 0.012 0.001 TYR F 105 PHE 0.022 0.001 PHE A 28 TRP 0.011 0.002 TRP I 136 Details of bonding type rmsd covalent geometry : bond 0.00338 (29060) covalent geometry : angle 0.70824 (39560) SS BOND : bond 0.00251 ( 20) SS BOND : angle 0.58510 ( 40) hydrogen bonds : bond 0.04483 ( 1600) hydrogen bonds : angle 4.82673 ( 4500) Misc. bond : bond 0.00181 ( 30) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 924 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 862 time to evaluate : 1.071 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: B 93 LYS cc_start: 0.5910 (mttt) cc_final: 0.5354 (mmtp) REVERT: C 93 LYS cc_start: 0.6672 (mttt) cc_final: 0.5964 (mmtm) REVERT: C 121 SER cc_start: 0.7922 (m) cc_final: 0.7111 (t) REVERT: C 172 PHE cc_start: 0.8315 (p90) cc_final: 0.8036 (p90) REVERT: D 40 LYS cc_start: 0.9467 (tptp) cc_final: 0.9078 (tptp) REVERT: D 43 GLU cc_start: 0.8037 (tm-30) cc_final: 0.7535 (tm-30) REVERT: D 85 GLU cc_start: 0.7680 (tp30) cc_final: 0.6857 (mm-30) REVERT: D 95 THR cc_start: 0.9264 (m) cc_final: 0.8800 (p) REVERT: D 138 TYR cc_start: 0.8530 (p90) cc_final: 0.8101 (p90) REVERT: D 172 PHE cc_start: 0.8733 (p90) cc_final: 0.8524 (p90) REVERT: E 46 GLN cc_start: 0.8978 (tt0) cc_final: 0.8519 (tm-30) REVERT: E 122 LYS cc_start: 0.8781 (tppt) cc_final: 0.8504 (tptp) REVERT: E 173 LYS cc_start: 0.8910 (tttt) cc_final: 0.8676 (tttm) REVERT: F 43 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7768 (tm-30) REVERT: F 57 GLU cc_start: 0.8149 (pt0) cc_final: 0.7875 (pt0) REVERT: F 170 GLU cc_start: 0.8424 (pm20) cc_final: 0.8112 (pm20) REVERT: G 19 PHE cc_start: 0.8556 (m-80) cc_final: 0.8272 (m-80) REVERT: G 46 GLN cc_start: 0.9008 (tt0) cc_final: 0.8680 (tm-30) REVERT: G 103 LYS cc_start: 0.7577 (mppt) cc_final: 0.7149 (mtmt) REVERT: H 19 PHE cc_start: 0.8531 (m-80) cc_final: 0.8288 (m-80) REVERT: H 93 LYS cc_start: 0.6652 (mttt) cc_final: 0.5732 (mmtp) REVERT: I 19 PHE cc_start: 0.8865 (m-80) cc_final: 0.8639 (m-80) REVERT: I 122 LYS cc_start: 0.7697 (mmmt) cc_final: 0.7396 (tptt) REVERT: I 138 TYR cc_start: 0.8348 (p90) cc_final: 0.7985 (p90) REVERT: J 19 PHE cc_start: 0.8624 (m-80) cc_final: 0.8365 (m-80) REVERT: J 50 GLU cc_start: 0.8175 (tm-30) cc_final: 0.7197 (tm-30) REVERT: J 148 ASN cc_start: 0.8003 (m-40) cc_final: 0.7748 (t0) REVERT: K 138 TYR cc_start: 0.8372 (p90) cc_final: 0.8107 (p90) REVERT: K 173 LYS cc_start: 0.8825 (tttt) cc_final: 0.8462 (tttm) REVERT: A 43 GLU cc_start: 0.8160 (tm-30) cc_final: 0.7875 (tm-30) REVERT: A 155 LYS cc_start: 0.9485 (mmtm) cc_final: 0.9269 (mmtt) REVERT: L 85 GLU cc_start: 0.7147 (tp30) cc_final: 0.6940 (mm-30) REVERT: L 173 LYS cc_start: 0.8872 (tttt) cc_final: 0.8568 (mtpt) REVERT: M 35 LEU cc_start: 0.8794 (mt) cc_final: 0.8563 (mt) REVERT: M 39 GLN cc_start: 0.8420 (OUTLIER) cc_final: 0.8015 (mp10) REVERT: M 171 GLU cc_start: 0.8302 (mt-10) cc_final: 0.8102 (mt-10) REVERT: N 122 LYS cc_start: 0.8320 (tptm) cc_final: 0.8029 (mmtt) REVERT: N 172 PHE cc_start: 0.8690 (p90) cc_final: 0.8482 (p90) REVERT: N 173 LYS cc_start: 0.8932 (tttt) cc_final: 0.8667 (tttm) REVERT: O 89 MET cc_start: 0.7533 (mmm) cc_final: 0.7229 (mmm) REVERT: O 105 TYR cc_start: 0.9106 (m-80) cc_final: 0.8684 (m-80) REVERT: P 173 LYS cc_start: 0.8865 (tttt) cc_final: 0.8603 (tttm) REVERT: Q 28 PHE cc_start: 0.8905 (t80) cc_final: 0.8605 (t80) REVERT: Q 39 GLN cc_start: 0.8760 (mm-40) cc_final: 0.8423 (mm110) REVERT: Q 95 THR cc_start: 0.9212 (m) cc_final: 0.8731 (p) REVERT: R 84 ARG cc_start: 0.7614 (mpt180) cc_final: 0.6953 (mpt180) REVERT: R 122 LYS cc_start: 0.7598 (mmmm) cc_final: 0.6907 (mptt) REVERT: R 155 LYS cc_start: 0.8945 (mmtm) cc_final: 0.7109 (tptm) REVERT: S 11 GLU cc_start: 0.7894 (pm20) cc_final: 0.7547 (pm20) REVERT: S 19 PHE cc_start: 0.8238 (m-80) cc_final: 0.7807 (m-80) REVERT: S 42 LYS cc_start: 0.9277 (tttt) cc_final: 0.8654 (tptt) REVERT: S 51 GLU cc_start: 0.8422 (tm-30) cc_final: 0.8155 (tm-30) REVERT: S 120 ASP cc_start: 0.6775 (t0) cc_final: 0.6415 (p0) REVERT: S 122 LYS cc_start: 0.8406 (mmmm) cc_final: 0.7061 (mmtt) REVERT: S 155 LYS cc_start: 0.8890 (mmtm) cc_final: 0.7630 (mmmt) REVERT: S 170 GLU cc_start: 0.8772 (pm20) cc_final: 0.8458 (pm20) REVERT: T 121 SER cc_start: 0.8612 (m) cc_final: 0.7880 (t) REVERT: T 122 LYS cc_start: 0.8374 (mmmm) cc_final: 0.8025 (mmtt) REVERT: T 138 TYR cc_start: 0.8704 (p90) cc_final: 0.8343 (p90) REVERT: T 171 GLU cc_start: 0.7267 (mt-10) cc_final: 0.7043 (tt0) outliers start: 62 outliers final: 43 residues processed: 882 average time/residue: 0.1837 time to fit residues: 252.6672 Evaluate side-chains 728 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 684 time to evaluate : 1.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 92 ASP Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 84 ARG Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 74 ILE Chi-restraints excluded: chain L residue 95 THR Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 136 TRP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 139 LEU Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 129 SER Chi-restraints excluded: chain T residue 180 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 72 optimal weight: 2.9990 chunk 243 optimal weight: 6.9990 chunk 331 optimal weight: 3.9990 chunk 270 optimal weight: 0.0670 chunk 116 optimal weight: 6.9990 chunk 362 optimal weight: 0.9980 chunk 259 optimal weight: 6.9990 chunk 56 optimal weight: 4.9990 chunk 340 optimal weight: 0.8980 chunk 134 optimal weight: 6.9990 chunk 4 optimal weight: 5.9990 overall best weight: 1.7922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN D 143 ASN G 180 GLN J 39 GLN M 143 ASN M 180 GLN O 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.096875 restraints weight = 57768.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100318 restraints weight = 28710.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.102590 restraints weight = 17465.421| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104101 restraints weight = 11919.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 48)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105151 restraints weight = 8824.552| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.2827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29110 Z= 0.155 Angle : 0.689 13.819 39600 Z= 0.351 Chirality : 0.047 0.170 4960 Planarity : 0.009 0.179 5020 Dihedral : 6.012 179.748 4080 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.16 % Favored : 93.32 % Rotamer: Outliers : 3.01 % Allowed : 11.36 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.14), residues: 3880 helix: 3.33 (0.15), residues: 1040 sheet: 1.81 (0.17), residues: 1080 loop : -1.46 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.002 ARG E 84 TYR 0.010 0.001 TYR K 105 PHE 0.022 0.002 PHE M 28 TRP 0.010 0.002 TRP I 136 Details of bonding type rmsd covalent geometry : bond 0.00365 (29060) covalent geometry : angle 0.68894 (39560) SS BOND : bond 0.00244 ( 20) SS BOND : angle 0.62077 ( 40) hydrogen bonds : bond 0.04259 ( 1600) hydrogen bonds : angle 4.63964 ( 4500) Misc. bond : bond 0.00287 ( 30) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 778 time to evaluate : 1.050 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 45 MET cc_start: 0.9052 (ptp) cc_final: 0.8771 (ptm) REVERT: C 93 LYS cc_start: 0.6675 (mttt) cc_final: 0.5984 (mmtm) REVERT: C 121 SER cc_start: 0.7818 (m) cc_final: 0.7032 (t) REVERT: D 40 LYS cc_start: 0.9409 (tptp) cc_final: 0.9202 (tptp) REVERT: D 95 THR cc_start: 0.9169 (m) cc_final: 0.8654 (p) REVERT: D 138 TYR cc_start: 0.8451 (p90) cc_final: 0.8087 (p90) REVERT: D 172 PHE cc_start: 0.8752 (p90) cc_final: 0.8528 (p90) REVERT: E 85 GLU cc_start: 0.8009 (tp30) cc_final: 0.7705 (mp0) REVERT: E 121 SER cc_start: 0.8634 (m) cc_final: 0.7807 (t) REVERT: E 173 LYS cc_start: 0.8891 (tttt) cc_final: 0.8638 (tttm) REVERT: F 59 ASP cc_start: 0.7987 (t0) cc_final: 0.7664 (t0) REVERT: F 138 TYR cc_start: 0.8458 (p90) cc_final: 0.8250 (p90) REVERT: G 19 PHE cc_start: 0.8535 (m-80) cc_final: 0.8297 (m-80) REVERT: G 46 GLN cc_start: 0.8893 (tt0) cc_final: 0.8285 (tm-30) REVERT: G 93 LYS cc_start: 0.6835 (mttt) cc_final: 0.6630 (mmtp) REVERT: G 138 TYR cc_start: 0.8698 (p90) cc_final: 0.8483 (p90) REVERT: H 43 GLU cc_start: 0.8392 (tm-30) cc_final: 0.8151 (tm-30) REVERT: H 93 LYS cc_start: 0.6769 (mttt) cc_final: 0.5870 (mmtp) REVERT: H 121 SER cc_start: 0.7824 (OUTLIER) cc_final: 0.6688 (t) REVERT: I 138 TYR cc_start: 0.8259 (p90) cc_final: 0.7204 (p90) REVERT: J 19 PHE cc_start: 0.8661 (m-80) cc_final: 0.8378 (m-80) REVERT: J 28 PHE cc_start: 0.9070 (t80) cc_final: 0.8864 (t80) REVERT: J 43 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7743 (tm-30) REVERT: J 85 GLU cc_start: 0.7609 (tp30) cc_final: 0.6989 (tp30) REVERT: J 103 LYS cc_start: 0.8141 (mmtt) cc_final: 0.7882 (mmmt) REVERT: J 148 ASN cc_start: 0.8035 (m-40) cc_final: 0.7812 (t0) REVERT: K 173 LYS cc_start: 0.8813 (tttt) cc_final: 0.8471 (tttm) REVERT: A 50 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7998 (tp30) REVERT: A 170 GLU cc_start: 0.8473 (pm20) cc_final: 0.8132 (pm20) REVERT: L 120 ASP cc_start: 0.6612 (t0) cc_final: 0.5966 (p0) REVERT: L 173 LYS cc_start: 0.8782 (tttt) cc_final: 0.8520 (mtpt) REVERT: M 50 GLU cc_start: 0.7978 (mm-30) cc_final: 0.7409 (mm-30) REVERT: M 106 GLU cc_start: 0.7761 (tp30) cc_final: 0.7528 (tp30) REVERT: N 19 PHE cc_start: 0.8358 (m-80) cc_final: 0.8109 (m-80) REVERT: N 50 GLU cc_start: 0.7774 (mm-30) cc_final: 0.7321 (mp0) REVERT: N 122 LYS cc_start: 0.8492 (tptm) cc_final: 0.8225 (tptp) REVERT: N 173 LYS cc_start: 0.8953 (tttt) cc_final: 0.8687 (tttm) REVERT: O 89 MET cc_start: 0.7666 (mmm) cc_final: 0.7400 (mmm) REVERT: P 121 SER cc_start: 0.8151 (m) cc_final: 0.7299 (t) REVERT: P 173 LYS cc_start: 0.8957 (tttt) cc_final: 0.8629 (tttm) REVERT: Q 28 PHE cc_start: 0.8994 (t80) cc_final: 0.8656 (t80) REVERT: Q 39 GLN cc_start: 0.8795 (mm-40) cc_final: 0.8384 (mm110) REVERT: Q 46 GLN cc_start: 0.8942 (tm-30) cc_final: 0.8630 (tm-30) REVERT: Q 95 THR cc_start: 0.9215 (m) cc_final: 0.8734 (p) REVERT: Q 138 TYR cc_start: 0.8342 (p90) cc_final: 0.8103 (p90) REVERT: R 84 ARG cc_start: 0.7500 (mpt180) cc_final: 0.6981 (mpt180) REVERT: R 103 LYS cc_start: 0.7842 (mptt) cc_final: 0.7209 (mptt) REVERT: R 122 LYS cc_start: 0.7767 (mmmm) cc_final: 0.7321 (mptt) REVERT: R 155 LYS cc_start: 0.9007 (mmtm) cc_final: 0.7173 (tttt) REVERT: S 19 PHE cc_start: 0.8164 (m-80) cc_final: 0.7718 (m-80) REVERT: S 42 LYS cc_start: 0.9231 (tttt) cc_final: 0.8460 (tptt) REVERT: S 51 GLU cc_start: 0.8450 (tm-30) cc_final: 0.8159 (tm-30) REVERT: S 122 LYS cc_start: 0.8472 (mmmm) cc_final: 0.6995 (mmtt) REVERT: S 155 LYS cc_start: 0.8928 (mmtm) cc_final: 0.7686 (mmmt) REVERT: T 121 SER cc_start: 0.8647 (m) cc_final: 0.7943 (t) REVERT: T 122 LYS cc_start: 0.8375 (mmmm) cc_final: 0.8050 (mmtt) outliers start: 95 outliers final: 51 residues processed: 833 average time/residue: 0.1790 time to fit residues: 233.8475 Evaluate side-chains 745 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 693 time to evaluate : 0.907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain D residue 129 SER Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 136 TRP Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 200 VAL Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 311 optimal weight: 2.9990 chunk 204 optimal weight: 7.9990 chunk 278 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 328 optimal weight: 6.9990 chunk 44 optimal weight: 7.9990 chunk 197 optimal weight: 9.9990 chunk 290 optimal weight: 6.9990 chunk 78 optimal weight: 5.9990 chunk 280 optimal weight: 10.0000 chunk 169 optimal weight: 8.9990 overall best weight: 3.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3598 r_free = 0.3598 target = 0.106019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.092269 restraints weight = 58118.859| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095707 restraints weight = 28286.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097917 restraints weight = 17034.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.099402 restraints weight = 11596.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3505 r_free = 0.3505 target = 0.100444 restraints weight = 8570.314| |-----------------------------------------------------------------------------| r_work (final): 0.3508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8251 moved from start: 0.3443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.061 29110 Z= 0.244 Angle : 0.759 15.503 39600 Z= 0.387 Chirality : 0.048 0.187 4960 Planarity : 0.008 0.166 5020 Dihedral : 6.146 179.259 4080 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.11 % Favored : 92.37 % Rotamer: Outliers : 3.42 % Allowed : 14.08 % Favored : 82.50 % 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: 0.78 (0.14), residues: 3880 helix: 3.10 (0.15), residues: 1040 sheet: 1.02 (0.16), residues: 1160 loop : -1.66 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.025 0.002 ARG C 84 TYR 0.028 0.002 TYR K 169 PHE 0.023 0.002 PHE F 28 TRP 0.016 0.003 TRP D 136 Details of bonding type rmsd covalent geometry : bond 0.00584 (29060) covalent geometry : angle 0.75854 (39560) SS BOND : bond 0.00363 ( 20) SS BOND : angle 0.72124 ( 40) hydrogen bonds : bond 0.04536 ( 1600) hydrogen bonds : angle 4.88872 ( 4500) Misc. bond : bond 0.00293 ( 30) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 850 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 742 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 171 GLU cc_start: 0.7856 (mt-10) cc_final: 0.7446 (mt-10) REVERT: C 103 LYS cc_start: 0.8169 (mmmt) cc_final: 0.7808 (tptp) REVERT: C 172 PHE cc_start: 0.8369 (p90) cc_final: 0.8154 (p90) REVERT: C 180 GLN cc_start: 0.8354 (pm20) cc_final: 0.8094 (pm20) REVERT: D 85 GLU cc_start: 0.7743 (OUTLIER) cc_final: 0.7175 (mp0) REVERT: D 95 THR cc_start: 0.9141 (m) cc_final: 0.8598 (p) REVERT: D 138 TYR cc_start: 0.8593 (p90) cc_final: 0.8137 (p90) REVERT: D 172 PHE cc_start: 0.8824 (p90) cc_final: 0.8605 (p90) REVERT: E 121 SER cc_start: 0.8674 (m) cc_final: 0.7786 (t) REVERT: E 173 LYS cc_start: 0.8971 (tttt) cc_final: 0.8706 (tttm) REVERT: F 57 GLU cc_start: 0.8373 (pt0) cc_final: 0.8164 (pt0) REVERT: F 106 GLU cc_start: 0.7896 (tp30) cc_final: 0.7681 (tp30) REVERT: G 19 PHE cc_start: 0.8628 (m-80) cc_final: 0.8414 (m-80) REVERT: G 43 GLU cc_start: 0.8453 (tm-30) cc_final: 0.8020 (tm-30) REVERT: G 138 TYR cc_start: 0.8875 (p90) cc_final: 0.8584 (p90) REVERT: G 170 GLU cc_start: 0.8648 (pm20) cc_final: 0.8399 (pm20) REVERT: H 93 LYS cc_start: 0.7027 (mttt) cc_final: 0.5990 (mmtp) REVERT: H 170 GLU cc_start: 0.8593 (pm20) cc_final: 0.8338 (pm20) REVERT: I 19 PHE cc_start: 0.9014 (m-80) cc_final: 0.8804 (m-80) REVERT: I 99 MET cc_start: 0.8500 (tmm) cc_final: 0.8133 (tmm) REVERT: J 19 PHE cc_start: 0.8776 (m-80) cc_final: 0.8459 (m-80) REVERT: J 170 GLU cc_start: 0.8504 (pm20) cc_final: 0.8195 (pm20) REVERT: K 138 TYR cc_start: 0.8529 (p90) cc_final: 0.8143 (p90) REVERT: K 173 LYS cc_start: 0.8860 (tttt) cc_final: 0.8497 (tttm) REVERT: A 103 LYS cc_start: 0.7510 (mppt) cc_final: 0.7282 (mmtp) REVERT: L 45 MET cc_start: 0.9136 (ptp) cc_final: 