Starting phenix.real_space_refine on Tue Aug 26 21:02:42 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/3jd6_6425/08_2025/3jd6_6425.cif Found real_map, /net/cci-nas-00/data/ceres_data/3jd6_6425/08_2025/3jd6_6425.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/3jd6_6425/08_2025/3jd6_6425.map" default_real_map = "/net/cci-nas-00/data/ceres_data/3jd6_6425/08_2025/3jd6_6425.map" model { file = "/net/cci-nas-00/data/ceres_data/3jd6_6425/08_2025/3jd6_6425.cif" } default_model = "/net/cci-nas-00/data/ceres_data/3jd6_6425/08_2025/3jd6_6425.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 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: 5 Type Number sf(0) Gaussians S 144 5.16 5 C 13904 2.51 5 N 3792 2.21 5 O 4032 1.98 5 H 21216 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 144 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 43088 Number of models: 1 Model: "" Number of chains: 1 Chain: "O" Number of atoms: 2693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 2693 Classifications: {'peptide': 167} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 158} Restraints were copied for chains: A, B, C, D, E, F, G, H, I, J, K, L, M, N, P Time building chain proxies: 4.81, per 1000 atoms: 0.11 Number of scatterers: 43088 At special positions: 0 Unit cell: (149.35, 149.35, 91.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 144 16.00 O 4032 8.00 N 3792 7.00 C 13904 6.00 H 21216 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=32, symmetry=0 Simple disulfide: pdb=" SG CYS O 63 " - pdb=" SG CYS O 219 " distance=2.04 Simple disulfide: pdb=" SG CYS O 110 " - pdb=" SG CYS O 142 " distance=2.04 Simple disulfide: pdb=" SG CYS A 63 " - pdb=" SG CYS A 219 " distance=2.04 Simple disulfide: pdb=" SG CYS B 63 " - pdb=" SG CYS B 219 " distance=2.04 Simple disulfide: pdb=" SG CYS C 63 " - pdb=" SG CYS C 219 " distance=2.04 Simple disulfide: pdb=" SG CYS D 63 " - pdb=" SG CYS D 219 " distance=2.04 Simple disulfide: pdb=" SG CYS E 63 " - pdb=" SG CYS E 219 " distance=2.04 Simple disulfide: pdb=" SG CYS F 63 " - pdb=" SG CYS F 219 " distance=2.04 Simple disulfide: pdb=" SG CYS G 63 " - pdb=" SG CYS G 219 " distance=2.04 Simple disulfide: pdb=" SG CYS H 63 " - pdb=" SG CYS H 219 " distance=2.04 Simple disulfide: pdb=" SG CYS I 63 " - pdb=" SG CYS I 219 " distance=2.04 Simple disulfide: pdb=" SG CYS J 63 " - pdb=" SG CYS J 219 " distance=2.04 Simple disulfide: pdb=" SG CYS K 63 " - pdb=" SG CYS K 219 " distance=2.04 Simple disulfide: pdb=" SG CYS L 63 " - pdb=" SG CYS L 219 " distance=2.04 Simple disulfide: pdb=" SG CYS M 63 " - pdb=" SG CYS M 219 " distance=2.04 Simple disulfide: pdb=" SG CYS N 63 " - pdb=" SG CYS N 219 " distance=2.04 Simple disulfide: pdb=" SG CYS P 63 " - pdb=" SG CYS P 219 " distance=2.04 Simple disulfide: pdb=" SG CYS A 110 " - pdb=" SG CYS A 142 " distance=2.04 Simple disulfide: pdb=" SG CYS B 110 " - pdb=" SG CYS B 142 " distance=2.04 Simple disulfide: pdb=" SG CYS C 110 " - pdb=" SG CYS C 142 " distance=2.04 Simple disulfide: pdb=" SG CYS D 110 " - pdb=" SG CYS D 142 " distance=2.04 Simple disulfide: pdb=" SG CYS E 110 " - pdb=" SG CYS E 142 " distance=2.04 Simple disulfide: pdb=" SG CYS F 110 " - pdb=" SG CYS F 142 " distance=2.04 Simple disulfide: pdb=" SG CYS G 110 " - pdb=" SG CYS G 142 " distance=2.04 Simple disulfide: pdb=" SG CYS H 110 " - pdb=" SG CYS H 142 " distance=2.04 Simple disulfide: pdb=" SG CYS I 110 " - pdb=" SG CYS I 142 " distance=2.04 Simple disulfide: pdb=" SG CYS J 110 " - pdb=" SG CYS J 142 " distance=2.04 Simple disulfide: pdb=" SG CYS K 110 " - pdb=" SG CYS K 142 " distance=2.04 Simple disulfide: pdb=" SG CYS L 110 " - pdb=" SG CYS L 142 " distance=2.04 Simple disulfide: pdb=" SG CYS M 110 " - pdb=" SG CYS M 142 " distance=2.04 Simple disulfide: pdb=" SG CYS N 110 " - pdb=" SG CYS N 142 " distance=2.04 Simple disulfide: pdb=" SG CYS P 110 " - pdb=" SG CYS P 142 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.91 Conformation dependent library (CDL) restraints added in 1.4 seconds Enol-peptide restraints added in 953.7 nanoseconds 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5024 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 32 sheets defined 1.8% alpha, 55.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.24 Creating SS restraints... Processing helix chain 'O' and resid 77 through 79 No H-bonds generated for 'chain 'O' and resid 77 through 79' Processing helix chain 'A' and resid 77 through 79 No H-bonds generated for 'chain 'A' and resid 77 through 79' Processing helix chain 'B' and resid 77 through 79 No H-bonds generated for 'chain 'B' and resid 77 through 79' Processing helix chain 'C' and resid 77 through 79 No H-bonds generated for 'chain 'C' and resid 77 through 79' Processing helix chain 'D' and resid 77 through 79 No H-bonds generated for 'chain 'D' and resid 77 through 79' Processing helix chain 'E' and resid 77 through 79 No H-bonds generated for 'chain 'E' and resid 77 through 79' Processing helix chain 'F' and resid 77 through 79 No H-bonds generated for 'chain 'F' and resid 77 through 79' Processing helix chain 'G' and resid 77 through 79 No H-bonds generated for 'chain 'G' and resid 77 through 79' Processing helix chain 'H' and resid 77 through 79 No H-bonds generated for 'chain 'H' and resid 77 through 79' Processing helix chain 'I' and resid 77 through 79 No H-bonds generated for 'chain 'I' and resid 77 through 79' Processing helix chain 'J' and resid 77 through 79 No H-bonds generated for 'chain 'J' and resid 77 through 79' Processing helix chain 'K' and resid 77 through 79 No H-bonds generated for 'chain 'K' and resid 77 through 79' Processing helix chain 'L' and resid 77 through 79 No H-bonds generated for 'chain 'L' and resid 77 through 79' Processing helix chain 'M' and resid 77 through 79 No H-bonds generated for 'chain 'M' and resid 77 through 79' Processing helix chain 'N' and resid 77 through 79 No H-bonds generated for 'chain 'N' and resid 77 through 79' Processing helix chain 'P' and resid 77 through 79 No H-bonds generated for 'chain 'P' and resid 77 through 79' Processing sheet with id=1, first strand: chain 'O' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN O 124 " --> pdb=" O ARG O 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG O 200 " --> pdb=" O GLN O 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP O 126 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE O 198 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS O 128 " --> pdb=" O SER O 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER O 196 " --> pdb=" O LYS O 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE O 130 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE O 194 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL O 132 " --> pdb=" O PRO O 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER O 134 " --> pdb=" O LEU O 190 " (cutoff:3.500A) Processing sheet with id=2, first strand: chain 'O' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN O 124 " --> pdb=" O ARG O 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG O 200 " --> pdb=" O GLN O 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP O 126 " --> pdb=" O PHE O 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE O 198 " --> pdb=" O ASP O 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS O 128 " --> pdb=" O SER O 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER O 196 " --> pdb=" O LYS O 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE O 130 " --> pdb=" O ILE O 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE O 194 " --> pdb=" O ILE O 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL O 132 " --> pdb=" O PRO O 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER O 134 " --> pdb=" O LEU O 190 " (cutoff:3.500A) Processing sheet with id=3, first strand: chain 'A' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN A 124 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG A 200 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP A 126 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 198 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A 128 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER A 196 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE A 130 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE A 194 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL A 132 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 134 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=4, first strand: chain 'A' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN A 124 " --> pdb=" O ARG A 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG A 200 " --> pdb=" O GLN A 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP A 126 " --> pdb=" O PHE A 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE A 198 " --> pdb=" O ASP A 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS A 128 " --> pdb=" O SER A 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER A 196 " --> pdb=" O LYS A 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE A 130 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE A 194 " --> pdb=" O ILE A 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL A 132 " --> pdb=" O PRO A 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER A 134 " --> pdb=" O LEU A 190 " (cutoff:3.500A) Processing sheet with id=5, first strand: chain 'B' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN B 124 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG B 200 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP B 126 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 198 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS B 128 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER B 196 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE B 130 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE B 194 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL B 132 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER B 134 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=6, first strand: chain 'B' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN B 124 " --> pdb=" O ARG B 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG B 200 " --> pdb=" O GLN B 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP B 126 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE B 198 " --> pdb=" O ASP B 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS B 128 " --> pdb=" O SER B 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER B 196 " --> pdb=" O LYS B 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE B 130 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE B 194 " --> pdb=" O ILE B 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL B 132 " --> pdb=" O PRO B 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER B 134 " --> pdb=" O LEU B 190 " (cutoff:3.500A) Processing sheet with id=7, first strand: chain 'C' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN C 124 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG C 200 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 126 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE C 198 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C 128 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER C 196 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE C 130 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE C 194 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL C 132 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER C 134 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=8, first strand: chain 'C' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN C 124 " --> pdb=" O ARG C 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG C 200 " --> pdb=" O GLN C 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP C 126 " --> pdb=" O PHE C 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE C 198 " --> pdb=" O ASP C 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS C 128 " --> pdb=" O SER C 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER C 196 " --> pdb=" O LYS C 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE C 130 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE C 194 " --> pdb=" O ILE C 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL C 132 " --> pdb=" O PRO C 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER C 134 " --> pdb=" O LEU C 190 " (cutoff:3.500A) Processing sheet with id=9, first strand: chain 'D' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN D 124 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG D 200 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 126 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE D 198 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D 128 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER D 196 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE D 130 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE D 194 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL D 132 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER D 134 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=10, first strand: chain 'D' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN D 124 " --> pdb=" O ARG D 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG D 200 " --> pdb=" O GLN D 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP D 126 " --> pdb=" O PHE D 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE D 198 " --> pdb=" O ASP D 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS D 128 " --> pdb=" O SER D 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER D 196 " --> pdb=" O LYS D 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE D 130 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE D 194 " --> pdb=" O ILE D 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL D 132 " --> pdb=" O PRO D 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER D 134 " --> pdb=" O LEU D 190 " (cutoff:3.500A) Processing sheet with id=11, first strand: chain 'E' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN E 124 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG E 200 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP E 126 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE E 198 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS E 128 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER E 196 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE E 130 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE E 194 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL E 132 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER E 134 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=12, first strand: chain 'E' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN E 124 " --> pdb=" O ARG E 