Starting phenix.real_space_refine on Mon Jun 23 22:52:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7txi_26158/06_2025/7txi_26158.cif Found real_map, /net/cci-nas-00/data/ceres_data/7txi_26158/06_2025/7txi_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7txi_26158/06_2025/7txi_26158.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7txi_26158/06_2025/7txi_26158.map" model { file = "/net/cci-nas-00/data/ceres_data/7txi_26158/06_2025/7txi_26158.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7txi_26158/06_2025/7txi_26158.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.11s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 28660 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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, B, E, D, G, F, I, H, K, J, M, L, O, N, Q, P, S, R, T Time building chain proxies: 7.27, per 1000 atoms: 0.25 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=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 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: 9.12 Conformation dependent library (CDL) restraints added in 4.9 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: 5.04 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: 14.49 Time building geometry restraints manager: 9.95 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 - 21.88: 1261 21.88 - 32.82: 620 32.82 - 43.76: 261 43.76 - 54.70: 101 Dihedral angle restraints: 17463 sinusoidal: 6363 harmonic: 11100 Sorted by residual: dihedral pdb=" CB CYS B 110 " pdb=" SG CYS B 110 " pdb=" SG CYS B 132 " pdb=" CB CYS B 132 " ideal model delta sinusoidal sigma weight residual 93.00 38.30 54.70 1 1.00e+01 1.00e-02 4.05e+01 dihedral pdb=" CA THR F 164 " pdb=" C THR F 164 " pdb=" N PRO F 165 " pdb=" CA PRO F 165 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 dihedral pdb=" CA THR K 164 " pdb=" C THR K 164 " pdb=" N PRO K 165 " pdb=" CA PRO K 165 " ideal model delta harmonic sigma weight residual 180.00 152.63 27.37 0 5.00e+00 4.00e-02 3.00e+01 ... (remaining 17460 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: 1483 2.72 - 3.45: 42225 3.45 - 4.17: 63553 4.17 - 4.90: 115335 Nonbonded interactions: 222694 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 222689 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: 0.38 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' selection = chain 'K' selection = chain 'J' selection = chain 'M' selection = chain 'L' selection = chain 'O' selection = chain 'N' selection = chain 'Q' selection = chain 'P' selection = chain 'S' selection = chain 'R' 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: 2.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 1.070 Check model and map are aligned: 0.200 Set scattering table: 0.270 Process input model: 61.710 Find NCS groups from input model: 1.240 Set up NCS constraints: 0.200 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:4.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 71.510 ------------------------------------------------------------------------------- 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 29091 Z= 2.489 Angle : 0.991 17.041 39562 Z= 0.537 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.012 0.003 TRP T 136 PHE 0.021 0.002 PHE T 28 TYR 0.010 0.002 TYR I 138 ARG 0.008 0.001 ARG T 84 Details of bonding type rmsd hydrogen bonds : bond 0.16371 ( 1600) hydrogen bonds : angle 6.63837 ( 4500) SS BOND : bond 0.00020 ( 1) SS BOND : angle 0.87286 ( 2) covalent geometry : bond 0.00756 (29060) covalent geometry : angle 0.99087 (39560) 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 : 6.834 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: 0.4330 time to fit residues: 728.0397 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 : 3.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 320 optimal weight: 5.9990 chunk 288 optimal weight: 0.6980 chunk 159 optimal weight: 8.9990 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 10.0000 chunk 153 optimal weight: 7.9990 chunk 297 optimal weight: 0.9980 chunk 115 optimal weight: 4.9990 chunk 181 optimal weight: 6.9990 chunk 221 optimal weight: 9.9990 chunk 345 optimal weight: 3.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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 = 0.3655 r_free = 0.3655 target = 0.109713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.095702 restraints weight = 58157.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.099198 restraints weight = 28375.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3526 r_free = 0.3526 target = 0.101491 restraints weight = 17120.967| |-----------------------------------------------------------------------------| r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 29091 Z= 0.194 Angle : 0.753 8.941 39562 Z= 0.381 Chirality : 0.048 0.164 4960 Planarity : 0.011 0.222 5020 Dihedral : 6.242 176.142 4080 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 1.03 % Allowed : 5.93 % Favored : 93.04 % Rotamer: Outliers : 2.09 % Allowed : 9.40 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 2.50 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.14), residues: 3880 helix: 3.49 (0.15), residues: 1040 sheet: 1.34 (0.16), residues: 1160 loop : -1.40 (0.15), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP I 136 PHE 0.020 0.002 PHE A 28 TYR 0.012 0.002 TYR F 105 ARG 0.030 0.002 ARG K 47 Details of bonding type rmsd hydrogen bonds : bond 0.04750 ( 1600) hydrogen bonds : angle 4.96937 ( 4500) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.63521 ( 2) covalent geometry : bond 0.00461 (29060) covalent geometry : angle 0.75301 (39560) Misc. bond : bond 0.00203 ( 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 893 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 827 time to evaluate : 3.424 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: 0.6074 (mttt) cc_final: 0.5466 (mmtp) REVERT: C 93 LYS cc_start: 0.6769 (mttt) cc_final: 0.6060 (mmtm) REVERT: C 121 SER cc_start: 0.7994 (m) cc_final: 0.7144 (t) REVERT: C 172 PHE cc_start: 0.8393 (p90) cc_final: 0.8161 (p90) REVERT: D 40 LYS cc_start: 0.9489 (tptp) cc_final: 0.9224 (tptp) REVERT: D 95 THR cc_start: 0.9267 (m) cc_final: 0.8773 (p) REVERT: D 138 TYR cc_start: 0.8670 (p90) cc_final: 0.8138 (p90) REVERT: D 172 PHE cc_start: 0.8785 (p90) cc_final: 0.8560 (p90) REVERT: E 46 GLN cc_start: 0.9026 (tt0) cc_final: 0.8613 (tm-30) REVERT: E 76 ILE cc_start: 0.9473 (mt) cc_final: 0.9039 (tt) REVERT: E 138 TYR cc_start: 0.8932 (p90) cc_final: 0.8561 (p90) REVERT: E 173 LYS cc_start: 0.8926 (tttt) cc_final: 0.8664 (tttm) REVERT: E 185 THR cc_start: 0.8941 (m) cc_final: 0.8737 (t) REVERT: F 59 ASP cc_start: 0.8019 (t0) cc_final: 0.7793 (t0) REVERT: F 170 GLU cc_start: 0.8461 (pm20) cc_final: 0.8086 (pm20) REVERT: G 19 PHE cc_start: 0.8634 (m-80) cc_final: 0.8361 (m-80) REVERT: G 46 GLN cc_start: 0.9087 (tt0) cc_final: 0.8702 (tm-30) REVERT: G 103 LYS cc_start: 0.7777 (mppt) cc_final: 0.7416 (mtmt) REVERT: G 138 TYR cc_start: 0.8856 (p90) cc_final: 0.8599 (p90) REVERT: H 93 LYS cc_start: 0.6867 (mttt) cc_final: 0.5954 (mmtp) REVERT: I 19 PHE cc_start: 0.8873 (m-80) cc_final: 0.8637 (m-80) REVERT: I 39 GLN cc_start: 0.8668 (mm-40) cc_final: 0.8419 (mm-40) REVERT: J 19 PHE cc_start: 0.8711 (m-80) cc_final: 0.8444 (m-80) REVERT: J 50 GLU cc_start: 0.8294 (tm-30) cc_final: 0.7140 (tm-30) REVERT: J 85 GLU cc_start: 0.7647 (tp30) cc_final: 0.7366 (tp30) REVERT: J 122 LYS cc_start: 0.7866 (tppp) cc_final: 0.7415 (tptt) REVERT: J 148 ASN cc_start: 0.8146 (m-40) cc_final: 0.7859 (t0) REVERT: K 138 TYR cc_start: 0.8570 (p90) cc_final: 0.8122 (p90) REVERT: K 173 LYS cc_start: 0.8839 (tttt) cc_final: 0.8472 (tttm) REVERT: L 85 GLU cc_start: 0.7430 (tp30) cc_final: 0.7211 (mm-30) REVERT: L 106 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7657 (tm-30) REVERT: L 120 ASP cc_start: 0.6770 (t0) cc_final: 0.6055 (p0) REVERT: L 172 PHE cc_start: 0.8473 (p90) cc_final: 0.8256 (p90) REVERT: M 28 PHE cc_start: 0.8921 (t80) cc_final: 0.8709 (t80) REVERT: M 39 GLN cc_start: 0.8505 (OUTLIER) cc_final: 0.8198 (mp10) REVERT: M 171 GLU cc_start: 0.8374 (mt-10) cc_final: 0.8124 (mt-10) REVERT: N 19 PHE cc_start: 0.8051 (m-80) cc_final: 0.7823 (m-80) REVERT: N 122 LYS cc_start: 0.8473 (tptm) cc_final: 0.8235 (tptp) REVERT: N 173 LYS cc_start: 0.8955 (tttt) cc_final: 0.8685 (tttm) REVERT: O 89 MET cc_start: 0.7633 (mmm) cc_final: 0.7323 (mmm) REVERT: O 120 ASP cc_start: 0.6898 (t0) cc_final: 0.6633 (p0) REVERT: P 173 LYS cc_start: 0.8888 (tttt) cc_final: 0.8615 (tttm) REVERT: Q 39 GLN cc_start: 0.8895 (mm-40) cc_final: 0.8511 (mm110) REVERT: Q 95 THR cc_start: 0.9245 (m) cc_final: 0.8731 (p) REVERT: R 120 ASP cc_start: 0.7241 (t0) cc_final: 0.6845 (p0) REVERT: R 122 LYS cc_start: 0.7927 (mmmm) cc_final: 0.7112 (mmtt) REVERT: R 148 ASN cc_start: 0.8021 (m-40) cc_final: 0.7818 (m-40) REVERT: R 155 LYS cc_start: 0.8965 (mmtm) cc_final: 0.7128 (tptm) REVERT: S 11 GLU cc_start: 