0.8770 (ptm) REVERT: L 88 ASP cc_start: 0.8463 (t0) cc_final: 0.8236 (t0) REVERT: L 92 ASP cc_start: 0.8271 (p0) cc_final: 0.7628 (p0) REVERT: L 103 LYS cc_start: 0.8213 (mppt) cc_final: 0.7711 (mttt) REVERT: L 120 ASP cc_start: 0.6632 (t0) cc_final: 0.6075 (p0) REVERT: M 39 GLN cc_start: 0.8491 (OUTLIER) cc_final: 0.8201 (mp10) REVERT: M 46 GLN cc_start: 0.8914 (tm-30) cc_final: 0.8343 (tm-30) REVERT: M 106 GLU cc_start: 0.7838 (tp30) cc_final: 0.7632 (tp30) REVERT: N 122 LYS cc_start: 0.8682 (tptm) cc_final: 0.8474 (tptp) REVERT: N 173 LYS cc_start: 0.9020 (tttt) cc_final: 0.8650 (tttm) REVERT: P 121 SER cc_start: 0.8234 (m) cc_final: 0.6957 (t) REVERT: P 173 LYS cc_start: 0.8972 (tttt) cc_final: 0.8640 (tttm) REVERT: P 187 GLU cc_start: 0.8216 (tm-30) cc_final: 0.7640 (tm-30) REVERT: Q 59 ASP cc_start: 0.7857 (t0) cc_final: 0.7587 (t0) REVERT: Q 95 THR cc_start: 0.9259 (m) cc_final: 0.8789 (p) REVERT: Q 103 LYS cc_start: 0.7944 (mppt) cc_final: 0.7605 (mtmt) REVERT: Q 138 TYR cc_start: 0.8442 (p90) cc_final: 0.8217 (p90) REVERT: R 50 GLU cc_start: 0.7982 (tp30) cc_final: 0.6287 (mm-30) REVERT: R 84 ARG cc_start: 0.7716 (mpt180) cc_final: 0.7210 (mpt180) REVERT: R 92 ASP cc_start: 0.8511 (p0) cc_final: 0.7989 (p0) REVERT: R 105 TYR cc_start: 0.8548 (m-80) cc_final: 0.8261 (m-80) REVERT: R 122 LYS cc_start: 0.8023 (mmmm) cc_final: 0.7596 (mptt) REVERT: R 155 LYS cc_start: 0.9052 (mmtm) cc_final: 0.7253 (tptm) REVERT: S 19 PHE cc_start: 0.8302 (m-80) cc_final: 0.7815 (m-80) REVERT: S 42 LYS cc_start: 0.9162 (tttt) cc_final: 0.8313 (tptt) REVERT: S 51 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8187 (tm-30) REVERT: S 84 ARG cc_start: 0.7975 (mpt180) cc_final: 0.7506 (mtt90) REVERT: S 122 LYS cc_start: 0.8864 (mmmm) cc_final: 0.7556 (mmtt) REVERT: S 155 LYS cc_start: 0.8929 (mmtm) cc_final: 0.7804 (mmmt) REVERT: T 45 MET cc_start: 0.8790 (OUTLIER) cc_final: 0.8464 (ptt) REVERT: T 121 SER cc_start: 0.8761 (m) cc_final: 0.8036 (t) REVERT: T 122 LYS cc_start: 0.8497 (mmmm) cc_final: 0.8093 (mmtt) outliers start: 108 outliers final: 63 residues processed: 810 average time/residue: 0.1828 time to fit residues: 229.6571 Evaluate side-chains 728 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 662 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 160 LEU Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 66 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 187 GLU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 66 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain T residue 45 MET Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 125 optimal weight: 6.9990 chunk 25 optimal weight: 3.9990 chunk 148 optimal weight: 0.6980 chunk 159 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 126 optimal weight: 3.9990 chunk 304 optimal weight: 1.9990 chunk 285 optimal weight: 0.7980 chunk 183 optimal weight: 7.9990 chunk 87 optimal weight: 5.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN G 143 ASN J 39 GLN M 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.108958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.095326 restraints weight = 57868.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.098798 restraints weight = 27900.675| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.101047 restraints weight = 16652.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.102540 restraints weight = 11261.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.103537 restraints weight = 8265.050| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29110 Z= 0.145 Angle : 0.729 15.153 39600 Z= 0.365 Chirality : 0.047 0.189 4960 Planarity : 0.007 0.190 5020 Dihedral : 5.991 179.907 4080 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.29 % Favored : 93.20 % Rotamer: Outliers : 2.97 % Allowed : 15.82 % Favored : 81.20 % 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: 0.82 (0.14), residues: 3880 helix: 3.13 (0.15), residues: 1040 sheet: 0.92 (0.16), residues: 1180 loop : -1.56 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.002 ARG E 84 TYR 0.027 0.001 TYR K 169 PHE 0.022 0.002 PHE M 28 TRP 0.010 0.002 TRP P 136 Details of bonding type rmsd covalent geometry : bond 0.00337 (29060) covalent geometry : angle 0.72881 (39560) SS BOND : bond 0.00194 ( 20) SS BOND : angle 0.47111 ( 40) hydrogen bonds : bond 0.04118 ( 1600) hydrogen bonds : angle 4.57036 ( 4500) Misc. bond : bond 0.00339 ( 30) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 870 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 776 time to evaluate : 0.998 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 40 LYS cc_start: 0.9517 (tptp) cc_final: 0.9278 (tptm) REVERT: C 93 LYS cc_start: 0.6557 (mttt) cc_final: 0.5890 (mmtm) REVERT: C 172 PHE cc_start: 0.8248 (p90) cc_final: 0.8018 (p90) REVERT: D 76 ILE cc_start: 0.9378 (mt) cc_final: 0.9164 (tt) REVERT: D 85 GLU cc_start: 0.7682 (OUTLIER) cc_final: 0.7174 (mp0) REVERT: D 95 THR cc_start: 0.9112 (m) cc_final: 0.8674 (p) REVERT: D 138 TYR cc_start: 0.8362 (p90) cc_final: 0.7913 (p90) REVERT: D 172 PHE cc_start: 0.8773 (p90) cc_final: 0.8549 (p90) REVERT: E 120 ASP cc_start: 0.7563 (t0) cc_final: 0.7277 (p0) REVERT: E 121 SER cc_start: 0.8603 (m) cc_final: 0.7060 (t) REVERT: G 19 PHE cc_start: 0.8574 (m-80) cc_final: 0.8243 (m-80) REVERT: G 46 GLN cc_start: 0.9044 (tt0) cc_final: 0.8641 (tm-30) REVERT: G 138 TYR cc_start: 0.8749 (p90) cc_final: 0.8415 (p90) REVERT: H 93 LYS cc_start: 0.6954 (mttt) cc_final: 0.5967 (mmtp) REVERT: H 170 GLU cc_start: 0.8486 (pm20) cc_final: 0.8248 (pm20) REVERT: I 19 PHE cc_start: 0.8995 (m-80) cc_final: 0.8783 (m-80) REVERT: I 99 MET cc_start: 0.8471 (tmm) cc_final: 0.8123 (tmm) REVERT: I 138 TYR cc_start: 0.8203 (p90) cc_final: 0.7247 (p90) REVERT: J 19 PHE cc_start: 0.8738 (m-80) cc_final: 0.8361 (m-80) REVERT: J 103 LYS cc_start: 0.8459 (mmtt) cc_final: 0.8107 (mmmt) REVERT: J 148 ASN cc_start: 0.7779 (m-40) cc_final: 0.7518 (t0) REVERT: J 169 TYR cc_start: 0.7393 (m-80) cc_final: 0.7177 (m-80) REVERT: K 33 MET cc_start: 0.8690 (OUTLIER) cc_final: 0.8228 (tpp) REVERT: K 173 LYS cc_start: 0.8859 (tttt) cc_final: 0.8495 (tttm) REVERT: A 50 GLU cc_start: 0.8405 (tm-30) cc_final: 0.8016 (tp30) REVERT: A 152 LEU cc_start: 0.8499 (OUTLIER) cc_final: 0.8204 (tt) REVERT: A 170 GLU cc_start: 0.8367 (pm20) cc_final: 0.8057 (mp0) REVERT: L 103 LYS cc_start: 0.8150 (mppt) cc_final: 0.7614 (mttt) REVERT: L 120 ASP cc_start: 0.6572 (t0) cc_final: 0.6146 (p0) REVERT: M 39 GLN cc_start: 0.8469 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: M 50 GLU cc_start: 0.7860 (mm-30) cc_final: 0.7367 (tp30) REVERT: M 85 GLU cc_start: 0.7925 (tp30) cc_final: 0.6643 (tp30) REVERT: M 172 PHE cc_start: 0.8656 (p90) cc_final: 0.8388 (p90) REVERT: N 122 LYS cc_start: 0.8695 (tptm) cc_final: 0.8440 (tptp) REVERT: N 173 LYS cc_start: 0.9030 (tttt) cc_final: 0.8623 (tttm) REVERT: O 84 ARG cc_start: 0.6056 (mpt-90) cc_final: 0.5814 (mpt-90) REVERT: P 173 LYS cc_start: 0.9029 (tttt) cc_final: 0.8648 (tttm) REVERT: P 187 GLU cc_start: 0.8188 (tm-30) cc_final: 0.7632 (tm-30) REVERT: Q 39 GLN cc_start: 0.8739 (mm-40) cc_final: 0.8477 (mm110) REVERT: Q 95 THR cc_start: 0.9165 (m) cc_final: 0.8656 (p) REVERT: Q 103 LYS cc_start: 0.7648 (mppt) cc_final: 0.7270 (mtmt) REVERT: Q 138 TYR cc_start: 0.8266 (p90) cc_final: 0.8025 (p90) REVERT: R 19 PHE cc_start: 0.8488 (m-80) cc_final: 0.8276 (m-80) REVERT: R 50 GLU cc_start: 0.7524 (tp30) cc_final: 0.7289 (mm-30) REVERT: R 84 ARG cc_start: 0.7698 (mpt180) cc_final: 0.7287 (mpt180) REVERT: R 92 ASP cc_start: 0.8347 (p0) cc_final: 0.7927 (p0) REVERT: R 122 LYS cc_start: 