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG E 200 " --> pdb=" O GLN E 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP E 126 " --> pdb=" O PHE E 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE E 198 " --> pdb=" O ASP E 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS E 128 " --> pdb=" O SER E 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER E 196 " --> pdb=" O LYS E 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE E 130 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE E 194 " --> pdb=" O ILE E 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL E 132 " --> pdb=" O PRO E 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER E 134 " --> pdb=" O LEU E 190 " (cutoff:3.500A) Processing sheet with id=13, first strand: chain 'F' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN F 124 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG F 200 " --> pdb=" O GLN F 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 126 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE F 198 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS F 128 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER F 196 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F 130 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE F 194 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL F 132 " --> pdb=" O PRO F 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER F 134 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=14, first strand: chain 'F' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN F 124 " --> pdb=" O ARG F 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG F 200 " --> pdb=" O GLN F 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP F 126 " --> pdb=" O PHE F 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE F 198 " --> pdb=" O ASP F 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS F 128 " --> pdb=" O SER F 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER F 196 " --> pdb=" O LYS F 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F 130 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE F 194 " --> pdb=" O ILE F 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL F 132 " --> pdb=" O PRO F 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER F 134 " --> pdb=" O LEU F 190 " (cutoff:3.500A) Processing sheet with id=15, first strand: chain 'G' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN G 124 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG G 200 " --> pdb=" O GLN G 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP G 126 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE G 198 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 128 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER G 196 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE G 130 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE G 194 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL G 132 " --> pdb=" O PRO G 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER G 134 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id=16, first strand: chain 'G' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN G 124 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG G 200 " --> pdb=" O GLN G 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP G 126 " --> pdb=" O PHE G 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE G 198 " --> pdb=" O ASP G 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS G 128 " --> pdb=" O SER G 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER G 196 " --> pdb=" O LYS G 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE G 130 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE G 194 " --> pdb=" O ILE G 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL G 132 " --> pdb=" O PRO G 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER G 134 " --> pdb=" O LEU G 190 " (cutoff:3.500A) Processing sheet with id=17, first strand: chain 'H' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN H 124 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG H 200 " --> pdb=" O GLN H 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP H 126 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE H 198 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS H 128 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER H 196 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE H 130 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE H 194 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL H 132 " --> pdb=" O PRO H 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER H 134 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id=18, first strand: chain 'H' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN H 124 " --> pdb=" O ARG H 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG H 200 " --> pdb=" O GLN H 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP H 126 " --> pdb=" O PHE H 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE H 198 " --> pdb=" O ASP H 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS H 128 " --> pdb=" O SER H 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER H 196 " --> pdb=" O LYS H 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE H 130 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE H 194 " --> pdb=" O ILE H 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL H 132 " --> pdb=" O PRO H 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER H 134 " --> pdb=" O LEU H 190 " (cutoff:3.500A) Processing sheet with id=19, first strand: chain 'I' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN I 124 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG I 200 " --> pdb=" O GLN I 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP I 126 " --> pdb=" O PHE I 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE I 198 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS I 128 " --> pdb=" O SER I 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER I 196 " --> pdb=" O LYS I 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE I 130 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE I 194 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL I 132 " --> pdb=" O PRO I 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER I 134 " --> pdb=" O LEU I 190 " (cutoff:3.500A) Processing sheet with id=20, first strand: chain 'I' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN I 124 " --> pdb=" O ARG I 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG I 200 " --> pdb=" O GLN I 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP I 126 " --> pdb=" O PHE I 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE I 198 " --> pdb=" O ASP I 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS I 128 " --> pdb=" O SER I 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER I 196 " --> pdb=" O LYS I 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE I 130 " --> pdb=" O ILE I 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE I 194 " --> pdb=" O ILE I 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL I 132 " --> pdb=" O PRO I 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER I 134 " --> pdb=" O LEU I 190 " (cutoff:3.500A) Processing sheet with id=21, first strand: chain 'J' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN J 124 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG J 200 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP J 126 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE J 198 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS J 128 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER J 196 " --> pdb=" O LYS J 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE J 130 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE J 194 " --> pdb=" O ILE J 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL J 132 " --> pdb=" O PRO J 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER J 134 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing sheet with id=22, first strand: chain 'J' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN J 124 " --> pdb=" O ARG J 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG J 200 " --> pdb=" O GLN J 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP J 126 " --> pdb=" O PHE J 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE J 198 " --> pdb=" O ASP J 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS J 128 " --> pdb=" O SER J 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER J 196 " --> pdb=" O LYS J 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE J 130 " --> pdb=" O ILE J 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE J 194 " --> pdb=" O ILE J 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL J 132 " --> pdb=" O PRO J 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER J 134 " --> pdb=" O LEU J 190 " (cutoff:3.500A) Processing sheet with id=23, first strand: chain 'K' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN K 124 " --> pdb=" O ARG K 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG K 200 " --> pdb=" O GLN K 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP K 126 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE K 198 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS K 128 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER K 196 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE K 130 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE K 194 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL K 132 " --> pdb=" O PRO K 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER K 134 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing sheet with id=24, first strand: chain 'K' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN K 124 " --> pdb=" O ARG K 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG K 200 " --> pdb=" O GLN K 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP K 126 " --> pdb=" O PHE K 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE K 198 " --> pdb=" O ASP K 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS K 128 " --> pdb=" O SER K 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER K 196 " --> pdb=" O LYS K 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE K 130 " --> pdb=" O ILE K 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE K 194 " --> pdb=" O ILE K 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL K 132 " --> pdb=" O PRO K 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER K 134 " --> pdb=" O LEU K 190 " (cutoff:3.500A) Processing sheet with id=25, first strand: chain 'L' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN L 124 " --> pdb=" O ARG L 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG L 200 " --> pdb=" O GLN L 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP L 126 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE L 198 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS L 128 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER L 196 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE L 130 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE L 194 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL L 132 " --> pdb=" O PRO L 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER L 134 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing sheet with id=26, first strand: chain 'L' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN L 124 " --> pdb=" O ARG L 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG L 200 " --> pdb=" O GLN L 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP L 126 " --> pdb=" O PHE L 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE L 198 " --> pdb=" O ASP L 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS L 128 " --> pdb=" O SER L 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER L 196 " --> pdb=" O LYS L 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE L 130 " --> pdb=" O ILE L 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE L 194 " --> pdb=" O ILE L 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL L 132 " --> pdb=" O PRO L 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER L 134 " --> pdb=" O LEU L 190 " (cutoff:3.500A) Processing sheet with id=27, first strand: chain 'M' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN M 124 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG M 200 " --> pdb=" O GLN M 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP M 126 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE M 198 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS M 128 " --> pdb=" O SER M 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER M 196 " --> pdb=" O LYS M 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE M 130 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE M 194 " --> pdb=" O ILE M 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL M 132 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER M 134 " --> pdb=" O LEU M 190 " (cutoff:3.500A) Processing sheet with id=28, first strand: chain 'M' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN M 124 " --> pdb=" O ARG M 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG M 200 " --> pdb=" O GLN M 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP M 126 " --> pdb=" O PHE M 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE M 198 " --> pdb=" O ASP M 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS M 128 " --> pdb=" O SER M 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER M 196 " --> pdb=" O LYS M 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE M 130 " --> pdb=" O ILE M 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE M 194 " --> pdb=" O ILE M 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL M 132 " --> pdb=" O PRO M 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER M 134 " --> pdb=" O LEU M 190 " (cutoff:3.500A) Processing sheet with id=29, first strand: chain 'N' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN N 124 " --> pdb=" O ARG N 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG N 200 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP N 126 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE N 198 " --> pdb=" O ASP N 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS N 128 " --> pdb=" O SER N 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER N 196 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE N 130 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE N 194 " --> pdb=" O ILE N 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL N 132 " --> pdb=" O PRO N 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER N 134 " --> pdb=" O LEU N 190 " (cutoff:3.500A) Processing sheet with id=30, first strand: chain 'N' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN N 124 " --> pdb=" O ARG N 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG N 200 " --> pdb=" O GLN N 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP N 126 " --> pdb=" O PHE N 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE N 198 " --> pdb=" O ASP N 126 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N LYS N 128 " --> pdb=" O SER N 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER N 196 " --> pdb=" O LYS N 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE N 130 " --> pdb=" O ILE N 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE N 194 " --> pdb=" O ILE N 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL N 132 " --> pdb=" O PRO N 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER N 134 " --> pdb=" O LEU N 190 " (cutoff:3.500A) Processing sheet with id=31, first strand: chain 'P' and resid 67 through 68 removed outlier: 6.933A pdb=" N GLN P 124 " --> pdb=" O ARG P 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG P 200 " --> pdb=" O GLN P 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP P 126 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE P 198 " --> pdb=" O ASP P 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS P 128 " --> pdb=" O SER P 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER P 196 " --> pdb=" O LYS P 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE P 130 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE P 194 " --> pdb=" O ILE P 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL P 132 " --> pdb=" O PRO P 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER P 134 " --> pdb=" O LEU P 190 " (cutoff:3.500A) Processing sheet with id=32, first strand: chain 'P' and resid 81 through 83 removed outlier: 6.933A pdb=" N GLN P 124 " --> pdb=" O ARG P 200 " (cutoff:3.500A) removed outlier: 6.816A pdb=" N ARG P 200 " --> pdb=" O GLN P 124 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ASP P 126 " --> pdb=" O PHE P 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N PHE P 198 " --> pdb=" O ASP P 126 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N LYS P 128 " --> pdb=" O SER P 196 " (cutoff:3.500A) removed outlier: 10.734A pdb=" N SER P 196 " --> pdb=" O LYS P 128 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE P 130 " --> pdb=" O ILE P 194 " (cutoff:3.500A) removed outlier: 9.991A pdb=" N ILE P 194 " --> pdb=" O ILE P 130 " (cutoff:3.500A) removed outlier: 9.405A pdb=" N VAL P 132 " --> pdb=" O PRO P 192 " (cutoff:3.500A) removed outlier: 5.442A pdb=" N SER P 134 " --> pdb=" O LEU P 190 " (cutoff:3.500A) 640 hydrogen bonds defined for protein. 1632 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: 11.68 Time building geometry restraints manager: 5.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.96 - 1.13: 20952 1.13 - 1.30: 3816 1.30 - 1.47: 9288 1.47 - 1.64: 9432 1.64 - 1.81: 176 Bond restraints: 43664 Sorted by residual: bond pdb=" CE2 PHE P 198 " pdb=" HE2 PHE P 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE K 198 " pdb=" HE2 PHE K 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE E 198 " pdb=" HE2 PHE E 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE I 198 " pdb=" HE2 PHE I 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 bond pdb=" CE2 PHE A 198 " pdb=" HE2 PHE A 198 " ideal model delta sigma weight residual 0.930 1.144 -0.214 2.00e-02 2.50e+03 1.15e+02 ... (remaining 43659 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 65848 3.70 - 7.40: 10136 7.40 - 11.10: 2144 11.10 - 14.81: 432 14.81 - 18.51: 48 Bond angle restraints: 78608 Sorted by residual: angle pdb=" C ILE A 60 " pdb=" CA ILE A 60 " pdb=" CB ILE A 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE P 60 " pdb=" CA ILE P 60 " pdb=" CB ILE P 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE M 60 " pdb=" CA ILE M 60 " pdb=" CB ILE M 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE G 60 " pdb=" CA ILE G 60 " pdb=" CB ILE G 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 angle pdb=" C ILE E 60 " pdb=" CA ILE E 60 " pdb=" CB ILE E 60 " ideal model delta sigma weight residual 110.88 120.63 -9.75 9.80e-01 1.04e+00 9.90e+01 ... (remaining 78603 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.13: 19680 24.13 - 48.26: 784 48.26 - 72.39: 96 72.39 - 96.52: 48 96.52 - 120.65: 48 Dihedral angle restraints: 20656 sinusoidal: 11168 harmonic: 9488 Sorted by residual: dihedral pdb=" CA SER A 95 " pdb=" C SER A 95 " pdb=" N TRP A 96 " pdb=" CA TRP A 96 " ideal model delta harmonic sigma weight residual 180.00 59.35 120.65 0 5.00e+00 4.00e-02 5.82e+02 dihedral pdb=" CA SER M 95 " pdb=" C SER M 95 " pdb=" N TRP M 96 " pdb=" CA TRP M 96 " ideal model delta harmonic sigma weight residual 180.00 59.35 120.65 0 5.00e+00 4.00e-02 5.82e+02 dihedral pdb=" CA SER K 95 " pdb=" C SER K 95 " pdb=" N TRP K 96 " pdb=" CA TRP K 96 " ideal model delta harmonic sigma weight residual 180.00 59.35 120.65 0 5.00e+00 4.00e-02 5.82e+02 ... (remaining 20653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.109: 2216 0.109 - 0.218: 824 0.218 - 0.327: 128 0.327 - 0.436: 16 0.436 - 0.545: 32 Chirality restraints: 3216 Sorted by residual: chirality pdb=" CA ALA A 111 " pdb=" N ALA A 111 " pdb=" C ALA A 111 " pdb=" CB ALA A 111 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA ALA E 111 " pdb=" N ALA E 111 " pdb=" C ALA E 111 " pdb=" CB ALA E 111 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.42e+00 chirality pdb=" CA ALA P 111 " pdb=" N ALA P 111 " pdb=" C ALA P 111 " pdb=" CB ALA P 111 " both_signs ideal model delta sigma weight residual False 2.48 1.94 0.54 2.00e-01 2.50e+01 7.42e+00 ... (remaining 3213 not shown) Planarity restraints: 6416 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 112 " -0.038 2.00e-02 2.50e+03 1.01e-01 4.10e+02 pdb=" CG TRP A 112 " -0.162 2.00e-02 2.50e+03 pdb=" CD1 TRP A 112 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP A 112 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP A 112 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP A 112 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP A 112 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 112 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 112 " 0.117 2.00e-02 2.50e+03 pdb=" CH2 TRP A 112 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP A 112 " 0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP A 112 " 0.147 2.00e-02 2.50e+03 pdb=" HZ2 TRP A 112 " 0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP A 112 " 0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP A 112 " -0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 112 " 0.038 2.00e-02 2.50e+03 1.01e-01 4.10e+02 pdb=" CG TRP P 112 " 0.162 2.00e-02 2.50e+03 pdb=" CD1 TRP P 112 " 0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP P 112 " 0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP P 112 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP P 112 " 0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP P 112 " -0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 112 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 112 " -0.117 2.00e-02 2.50e+03 pdb=" CH2 TRP P 112 " -0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP P 112 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP P 112 " -0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP P 112 " -0.147 2.00e-02 2.50e+03 pdb=" HZ2 TRP P 112 " -0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP P 112 " -0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP P 112 " 0.239 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 112 " -0.038 2.00e-02 2.50e+03 1.01e-01 4.10e+02 pdb=" CG TRP C 112 " -0.162 2.00e-02 2.50e+03 pdb=" CD1 TRP C 112 " -0.077 2.00e-02 2.50e+03 pdb=" CD2 TRP C 112 " -0.033 2.00e-02 2.50e+03 pdb=" NE1 TRP C 112 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 112 " -0.013 2.00e-02 2.50e+03 pdb=" CE3 TRP C 112 " 0.037 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 112 " -0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 112 " 0.117 2.00e-02 2.50e+03 pdb=" CH2 TRP C 112 " 0.005 2.00e-02 2.50e+03 pdb=" HD1 TRP C 112 " 0.001 2.00e-02 2.50e+03 pdb=" HE1 TRP C 112 " 0.176 2.00e-02 2.50e+03 pdb=" HE3 TRP C 112 " 0.147 2.00e-02 2.50e+03 pdb=" HZ2 TRP C 112 " 0.059 2.00e-02 2.50e+03 pdb=" HZ3 TRP C 112 " 0.020 2.00e-02 2.50e+03 pdb=" HH2 TRP C 112 " -0.239 2.00e-02 2.50e+03 ... (remaining 6413 not shown) Histogram of nonbonded interaction distances: 0.54 - 1.35: 24 1.35 - 2.16: 4968 2.16 - 2.98: 110488 2.98 - 3.79: 184896 3.79 - 4.60: 307560 Warning: very small nonbonded interaction distances. Nonbonded interactions: 607936 Sorted by model distance: nonbonded pdb=" HE3 TRP O 147 " pdb=" HE3 TRP H 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP B 147 " pdb=" HE3 TRP N 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP D 147 " pdb=" HE3 TRP L 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP F 147 " pdb=" HE3 TRP J 147 " model vdw 0.540 2.100 nonbonded pdb=" HE3 TRP E 147 " pdb=" HE3 TRP K 147 " model vdw 0.540 2.100 ... (remaining 607931 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: 0.10 Found NCS groups: ncs_group { reference = chain 'O' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'P' } 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.210 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: 0.260 Extract box with map and model: 0.630 Check model and map are aligned: 0.130 Set scattering table: 0.120 Process input model: 38.890 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.110 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4494 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 0.112 22480 Z= 1.941 Angle : 2.695 14.259 30544 Z= 1.910 Chirality : 0.119 0.545 3216 Planarity : 0.017 0.109 3888 Dihedral : 14.706 120.648 8288 Min Nonbonded Distance : 1.693 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.61 % Allowed : 13.33 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 1.27 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.14 (0.13), residues: 2640 helix: None (None), residues: 0 sheet: -0.77 (0.16), residues: 656 loop : -2.80 (0.11), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 156 TYR 0.001 0.000 TYR G 89 PHE 0.061 0.007 PHE A 198 TRP 0.105 0.008 TRP P 112 HIS 0.001 0.000 HIS H 66 Details of bonding type rmsd covalent geometry : bond 0.02643 (22448) covalent geometry : angle 2.69661 (30480) SS BOND : bond 0.00608 ( 32) SS BOND : angle 1.55866 ( 64) hydrogen bonds : bond 0.18675 ( 432) hydrogen bonds : angle 11.32281 ( 1632) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1040 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 1040 time to evaluate : 1.286 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: 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revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 1040 average time/residue: 0.4104 time to fit residues: 633.0912 Evaluate side-chains 616 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 616 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 8.9990 chunk 155 optimal weight: 10.0000 chunk 244 optimal weight: 7.9990 chunk 183 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 71 optimal weight: 7.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 162 ASN O 172 ASN O 187 GLN A 162 ASN A 187 GLN B 162 ASN B 187 GLN C 162 ASN C 187 GLN D 162 ASN D 187 GLN E 162 ASN E 187 GLN F 162 ASN F 187 GLN G 162 ASN G 187 GLN H 162 ASN H 172 ASN H 187 GLN I 162 ASN I 187 GLN J 162 ASN J 187 GLN K 162 ASN K 187 GLN L 162 ASN L 187 GLN M 162 ASN M 187 GLN N 162 ASN N 187 GLN P 162 ASN P 187 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.078184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.062440 restraints weight = 284876.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3769 r_free = 0.3769 target = 0.066006 restraints weight = 162057.123| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.068807 restraints weight = 103879.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.070751 restraints weight = 70377.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.072194 restraints weight = 49826.920| |-----------------------------------------------------------------------------| r_work (final): 0.3872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.5046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 22480 Z= 0.236 Angle : 0.841 8.207 30544 Z= 0.467 Chirality : 0.048 0.162 3216 Planarity : 0.006 0.060 3888 Dihedral : 10.040 67.469 2960 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer: Outliers : 0.66 % Allowed : 3.95 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.78 (0.14), residues: 2640 helix: -4.64 (0.21), residues: 96 sheet: 0.22 (0.20), residues: 576 loop : -2.58 (0.11), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 213 TYR 0.011 0.001 TYR C 155 PHE 0.031 0.004 PHE L 198 TRP 0.008 0.002 TRP D 147 HIS 0.003 0.002 HIS O 66 Details of bonding type rmsd covalent geometry : bond 0.00469 (22448) covalent geometry : angle 0.84110 (30480) SS BOND : bond 0.00600 ( 32) SS BOND : angle 0.79458 ( 64) hydrogen bonds : bond 0.05075 ( 432) hydrogen bonds : angle 8.26420 ( 1632) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 752 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 736 time to evaluate : 1.255 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry 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clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 145 ASP cc_start: 0.8826 (t0) cc_final: 0.8585 (t0) REVERT: A 164 ILE cc_start: 0.9697 (pt) cc_final: 0.9075 (mm) REVERT: C 145 ASP cc_start: 0.8807 (t0) cc_final: 0.8561 (t0) REVERT: C 164 ILE cc_start: 0.9691 (pt) cc_final: 0.9060 (mm) REVERT: E 145 ASP cc_start: 0.8806 (t0) cc_final: 0.8561 (t0) REVERT: E 164 ILE cc_start: 0.9693 (pt) cc_final: 0.9064 (mm) REVERT: G 145 ASP cc_start: 0.8812 (t0) cc_final: 0.8570 (t0) REVERT: G 164 ILE cc_start: 0.9695 (pt) cc_final: 0.9069 (mm) REVERT: I 145 ASP cc_start: 0.8834 (t0) cc_final: 0.8594 (t0) REVERT: I 164 ILE cc_start: 0.9690 (pt) cc_final: 0.9060 (mm) REVERT: K 145 ASP cc_start: 0.8834 (t0) cc_final: 0.8595 (t0) REVERT: K 164 ILE cc_start: 0.9684 (pt) cc_final: 0.9047 (mm) REVERT: M 145 ASP cc_start: 0.8839 (t0) cc_final: 0.8600 (t0) REVERT: M 164 ILE cc_start: 0.9689 (pt) cc_final: 0.9056 (mm) REVERT: P 145 ASP cc_start: 0.8853 (t0) cc_final: 0.8618 (t0) REVERT: P 164 ILE cc_start: 0.9690 (pt) cc_final: 0.9057 (mm) outliers start: 16 outliers final: 8 residues processed: 752 average time/residue: 0.3834 time to fit residues: 428.7536 Evaluate side-chains 582 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 574 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 172 optimal weight: 9.9990 chunk 114 optimal weight: 30.0000 chunk 31 optimal weight: 20.0000 chunk 96 optimal weight: 5.9990 chunk 176 optimal weight: 2.9990 chunk 69 optimal weight: 20.0000 chunk 228 optimal weight: 20.0000 chunk 183 optimal weight: 20.0000 chunk 92 optimal weight: 6.9990 chunk 78 optimal weight: 30.0000 chunk 138 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 172 ASN A 172 ASN B 172 ASN C 172 ASN D 172 ASN E 172 ASN F 172 ASN G 172 ASN H 172 ASN I 172 ASN J 172 ASN K 172 ASN L 172 ASN M 172 ASN N 172 ASN P 172 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3935 r_free = 0.3935 target = 0.075692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.061692 restraints weight = 305604.