0.8061 (pm20) cc_final: 0.7634 (pm20) REVERT: S 19 PHE cc_start: 0.8386 (m-80) cc_final: 0.7917 (m-80) REVERT: S 42 LYS cc_start: 0.9325 (tttt) cc_final: 0.8648 (tptt) REVERT: S 51 GLU cc_start: 0.8550 (tm-30) cc_final: 0.8251 (tm-30) REVERT: S 84 ARG cc_start: 0.7968 (mpt180) cc_final: 0.7404 (mtt90) REVERT: S 120 ASP cc_start: 0.6873 (t0) cc_final: 0.6409 (p0) REVERT: S 122 LYS cc_start: 0.8606 (mmmm) cc_final: 0.7290 (mmtt) REVERT: S 155 LYS cc_start: 0.8879 (mmtm) cc_final: 0.7721 (mmmt) REVERT: S 170 GLU cc_start: 0.8771 (pm20) cc_final: 0.8419 (pm20) REVERT: T 121 SER cc_start: 0.8765 (m) cc_final: 0.8046 (t) REVERT: T 122 LYS cc_start: 0.8493 (mmmm) cc_final: 0.8082 (mmtt) REVERT: T 171 GLU cc_start: 0.7380 (mt-10) cc_final: 0.7081 (tt0) REVERT: T 173 LYS cc_start: 0.8581 (tttt) cc_final: 0.8198 (tttp) outliers start: 66 outliers final: 44 residues processed: 853 average time/residue: 0.4340 time to fit residues: 571.1203 Evaluate side-chains 755 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 710 time to evaluate : 2.912 ------------------------------------------------------------------------------- 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 28 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 132 CYS Chi-restraints excluded: chain F residue 118 LEU Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 110 CYS 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 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 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 324 optimal weight: 0.9990 chunk 31 optimal weight: 0.3980 chunk 123 optimal weight: 2.9990 chunk 281 optimal weight: 2.9990 chunk 305 optimal weight: 0.9990 chunk 184 optimal weight: 1.9990 chunk 269 optimal weight: 5.9990 chunk 358 optimal weight: 5.9990 chunk 167 optimal weight: 0.9990 chunk 52 optimal weight: 4.9990 chunk 348 optimal weight: 10.0000 overall best weight: 1.0788 ------------------------------------------------------------------------------- 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 O 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.111039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.097222 restraints weight = 58149.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3513 r_free = 0.3513 target = 0.100698 restraints weight = 28957.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.102942 restraints weight = 17576.494| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8200 moved from start: 0.2904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 29091 Z= 0.133 Angle : 0.671 13.982 39562 Z= 0.342 Chirality : 0.046 0.176 4960 Planarity : 0.008 0.157 5020 Dihedral : 6.004 178.939 4080 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 8.36 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.21 % Favored : 93.27 % Rotamer: Outliers : 3.39 % Allowed : 11.55 % Favored : 85.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.34 (0.14), residues: 3880 helix: 3.43 (0.15), residues: 1040 sheet: 1.83 (0.17), residues: 1080 loop : -1.46 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 136 PHE 0.022 0.001 PHE J 28 TYR 0.015 0.001 TYR I 169 ARG 0.029 0.002 ARG E 84 Details of bonding type rmsd hydrogen bonds : bond 0.04237 ( 1600) hydrogen bonds : angle 4.58038 ( 4500) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.40983 ( 2) covalent geometry : bond 0.00309 (29060) covalent geometry : angle 0.67059 (39560) Misc. bond : bond 0.00254 ( 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 917 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 810 time to evaluate : 3.102 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: C 93 LYS cc_start: 0.6744 (mttt) cc_final: 0.6048 (mmtm) REVERT: C 103 LYS cc_start: 0.8020 (mmmt) cc_final: 0.7816 (tptp) REVERT: C 121 SER cc_start: 0.7808 (m) cc_final: 0.7041 (t) REVERT: D 33 MET cc_start: 0.8565 (tpt) cc_final: 0.8363 (tpp) REVERT: D 40 LYS cc_start: 0.9426 (tptp) cc_final: 0.9213 (tptp) REVERT: D 95 THR cc_start: 0.9179 (m) cc_final: 0.8662 (p) REVERT: D 103 LYS cc_start: 0.7170 (OUTLIER) cc_final: 0.6773 (tptp) REVERT: D 138 TYR cc_start: 0.8472 (p90) cc_final: 0.8134 (p90) REVERT: D 172 PHE cc_start: 0.8736 (p90) cc_final: 0.8514 (p90) REVERT: E 76 ILE cc_start: 0.9426 (mt) cc_final: 0.9022 (tt) REVERT: E 85 GLU cc_start: 0.8157 (tp30) cc_final: 0.7827 (mp0) REVERT: E 122 LYS cc_start: 0.8657 (tppt) cc_final: 0.8388 (tptp) REVERT: E 173 LYS cc_start: 0.8881 (tttt) cc_final: 0.8628 (tttm) REVERT: F 59 ASP cc_start: 0.8040 (t0) cc_final: 0.7799 (t0) REVERT: G 19 PHE cc_start: 0.8560 (m-80) cc_final: 0.8320 (m-80) REVERT: G 46 GLN cc_start: 0.8980 (tt0) cc_final: 0.8661 (tm-30) REVERT: G 138 TYR cc_start: 0.8641 (p90) cc_final: 0.8392 (p90) REVERT: H 51 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8474 (tm-30) REVERT: H 93 LYS cc_start: 0.6882 (mttt) cc_final: 0.5946 (mmtp) REVERT: I 19 PHE cc_start: 0.8806 (m-80) cc_final: 0.8579 (m-80) REVERT: I 39 GLN cc_start: 0.8643 (mm-40) cc_final: 0.8184 (mm-40) REVERT: I 138 TYR cc_start: 0.8321 (p90) cc_final: 0.7525 (p90) REVERT: J 19 PHE cc_start: 0.8679 (m-80) cc_final: 0.8389 (m-80) REVERT: J 148 ASN cc_start: 0.8007 (m-40) cc_final: 0.7751 (t0) REVERT: K 173 LYS cc_start: 0.8794 (tttt) cc_final: 0.8462 (tttm) REVERT: A 43 GLU cc_start: 0.8205 (tm-30) cc_final: 0.7974 (tm-30) REVERT: A 170 GLU cc_start: 0.8314 (pm20) cc_final: 0.7923 (pm20) REVERT: L 170 GLU cc_start: 0.8490 (pm20) cc_final: 0.8263 (pm20) REVERT: L 173 LYS cc_start: 0.8850 (tttt) cc_final: 0.8583 (mtpt) REVERT: M 28 PHE cc_start: 0.8959 (t80) cc_final: 0.8757 (t80) REVERT: M 84 ARG cc_start: 0.7102 (OUTLIER) cc_final: 0.6105 (ptp-110) REVERT: M 106 GLU cc_start: 0.7789 (tp30) cc_final: 0.7586 (tp30) REVERT: M 171 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8094 (mt-10) REVERT: N 50 GLU cc_start: 0.7917 (mm-30) cc_final: 0.7435 (mp0) REVERT: N 122 LYS cc_start: 0.8491 (tptm) cc_final: 0.8221 (tptp) REVERT: N 173 LYS cc_start: 0.8932 (tttt) cc_final: 0.8647 (tttm) REVERT: O 120 ASP cc_start: 0.6910 (t0) cc_final: 0.6706 (p0) REVERT: P 136 TRP cc_start: 0.7711 (m-90) cc_final: 0.7411 (m-10) REVERT: P 173 LYS cc_start: 0.8972 (tttt) cc_final: 0.8697 (tttm) REVERT: Q 39 GLN cc_start: 0.8835 (mm-40) cc_final: 0.8448 (mm110) REVERT: Q 46 GLN cc_start: 0.8997 (tm-30) cc_final: 0.8667 (tm-30) REVERT: Q 95 THR cc_start: 0.9229 (m) cc_final: 0.8732 (p) REVERT: Q 138 TYR cc_start: 0.8359 (p90) cc_final: 0.8104 (p90) REVERT: R 84 ARG cc_start: 0.7285 (mmt180) cc_final: 0.6616 (mpt180) REVERT: R 103 LYS cc_start: 0.8180 (mmtt) cc_final: 0.7927 (mptt) REVERT: R 120 ASP cc_start: 0.7051 (t0) cc_final: 0.6759 (p0) REVERT: R 122 LYS cc_start: 0.7775 (mmmm) cc_final: 0.7099 (mptt) REVERT: R 155 LYS cc_start: 0.9006 (mmtm) cc_final: 0.7184 (tttt) REVERT: S 19 PHE cc_start: 0.8246 (m-80) cc_final: 0.7787 (m-80) REVERT: S 42 LYS cc_start: 0.9220 (tttt) cc_final: 0.8419 (tptt) REVERT: S 51 GLU cc_start: 0.8562 (tm-30) cc_final: 0.8241 (tm-30) REVERT: S 120 ASP cc_start: 0.6722 (t0) cc_final: 0.6417 (p0) REVERT: S 122 LYS cc_start: 0.8534 (mmmm) cc_final: 0.7201 (mmtt) REVERT: S 155 LYS cc_start: 0.8947 (mmtm) cc_final: 0.7748 (mtpt) REVERT: T 121 SER cc_start: 0.8726 (m) cc_final: 0.8010 (t) REVERT: T 122 LYS cc_start: 0.8327 (mmmm) cc_final: 0.7975 (mmtt) REVERT: T 173 LYS cc_start: 0.8530 (tttt) cc_final: 0.8285 (tttt) outliers start: 107 outliers final: 56 residues processed: 875 average time/residue: 0.4240 time to fit residues: 581.9433 Evaluate side-chains 764 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 706 time to evaluate : 3.387 ------------------------------------------------------------------------------- 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 85 GLU Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 189 ILE Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 103 LYS Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E 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 66 VAL Chi-restraints excluded: chain G residue 110 CYS Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 132 CYS Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 132 CYS Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 129 SER Chi-restraints excluded: chain K residue 132 CYS 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 132 CYS Chi-restraints excluded: chain L residue 136 TRP Chi-restraints excluded: chain M residue 66 VAL Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 132 CYS 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 O residue 112 VAL 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 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 92 ASP 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 320 optimal weight: 4.9990 chunk 24 optimal weight: 9.9990 chunk 67 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 101 optimal weight: 2.9990 chunk 246 optimal weight: 8.9990 chunk 170 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 155 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 180 GLN R 180 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.103469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3329 r_free = 0.3329 target = 0.089764 restraints weight = 59455.