0.7998 (mmmm) cc_final: 0.7582 (mptt) REVERT: R 155 LYS cc_start: 0.9069 (mmtm) cc_final: 0.7179 (tptt) REVERT: S 19 PHE cc_start: 0.8300 (m-80) cc_final: 0.7799 (m-80) REVERT: S 42 LYS cc_start: 0.9119 (tttt) cc_final: 0.8256 (tptt) REVERT: S 84 ARG cc_start: 0.7988 (mpt180) cc_final: 0.7599 (mtt90) REVERT: S 122 LYS cc_start: 0.8838 (mmmm) cc_final: 0.7530 (mmtt) REVERT: S 155 LYS cc_start: 0.8945 (mmtm) cc_final: 0.7847 (mtpt) REVERT: T 45 MET cc_start: 0.8676 (ptm) cc_final: 0.8300 (ptm) REVERT: T 121 SER cc_start: 0.8728 (m) cc_final: 0.7989 (t) REVERT: T 122 LYS cc_start: 0.8489 (mmmm) cc_final: 0.8047 (mmtt) outliers start: 94 outliers final: 65 residues processed: 829 average time/residue: 0.1816 time to fit residues: 234.4995 Evaluate side-chains 753 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 684 time to evaluate : 1.007 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 42 LYS Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 152 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 39 GLN Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 92 ASP Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 169 TYR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 26 optimal weight: 0.4980 chunk 223 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 chunk 317 optimal weight: 6.9990 chunk 359 optimal weight: 9.9990 chunk 28 optimal weight: 0.3980 chunk 102 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 306 optimal weight: 3.9990 chunk 35 optimal weight: 7.9990 chunk 345 optimal weight: 5.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 180 GLN P 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.109717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096121 restraints weight = 58116.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.099588 restraints weight = 27953.420| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.101848 restraints weight = 16662.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3554 r_free = 0.3554 target = 0.103341 restraints weight = 11221.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.104385 restraints weight = 8224.412| |-----------------------------------------------------------------------------| r_work (final): 0.3569 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8187 moved from start: 0.3798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 29110 Z= 0.140 Angle : 0.721 15.641 39600 Z= 0.361 Chirality : 0.047 0.200 4960 Planarity : 0.009 0.245 5020 Dihedral : 6.415 178.390 4080 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.24 % Favored : 93.25 % Rotamer: Outliers : 3.07 % Allowed : 17.41 % Favored : 79.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3880 helix: 3.11 (0.15), residues: 1040 sheet: 0.88 (0.16), residues: 1180 loop : -1.53 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.037 0.002 ARG A 84 TYR 0.019 0.001 TYR A 169 PHE 0.027 0.001 PHE A 28 TRP 0.010 0.002 TRP P 136 Details of bonding type rmsd covalent geometry : bond 0.00322 (29060) covalent geometry : angle 0.72108 (39560) SS BOND : bond 0.00198 ( 20) SS BOND : angle 0.66377 ( 40) hydrogen bonds : bond 0.03947 ( 1600) hydrogen bonds : angle 4.45348 ( 4500) Misc. bond : bond 0.00308 ( 30) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 846 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 749 time to evaluate : 0.885 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 170 GLU cc_start: 0.8355 (pm20) cc_final: 0.8062 (pm20) REVERT: C 93 LYS cc_start: 0.6570 (mttt) cc_final: 0.5908 (mmtm) REVERT: C 172 PHE cc_start: 0.8218 (p90) cc_final: 0.7996 (p90) REVERT: C 180 GLN cc_start: 0.8361 (pm20) cc_final: 0.8015 (pm20) REVERT: D 76 ILE cc_start: 0.9379 (mt) cc_final: 0.9154 (tt) REVERT: D 85 GLU cc_start: 0.7666 (OUTLIER) cc_final: 0.7285 (tp30) REVERT: D 138 TYR cc_start: 0.8312 (p90) cc_final: 0.7872 (p90) REVERT: D 172 PHE cc_start: 0.8737 (p90) cc_final: 0.8517 (p90) REVERT: E 85 GLU cc_start: 0.7988 (mm-30) cc_final: 0.7702 (mp0) REVERT: E 121 SER cc_start: 0.8569 (m) cc_final: 0.7225 (t) REVERT: G 19 PHE cc_start: 0.8381 (m-80) cc_final: 0.8146 (m-80) REVERT: G 46 GLN cc_start: 0.8943 (tt0) cc_final: 0.8662 (tm-30) REVERT: G 138 TYR cc_start: 0.8670 (p90) cc_final: 0.8342 (p90) REVERT: H 59 ASP cc_start: 0.8318 (t0) cc_final: 0.8066 (t0) REVERT: H 93 LYS cc_start: 0.6982 (mttt) cc_final: 0.6004 (mmtp) REVERT: H 170 GLU cc_start: 0.8464 (pm20) cc_final: 0.8173 (pm20) REVERT: I 16 LEU cc_start: 0.9180 (tp) cc_final: 0.8913 (tp) REVERT: I 19 PHE cc_start: 0.8921 (m-80) cc_final: 0.8669 (m-80) REVERT: I 99 MET cc_start: 0.8414 (tmm) cc_final: 0.8098 (tmm) REVERT: I 138 TYR cc_start: 0.8142 (p90) cc_final: 0.7202 (p90) REVERT: J 19 PHE cc_start: 0.8635 (m-80) cc_final: 0.8258 (m-80) REVERT: J 148 ASN cc_start: 0.7606 (m-40) cc_final: 0.7369 (t0) REVERT: J 169 TYR cc_start: 0.7466 (m-80) cc_final: 0.7260 (m-80) REVERT: K 33 MET cc_start: 0.8616 (OUTLIER) cc_final: 0.8134 (tpp) REVERT: K 173 LYS cc_start: 0.8837 (tttt) cc_final: 0.8532 (tttm) REVERT: A 170 GLU cc_start: 0.8090 (pm20) cc_final: 0.7858 (mp0) REVERT: L 40 LYS cc_start: 0.9360 (tptt) cc_final: 0.9142 (tppt) REVERT: L 103 LYS cc_start: 0.7930 (mppt) cc_final: 0.7598 (mttt) REVERT: L 120 ASP cc_start: 0.6407 (t0) cc_final: 0.6137 (p0) REVERT: M 172 PHE cc_start: 0.8657 (p90) cc_final: 0.8393 (p90) REVERT: N 122 LYS cc_start: 0.8671 (tptm) cc_final: 0.8390 (tptp) REVERT: N 173 LYS cc_start: 0.8995 (tttt) cc_final: 0.8657 (tttm) REVERT: P 19 PHE cc_start: 0.8368 (m-80) cc_final: 0.8142 (m-80) REVERT: P 136 TRP cc_start: 0.8014 (m-90) cc_final: 0.7711 (m-10) REVERT: P 173 LYS cc_start: 0.9003 (tttt) cc_final: 0.8653 (tttm) REVERT: P 187 GLU cc_start: 0.8144 (tm-30) cc_final: 0.7647 (tm-30) REVERT: Q 39 GLN cc_start: 0.8692 (mm-40) cc_final: 0.8459 (mm110) REVERT: Q 93 LYS cc_start: 0.7268 (mmtt) cc_final: 0.6675 (mmtt) REVERT: Q 95 THR cc_start: 0.9141 (m) cc_final: 0.8623 (p) REVERT: Q 103 LYS cc_start: 0.7539 (mppt) cc_final: 0.7303 (mtmt) REVERT: R 19 PHE cc_start: 0.8428 (m-80) cc_final: 0.8211 (m-80) REVERT: R 84 ARG cc_start: 0.7604 (mpt180) cc_final: 0.7300 (mpt180) REVERT: R 122 LYS cc_start: 0.8069 (mmmm) cc_final: 0.7677 (mptt) REVERT: R 155 LYS cc_start: 0.9093 (mmtm) cc_final: 0.7350 (tttt) REVERT: S 19 PHE cc_start: 0.8188 (m-80) cc_final: 0.7712 (m-80) REVERT: S 42 LYS cc_start: 0.9086 (tttt) cc_final: 0.8248 (tptt) REVERT: S 84 ARG cc_start: 0.7904 (mpt180) cc_final: 0.7599 (mtt90) REVERT: S 122 LYS cc_start: 0.8856 (mmmm) cc_final: 0.7569 (mmtt) REVERT: S 155 LYS cc_start: 0.8938 (mmtm) cc_final: 0.7064 (tttt) REVERT: T 45 MET cc_start: 0.8587 (OUTLIER) cc_final: 0.8237 (ptm) REVERT: T 121 SER cc_start: 0.8694 (m) cc_final: 0.7934 (t) REVERT: T 122 LYS cc_start: 0.8457 (mmmm) cc_final: 0.8025 (mmtt) outliers start: 97 outliers final: 71 residues processed: 799 average time/residue: 0.1830 time to fit residues: 228.4984 Evaluate side-chains 766 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 692 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 169 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 169 TYR Chi-restraints excluded: chain T residue 45 MET Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 72 ASP Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 129 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 70 optimal weight: 1.9990 chunk 299 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 62 optimal weight: 0.6980 chunk 265 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 6.9990 chunk 110 optimal weight: 3.9990 chunk 294 optimal weight: 0.3980 chunk 128 optimal weight: 6.9990 chunk 268 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN K 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.110781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.097139 restraints weight = 57782.