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.064924 restraints weight = 175981.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.067205 restraints weight = 112176.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.069112 restraints weight = 76014.627| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.070466 restraints weight = 52313.028| |-----------------------------------------------------------------------------| r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7512 moved from start: 0.6469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 22480 Z= 0.186 Angle : 0.748 5.484 30544 Z= 0.416 Chirality : 0.047 0.162 3216 Planarity : 0.005 0.030 3888 Dihedral : 8.485 55.339 2960 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.30 % Favored : 89.70 % Rotamer: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.90 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.07 (0.14), residues: 2640 helix: -3.10 (0.51), residues: 96 sheet: 0.32 (0.22), residues: 576 loop : -1.98 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 160 TYR 0.011 0.001 TYR D 155 PHE 0.015 0.002 PHE D 108 TRP 0.014 0.002 TRP D 96 HIS 0.003 0.002 HIS F 207 Details of bonding type rmsd covalent geometry : bond 0.00377 (22448) covalent geometry : angle 0.74668 (30480) SS BOND : bond 0.00778 ( 32) SS BOND : angle 1.10123 ( 64) hydrogen bonds : bond 0.03917 ( 432) hydrogen bonds : angle 7.29453 ( 1632) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 590 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 103 LEU cc_start: 0.9171 (tp) cc_final: 0.8877 (tp) REVERT: O 125 ILE cc_start: 0.9722 (mm) cc_final: 0.9497 (tp) REVERT: O 214 MET cc_start: 0.9165 (ppp) cc_final: 0.8924 (ppp) REVERT: O 215 GLU cc_start: 0.9187 (tt0) cc_final: 0.8902 (tt0) REVERT: A 214 MET cc_start: 0.9205 (ppp) cc_final: 0.8871 (ppp) REVERT: B 103 LEU cc_start: 0.9166 (tp) cc_final: 0.8876 (tp) REVERT: B 125 ILE cc_start: 0.9723 (mm) cc_final: 0.9497 (tp) REVERT: B 214 MET cc_start: 0.9173 (ppp) cc_final: 0.8928 (ppp) REVERT: B 215 GLU cc_start: 0.9188 (tt0) cc_final: 0.8905 (tt0) REVERT: C 214 MET cc_start: 0.9207 (ppp) cc_final: 0.8873 (ppp) REVERT: D 103 LEU cc_start: 0.9165 (tp) cc_final: 0.8872 (tp) REVERT: D 125 ILE cc_start: 0.9725 (mm) cc_final: 0.9498 (tp) REVERT: D 214 MET cc_start: 0.9181 (ppp) cc_final: 0.8932 (ppp) REVERT: D 215 GLU cc_start: 0.9194 (tt0) cc_final: 0.8909 (tt0) REVERT: E 214 MET cc_start: 0.9198 (ppp) cc_final: 0.8867 (ppp) REVERT: F 103 LEU cc_start: 0.9173 (tp) cc_final: 0.8884 (tp) REVERT: F 125 ILE cc_start: 0.9717 (mm) cc_final: 0.9490 (tp) REVERT: F 214 MET cc_start: 0.9169 (ppp) cc_final: 0.8922 (ppp) REVERT: F 215 GLU cc_start: 0.9189 (tt0) cc_final: 0.8904 (tt0) REVERT: G 214 MET cc_start: 0.9217 (ppp) cc_final: 0.8876 (ppp) REVERT: H 103 LEU cc_start: 0.9172 (tp) cc_final: 0.8881 (tp) REVERT: H 125 ILE cc_start: 0.9723 (mm) cc_final: 0.9495 (tp) REVERT: H 214 MET cc_start: 0.9166 (ppp) cc_final: 0.8922 (ppp) REVERT: H 215 GLU cc_start: 0.9192 (tt0) cc_final: 0.8906 (tt0) REVERT: I 214 MET cc_start: 0.9214 (ppp) cc_final: 0.8876 (ppp) REVERT: J 103 LEU cc_start: 0.9173 (tp) cc_final: 0.8882 (tp) REVERT: J 125 ILE cc_start: 0.9719 (mm) cc_final: 0.9491 (tp) REVERT: J 214 MET cc_start: 0.9164 (ppp) cc_final: 0.8920 (ppp) REVERT: J 215 GLU cc_start: 0.9189 (tt0) cc_final: 0.8905 (tt0) REVERT: K 214 MET cc_start: 0.9210 (ppp) cc_final: 0.8875 (ppp) REVERT: L 103 LEU cc_start: 0.9172 (tp) cc_final: 0.8879 (tp) REVERT: L 125 ILE cc_start: 0.9718 (mm) cc_final: 0.9492 (tp) REVERT: L 214 MET cc_start: 0.9162 (ppp) cc_final: 0.8915 (ppp) REVERT: L 215 GLU cc_start: 0.9187 (tt0) cc_final: 0.8903 (tt0) REVERT: M 214 MET cc_start: 0.9206 (ppp) cc_final: 0.8871 (ppp) REVERT: N 103 LEU cc_start: 0.9177 (tp) cc_final: 0.8886 (tp) REVERT: N 125 ILE cc_start: 0.9710 (mm) cc_final: 0.9484 (tp) REVERT: N 214 MET cc_start: 0.9155 (ppp) cc_final: 0.8908 (ppp) REVERT: N 215 GLU cc_start: 0.9176 (tt0) cc_final: 0.8893 (tt0) REVERT: P 214 MET cc_start: 0.9231 (ppp) cc_final: 0.8883 (ppp) outliers start: 0 outliers final: 0 residues processed: 590 average time/residue: 0.4189 time to fit residues: 365.6199 Evaluate side-chains 452 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 452 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 151 optimal weight: 10.0000 chunk 175 optimal weight: 20.0000 chunk 187 optimal weight: 7.9990 chunk 231 optimal weight: 20.0000 chunk 123 optimal weight: 10.0000 chunk 248 optimal weight: 30.0000 chunk 125 optimal weight: 20.0000 chunk 74 optimal weight: 10.0000 chunk 189 optimal weight: 9.9990 chunk 236 optimal weight: 8.9990 chunk 164 optimal weight: 9.9990 overall best weight: 9.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 172 ASN A 172 ASN B 172 ASN C 172 ASN D 172 ASN E 172 ASN F 172 ASN G 172 ASN H 172 ASN I 172 ASN J 172 ASN K 172 ASN L 172 ASN M 172 ASN N 172 ASN P 172 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.070048 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.057181 restraints weight = 325366.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.060111 restraints weight = 185374.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.062289 restraints weight = 118183.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.063834 restraints weight = 80090.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.065211 restraints weight = 56837.572| |-----------------------------------------------------------------------------| r_work (final): 0.3697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.7643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 22480 Z= 0.222 Angle : 0.696 4.737 30544 Z= 0.386 Chirality : 0.044 0.145 3216 Planarity : 0.005 0.030 3888 Dihedral : 7.389 43.539 2960 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.91 % Favored : 89.09 % Rotamer: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.98 (0.14), residues: 2640 helix: -3.45 (0.43), residues: 96 sheet: 1.16 (0.22), residues: 528 loop : -2.10 (0.12), residues: 2016 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG O 213 TYR 0.010 0.001 TYR O 155 PHE 0.011 0.002 PHE I 176 TRP 0.016 0.001 TRP N 122 HIS 0.004 0.002 HIS B 66 Details of bonding type rmsd covalent geometry : bond 0.00472 (22448) covalent geometry : angle 0.69591 (30480) SS BOND : bond 0.00830 ( 32) SS BOND : angle 0.88348 ( 64) hydrogen bonds : bond 0.03642 ( 432) hydrogen bonds : angle 6.98362 ( 1632) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 560 time to evaluate : 1.288 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 214 MET cc_start: 0.9233 (ppp) cc_final: 0.8841 (ppp) REVERT: A 136 ILE cc_start: 0.9671 (tp) cc_final: 0.9430 (tp) REVERT: A 151 TYR cc_start: 0.8203 (m-80) cc_final: 0.7798 (m-10) REVERT: A 214 MET cc_start: 0.9297 (ppp) cc_final: 0.8953 (ppp) REVERT: B 214 MET cc_start: 0.9227 (ppp) cc_final: 0.8833 (ppp) REVERT: C 136 