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.093139 restraints weight = 28801.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095322 restraints weight = 17350.571| |-----------------------------------------------------------------------------| r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.3566 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.064 29091 Z= 0.300 Angle : 0.800 13.883 39562 Z= 0.412 Chirality : 0.050 0.193 4960 Planarity : 0.008 0.174 5020 Dihedral : 5.675 179.374 4080 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.52 % Allowed : 7.50 % Favored : 91.98 % Rotamer: Outliers : 3.70 % Allowed : 14.34 % Favored : 81.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.14), residues: 3880 helix: 3.05 (0.15), residues: 1040 sheet: 0.85 (0.16), residues: 1160 loop : -1.78 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 136 PHE 0.021 0.002 PHE A 28 TYR 0.014 0.002 TYR F 169 ARG 0.036 0.002 ARG E 84 Details of bonding type rmsd hydrogen bonds : bond 0.04772 ( 1600) hydrogen bonds : angle 5.08816 ( 4500) SS BOND : bond 0.00100 ( 1) SS BOND : angle 1.03762 ( 2) covalent geometry : bond 0.00716 (29060) covalent geometry : angle 0.79967 (39560) Misc. bond : bond 0.00418 ( 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 849 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 117 poor density : 732 time to evaluate : 3.040 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: B 103 LYS cc_start: 0.8294 (mppt) cc_final: 0.8064 (mmmt) REVERT: C 11 GLU cc_start: 0.8653 (pm20) cc_final: 0.7979 (mm-30) REVERT: C 180 GLN cc_start: 0.8452 (pm20) cc_final: 0.8217 (pm20) REVERT: D 95 THR cc_start: 0.9157 (m) cc_final: 0.8631 (p) REVERT: D 138 TYR cc_start: 0.8709 (p90) cc_final: 0.8247 (p90) REVERT: D 172 PHE cc_start: 0.8857 (p90) cc_final: 0.8650 (p90) REVERT: E 46 GLN cc_start: 0.8976 (tt0) cc_final: 0.8519 (tm-30) REVERT: E 122 LYS cc_start: 0.8967 (tppt) cc_final: 0.8696 (tttp) REVERT: E 173 LYS cc_start: 0.8915 (tttt) cc_final: 0.8690 (tttm) REVERT: F 51 GLU cc_start: 0.9054 (tp30) cc_final: 0.8778 (tp30) REVERT: G 19 PHE cc_start: 0.8686 (m-80) cc_final: 0.8399 (m-80) REVERT: G 43 GLU cc_start: 0.8626 (tm-30) cc_final: 0.8307 (tm-30) REVERT: G 46 GLN cc_start: 0.9027 (tt0) cc_final: 0.8772 (tm-30) REVERT: G 138 TYR cc_start: 0.8988 (p90) cc_final: 0.8717 (p90) REVERT: G 170 GLU cc_start: 0.8686 (pm20) cc_final: 0.8428 (pm20) REVERT: H 93 LYS cc_start: 0.7081 (mttt) cc_final: 0.6144 (mmtp) REVERT: I 19 PHE cc_start: 0.8825 (m-80) cc_final: 0.8561 (m-80) REVERT: I 99 MET cc_start: 0.8485 (tmm) cc_final: 0.8107 (tmm) REVERT: J 19 PHE cc_start: 0.8822 (m-80) cc_final: 0.8461 (m-80) REVERT: J 28 PHE cc_start: 0.9288 (t80) cc_final: 0.8959 (t80) REVERT: J 103 LYS cc_start: 0.8766 (mmtt) cc_final: 0.8497 (mmtt) REVERT: J 148 ASN cc_start: 0.8198 (m-40) cc_final: 0.7950 (t0) REVERT: K 138 TYR cc_start: 0.8637 (p90) cc_final: 0.8163 (p90) REVERT: K 173 LYS cc_start: 0.8872 (tttt) cc_final: 0.8529 (tttm) REVERT: A 36 PHE cc_start: 0.8824 (t80) cc_final: 0.7496 (t80) REVERT: L 45 MET cc_start: 0.9204 (ptp) cc_final: 0.8861 (ptm) REVERT: L 88 ASP cc_start: 0.8478 (t0) cc_final: 0.8207 (t0) REVERT: L 92 ASP cc_start: 0.8356 (p0) cc_final: 0.8108 (p0) REVERT: L 103 LYS cc_start: 0.8400 (mppt) cc_final: 0.7897 (mttt) REVERT: L 120 ASP cc_start: 0.6984 (t0) cc_final: 0.6248 (p0) REVERT: L 172 PHE cc_start: 0.8692 (p90) cc_final: 0.8473 (p90) REVERT: M 39 GLN cc_start: 0.8548 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: M 103 LYS cc_start: 0.7931 (mppt) cc_final: 0.7710 (mtmt) REVERT: M 110 CYS cc_start: 0.8703 (OUTLIER) cc_final: 0.7983 (t) REVERT: M 136 TRP cc_start: 0.8393 (m-90) cc_final: 0.8101 (m-90) REVERT: N 19 PHE cc_start: 0.8437 (m-80) cc_final: 0.8179 (m-80) REVERT: N 122 LYS cc_start: 0.8713 (tptm) cc_final: 0.8381 (tptp) REVERT: N 173 LYS cc_start: 0.8969 (tttt) cc_final: 0.8594 (tttm) REVERT: P 173 LYS cc_start: 0.8931 (tttt) cc_final: 0.8633 (tttm) REVERT: Q 59 ASP cc_start: 0.7951 (t0) cc_final: 0.7704 (t0) REVERT: Q 95 THR cc_start: 0.9294 (m) cc_final: 0.8838 (p) REVERT: Q 138 TYR cc_start: 0.8531 (p90) cc_final: 0.8259 (p90) REVERT: R 105 TYR cc_start: 0.8724 (m-80) cc_final: 0.8496 (m-80) REVERT: R 122 LYS cc_start: 0.8088 (mmmm) cc_final: 0.7765 (mptt) REVERT: R 148 ASN cc_start: 0.8469 (m-40) cc_final: 0.8257 (m-40) REVERT: R 155 LYS cc_start: 0.9058 (mmtm) cc_final: 0.7211 (tptm) REVERT: S 19 PHE cc_start: 0.8372 (m-80) cc_final: 0.7877 (m-80) REVERT: S 42 LYS cc_start: 0.9169 (tttt) cc_final: 0.8310 (tptt) REVERT: S 84 ARG cc_start: 0.8161 (mpt180) cc_final: 0.7552 (mtt90) REVERT: S 120 ASP cc_start: 0.6860 (t0) cc_final: 0.6582 (p0) REVERT: S 122 LYS cc_start: 0.8968 (mmmm) cc_final: 0.7525 (mmtt) REVERT: S 155 LYS cc_start: 0.8902 (mmtm) cc_final: 0.7765 (mmmt) REVERT: T 45 MET cc_start: 0.8882 (OUTLIER) cc_final: 0.8542 (ptt) REVERT: T 121 SER cc_start: 0.8846 (m) cc_final: 0.8128 (t) REVERT: T 122 LYS cc_start: 0.8552 (mmmm) cc_final: 0.8110 (mmtt) REVERT: T 173 LYS cc_start: 0.8587 (tttt) cc_final: 0.8370 (tttt) outliers start: 117 outliers final: 69 residues processed: 812 average time/residue: 0.4243 time to fit residues: 530.3762 Evaluate side-chains 726 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 654 time to evaluate : 3.053 ------------------------------------------------------------------------------- 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 118 LEU Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 66 VAL 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 G residue 66 VAL Chi-restraints excluded: chain G residue 110 CYS Chi-restraints excluded: chain G residue 112 VAL Chi-restraints excluded: chain G residue 129 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 121 SER Chi-restraints excluded: chain H residue 189 ILE Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J 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 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 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 110 CYS 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG 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 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 129 SER Chi-restraints excluded: chain Q residue 132 CYS 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 110 CYS 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 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 19 optimal weight: 9.9990 chunk 332 optimal weight: 3.9990 chunk 349 optimal weight: 9.9990 chunk 233 optimal weight: 5.9990 chunk 56 optimal weight: 0.0020 chunk 44 optimal weight: 4.9990 chunk 301 optimal weight: 3.9990 chunk 181 optimal weight: 7.9990 chunk 142 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 226 optimal weight: 9.9990 overall best weight: 3.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 143 ASN J 39 GLN M 180 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.104463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3342 r_free = 0.3342 target = 0.090736 restraints weight = 59342.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.094134 restraints weight = 28947.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.096344 restraints weight = 17366.666| |-----------------------------------------------------------------------------| r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.063 29091 Z= 0.232 Angle : 0.770 14.849 39562 Z= 0.394 Chirality : 0.048 0.164 4960 Planarity : 0.008 0.255 5020 Dihedral : 6.022 179.144 4080 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.68 % Favored : 92.81 % Rotamer: Outliers : 3.80 % Allowed : 16.58 % Favored : 79.