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.100628 restraints weight = 28090.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.102891 restraints weight = 16831.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.104385 restraints weight = 11359.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.105439 restraints weight = 8350.655| |-----------------------------------------------------------------------------| r_work (final): 0.3582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29110 Z= 0.134 Angle : 0.728 15.834 39600 Z= 0.362 Chirality : 0.046 0.176 4960 Planarity : 0.008 0.161 5020 Dihedral : 6.353 179.622 4080 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.42 % Favored : 93.07 % Rotamer: Outliers : 3.29 % Allowed : 18.70 % Favored : 78.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.14), residues: 3880 helix: 3.12 (0.15), residues: 1040 sheet: 0.86 (0.16), residues: 1180 loop : -1.51 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.027 0.002 ARG P 47 TYR 0.018 0.001 TYR A 169 PHE 0.025 0.001 PHE M 28 TRP 0.010 0.002 TRP P 136 Details of bonding type rmsd covalent geometry : bond 0.00306 (29060) covalent geometry : angle 0.72838 (39560) SS BOND : bond 0.00446 ( 20) SS BOND : angle 0.59042 ( 40) hydrogen bonds : bond 0.03801 ( 1600) hydrogen bonds : angle 4.35085 ( 4500) Misc. bond : bond 0.00291 ( 30) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 853 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 749 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 152 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7499 (tp) REVERT: C 93 LYS cc_start: 0.6554 (mttt) cc_final: 0.5863 (mmtm) REVERT: C 172 PHE cc_start: 0.8241 (p90) cc_final: 0.8035 (p90) REVERT: C 180 GLN cc_start: 0.8429 (pm20) cc_final: 0.8090 (pm20) REVERT: D 76 ILE cc_start: 0.9355 (mt) cc_final: 0.9121 (tt) REVERT: D 85 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7262 (tp30) REVERT: D 138 TYR cc_start: 0.8317 (p90) cc_final: 0.7850 (p90) REVERT: D 172 PHE cc_start: 0.8760 (p90) cc_final: 0.8534 (p90) REVERT: E 43 GLU cc_start: 0.8503 (tm-30) cc_final: 0.7986 (tm-30) REVERT: E 76 ILE cc_start: 0.9308 (mt) cc_final: 0.8928 (tt) REVERT: G 19 PHE cc_start: 0.8421 (m-80) cc_final: 0.8059 (m-80) REVERT: G 46 GLN cc_start: 0.9019 (tt0) cc_final: 0.8698 (tm-30) REVERT: G 138 TYR cc_start: 0.8695 (p90) cc_final: 0.8365 (p90) REVERT: H 59 ASP cc_start: 0.8289 (t0) cc_final: 0.8042 (t0) REVERT: H 93 LYS cc_start: 0.7018 (mttt) cc_final: 0.6097 (mmtp) REVERT: H 170 GLU cc_start: 0.8374 (pm20) cc_final: 0.8150 (pm20) REVERT: I 19 PHE cc_start: 0.8932 (m-80) cc_final: 0.8676 (m-80) REVERT: I 39 GLN cc_start: 0.8664 (mm-40) cc_final: 0.8408 (tp40) REVERT: I 99 MET cc_start: 0.8414 (tmm) cc_final: 0.8090 (tmm) REVERT: I 105 TYR cc_start: 0.8724 (m-80) cc_final: 0.8336 (m-80) REVERT: I 138 TYR cc_start: 0.8122 (p90) cc_final: 0.7070 (p90) REVERT: J 19 PHE cc_start: 0.8624 (m-80) cc_final: 0.8227 (m-80) REVERT: J 103 LYS cc_start: 0.8415 (mmtt) cc_final: 0.8067 (mmmt) REVERT: J 148 ASN cc_start: 0.7545 (m-40) cc_final: 0.7286 (t0) REVERT: J 169 TYR cc_start: 0.7445 (m-80) cc_final: 0.7167 (m-80) REVERT: K 33 MET cc_start: 0.8592 (OUTLIER) cc_final: 0.8175 (tpp) REVERT: K 173 LYS cc_start: 0.8858 (tttt) cc_final: 0.8523 (tttm) REVERT: A 170 GLU cc_start: 0.8162 (pm20) cc_final: 0.7797 (mp0) REVERT: L 40 LYS cc_start: 0.9406 (tptt) cc_final: 0.9188 (tppt) REVERT: L 103 LYS cc_start: 0.7851 (mppt) cc_final: 0.7550 (mttt) REVERT: M 170 GLU cc_start: 0.8571 (OUTLIER) cc_final: 0.8207 (pm20) REVERT: M 172 PHE cc_start: 0.8673 (p90) cc_final: 0.8400 (p90) REVERT: N 19 PHE cc_start: 0.8341 (m-80) cc_final: 0.8039 (m-80) REVERT: N 33 MET cc_start: 0.8902 (OUTLIER) cc_final: 0.8652 (tpp) REVERT: N 122 LYS cc_start: 0.8640 (tptm) cc_final: 0.8344 (tptp) REVERT: N 170 GLU cc_start: 0.8117 (pm20) cc_final: 0.7865 (pm20) REVERT: N 173 LYS cc_start: 0.8953 (tttt) cc_final: 0.8609 (tttm) REVERT: P 19 PHE cc_start: 0.8369 (m-80) cc_final: 0.8121 (m-80) REVERT: P 121 SER cc_start: 0.8354 (m) cc_final: 0.7286 (t) REVERT: P 136 TRP cc_start: 0.7868 (m-90) cc_final: 0.7595 (m-10) REVERT: P 173 LYS cc_start: 0.9001 (tttt) cc_final: 0.8642 (tttm) REVERT: P 187 GLU cc_start: 0.8152 (tm-30) cc_final: 0.7661 (tm-30) REVERT: Q 39 GLN cc_start: 0.8733 (mm-40) cc_final: 0.8485 (mm110) REVERT: Q 95 THR cc_start: 0.9104 (m) cc_final: 0.8583 (p) REVERT: Q 103 LYS cc_start: 0.7538 (mppt) cc_final: 0.7288 (mtmt) REVERT: R 19 PHE cc_start: 0.8463 (m-80) cc_final: 0.8245 (m-80) REVERT: R 84 ARG cc_start: 0.7642 (mpt180) cc_final: 0.7350 (mpt180) REVERT: R 122 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7683 (mptt) REVERT: R 155 LYS cc_start: 0.9023 (mmtm) cc_final: 0.7336 (tttt) REVERT: S 19 PHE cc_start: 0.8198 (m-80) cc_final: 0.7722 (m-80) REVERT: S 42 LYS cc_start: 0.9083 (tttt) cc_final: 0.8301 (tptt) REVERT: S 51 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8169 (tm-30) REVERT: S 84 ARG cc_start: 0.7823 (mpt180) cc_final: 0.7577 (mtt90) REVERT: S 122 LYS cc_start: 0.8888 (mmmm) cc_final: 0.7600 (mmtt) REVERT: S 138 TYR cc_start: 0.8206 (p90) cc_final: 0.7096 (p90) REVERT: S 155 LYS cc_start: 0.8952 (mmtm) cc_final: 0.7809 (mtpt) REVERT: T 45 MET cc_start: 0.8517 (ptm) cc_final: 0.8154 (ptm) REVERT: T 121 SER cc_start: 0.8691 (m) cc_final: 0.7915 (t) REVERT: T 122 LYS cc_start: 0.8470 (mmmm) cc_final: 0.8018 (mmtt) outliers start: 104 outliers final: 76 residues processed: 806 average time/residue: 0.1744 time to fit residues: 220.7894 Evaluate side-chains 770 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 689 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 112 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 169 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 66 VAL Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 169 TYR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 314 optimal weight: 3.9990 chunk 96 optimal weight: 0.9990 chunk 137 optimal weight: 10.0000 chunk 157 optimal weight: 9.9990 chunk 260 optimal weight: 3.9990 chunk 315 optimal weight: 0.0870 chunk 16 optimal weight: 2.9990 chunk 338 optimal weight: 0.2980 chunk 242 optimal weight: 7.9990 chunk 362 optimal weight: 2.9990 chunk 247 optimal weight: 0.9990 overall best weight: 1.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 143 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.110939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.097489 restraints weight = 57830.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.100883 restraints weight = 28446.019| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.103091 restraints weight = 17179.862| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104574 restraints weight = 11686.