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.14), residues: 3880 helix: 3.01 (0.15), residues: 1040 sheet: 0.72 (0.16), residues: 1160 loop : -1.90 (0.14), residues: 1680 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP D 136 PHE 0.022 0.002 PHE O 28 TYR 0.023 0.002 TYR F 169 ARG 0.031 0.001 ARG E 84 Details of bonding type rmsd hydrogen bonds : bond 0.04548 ( 1600) hydrogen bonds : angle 4.91106 ( 4500) SS BOND : bond 0.00088 ( 1) SS BOND : angle 0.75023 ( 2) covalent geometry : bond 0.00552 (29060) covalent geometry : angle 0.76990 (39560) Misc. bond : bond 0.00277 ( 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 878 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 758 time to evaluate : 3.229 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: B 103 LYS cc_start: 0.8492 (mppt) cc_final: 0.8225 (mmmt) REVERT: C 11 GLU cc_start: 0.8656 (pm20) cc_final: 0.7951 (mm-30) REVERT: D 138 TYR cc_start: 0.8645 (p90) cc_final: 0.8227 (p90) REVERT: D 172 PHE cc_start: 0.8873 (p90) cc_final: 0.8663 (p90) REVERT: E 46 GLN cc_start: 0.9017 (tt0) cc_final: 0.8598 (tm-30) REVERT: E 122 LYS cc_start: 0.9001 (tppt) cc_final: 0.8800 (tttp) REVERT: E 173 LYS cc_start: 0.8962 (tttt) cc_final: 0.8653 (tttm) REVERT: G 19 PHE cc_start: 0.8737 (m-80) cc_final: 0.8528 (m-80) REVERT: G 46 GLN cc_start: 0.9008 (tt0) cc_final: 0.8784 (tm-30) REVERT: G 136 TRP cc_start: 0.7959 (m-10) cc_final: 0.7636 (m-10) REVERT: G 138 TYR cc_start: 0.8932 (p90) cc_final: 0.8570 (p90) REVERT: H 93 LYS cc_start: 0.7155 (mttt) cc_final: 0.6187 (mmtp) REVERT: H 106 GLU cc_start: 0.8139 (tm-30) cc_final: 0.7933 (tm-30) REVERT: H 180 GLN cc_start: 0.7932 (pp30) cc_final: 0.7732 (pp30) REVERT: I 11 GLU cc_start: 0.8390 (pm20) cc_final: 0.7561 (pt0) REVERT: I 19 PHE cc_start: 0.8880 (m-80) cc_final: 0.8661 (m-80) REVERT: I 99 MET cc_start: 0.8446 (tmm) cc_final: 0.8095 (tmm) REVERT: I 103 LYS cc_start: 0.7132 (mppt) cc_final: 0.6894 (mmtp) REVERT: J 19 PHE cc_start: 0.8855 (m-80) cc_final: 0.8480 (m-80) REVERT: J 28 PHE cc_start: 0.9288 (t80) cc_final: 0.8888 (t80) REVERT: J 169 TYR cc_start: 0.7660 (m-80) cc_final: 0.7446 (m-80) REVERT: J 170 GLU cc_start: 0.8495 (pm20) cc_final: 0.8058 (pm20) REVERT: K 138 TYR cc_start: 0.8591 (p90) cc_final: 0.8023 (p90) REVERT: K 173 LYS cc_start: 0.8936 (tttt) cc_final: 0.8638 (tttm) REVERT: A 11 GLU cc_start: 0.8150 (pm20) cc_final: 0.7936 (pm20) REVERT: A 50 GLU cc_start: 0.8441 (tm-30) cc_final: 0.7887 (tp30) REVERT: A 170 GLU cc_start: 0.8348 (pm20) cc_final: 0.8012 (pm20) REVERT: L 45 MET cc_start: 0.9157 (ptp) cc_final: 0.8809 (ptm) REVERT: L 103 LYS cc_start: 0.8166 (mppt) cc_final: 0.7700 (mttt) REVERT: L 120 ASP cc_start: 0.6921 (t0) cc_final: 0.6325 (p0) REVERT: L 172 PHE cc_start: 0.8760 (p90) cc_final: 0.8517 (p90) REVERT: M 39 GLN cc_start: 0.8512 (OUTLIER) cc_final: 0.8235 (mp10) REVERT: M 43 GLU cc_start: 0.8074 (tm-30) cc_final: 0.7726 (tm-30) REVERT: M 50 GLU cc_start: 0.8015 (mm-30) cc_final: 0.7811 (tp30) REVERT: M 136 TRP cc_start: 0.8440 (m-90) cc_final: 0.8176 (m-90) REVERT: M 171 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8070 (mt-10) REVERT: M 172 PHE cc_start: 0.8690 (p90) cc_final: 0.8481 (p90) REVERT: N 122 LYS cc_start: 0.8761 (tptm) cc_final: 0.8349 (tptp) REVERT: N 173 LYS cc_start: 0.9011 (tttt) cc_final: 0.8591 (tttm) REVERT: P 121 SER cc_start: 0.8404 (m) cc_final: 0.7610 (t) REVERT: P 173 LYS cc_start: 0.8947 (tttt) cc_final: 0.8622 (tttm) REVERT: Q 95 THR cc_start: 0.9266 (m) cc_final: 0.8797 (p) REVERT: Q 121 SER cc_start: 0.8605 (m) cc_final: 0.7405 (t) REVERT: Q 138 TYR cc_start: 0.8467 (p90) cc_final: 0.8214 (p90) REVERT: R 122 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7784 (mptt) REVERT: R 155 LYS cc_start: 0.9096 (mmtm) cc_final: 0.7252 (tptt) REVERT: S 19 PHE cc_start: 0.8482 (m-80) cc_final: 0.7978 (m-80) REVERT: S 42 LYS cc_start: 0.9174 (tttt) cc_final: 0.8309 (tptt) REVERT: S 84 ARG cc_start: 0.8083 (mpt180) cc_final: 0.7803 (mtt90) REVERT: S 120 ASP cc_start: 0.6803 (t0) cc_final: 0.6577 (p0) REVERT: S 122 LYS cc_start: 0.9041 (mmmm) cc_final: 0.7727 (mmtt) REVERT: S 152 LEU cc_start: 0.8954 (OUTLIER) cc_final: 0.8583 (tt) REVERT: S 155 LYS cc_start: 0.8933 (mmtm) cc_final: 0.7779 (mmmt) REVERT: T 45 MET cc_start: 0.8808 (OUTLIER) cc_final: 0.8424 (ptt) REVERT: T 121 SER cc_start: 0.8888 (m) cc_final: 0.8168 (t) REVERT: T 122 LYS cc_start: 0.8568 (mmmm) cc_final: 0.8090 (mmtt) REVERT: T 173 LYS cc_start: 0.8568 (tttt) cc_final: 0.8355 (tttt) outliers start: 120 outliers final: 84 residues processed: 829 average time/residue: 0.4524 time to fit residues: 579.3161 Evaluate side-chains 772 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 685 time to evaluate : 3.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain B residue 152 LEU Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 141 ILE 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 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 84 ARG 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 66 VAL Chi-restraints excluded: chain G residue 110 CYS 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 74 ILE 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 110 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain J residue 66 VAL Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 132 CYS 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 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 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 139 LEU 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 76 ILE Chi-restraints excluded: chain M residue 84 ARG Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 110 CYS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 114 ASP 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG 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 Q residue 132 CYS 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 31 LEU Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain S residue 152 LEU 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 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 195 optimal weight: 7.9990 chunk 339 optimal weight: 5.9990 chunk 80 optimal weight: 4.9990 chunk 186 optimal weight: 0.8980 chunk 16 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 287 optimal weight: 5.9990 chunk 216 optimal weight: 7.9990 chunk 273 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 315 optimal weight: 6.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 180 GLN K 143 ASN Q 180 GLN R 180 GLN T 39 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.106351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3379 r_free = 0.3379 target = 0.092751 restraints weight = 59117.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.096132 restraints weight = 28567.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.098345 restraints weight = 17185.804| |-----------------------------------------------------------------------------| r_work (final): 0.3469 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8282 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 29091 Z= 0.162 Angle : 0.735 15.633 39562 Z= 0.373 Chirality : 0.047 0.197 4960 Planarity : 0.009 0.340 5020 Dihedral : 6.083 179.251 4080 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.65 % Favored : 92.84 % Rotamer: Outliers : 3.51 % Allowed : 18.23 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.14), residues: 3880 helix: 3.08 (0.15), residues: 1040 sheet: 0.62 (0.16), residues: 1180 loop : -1.79 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 136 PHE 0.026 0.002 PHE A 28 TYR 0.027 0.001 TYR A 169 ARG 0.034 0.001 ARG Q 84 Details of bonding type rmsd hydrogen bonds : bond 0.04269 ( 1600) hydrogen bonds : angle 4.67508 ( 4500) SS BOND : bond 0.00425 ( 1) SS BOND : angle 1.25398 ( 2) covalent geometry : bond 0.00376 (29060) covalent geometry : angle 0.73486 (39560) Misc. bond : bond 0.00367 ( 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 856 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 745 time to evaluate : 3.021 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: B 103 LYS cc_start: 0.8452 (mppt) cc_final: 0.8214 (mmmt) REVERT: B 170 GLU cc_start: 0.8386 (pm20) cc_final: 0.8070 (pm20) REVERT: C 11 GLU cc_start: 0.8562 (pm20) cc_final: 0.7873 (mm-30) REVERT: C 180 GLN cc_start: 0.8468 (pm20) cc_final: 0.8204 (pm20) REVERT: D 138 TYR cc_start: 0.8533 (p90) cc_final: 0.8094 (p90) REVERT: D 172 PHE cc_start: 0.8842 (p90) cc_final: 0.8642 (p90) REVERT: E 46 GLN cc_start: 0.8996 (tt0) cc_final: 0.8525 (tm-30) REVERT: E 122 LYS cc_start: 0.8994 (tppt) cc_final: 0.8697 (tttp) REVERT: E 173 LYS cc_start: 0.8884 (tttt) cc_final: 0.8650 (tttm) REVERT: G 19 PHE cc_start: 0.8665 (m-80) cc_final: 0.8428 (m-80) REVERT: G 46 GLN cc_start: 0.8979 (tt0) cc_final: 0.8696 (tm-30) REVERT: G 138 TYR cc_start: 0.8838 (p90) cc_final: 0.8437 (p90) REVERT: H 93 LYS cc_start: 0.7189 (mttt) cc_final: 0.6199 (mmtp) REVERT: H 106 GLU cc_start: 0.8075 (tm-30) cc_final: 0.7813 (tm-30) REVERT: I 19 PHE cc_start: 0.8807 (m-80) cc_final: 0.8507 (m-80) REVERT: I 99 MET cc_start: 0.8424 (tmm) cc_final: 0.8086 (tmm) REVERT: I 105 TYR cc_start: 0.8837 (m-80) cc_final: 0.8398 (m-80) REVERT: I 138 TYR cc_start: 0.8358 (p90) cc_final: 0.7964 (p90) REVERT: J 19 PHE cc_start: 0.8794 (m-80) cc_final: 0.8392 (m-80) REVERT: J 103 LYS cc_start: 0.8548 (mmtt) cc_final: 0.8222 (mmmt) REVERT: J 169 TYR cc_start: 0.7643 (m-80) cc_final: 0.7397 (m-80) REVERT: J 170 GLU cc_start: 0.8454 (pm20) cc_final: 0.7966 (pm20) REVERT: K 173 LYS cc_start: 0.8903 (tttt) cc_final: 0.8601 (tttm) REVERT: A 170 GLU cc_start: 0.8407 (pm20) cc_final: 0.8070 (mp0) REVERT: L 103 LYS cc_start: 0.7936 (mppt) cc_final: 0.7669 (mttt) REVERT: L 120 ASP cc_start: 0.6787 (t0) cc_final: 0.6192 (p0) REVERT: L 172 PHE cc_start: 0.8737 (p90) cc_final: 0.8506 (p90) REVERT: M 39 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.8187 (mp10) REVERT: M 172 PHE cc_start: 0.8705 (p90) cc_final: 0.8490 (p90) REVERT: N 122 LYS cc_start: 0.8786 (tptm) cc_final: 0.8437 (tptp) REVERT: N 172 PHE cc_start: 0.8775 (p90) cc_final: 0.8518 (p90) REVERT: N 173 LYS cc_start: 0.9028 (tttt) cc_final: 0.8589 (tttm) REVERT: O 120 ASP cc_start: 0.6898 (t0) cc_final: 0.6578 (p0) REVERT: P 110 CYS cc_start: 0.9253 (OUTLIER) cc_final: 0.8759 (t) REVERT: P 121 SER cc_start: 0.8349 (m) cc_final: 0.7493 (t) REVERT: P 173 LYS cc_start: 0.8968 (tttt) cc_final: 0.8624 (tttm) REVERT: Q 95 THR cc_start: 0.9243 (m) cc_final: 0.8762 (p) REVERT: Q 103 LYS cc_start: 0.8342 (mmtt) cc_final: 0.7173 (mtmt) REVERT: Q 138 TYR cc_start: 0.8395 (p90) cc_final: 0.8132 (p90) REVERT: R 122 LYS cc_start: 0.8082 (mmmm) cc_final: 0.7741 (mptt) REVERT: R 148 ASN cc_start: 0.8301 (m-40) cc_final: 0.8038 (m-40) REVERT: R 155 LYS cc_start: 0.9095 (mmtm) cc_final: 0.7281 (tptt) REVERT: S 19 PHE cc_start: 0.8448 (m-80) cc_final: 0.7941 (m-80) REVERT: S 42 LYS cc_start: 0.9143 (tttt) cc_final: 0.8257 (tptt) REVERT: S 51 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8251 (tm-30) REVERT: S 84 ARG cc_start: 0.8052 (mpt180) cc_final: 0.7523 (mpp-170) REVERT: S 122 LYS cc_start: 0.9044 (mmmm) cc_final: 0.7737 (mmtt) REVERT: S 155 LYS cc_start: 0.8951 (mmtm) cc_final: 0.7746 (mtpt) REVERT: T 45 MET cc_start: 0.8745 (ptm) cc_final: 0.8376 (ptt) REVERT: T 121 SER cc_start: 0.8845 (m) cc_final: 0.8107 (t) REVERT: T 122 LYS cc_start: 0.8549 (mmmm) cc_final: 0.8065 (mmtt) outliers start: 111 outliers final: 83 residues processed: 811 average time/residue: 0.4162 time to fit residues: 521.5216 Evaluate side-chains 763 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 678 time to evaluate : 3.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 66 VAL Chi-restraints excluded: chain B residue 129 SER Chi-restraints excluded: chain C residue 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 141 ILE 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 E residue 16 LEU Chi-restraints excluded: chain E residue 66 VAL 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 84 ARG 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 66 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 110 CYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 ILE Chi-restraints excluded: chain H residue 121 SER 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 I residue 118 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 110 CYS 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 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain L residue 66 VAL Chi-restraints excluded: chain L residue 112 VAL Chi-restraints excluded: chain M residue 16 LEU 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 84 ARG Chi-restraints excluded: chain M residue 110 CYS 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG 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 Q residue 132 CYS Chi-restraints excluded: chain Q residue 180 GLN Chi-restraints excluded: chain Q residue 187 GLU 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 R residue 180 GLN 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 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 29 optimal weight: 0.9980 chunk 114 optimal weight: 4.9990 chunk 279 optimal weight: 6.9990 chunk 160 optimal weight: 3.9990 chunk 212 optimal weight: 0.9980 chunk 284 optimal weight: 0.9980 chunk 140 optimal weight: 7.9990 chunk 93 optimal weight: 10.0000 chunk 327 optimal weight: 8.9990 chunk 216 optimal weight: 4.9990 chunk 25 optimal weight: 5.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 46 GLN E 180 GLN J 39 GLN P 180 GLN Q 180 GLN R 180 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.105789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.092274 restraints weight = 58945.158| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.095621 restraints weight = 28348.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.097805 restraints weight = 17017.622| |-----------------------------------------------------------------------------| r_work (final): 0.3464 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29091 Z= 0.181 Angle : 0.764 15.514 39562 Z= 0.387 Chirality : 0.047 0.176 4960 Planarity : 0.009 0.261 5020 Dihedral : 6.092 179.095 4080 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 9.76 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.75 % Favored : 92.73 % Rotamer: Outliers : 3.58 % Allowed : 19.97 % Favored : 76.46 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.14), residues: 3880 helix: 3.04 (0.15), residues: 1040 sheet: 0.55 (0.16), residues: 1180 loop : -1.83 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 136 PHE 0.020 0.002 PHE P 28 TYR 0.018 0.001 TYR A 169 ARG 0.049 0.002 ARG A 84 Details of bonding type rmsd hydrogen bonds : bond 0.04242 ( 1600) hydrogen bonds : angle 4.66238 ( 4500) SS BOND : bond 0.00379 ( 1) SS BOND : angle 0.70653 ( 2) covalent geometry : bond 0.00426 (29060) covalent geometry : angle 0.76362 (39560) Misc. bond : bond 0.00378 ( 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 838 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 725 time to evaluate : 3.172 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: B 103 LYS cc_start: 0.8527 (mppt) cc_final: 0.8294 (mmmt) REVERT: C 11 GLU cc_start: 0.8610 (pm20) cc_final: 0.7921 (mm-30) REVERT: C 180 GLN cc_start: 0.8561 (pm20) cc_final: 0.8309 (pm20) REVERT: D 138 TYR cc_start: 0.8565 (p90) cc_final: 0.8184 (p90) REVERT: D 172 PHE cc_start: 0.8873 (p90) cc_final: 0.8672 (p90) REVERT: E 46 GLN cc_start: 0.9026 (tt0) cc_final: 0.8595 (tm-30) REVERT: E 122 LYS cc_start: 0.9019 (tppt) cc_final: 0.8687 (tttp) REVERT: F 50 GLU cc_start: 0.8146 (mt-10) cc_final: 0.7911 (mt-10) REVERT: G 19 PHE cc_start: 0.8666 (m-80) cc_final: 0.8350 (m-80) REVERT: G 46 GLN cc_start: 0.8972 (tt0) cc_final: 0.8679 (tm-30) REVERT: G 138 TYR cc_start: 0.8886 (p90) cc_final: 0.8497 (p90) REVERT: H 93 LYS cc_start: 0.7208 (mttt) cc_final: 0.6265 (mmtp) REVERT: H 106 GLU cc_start: 0.8106 (tm-30) cc_final: 0.7902 (tm-30) REVERT: H 170 GLU cc_start: 0.8478 (pm20) cc_final: 0.8170 (pm20) REVERT: I 19 PHE cc_start: 0.8805 (m-80) cc_final: 0.8546 (m-80) REVERT: I 99 MET cc_start: 0.8426 (tmm) cc_final: 0.8088 (tmm) REVERT: I 103 LYS cc_start: 0.6875 (mppt) cc_final: 0.6463 (mmtp) REVERT: I 105 TYR cc_start: 0.8834 (m-80) cc_final: 0.8438 (m-80) REVERT: I 138 TYR cc_start: 0.8367 (p90) cc_final: 0.8023 (p90) REVERT: J 19 PHE cc_start: 0.8799 (m-80) cc_final: 0.8405 (m-80) REVERT: J 103 LYS cc_start: 0.8644 (mmtt) cc_final: 0.8323 (mmmt) REVERT: K 173 LYS cc_start: 0.8905 (tttt) cc_final: 0.8598 (tttm) REVERT: A 50 GLU cc_start: 0.8426 (tm-30) cc_final: 0.8179 (tm-30) REVERT: A 170 GLU cc_start: 0.8374 (pm20) cc_final: 0.8010 (mp0) REVERT: L 88 ASP cc_start: 0.8368 (t0) cc_final: 0.8040 (t0) REVERT: L 103 LYS cc_start: 0.7956 (mppt) cc_final: 0.7623 (mttt) REVERT: L 120 ASP cc_start: 0.6555 (t0) cc_final: 0.6129 (p0) REVERT: L 172 PHE cc_start: 0.8734 (p90) cc_final: 0.8511 (p90) REVERT: M 39 GLN cc_start: 0.8465 (OUTLIER) cc_final: 0.8214 (mp10) REVERT: M 171 GLU cc_start: 0.8373 (mt-10) cc_final: 0.8151 (mt-10) REVERT: M 172 PHE cc_start: 0.8712 (p90) cc_final: 0.8488 (p90) REVERT: N 122 LYS cc_start: 0.8818 (tptm) cc_final: 0.8556 (tptp) REVERT: N 173 LYS cc_start: 0.9027 (tttt) cc_final: 0.8599 (tttm) REVERT: O 120 ASP cc_start: 0.6910 (t0) cc_final: 0.6690 (p0) REVERT: P 50 GLU cc_start: 0.7769 (tm-30) cc_final: 0.5560 (tm-30) REVERT: P 103 LYS cc_start: 0.7931 (mppt) cc_final: 0.7616 (mmtm) REVERT: P 110 CYS cc_start: 0.9218 (OUTLIER) cc_final: 0.8852 (t) REVERT: P 121 SER cc_start: 0.8366 (m) cc_final: 0.7397 (t) REVERT: P 173 LYS cc_start: 0.8966 (tttt) cc_final: 0.8632 (tttm) REVERT: Q 95 THR cc_start: 0.9225 (m) cc_final: 0.8759 (p) REVERT: Q 103 LYS cc_start: 0.8400 (mmtt) cc_final: 0.7239 (mtmt) REVERT: Q 138 TYR cc_start: 0.8358 (p90) cc_final: 0.8136 (p90) REVERT: R 50 GLU cc_start: 0.8233 (tp30) cc_final: 0.7999 (tp30) REVERT: R 122 LYS cc_start: 0.8165 (mmmm) cc_final: 0.7802 (mptt) REVERT: R 148 ASN cc_start: 0.8315 (m-40) cc_final: 0.8068 (m-40) REVERT: R 155 LYS cc_start: 0.9057 (mmtm) cc_final: 0.7248 (tptt) REVERT: S 19 PHE cc_start: 0.8447 (m-80) cc_final: 0.7929 (m-80) REVERT: S 42 LYS cc_start: 0.9158 (tttt) cc_final: 0.8272 (tptt) REVERT: S 51 GLU cc_start: 0.8610 (tm-30) cc_final: 0.8213 (tm-30) REVERT: S 84 ARG cc_start: 0.8062 (mpt180) cc_final: 0.7641 (mpp-170) REVERT: S 122 LYS cc_start: 0.8995 (mmmm) cc_final: 0.7684 (mmtt) REVERT: S 152 LEU cc_start: 0.8909 (OUTLIER) cc_final: 0.8584 (tt) REVERT: S 155 LYS cc_start: 0.8967 (mmtm) cc_final: 0.7748 (mtpt) REVERT: T 45 MET cc_start: 0.8762 (ptm) cc_final: 0.8370 (ptt) REVERT: T 121 SER cc_start: 0.8821 (m) cc_final: 0.8069 (t) REVERT: T 122 LYS cc_start: 0.8558 (mmmm) cc_final: 0.8067 (mmtt) outliers start: 113 outliers final: 86 residues processed: 788 average time/residue: 0.4288 time to fit residues: 520.7007 Evaluate side-chains 769 