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.105553 restraints weight = 8588.746| |-----------------------------------------------------------------------------| r_work (final): 0.3589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.4031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 29110 Z= 0.134 Angle : 0.734 16.336 39600 Z= 0.363 Chirality : 0.047 0.181 4960 Planarity : 0.009 0.184 5020 Dihedral : 5.718 173.622 4080 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.03 % Favored : 93.45 % Rotamer: Outliers : 3.10 % Allowed : 19.97 % Favored : 76.93 % 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: 0.80 (0.14), residues: 3880 helix: 3.07 (0.15), residues: 1040 sheet: 0.86 (0.16), residues: 1180 loop : -1.49 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.032 0.002 ARG P 47 TYR 0.014 0.001 TYR A 169 PHE 0.033 0.001 PHE J 28 TRP 0.010 0.002 TRP A 136 Details of bonding type rmsd covalent geometry : bond 0.00306 (29060) covalent geometry : angle 0.73412 (39560) SS BOND : bond 0.00158 ( 20) SS BOND : angle 0.40276 ( 40) hydrogen bonds : bond 0.03699 ( 1600) hydrogen bonds : angle 4.31862 ( 4500) Misc. bond : bond 0.00286 ( 30) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 843 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 98 poor density : 745 time to evaluate : 1.103 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 170 GLU cc_start: 0.8341 (pm20) cc_final: 0.7997 (pm20) REVERT: B 171 GLU cc_start: 0.7859 (mt-10) cc_final: 0.7343 (mt-10) REVERT: C 93 LYS cc_start: 0.6724 (mttt) cc_final: 0.5997 (mmtm) REVERT: C 180 GLN cc_start: 0.8501 (pm20) cc_final: 0.8188 (pm20) REVERT: D 76 ILE cc_start: 0.9351 (mt) cc_final: 0.9127 (tt) REVERT: D 85 GLU cc_start: 0.7684 (OUTLIER) cc_final: 0.7282 (tp30) REVERT: D 138 TYR cc_start: 0.8272 (p90) cc_final: 0.7820 (p90) REVERT: D 172 PHE cc_start: 0.8713 (p90) cc_final: 0.8479 (p90) REVERT: E 19 PHE cc_start: 0.9109 (m-80) cc_final: 0.8892 (m-80) REVERT: E 76 ILE cc_start: 0.9317 (mt) cc_final: 0.8957 (tt) REVERT: G 19 PHE cc_start: 0.8393 (m-80) cc_final: 0.8056 (m-80) REVERT: G 46 GLN cc_start: 0.8946 (tt0) cc_final: 0.8727 (tm-30) REVERT: G 138 TYR cc_start: 0.8653 (p90) cc_final: 0.8288 (p90) REVERT: H 59 ASP cc_start: 0.8257 (t0) cc_final: 0.8053 (t0) REVERT: H 93 LYS cc_start: 0.7150 (mttt) cc_final: 0.6176 (mmtp) REVERT: H 170 GLU cc_start: 0.8360 (pm20) cc_final: 0.8117 (pm20) REVERT: I 19 PHE cc_start: 0.8923 (m-80) cc_final: 0.8651 (m-80) REVERT: I 99 MET cc_start: 0.8382 (tmm) cc_final: 0.8085 (tmm) REVERT: I 105 TYR cc_start: 0.8692 (m-80) cc_final: 0.8417 (m-80) REVERT: J 19 PHE cc_start: 0.8547 (m-80) cc_final: 0.8198 (m-80) REVERT: J 103 LYS cc_start: 0.8441 (mmtt) cc_final: 0.8112 (mmtt) REVERT: J 148 ASN cc_start: 0.7459 (m-40) cc_final: 0.7222 (t0) REVERT: J 170 GLU cc_start: 0.8407 (pm20) cc_final: 0.7952 (pm20) REVERT: K 173 LYS cc_start: 0.8870 (tttt) cc_final: 0.8507 (tttm) REVERT: A 170 GLU cc_start: 0.8169 (pm20) cc_final: 0.7826 (pm20) REVERT: L 40 LYS cc_start: 0.9362 (tptt) cc_final: 0.9160 (tppt) REVERT: L 103 LYS cc_start: 0.7832 (mppt) cc_final: 0.7548 (mttt) REVERT: L 170 GLU cc_start: 0.8347 (OUTLIER) cc_final: 0.7871 (pm20) REVERT: M 170 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8219 (pm20) REVERT: M 172 PHE cc_start: 0.8668 (p90) cc_final: 0.8402 (p90) REVERT: N 19 PHE cc_start: 0.8225 (m-80) cc_final: 0.7979 (m-80) REVERT: N 33 MET cc_start: 0.8896 (OUTLIER) cc_final: 0.8639 (tpp) REVERT: N 122 LYS cc_start: 0.8626 (tptm) cc_final: 0.8347 (tptp) REVERT: N 173 LYS cc_start: 0.8933 (tttt) cc_final: 0.8624 (tttm) REVERT: P 19 PHE cc_start: 0.8298 (m-80) cc_final: 0.8079 (m-80) REVERT: P 136 TRP cc_start: 0.7845 (m-90) cc_final: 0.7581 (m-10) REVERT: P 173 LYS cc_start: 0.9007 (tttt) cc_final: 0.8654 (tttm) REVERT: P 187 GLU cc_start: 0.8156 (tm-30) cc_final: 0.7653 (tm-30) REVERT: Q 28 PHE cc_start: 0.9072 (t80) cc_final: 0.8843 (t80) REVERT: Q 95 THR cc_start: 0.9113 (m) cc_final: 0.8612 (p) REVERT: Q 103 LYS cc_start: 0.7500 (mppt) cc_final: 0.7265 (mtmt) REVERT: R 84 ARG cc_start: 0.7646 (mpt180) cc_final: 0.7341 (mpt180) REVERT: R 122 LYS cc_start: 0.8199 (mmmm) cc_final: 0.7600 (mptt) REVERT: R 155 LYS cc_start: 0.9031 (mmtm) cc_final: 0.7364 (tttt) REVERT: S 19 PHE cc_start: 0.8156 (m-80) cc_final: 0.7639 (m-80) REVERT: S 42 LYS cc_start: 0.9088 (tttt) cc_final: 0.8265 (tptt) REVERT: S 51 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8190 (tm-30) REVERT: S 84 ARG cc_start: 0.7749 (mpt180) cc_final: 0.7443 (mpp-170) REVERT: S 122 LYS cc_start: 0.8857 (mmmm) cc_final: 0.7670 (mmtt) REVERT: S 138 TYR cc_start: 0.8155 (p90) cc_final: 0.7076 (p90) REVERT: S 155 LYS cc_start: 0.8965 (mmtm) cc_final: 0.7836 (mtpt) REVERT: T 45 MET cc_start: 0.8515 (ptm) cc_final: 0.8219 (ptm) REVERT: T 121 SER cc_start: 0.8686 (m) cc_final: 0.7878 (t) REVERT: T 122 LYS cc_start: 0.8478 (mmmm) cc_final: 0.8000 (mmtt) outliers start: 98 outliers final: 80 residues processed: 801 average time/residue: 0.1723 time to fit residues: 216.7935 Evaluate side-chains 766 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 682 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 42 LYS Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain E residue 180 GLN Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain L residue 170 GLU Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 169 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 136 TRP Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 8 VAL Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 350 optimal weight: 2.9990 chunk 157 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 205 optimal weight: 0.9990 chunk 278 optimal weight: 2.9990 chunk 337 optimal weight: 6.9990 chunk 150 optimal weight: 3.9990 chunk 240 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 93 optimal weight: 3.9990 chunk 172 optimal weight: 0.6980 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 39 GLN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 143 ASN Q 39 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.110148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.096545 restraints weight = 57820.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.099982 restraints weight = 28112.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.102202 restraints weight = 16882.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3559 r_free = 0.3559 target = 0.103692 restraints weight = 11458.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.104743 restraints weight = 8431.737| |-----------------------------------------------------------------------------| r_work (final): 0.3575 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.4056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 29110 Z= 0.151 Angle : 0.767 17.427 39600 Z= 0.380 Chirality : 0.047 0.310 4960 Planarity : 0.010 0.319 5020 Dihedral : 5.212 174.559 4080 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 9.47 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.26 % Favored : 93.22 % Rotamer: Outliers : 3.04 % Allowed : 20.79 % Favored : 76.17 % 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: 0.76 (0.14), residues: 3880 helix: 3.08 (0.15), residues: 1040 sheet: 0.83 (0.16), residues: 1180 loop : -1.53 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG P 84 TYR 0.029 0.001 TYR J 169 PHE 0.033 0.002 PHE J 28 TRP 0.010 0.002 TRP T 136 Details of bonding type rmsd covalent geometry : bond 0.00354 (29060) covalent geometry : angle 0.76776 (39560) SS BOND : bond 0.00193 ( 20) SS BOND : angle 0.42884 ( 40) hydrogen bonds : bond 0.03758 ( 1600) hydrogen bonds : angle 4.35169 ( 4500) Misc. bond : bond 0.00341 ( 30) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 721 time to evaluate : 1.089 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 93 LYS cc_start: 0.6352 (mttt) cc_final: 0.5751 (mmtp) REVERT: C 93 LYS cc_start: 0.6622 (mttt) cc_final: 0.5919 (mmtm) REVERT: C 170 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8152 (pm20) REVERT: C 180 GLN cc_start: 0.8527 (pm20) cc_final: 0.8257 (pm20) REVERT: D 33 MET cc_start: 0.8432 (tpp) cc_final: 0.8193 (tpp) REVERT: D 76 ILE cc_start: 0.9346 (mt) cc_final: 0.9132 (tt) REVERT: D 85 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: D 138 TYR cc_start: 0.8329 (p90) cc_final: 0.7906 (p90) REVERT: D 172 PHE cc_start: 0.8765 (p90) cc_final: 0.8541 (p90) REVERT: E 46 GLN cc_start: 0.8824 (tt0) cc_final: 0.8588 (tp-100) REVERT: E 76 ILE cc_start: 0.9316 (mt) cc_final: 0.8954 (tt) REVERT: E 122 LYS cc_start: 0.8491 (tptp) cc_final: 0.7991 (tppt) REVERT: G 19 PHE cc_start: 0.8351 (m-80) cc_final: 0.7984 (m-80) REVERT: G 46 GLN cc_start: 0.8992 (tt0) cc_final: 0.8713 (tm-30) REVERT: G 138 TYR cc_start: 0.8672 (p90) cc_final: 0.8299 (p90) REVERT: H 59 ASP cc_start: 0.8268 (t0) cc_final: 0.8056 (t0) REVERT: H 93 LYS cc_start: 0.7154 (mttt) cc_final: 0.6158 (mmtp) REVERT: H 170 GLU cc_start: 0.8371 (pm20) cc_final: 0.8148 (pm20) REVERT: I 19 PHE cc_start: 0.8930 (m-80) cc_final: 0.8657 (m-80) REVERT: I 99 MET cc_start: 0.8376 (tmm) cc_final: 0.8025 (tmm) REVERT: I 105 TYR cc_start: 0.8692 (m-80) cc_final: 0.8357 (m-80) REVERT: I 138 TYR cc_start: 0.8099 (p90) cc_final: 0.7048 (p90) REVERT: J 19 PHE cc_start: 0.8574 (m-80) cc_final: 0.8226 (m-80) REVERT: J 103 LYS cc_start: 0.8543 (mmtt) cc_final: 0.8166 (mmmt) REVERT: J 148 ASN cc_start: 0.7536 (m-40) cc_final: 0.7297 (t0) REVERT: K 173 LYS cc_start: 0.8884 (tttt) cc_final: 0.8648 (tttm) REVERT: A 170 GLU cc_start: 0.8306 (pm20) cc_final: 0.7920 (pm20) REVERT: L 40 LYS cc_start: 0.9362 (tptt) cc_final: 0.9162 (tppt) REVERT: L 103 LYS cc_start: 0.7903 (mppt) cc_final: 0.7614 (mttt) REVERT: M 170 GLU cc_start: 0.8580 (OUTLIER) cc_final: 0.8222 (pm20) REVERT: N 19 PHE cc_start: 0.8151 (m-80) cc_final: 0.7909 (m-80) REVERT: N 33 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8671 (tpp) REVERT: N 122 LYS cc_start: 0.8641 (tptm) cc_final: 0.8371 (tptp) REVERT: N 170 GLU cc_start: 0.8154 (pm20) cc_final: 0.7871 (pm20) REVERT: N 173 LYS cc_start: 0.8903 (tttt) cc_final: 0.8575 (tttm) REVERT: P 19 PHE cc_start: 0.8329 (m-80) cc_final: 0.8102 (m-80) REVERT: P 121 SER cc_start: 0.8366 (m) cc_final: 0.7465 (t) REVERT: P 136 TRP cc_start: 0.7907 (m-90) cc_final: 0.7652 (m-10) REVERT: P 173 LYS cc_start: 0.9017 (tttt) cc_final: 0.8651 (tttm) REVERT: P 187 GLU cc_start: 0.8183 (tm-30) cc_final: 0.7663 (tm-30) REVERT: Q 28 PHE cc_start: 0.9107 (t80) cc_final: 0.8871 (t80) REVERT: Q 95 THR cc_start: 0.9155 (m) cc_final: 0.8624 (p) REVERT: Q 103 LYS cc_start: 0.7609 (mppt) cc_final: 0.7388 (mtmt) REVERT: Q 121 SER cc_start: 0.7931 (OUTLIER) cc_final: 0.6790 (t) REVERT: Q 170 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8247 (pt0) REVERT: R 19 PHE cc_start: 0.8373 (m-80) cc_final: 0.8122 (m-80) REVERT: R 122 LYS cc_start: 0.8237 (mmmm) cc_final: 0.7696 (mptt) REVERT: R 155 LYS cc_start: 0.9028 (mmtm) cc_final: 0.7335 (tttt) REVERT: S 19 PHE cc_start: 0.8166 (m-80) cc_final: 0.7623 (m-80) REVERT: S 42 LYS cc_start: 0.9087 (tttt) cc_final: 0.8274 (tptt) REVERT: S 51 GLU cc_start: 0.8436 (tm-30) cc_final: 0.8201 (tm-30) REVERT: S 84 ARG cc_start: 0.7785 (mpt180) cc_final: 0.7475 (mpp-170) REVERT: S 122 LYS cc_start: 0.8978 (mmmm) cc_final: 0.7705 (mmtt) REVERT: S 138 TYR cc_start: 0.8240 (p90) cc_final: 0.7123 (p90) REVERT: S 155 LYS cc_start: 0.8983 (mmtm) cc_final: 0.7887 (mtpt) REVERT: T 45 MET cc_start: 0.8619 (ptm) cc_final: 0.8269 (ptm) REVERT: T 121 SER cc_start: 0.8669 (m) cc_final: 0.7851 (t) REVERT: T 122 LYS cc_start: 0.8461 (mmmm) cc_final: 0.7977 (mmtt) outliers start: 96 outliers final: 80 residues processed: 777 average time/residue: 0.1773 time to fit residues: 215.5474 Evaluate side-chains 785 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 699 time to evaluate : 0.724 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 141 ILE Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 93 LYS Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 169 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 121 SER Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 160 LEU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain S residue 169 TYR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 58 optimal weight: 3.9990 chunk 91 optimal weight: 6.9990 chunk 133 optimal weight: 0.8980 chunk 41 optimal weight: 1.9990 chunk 308 optimal weight: 9.9990 chunk 68 optimal weight: 0.9980 chunk 36 optimal weight: 9.9990 chunk 339 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 145 optimal weight: 0.6980 chunk 234 optimal weight: 2.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 143 ASN ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 143 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3668 r_free = 0.3668 target = 0.110508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.096889 restraints weight = 57690.867| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.100313 restraints weight = 28083.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.102537 restraints weight = 16895.719| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.104031 restraints weight = 11477.007| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3580 r_free = 0.3580 target = 0.105034 restraints weight = 8443.917| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.4174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29110 Z= 0.146 Angle : 0.774 17.803 39600 Z= 0.382 Chirality : 0.047 0.300 4960 Planarity : 0.010 0.280 5020 Dihedral : 5.250 175.716 4080 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.24 % Favored : 93.25 % Rotamer: Outliers : 2.88 % Allowed : 21.08 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3880 helix: 3.04 (0.15), residues: 1040 sheet: 0.81 (0.16), residues: 1180 loop : -1.55 (0.15), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.043 0.002 ARG C 84 TYR 0.022 0.001 TYR J 169 PHE 0.033 0.002 PHE J 28 TRP 0.010 0.002 TRP P 136 Details of bonding type rmsd covalent geometry : bond 0.00341 (29060) covalent geometry : angle 0.77384 (39560) SS BOND : bond 0.00170 ( 20) SS BOND : angle 0.38261 ( 40) hydrogen bonds : bond 0.03745 ( 1600) hydrogen bonds : angle 4.36016 ( 4500) Misc. bond : bond 0.00366 ( 30) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7760 Ramachandran restraints generated. 3880 Oldfield, 0 Emsley, 3880 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 817 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 726 time to evaluate : 0.938 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: B 93 LYS cc_start: 0.6380 (mttt) cc_final: 0.5740 (mmtp) REVERT: B 171 GLU cc_start: 0.7889 (mt-10) cc_final: 0.7381 (mt-10) REVERT: C 89 MET cc_start: 0.7943 (mmm) cc_final: 0.7708 (mmm) REVERT: C 93 LYS cc_start: 0.6626 (mttt) cc_final: 0.5916 (mmtm) REVERT: C 170 GLU cc_start: 0.8522 (OUTLIER) cc_final: 0.8111 (pm20) REVERT: C 180 GLN cc_start: 0.8566 (pm20) cc_final: 0.8281 (pm20) REVERT: D 33 MET cc_start: 0.8450 (tpp) cc_final: 0.8225 (tpp) REVERT: D 76 ILE cc_start: 0.9338 (mt) cc_final: 0.9122 (tt) REVERT: D 85 GLU cc_start: 0.7716 (OUTLIER) cc_final: 0.7346 (tp30) REVERT: D 122 LYS cc_start: 0.8899 (tptt) cc_final: 0.8447 (mmmt) REVERT: D 138 TYR cc_start: 0.8297 (p90) cc_final: 0.7877 (p90) REVERT: D 172 PHE cc_start: 0.8763 (p90) cc_final: 0.8503 (p90) REVERT: E 46 GLN cc_start: 0.8932 (tt0) cc_final: 0.8650 (tp-100) REVERT: E 76 ILE cc_start: 0.9319 (mt) cc_final: 0.8954 (tt) REVERT: E 122 LYS cc_start: 0.8527 (tptp) cc_final: 0.8031 (tppt) REVERT: G 19 PHE cc_start: 0.8281 (m-80) cc_final: 0.7898 (m-80) REVERT: G 46 GLN cc_start: 0.9024 (tt0) cc_final: 0.8727 (tm-30) REVERT: G 138 TYR cc_start: 0.8652 (p90) cc_final: 0.8325 (p90) REVERT: H 19 PHE cc_start: 0.8411 (m-80) cc_final: 0.7994 (m-10) REVERT: H 88 ASP cc_start: 0.8615 (t0) cc_final: 0.8362 (t0) REVERT: H 93 LYS cc_start: 0.7133 (mttt) cc_final: 0.6026 (mmtp) REVERT: H 170 GLU cc_start: 0.8367 (pm20) cc_final: 0.8092 (pm20) REVERT: I 19 PHE cc_start: 0.8924 (m-80) cc_final: 0.8652 (m-80) REVERT: I 39 GLN cc_start: 0.8714 (mm-40) cc_final: 0.8473 (tp40) REVERT: I 99 MET cc_start: 0.8375 (tmm) cc_final: 0.8011 (tmm) REVERT: J 19 PHE cc_start: 0.8620 (m-80) cc_final: 0.8289 (m-80) REVERT: J 103 LYS cc_start: 0.8535 (mmtt) cc_final: 0.8269 (mmtt) REVERT: K 121 SER cc_start: 0.8235 (m) cc_final: 0.7030 (t) REVERT: K 173 LYS cc_start: 0.8996 (tttt) cc_final: 0.8538 (tttm) REVERT: A 170 GLU cc_start: 0.8368 (pm20) cc_final: 0.8013 (pm20) REVERT: L 103 LYS cc_start: 0.7852 (mppt) cc_final: 0.7593 (mttt) REVERT: M 46 GLN cc_start: 0.8957 (tm-30) cc_final: 0.8732 (tm-30) REVERT: M 170 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8214 (pm20) REVERT: N 19 PHE cc_start: 0.8164 (m-80) cc_final: 0.7933 (m-80) REVERT: N 33 MET cc_start: 0.8936 (OUTLIER) cc_final: 0.8679 (tpp) REVERT: N 122 LYS cc_start: 0.8636 (tptm) cc_final: 0.8377 (tptp) REVERT: N 170 GLU cc_start: 0.8118 (pm20) cc_final: 0.7831 (pm20) REVERT: N 173 LYS cc_start: 0.8949 (tttt) cc_final: 0.8573 (tttm) REVERT: P 19 PHE cc_start: 0.8286 (m-80) cc_final: 0.8059 (m-80) REVERT: P 121 SER cc_start: 0.8400 (m) cc_final: 0.7022 (t) REVERT: P 136 TRP cc_start: 0.7899 (m-90) cc_final: 0.7645 (m-10) REVERT: P 173 LYS cc_start: 0.9029 (tttt) cc_final: 0.8649 (tttm) REVERT: P 187 GLU cc_start: 0.8181 (tm-30) cc_final: 0.7659 (tm-30) REVERT: Q 28 PHE cc_start: 0.9131 (t80) cc_final: 0.8908 (t80) REVERT: Q 95 THR cc_start: 0.9148 (m) cc_final: 0.8626 (p) REVERT: Q 103 LYS cc_start: 0.7573 (mppt) cc_final: 0.7317 (mtmt) REVERT: Q 170 GLU cc_start: 0.8489 (OUTLIER) cc_final: 0.8243 (pt0) REVERT: R 19 PHE cc_start: 0.8406 (m-80) cc_final: 0.8159 (m-80) REVERT: R 122 LYS cc_start: 0.8169 (mmmm) cc_final: 0.7703 (mptt) REVERT: R 155 LYS cc_start: 0.8994 (mmtm) cc_final: 0.7290 (tttt) REVERT: S 19 PHE cc_start: 0.8255 (m-80) cc_final: 0.7703 (m-80) REVERT: S 42 LYS cc_start: 0.9119 (tttt) cc_final: 0.8289 (tptt) REVERT: S 51 GLU cc_start: 0.8486 (tm-30) cc_final: 0.8256 (tm-30) REVERT: S 84 ARG cc_start: 0.7772 (mpt180) cc_final: 0.7525 (mpp-170) REVERT: S 122 LYS cc_start: 0.9001 (mmmm) cc_final: 0.7723 (mmtt) REVERT: S 138 TYR cc_start: 0.8192 (p90) cc_final: 0.7086 (p90) REVERT: S 155 LYS cc_start: 0.8987 (mmtm) cc_final: 0.7892 (mtpt) REVERT: T 45 MET cc_start: 0.8561 (ptm) cc_final: 0.8262 (ptt) REVERT: T 121 SER cc_start: 0.8695 (m) cc_final: 0.7893 (t) REVERT: T 122 LYS cc_start: 0.8464 (mmmm) cc_final: 0.7952 (mmtt) outliers start: 91 outliers final: 79 residues processed: 776 average time/residue: 0.1765 time to fit residues: 214.5952 Evaluate side-chains 775 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 691 time to evaluate : 0.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 21 ILE Chi-restraints excluded: chain B residue 31 LEU Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 45 MET Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 170 GLU Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 85 GLU Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 66 VAL Chi-restraints excluded: chain F residue 110 CYS Chi-restraints excluded: chain F residue 112 VAL Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 8 VAL Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain G residue 189 ILE Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 89 MET Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 84 ARG Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 84 ARG Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain A residue 33 MET Chi-restraints excluded: chain A residue 84 ARG Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain M residue 31 LEU Chi-restraints excluded: chain M residue 33 MET Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 76 ILE Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 170 GLU Chi-restraints excluded: chain N residue 33 MET Chi-restraints excluded: chain N residue 66 VAL Chi-restraints excluded: chain N residue 76 ILE Chi-restraints excluded: chain N residue 112 VAL Chi-restraints excluded: chain N residue 187 GLU Chi-restraints excluded: chain O residue 66 VAL Chi-restraints excluded: chain O residue 110 CYS Chi-restraints excluded: chain O residue 112 VAL Chi-restraints excluded: chain P residue 8 VAL Chi-restraints excluded: chain P residue 110 CYS Chi-restraints excluded: chain P residue 112 VAL Chi-restraints excluded: chain P residue 129 SER Chi-restraints excluded: chain P residue 160 LEU Chi-restraints excluded: chain P residue 169 TYR Chi-restraints excluded: chain Q residue 66 VAL Chi-restraints excluded: chain Q residue 76 ILE Chi-restraints excluded: chain Q residue 112 VAL Chi-restraints excluded: chain Q residue 129 SER Chi-restraints excluded: chain Q residue 170 GLU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain R residue 33 MET Chi-restraints excluded: chain R residue 76 ILE Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain R residue 170 GLU Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain S residue 160 LEU Chi-restraints excluded: chain S residue 169 TYR Chi-restraints excluded: chain T residue 66 VAL Chi-restraints excluded: chain T residue 85 GLU Chi-restraints excluded: chain T residue 112 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 361 optimal weight: 2.9990 chunk 339 optimal weight: 6.9990 chunk 216 optimal weight: 7.9990 chunk 239 optimal weight: 0.5980 chunk 69 optimal weight: 0.2980 chunk 35 optimal weight: 3.9990 chunk 304 optimal weight: 0.0770 chunk 263 optimal weight: 0.0770 chunk 320 optimal weight: 0.9990 chunk 226 optimal weight: 0.8980 chunk 325 optimal weight: 1.9990 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 ASN F 143 ASN J 39 GLN O 39 GLN P 143 ASN Q 39 GLN T 180 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3706 r_free = 0.3706 target = 0.113181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.099769 restraints weight = 57664.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.103161 restraints weight = 28430.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.105363 restraints weight = 17137.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.106851 restraints weight = 11644.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.107875 restraints weight = 8553.772| |-----------------------------------------------------------------------------| r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 29110 Z= 0.137 Angle : 0.787 17.946 39600 Z= 0.387 Chirality : 0.047 0.299 4960 Planarity : 0.010 0.416 5020 Dihedral : 6.542 177.001 4080 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.66 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.08 % Favored : 93.40 % Rotamer: Outliers : 2.91 % Allowed : 21.30 % Favored : 75.79 % 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: 0.88 (0.14), residues: 3880 helix: 2.99 (0.15), residues: 1040 sheet: 1.27 (0.17), residues: 1100 loop : -1.51 (0.15), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.036 0.002 ARG B 84 TYR 0.019 0.001 TYR J 169 PHE 0.033 0.001 PHE J 28 TRP 0.011 0.001 TRP I 136 Details of bonding type rmsd covalent geometry : bond 0.00312 (29060) covalent geometry : angle 0.78725 (39560) SS BOND : bond 0.00093 ( 20) SS BOND : angle 0.29440 ( 40) hydrogen bonds : bond 0.03570 ( 1600) hydrogen bonds : angle 4.23083 ( 4500) Misc. bond : bond 0.00343 ( 30) =============================================================================== Job complete usr+sys time: 5150.84 seconds wall clock time: 89 minutes 22.81 seconds (5362.81 seconds total)