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 680 time to evaluate : 3.386 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain C residue 95 THR Chi-restraints excluded: chain C residue 141 ILE 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 E residue 16 LEU Chi-restraints excluded: chain E residue 28 PHE Chi-restraints excluded: chain E residue 66 VAL Chi-restraints excluded: chain E residue 84 ARG Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 84 ARG 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 66 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 110 CYS 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 121 SER Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 132 CYS Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL 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 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 180 GLN 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 16 LEU 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 84 ARG Chi-restraints excluded: chain M residue 92 ASP Chi-restraints excluded: chain M residue 110 CYS Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 118 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG 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 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 180 GLN Chi-restraints excluded: chain Q residue 187 GLU Chi-restraints excluded: chain R residue 8 VAL Chi-restraints excluded: chain S residue 31 LEU Chi-restraints excluded: chain S residue 110 CYS Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 152 LEU 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 175 optimal weight: 9.9990 chunk 63 optimal weight: 5.9990 chunk 19 optimal weight: 0.0000 chunk 186 optimal weight: 2.9990 chunk 52 optimal weight: 5.9990 chunk 331 optimal weight: 3.9990 chunk 163 optimal weight: 1.9990 chunk 372 optimal weight: 0.2980 chunk 354 optimal weight: 0.9990 chunk 112 optimal weight: 1.9990 chunk 278 optimal weight: 1.9990 overall best weight: 1.0590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 180 GLN T 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.103536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.089866 restraints weight = 58994.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.093089 restraints weight = 29639.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.095258 restraints weight = 18175.160| |-----------------------------------------------------------------------------| r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8223 moved from start: 0.4149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 29091 Z= 0.138 Angle : 0.738 16.959 39562 Z= 0.370 Chirality : 0.047 0.184 4960 Planarity : 0.008 0.218 5020 Dihedral : 5.304 179.284 4080 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.75 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.52 % Favored : 92.96 % Rotamer: Outliers : 3.13 % Allowed : 20.60 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.56 (0.14), residues: 3880 helix: 3.14 (0.15), residues: 1040 sheet: 0.63 (0.16), residues: 1180 loop : -1.76 (0.14), residues: 1660 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 136 PHE 0.029 0.001 PHE F 28 TYR 0.012 0.001 TYR F 138 ARG 0.030 0.002 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03912 ( 1600) hydrogen bonds : angle 4.39160 ( 4500) SS BOND : bond 0.00237 ( 1) SS BOND : angle 0.52122 ( 2) covalent geometry : bond 0.00310 (29060) covalent geometry : angle 0.73830 (39560) Misc. bond : bond 0.00281 ( 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 867 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 768 time to evaluate : 3.040 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 103 LYS cc_start: 0.8310 (mppt) cc_final: 0.8067 (mmmt) REVERT: B 170 GLU cc_start: 0.8287 (pm20) cc_final: 0.7916 (mp0) REVERT: B 171 GLU cc_start: 0.8074 (mt-10) cc_final: 0.7419 (mt-10) REVERT: B 187 GLU cc_start: 0.7880 (tt0) cc_final: 0.7586 (tt0) REVERT: C 180 GLN cc_start: 0.8602 (pm20) cc_final: 0.8335 (pm20) REVERT: D 138 TYR cc_start: 0.8415 (p90) cc_final: 0.7986 (p90) REVERT: D 172 PHE cc_start: 0.8928 (p90) cc_final: 0.8716 (p90) REVERT: E 59 ASP cc_start: 0.7649 (t0) cc_final: 0.7156 (p0) REVERT: E 122 LYS cc_start: 0.9000 (tppt) cc_final: 0.8713 (tttp) REVERT: G 19 PHE cc_start: 0.8496 (m-80) cc_final: 0.8161 (m-80) REVERT: G 46 GLN cc_start: 0.9002 (tt0) cc_final: 0.8666 (tm-30) REVERT: G 138 TYR cc_start: 0.8721 (p90) cc_final: 0.8303 (p90) REVERT: H 59 ASP cc_start: 0.8384 (t0) cc_final: 0.8093 (t0) REVERT: H 88 ASP cc_start: 0.8739 (t0) cc_final: 0.8539 (t0) REVERT: H 93 LYS cc_start: 0.7157 (mttt) cc_final: 0.6066 (mmtp) REVERT: H 106 GLU cc_start: 0.8064 (tm-30) cc_final: 0.7844 (tm-30) REVERT: H 170 GLU cc_start: 0.8381 (pm20) cc_final: 0.8146 (pm20) REVERT: I 19 PHE cc_start: 0.8796 (m-80) cc_final: 0.8542 (m-80) REVERT: I 99 MET cc_start: 0.8405 (tmm) cc_final: 0.8022 (tmm) REVERT: I 105 TYR cc_start: 0.8720 (m-80) cc_final: 0.8334 (m-80) REVERT: I 138 TYR cc_start: 0.8147 (p90) cc_final: 0.7224 (p90) REVERT: J 19 PHE cc_start: 0.8678 (m-80) cc_final: 0.8283 (m-80) REVERT: J 103 LYS cc_start: 0.8527 (mmtt) cc_final: 0.8170 (mmmt) REVERT: K 33 MET cc_start: 0.8686 (OUTLIER) cc_final: 0.8217 (tpp) REVERT: K 173 LYS cc_start: 0.8875 (tttt) cc_final: 0.8595 (tttm) REVERT: A 170 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7876 (mp0) REVERT: L 88 ASP cc_start: 0.8401 (t0) cc_final: 0.8109 (t0) REVERT: L 103 LYS cc_start: 0.7639 (mppt) cc_final: 0.7402 (mttt) REVERT: L 120 ASP cc_start: 0.6460 (t0) cc_final: 0.6023 (p0) REVERT: L 170 GLU cc_start: 0.8310 (OUTLIER) cc_final: 0.7773 (pm20) REVERT: L 172 PHE cc_start: 0.8692 (p90) cc_final: 0.8472 (p90) REVERT: M 170 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: M 171 GLU cc_start: 0.8367 (mt-10) cc_final: 0.8030 (mt-10) REVERT: M 172 PHE cc_start: 0.8745 (p90) cc_final: 0.8502 (p90) REVERT: N 19 PHE cc_start: 0.8483 (m-80) cc_final: 0.8159 (m-80) REVERT: N 103 LYS cc_start: 0.7563 (mmtp) cc_final: 0.7204 (mmtm) REVERT: N 122 LYS cc_start: 0.8771 (tptm) cc_final: 0.8360 (tptp) REVERT: N 173 LYS cc_start: 0.8945 (tttt) cc_final: 0.8637 (tttm) REVERT: O 89 MET cc_start: 0.7408 (mmm) cc_final: 0.7171 (mmm) REVERT: O 120 ASP cc_start: 0.6953 (t0) cc_final: 0.6601 (p0) REVERT: P 19 PHE cc_start: 0.8451 (m-80) cc_final: 0.8175 (m-80) REVERT: P 110 CYS cc_start: 0.9210 (OUTLIER) cc_final: 0.8710 (t) REVERT: P 121 SER cc_start: 0.8400 (m) cc_final: 0.7384 (t) REVERT: P 136 TRP cc_start: 0.8048 (m-90) cc_final: 0.7827 (m-10) REVERT: P 173 LYS cc_start: 0.9005 (tttt) cc_final: 0.8655 (tttm) REVERT: Q 28 PHE cc_start: 0.9221 (t80) cc_final: 0.8988 (t80) REVERT: Q 39 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8646 (mm110) REVERT: Q 95 THR cc_start: 0.9178 (m) cc_final: 0.8661 (p) REVERT: Q 103 LYS cc_start: 0.8242 (mmtt) cc_final: 0.7128 (mttt) REVERT: Q 170 GLU cc_start: 0.8595 (OUTLIER) cc_final: 0.8296 (pt0) REVERT: R 120 ASP cc_start: 0.7078 (t0) cc_final: 0.6850 (p0) REVERT: R 122 LYS cc_start: 0.8095 (mmmm) cc_final: 0.7443 (mptt) REVERT: R 148 ASN cc_start: 0.8188 (m-40) cc_final: 0.7949 (m-40) REVERT: R 155 LYS cc_start: 0.9031 (mmtm) cc_final: 0.7270 (tttt) REVERT: S 19 PHE cc_start: 0.8377 (m-80) cc_final: 0.7808 (m-80) REVERT: S 42 LYS cc_start: 0.9146 (tttt) cc_final: 0.8255 (tptt) REVERT: S 51 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8200 (tm-30) REVERT: S 84 ARG cc_start: 0.8016 (mpt180) cc_final: 0.7572 (mpp-170) REVERT: S 122 LYS cc_start: 0.8960 (mmmm) cc_final: 0.7583 (mmtt) REVERT: S 155 LYS cc_start: 0.8980 (mmtm) cc_final: 0.7753 (mtpt) REVERT: T 45 MET cc_start: 0.8679 (ptm) cc_final: 0.8293 (ptt) REVERT: T 121 SER cc_start: 0.8791 (m) cc_final: 0.8029 (t) REVERT: T 122 LYS cc_start: 0.8493 (mmmm) cc_final: 0.7970 (mmtt) outliers start: 99 outliers final: 79 residues processed: 821 average time/residue: 0.4103 time to fit residues: 520.9382 Evaluate side-chains 779 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 694 time to evaluate : 2.984 ------------------------------------------------------------------------------- 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 C residue 66 VAL Chi-restraints excluded: chain D residue 31 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 112 VAL 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 84 ARG 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 66 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 110 CYS Chi-restraints excluded: chain G residue 118 LEU Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 74 ILE 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 I residue 118 LEU Chi-restraints excluded: chain I residue 189 ILE Chi-restraints excluded: chain J residue 136 TRP Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL 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 16 LEU Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 180 GLN 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 L residue 170 GLU Chi-restraints excluded: chain M residue 16 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 84 ARG Chi-restraints excluded: chain M residue 112 VAL Chi-restraints excluded: chain M residue 118 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG 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 112 VAL Chi-restraints excluded: chain R residue 170 GLU 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 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 169 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 34 optimal weight: 0.8980 chunk 25 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 304 optimal weight: 0.6980 chunk 194 optimal weight: 0.0470 chunk 313 optimal weight: 5.9990 chunk 113 optimal weight: 0.0670 chunk 358 optimal weight: 0.9990 chunk 241 optimal weight: 7.9990 chunk 165 optimal weight: 3.9990 chunk 265 optimal weight: 6.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 39 GLN J 143 ASN P 143 ASN Q 180 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.105137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.091693 restraints weight = 58441.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.094891 restraints weight = 29752.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.097021 restraints weight = 18293.537| |-----------------------------------------------------------------------------| r_work (final): 0.3421 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 29091 Z= 0.135 Angle : 0.760 17.591 39562 Z= 0.378 Chirality : 0.047 0.182 4960 Planarity : 0.009 0.364 5020 Dihedral : 5.932 176.051 4080 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.34 % Favored : 93.14 % Rotamer: Outliers : 3.16 % Allowed : 21.80 % Favored : 75.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.14), residues: 3880 helix: 3.14 (0.15), residues: 1040 sheet: 1.23 (0.16), residues: 1080 loop : -1.76 (0.14), residues: 1760 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 136 PHE 0.028 0.001 PHE A 28 TYR 0.012 0.001 TYR G 105 ARG 0.025 0.001 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03704 ( 1600) hydrogen bonds : angle 4.26068 ( 4500) SS BOND : bond 0.00176 ( 1) SS BOND : angle 0.46901 ( 2) covalent geometry : bond 0.00308 (29060) covalent geometry : angle 0.76000 (39560) Misc. bond : bond 0.00269 ( 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 850 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 750 time to evaluate : 3.072 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: C 93 LYS cc_start: 0.7096 (mttt) cc_final: 0.6269 (mmtm) REVERT: C 180 GLN cc_start: 0.8582 (pm20) cc_final: 0.8276 (pm20) REVERT: D 33 MET cc_start: 0.8391 (tpp) cc_final: 0.8175 (tpp) REVERT: D 138 TYR cc_start: 0.8232 (p90) cc_final: 0.7934 (p90) REVERT: D 172 PHE cc_start: 0.8910 (p90) cc_final: 0.8672 (p90) REVERT: E 57 GLU cc_start: 0.8137 (pt0) cc_final: 0.7926 (pt0) REVERT: E 122 LYS cc_start: 0.8984 (tppt) cc_final: 0.8742 (tttp) REVERT: G 19 PHE cc_start: 0.8360 (m-80) cc_final: 0.8033 (m-80) REVERT: G 46 GLN cc_start: 0.8994 (tt0) cc_final: 0.8676 (tm-30) REVERT: G 138 TYR cc_start: 0.8545 (p90) cc_final: 0.8199 (p90) REVERT: H 93 LYS cc_start: 0.7195 (mttt) cc_final: 0.6096 (mmtp) REVERT: H 106 GLU cc_start: 0.8065 (tm-30) cc_final: 0.7833 (tm-30) REVERT: H 170 GLU cc_start: 0.8334 (pm20) cc_final: 0.8079 (pm20) REVERT: I 19 PHE cc_start: 0.8687 (m-80) cc_final: 0.8477 (m-80) REVERT: I 99 MET cc_start: 0.8376 (tmm) cc_final: 0.7977 (tmm) REVERT: I 138 TYR cc_start: 0.8140 (p90) cc_final: 0.7211 (p90) REVERT: J 19 PHE cc_start: 0.8668 (m-80) cc_final: 0.8313 (m-80) REVERT: J 170 GLU cc_start: 0.8479 (pm20) cc_final: 0.8039 (pm20) REVERT: K 39 GLN cc_start: 0.8746 (mm-40) cc_final: 0.8422 (tm-30) REVERT: K 173 LYS cc_start: 0.8876 (tttt) cc_final: 0.8607 (tttm) REVERT: K 187 GLU cc_start: 0.7716 (tp30) cc_final: 0.7437 (tp30) REVERT: A 170 GLU cc_start: 0.8216 (OUTLIER) cc_final: 0.7802 (mp0) REVERT: L 103 LYS cc_start: 0.7565 (mppt) cc_final: 0.7305 (mttt) REVERT: L 120 ASP cc_start: 0.6611 (t0) cc_final: 0.6085 (p0) REVERT: L 170 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7876 (pm20) REVERT: L 173 LYS cc_start: 0.8772 (tttt) cc_final: 0.8488 (mtpt) REVERT: M 40 LYS cc_start: 0.9076 (tptt) cc_final: 0.8814 (tptt) REVERT: M 50 GLU cc_start: 0.7831 (mm-30) cc_final: 0.7490 (tp30) REVERT: M 170 GLU cc_start: 0.8498 (OUTLIER) cc_final: 0.8155 (pm20) REVERT: M 171 GLU cc_start: 0.8293 (mt-10) cc_final: 0.7989 (mt-10) REVERT: M 172 PHE cc_start: 0.8732 (p90) cc_final: 0.8505 (p90) REVERT: N 19 PHE cc_start: 0.8229 (m-80) cc_final: 0.7977 (m-80) REVERT: N 122 LYS cc_start: 0.8739 (tptm) cc_final: 0.8351 (tptp) REVERT: N 173 LYS cc_start: 0.8888 (tttt) cc_final: 0.8594 (tttm) REVERT: O 89 MET cc_start: 0.7395 (mmm) cc_final: 0.7143 (mmm) REVERT: O 120 ASP cc_start: 0.6921 (t0) cc_final: 0.6677 (p0) REVERT: P 19 PHE cc_start: 0.8328 (m-80) cc_final: 0.8029 (m-80) REVERT: P 46 GLN cc_start: 0.8950 (tt0) cc_final: 0.8628 (tm-30) REVERT: P 110 CYS cc_start: 0.9157 (OUTLIER) cc_final: 0.8693 (t) REVERT: P 120 ASP cc_start: 0.7313 (t0) cc_final: 0.6978 (p0) REVERT: P 121 SER cc_start: 0.8201 (m) cc_final: 0.6774 (t) REVERT: P 136 TRP cc_start: 0.7868 (m-90) cc_final: 0.7666 (m-10) REVERT: P 173 LYS cc_start: 0.8985 (tttt) cc_final: 0.8629 (tttm) REVERT: Q 95 THR cc_start: 0.9149 (m) cc_final: 0.8647 (p) REVERT: Q 103 LYS cc_start: 0.8107 (mmtt) cc_final: 0.7113 (mtmt) REVERT: R 19 PHE cc_start: 0.8391 (m-80) cc_final: 0.8148 (m-80) REVERT: R 122 LYS cc_start: 0.8101 (mmmm) cc_final: 0.7444 (mptt) REVERT: R 148 ASN cc_start: 0.8102 (m-40) cc_final: 0.7901 (m-40) REVERT: R 155 LYS cc_start: 0.8984 (mmtm) cc_final: 0.7339 (tttt) REVERT: S 19 PHE cc_start: 0.8273 (m-80) cc_final: 0.7737 (m-80) REVERT: S 42 LYS cc_start: 0.9118 (tttt) cc_final: 0.8345 (tptt) REVERT: S 84 ARG cc_start: 0.7911 (mpt180) cc_final: 0.7545 (mpp-170) REVERT: S 122 LYS cc_start: 0.8831 (mmmm) cc_final: 0.7599 (mmtt) REVERT: S 138 TYR cc_start: 0.8153 (p90) cc_final: 0.7179 (p90) REVERT: S 155 LYS cc_start: 0.8991 (mmtm) cc_final: 0.7762 (mtpt) REVERT: T 45 MET cc_start: 0.8637 (ptm) cc_final: 0.8245 (ptt) REVERT: T 121 SER cc_start: 0.8762 (m) cc_final: 0.7968 (t) REVERT: T 122 LYS cc_start: 0.8288 (mmmm) cc_final: 0.7766 (mmtt) outliers start: 100 outliers final: 78 residues processed: 800 average time/residue: 0.4148 time to fit residues: 514.8697 Evaluate side-chains 784 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 702 time to evaluate : 3.161 ------------------------------------------------------------------------------- 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 66 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 84 ARG 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 66 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 110 CYS 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 74 ILE Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain I residue 141 ILE Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 136 TRP Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL 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 112 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 180 GLN 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 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 84 ARG Chi-restraints excluded: chain M residue 92 ASP 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 110 CYS 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 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 R residue 8 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 110 CYS 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 72 ASP Chi-restraints excluded: chain T residue 112 VAL Chi-restraints excluded: chain T residue 169 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 149 optimal weight: 0.9980 chunk 171 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 239 optimal weight: 4.9990 chunk 343 optimal weight: 0.6980 chunk 212 optimal weight: 2.9990 chunk 92 optimal weight: 8.9990 chunk 193 optimal weight: 3.9990 chunk 203 optimal weight: 6.9990 chunk 303 optimal weight: 0.0010 chunk 325 optimal weight: 4.9990 overall best weight: 1.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 143 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 143 ASN P 143 ASN Q 39 GLN T 39 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.104611 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.091389 restraints weight = 59012.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.094449 restraints weight = 30705.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.096516 restraints weight = 19192.338| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.4349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 29091 Z= 0.144 Angle : 0.801 21.271 39562 Z= 0.395 Chirality : 0.047 0.317 4960 Planarity : 0.010 0.274 5020 Dihedral : 6.823 176.040 4080 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.52 % Allowed : 6.31 % Favored : 93.17 % Rotamer: Outliers : 2.88 % Allowed : 22.94 % Favored : 74.18 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.14), residues: 3880 helix: 3.05 (0.15), residues: 1040 sheet: 1.10 (0.16), residues: 1100 loop : -1.75 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 136 PHE 0.036 0.002 PHE J 28 TYR 0.028 0.001 TYR J 169 ARG 0.026 0.001 ARG H 47 Details of bonding type rmsd hydrogen bonds : bond 0.03713 ( 1600) hydrogen bonds : angle 4.30611 ( 4500) SS BOND : bond 0.00217 ( 1) SS BOND : angle 0.50995 ( 2) covalent geometry : bond 0.00337 (29060) covalent geometry : angle 0.80134 (39560) Misc. bond : bond 0.00301 ( 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 794 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 703 time to evaluate : 3.181 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: C 93 LYS cc_start: 0.7155 (mttt) cc_final: 0.6371 (mmtm) REVERT: C 180 GLN cc_start: 0.8546 (pm20) cc_final: 0.8300 (pm20) REVERT: D 138 TYR cc_start: 0.8278 (p90) cc_final: 0.8014 (p90) REVERT: D 172 PHE cc_start: 0.8790 (p90) cc_final: 0.8584 (p90) REVERT: G 19 PHE cc_start: 0.8291 (m-80) cc_final: 0.7962 (m-80) REVERT: G 46 GLN cc_start: 0.8885 (tt0) cc_final: 0.8654 (tm-30) REVERT: G 138 TYR cc_start: 0.8568 (p90) cc_final: 0.8196 (p90) REVERT: G 173 LYS cc_start: 0.8745 (tptt) cc_final: 0.8491 (tptt) REVERT: H 89 MET cc_start: 0.7981 (tpt) cc_final: 0.7590 (tpt) REVERT: H 93 LYS cc_start: 0.7167 (mttt) cc_final: 0.6243 (mmtp) REVERT: H 170 GLU cc_start: 0.8327 (pm20) cc_final: 0.8093 (pm20) REVERT: I 99 MET cc_start: 0.8363 (tmm) cc_final: 0.8028 (tmm) REVERT: I 138 TYR cc_start: 0.8056 (p90) cc_final: 0.7141 (p90) REVERT: J 19 PHE cc_start: 0.8591 (m-80) cc_final: 0.8347 (m-80) REVERT: K 39 GLN cc_start: 0.8707 (mm-40) cc_final: 0.8398 (tm-30) REVERT: K 59 ASP cc_start: 0.8176 (t0) cc_final: 0.7820 (p0) REVERT: K 173 LYS cc_start: 0.8887 (tttt) cc_final: 0.8562 (tttm) REVERT: A 170 GLU cc_start: 0.8326 (OUTLIER) cc_final: 0.7993 (pm20) REVERT: L 103 LYS cc_start: 0.7588 (mppt) cc_final: 0.7338 (mttt) REVERT: L 120 ASP cc_start: 0.6553 (t0) cc_final: 0.6107 (p0) REVERT: L 170 GLU cc_start: 0.8335 (OUTLIER) cc_final: 0.7952 (pm20) REVERT: M 50 GLU cc_start: 0.7662 (mm-30) cc_final: 0.7225 (tp30) REVERT: M 170 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8193 (pm20) REVERT: M 171 GLU cc_start: 0.8224 (mt-10) cc_final: 0.7933 (mt-10) REVERT: M 172 PHE cc_start: 0.8715 (p90) cc_final: 0.8496 (p90) REVERT: N 19 PHE cc_start: 0.8075 (m-80) cc_final: 0.7864 (m-80) REVERT: N 46 GLN cc_start: 0.8777 (tt0) cc_final: 0.8100 (tm-30) REVERT: N 122 LYS cc_start: 0.8707 (tptm) cc_final: 0.8473 (tptp) REVERT: N 173 LYS cc_start: 0.8874 (tttt) cc_final: 0.8567 (tttm) REVERT: O 89 MET cc_start: 0.7383 (mmm) cc_final: 0.7142 (mmm) REVERT: P 19 PHE cc_start: 0.8207 (m-80) cc_final: 0.7939 (m-80) REVERT: P 110 CYS cc_start: 0.9103 (OUTLIER) cc_final: 0.8727 (t) REVERT: P 121 SER cc_start: 0.8220 (m) cc_final: 0.6846 (t) REVERT: P 173 LYS cc_start: 0.8957 (tttt) cc_final: 0.8628 (tttm) REVERT: Q 95 THR cc_start: 0.9170 (m) cc_final: 0.8712 (p) REVERT: Q 103 LYS cc_start: 0.8167 (mmtt) cc_final: 0.7224 (mttt) REVERT: R 19 PHE cc_start: 0.8288 (m-80) cc_final: 0.8058 (m-80) REVERT: R 122 LYS cc_start: 0.8150 (mmmm) cc_final: 0.7722 (mptt) REVERT: R 155 LYS cc_start: 0.8993 (mmtm) cc_final: 0.7405 (tttt) REVERT: S 19 PHE cc_start: 0.8166 (m-80) cc_final: 0.7672 (m-80) REVERT: S 42 LYS cc_start: 0.9116 (tttt) cc_final: 0.8263 (tptt) REVERT: S 51 GLU cc_start: 0.8488 (tm-30) cc_final: 0.8139 (tm-30) REVERT: S 59 ASP cc_start: 0.7957 (t0) cc_final: 0.7645 (p0) REVERT: S 84 ARG cc_start: 0.7881 (mpt180) cc_final: 0.7656 (mpp-170) REVERT: S 122 LYS cc_start: 0.8846 (mmmm) cc_final: 0.7647 (mmtt) REVERT: S 138 TYR cc_start: 0.8141 (p90) cc_final: 0.7225 (p90) REVERT: S 152 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8556 (tt) REVERT: S 155 LYS cc_start: 0.9019 (mmtm) cc_final: 0.7811 (mtpt) REVERT: T 45 MET cc_start: 0.8572 (ptm) cc_final: 0.8203 (ptt) REVERT: T 121 SER cc_start: 0.8750 (m) cc_final: 0.7967 (t) REVERT: T 122 LYS cc_start: 0.8281 (mmmm) cc_final: 0.7773 (mmtt) outliers start: 91 outliers final: 78 residues processed: 757 average time/residue: 0.4311 time to fit residues: 507.4390 Evaluate side-chains 764 residues out of total 3160 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 681 time to evaluate : 3.496 ------------------------------------------------------------------------------- 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 C residue 66 VAL Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 95 THR Chi-restraints excluded: chain D residue 112 VAL Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain E residue 129 SER Chi-restraints excluded: chain F residue 84 ARG 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 122 LYS Chi-restraints excluded: chain F residue 129 SER Chi-restraints excluded: chain F residue 170 GLU Chi-restraints excluded: chain G residue 66 VAL Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 110 CYS 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 74 ILE Chi-restraints excluded: chain H residue 110 CYS Chi-restraints excluded: chain H residue 162 LEU Chi-restraints excluded: chain I residue 8 VAL Chi-restraints excluded: chain I residue 66 VAL Chi-restraints excluded: chain I residue 110 CYS Chi-restraints excluded: chain I residue 112 VAL Chi-restraints excluded: chain I residue 118 LEU Chi-restraints excluded: chain J residue 110 CYS Chi-restraints excluded: chain J residue 129 SER Chi-restraints excluded: chain J residue 136 TRP Chi-restraints excluded: chain K residue 33 MET Chi-restraints excluded: chain K residue 66 VAL Chi-restraints excluded: chain K residue 92 ASP Chi-restraints excluded: chain K residue 112 VAL Chi-restraints excluded: chain K residue 134 THR Chi-restraints excluded: chain A residue 112 VAL Chi-restraints excluded: chain A residue 170 GLU Chi-restraints excluded: chain A residue 180 GLN 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 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 84 ARG 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 76 ILE Chi-restraints excluded: chain O residue 84 ARG Chi-restraints excluded: chain O residue 110 CYS 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 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 R residue 8 VAL Chi-restraints excluded: chain R residue 112 VAL Chi-restraints excluded: chain S residue 110 CYS Chi-restraints excluded: chain S residue 112 VAL Chi-restraints excluded: chain S residue 129 SER Chi-restraints excluded: chain S residue 152 LEU 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 169 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 380 random chunks: chunk 218 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 344 optimal weight: 4.9990 chunk 115 optimal weight: 0.8980 chunk 345 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 89 optimal weight: 0.9990 chunk 191 optimal weight: 1.9990 chunk 356 optimal weight: 4.9990 chunk 240 optimal weight: 2.9990 chunk 241 optimal weight: 3.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 39 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 = 0.3543 r_free = 0.3543 target = 0.104476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3320 r_free = 0.3320 target = 0.090936 restraints weight = 59239.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.094119 restraints weight = 30278.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.096236 restraints weight = 18691.214| |-----------------------------------------------------------------------------| r_work (final): 0.3413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.4378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 29091 Z= 0.146 Angle : 0.805 19.694 39562 Z= 0.395 Chirality : 0.047 0.319 4960 Planarity : 0.009 0.274 5020 Dihedral : 6.518 178.308 4080 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 9.89 Ramachandran Plot: Outliers : 0.49 % Allowed : 6.37 % Favored : 93.14 % Rotamer: Outliers : 2.97 % Allowed : 23.35 % Favored : 73.67 % Cbeta Deviations : 0.03 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.66 (0.14), residues: 3880 helix: 3.00 (0.15), residues: 1040 sheet: 1.09 (0.16), residues: 1100 loop : -1.75 (0.14), residues: 1740 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 136 PHE 0.035 0.001 PHE J 28 TYR 0.027 0.001 TYR J 169 ARG 0.029 0.001 ARG C 84 Details of bonding type rmsd hydrogen bonds : bond 0.03722 ( 1600) hydrogen bonds : angle 4.31153 ( 4500) SS BOND : bond 0.00214 ( 1) SS BOND : angle 0.50058 ( 2) covalent geometry : bond 0.00340 (29060) covalent geometry : angle 0.80481 (39560) Misc. bond : bond 0.00403 ( 30) =============================================================================== Job complete usr+sys time: 11574.35 seconds wall clock time: 201 minutes 9.43 seconds (12069.43 seconds total)