ILE cc_start: 0.9677 (tp) cc_final: 0.9434 (tp) REVERT: C 151 TYR cc_start: 0.8239 (m-80) cc_final: 0.7826 (m-10) REVERT: C 214 MET cc_start: 0.9312 (ppp) cc_final: 0.8966 (ppp) REVERT: D 214 MET cc_start: 0.9224 (ppp) cc_final: 0.8829 (ppp) REVERT: E 136 ILE cc_start: 0.9671 (tp) cc_final: 0.9431 (tp) REVERT: E 151 TYR cc_start: 0.8209 (m-80) cc_final: 0.7801 (m-10) REVERT: E 214 MET cc_start: 0.9305 (ppp) cc_final: 0.8959 (ppp) REVERT: F 214 MET cc_start: 0.9222 (ppp) cc_final: 0.8828 (ppp) REVERT: G 136 ILE cc_start: 0.9671 (tp) cc_final: 0.9428 (tp) REVERT: G 151 TYR cc_start: 0.8198 (m-80) cc_final: 0.7793 (m-10) REVERT: G 214 MET cc_start: 0.9299 (ppp) cc_final: 0.8952 (ppp) REVERT: H 214 MET cc_start: 0.9243 (ppp) cc_final: 0.8846 (ppp) REVERT: I 136 ILE cc_start: 0.9673 (tp) cc_final: 0.9432 (tp) REVERT: I 151 TYR cc_start: 0.8231 (m-80) cc_final: 0.7825 (m-10) REVERT: I 214 MET cc_start: 0.9310 (ppp) cc_final: 0.8964 (ppp) REVERT: J 214 MET cc_start: 0.9244 (ppp) cc_final: 0.8849 (ppp) REVERT: K 136 ILE cc_start: 0.9678 (tp) cc_final: 0.9436 (tp) REVERT: K 151 TYR cc_start: 0.8232 (m-80) cc_final: 0.7820 (m-10) REVERT: K 214 MET cc_start: 0.9321 (ppp) cc_final: 0.8970 (ppp) REVERT: L 214 MET cc_start: 0.9239 (ppp) cc_final: 0.8840 (ppp) REVERT: M 136 ILE cc_start: 0.9679 (tp) cc_final: 0.9443 (tp) REVERT: M 151 TYR cc_start: 0.8223 (m-80) cc_final: 0.7813 (m-10) REVERT: M 214 MET cc_start: 0.9303 (ppp) cc_final: 0.8961 (ppp) REVERT: N 214 MET cc_start: 0.9237 (ppp) cc_final: 0.8838 (ppp) REVERT: P 136 ILE cc_start: 0.9677 (tp) cc_final: 0.9432 (tp) REVERT: P 151 TYR cc_start: 0.8223 (m-80) cc_final: 0.7811 (m-10) REVERT: P 214 MET cc_start: 0.9323 (ppp) cc_final: 0.8971 (ppp) outliers start: 0 outliers final: 0 residues processed: 560 average time/residue: 0.4092 time to fit residues: 336.7930 Evaluate side-chains 456 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 456 time to evaluate : 1.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 87 optimal weight: 8.9990 chunk 241 optimal weight: 10.0000 chunk 54 optimal weight: 4.9990 chunk 109 optimal weight: 20.0000 chunk 254 optimal weight: 9.9990 chunk 191 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 192 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 253 optimal weight: 20.0000 chunk 166 optimal weight: 20.0000 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 172 ASN A 172 ASN A 179 ASN B 172 ASN C 172 ASN C 179 ASN D 172 ASN E 172 ASN E 179 ASN F 172 ASN G 172 ASN H 172 ASN I 172 ASN I 179 ASN J 172 ASN K 172 ASN K 179 ASN L 172 ASN M 172 ASN M 179 ASN N 172 ASN P 172 ASN Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3807 r_free = 0.3807 target = 0.070418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.057202 restraints weight = 313575.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.060109 restraints weight = 179286.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3646 r_free = 0.3646 target = 0.062216 restraints weight = 114956.034| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3679 r_free = 0.3679 target = 0.063911 restraints weight = 78700.953| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.065234 restraints weight = 55146.032| |-----------------------------------------------------------------------------| r_work (final): 0.3696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.8176 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22480 Z= 0.133 Angle : 0.612 4.456 30544 Z= 0.336 Chirality : 0.044 0.126 3216 Planarity : 0.005 0.036 3888 Dihedral : 6.905 43.084 2960 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.61 % Favored : 89.39 % Rotamer: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.27 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.95 (0.15), residues: 2640 helix: -3.57 (0.41), residues: 96 sheet: 0.73 (0.22), residues: 560 loop : -1.96 (0.12), residues: 1984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG I 191 TYR 0.012 0.001 TYR N 155 PHE 0.008 0.001 PHE A 176 TRP 0.010 0.001 TRP H 122 HIS 0.003 0.001 HIS B 207 Details of bonding type rmsd covalent geometry : bond 0.00284 (22448) covalent geometry : angle 0.61050 (30480) SS BOND : bond 0.00532 ( 32) SS BOND : angle 1.09975 ( 64) hydrogen bonds : bond 0.03276 ( 432) hydrogen bonds : angle 6.35856 ( 1632) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 566 time to evaluate : 1.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 125 ILE cc_start: 0.9694 (mm) cc_final: 0.9329 (tp) REVERT: O 136 ILE cc_start: 0.9652 (tp) cc_final: 0.9412 (tp) REVERT: A 136 ILE cc_start: 0.9670 (tp) cc_final: 0.9463 (tp) REVERT: A 151 TYR cc_start: 0.7859 (m-80) cc_final: 0.7474 (m-10) REVERT: A 177 TYR cc_start: 0.8062 (m-80) cc_final: 0.7669 (m-80) REVERT: A 214 MET cc_start: 0.9337 (ppp) cc_final: 0.8950 (ppp) REVERT: B 125 ILE cc_start: 0.9691 (mm) cc_final: 0.9328 (tp) REVERT: B 136 ILE cc_start: 0.9651 (tp) cc_final: 0.9413 (tp) REVERT: C 136 ILE cc_start: 0.9671 (tp) cc_final: 0.9463 (tp) REVERT: C 151 TYR cc_start: 0.7869 (m-80) cc_final: 0.7483 (m-10) REVERT: C 177 TYR cc_start: 0.8055 (m-80) cc_final: 0.7665 (m-80) REVERT: C 214 MET cc_start: 0.9352 (ppp) cc_final: 0.8961 (ppp) REVERT: D 125 ILE cc_start: 0.9692 (mm) cc_final: 0.9329 (tp) REVERT: D 136 ILE cc_start: 0.9653 (tp) cc_final: 0.9413 (tp) REVERT: E 136 ILE cc_start: 0.9669 (tp) cc_final: 0.9462 (tp) REVERT: E 151 TYR cc_start: 0.7885 (m-80) cc_final: 0.7494 (m-10) REVERT: E 177 TYR cc_start: 0.8055 (m-80) cc_final: 0.7664 (m-80) REVERT: E 214 MET cc_start: 0.9345 (ppp) cc_final: 0.8956 (ppp) REVERT: F 125 ILE cc_start: 0.9690 (mm) cc_final: 0.9324 (tp) REVERT: F 136 ILE cc_start: 0.9654 (tp) cc_final: 0.9414 (tp) REVERT: G 151 TYR cc_start: 0.7836 (m-80) cc_final: 0.7414 (m-10) REVERT: G 177 TYR cc_start: 0.8058 (m-80) cc_final: 0.7535 (m-80) REVERT: G 214 MET cc_start: 0.9346 (ppp) cc_final: 0.8952 (ppp) REVERT: H 125 ILE cc_start: 0.9690 (mm) cc_final: 0.9327 (tp) REVERT: H 136 ILE cc_start: 0.9653 (tp) cc_final: 0.9412 (tp) REVERT: I 136 ILE cc_start: 0.9675 (tp) cc_final: 0.9466 (tp) REVERT: I 151 TYR cc_start: 0.7884 (m-80) cc_final: 0.7498 (m-10) REVERT: I 177 TYR cc_start: 0.8061 (m-80) cc_final: 0.7671 (m-80) REVERT: I 214 MET cc_start: 0.9362 (ppp) cc_final: 0.8969 (ppp) REVERT: J 125 ILE cc_start: 0.9689 (mm) cc_final: 0.9325 (tp) REVERT: J 136 ILE cc_start: 0.9658 (tp) cc_final: 0.9419 (tp) REVERT: K 136 ILE cc_start: 0.9674 (tp) cc_final: 0.9465 (tp) REVERT: K 151 TYR cc_start: 0.7875 (m-80) cc_final: 0.7490 (m-10) REVERT: K 177 TYR cc_start: 0.8060 (m-80) cc_final: 0.7672 (m-80) REVERT: K 214 MET cc_start: 0.9368 (ppp) cc_final: 0.8973 (ppp) REVERT: L 125 ILE cc_start: 0.9694 (mm) cc_final: 0.9329 (tp) REVERT: L 136 ILE cc_start: 0.9658 (tp) cc_final: 0.9414 (tp) REVERT: L 214 MET cc_start: 0.9316 (ppp) cc_final: 0.9116 (ppp) REVERT: M 136 ILE cc_start: 0.9673 (tp) cc_final: 0.9465 (tp) REVERT: M 151 TYR cc_start: 0.7884 (m-80) cc_final: 0.7537 (m-10) REVERT: M 177 TYR cc_start: 0.8057 (m-80) cc_final: 0.7676 (m-80) REVERT: M 214 MET cc_start: 0.9363 (ppp) cc_final: 0.8972 (ppp) REVERT: N 125 ILE cc_start: 0.9693 (mm) cc_final: 0.9325 (tp) REVERT: N 136 ILE cc_start: 0.9658 (tp) cc_final: 0.9415 (tp) REVERT: P 151 TYR cc_start: 0.7839 (m-80) cc_final: 0.7415 (m-10) REVERT: P 177 TYR cc_start: 0.8061 (m-80) cc_final: 0.7532 (m-80) REVERT: P 214 MET cc_start: 0.9365 (ppp) cc_final: 0.8971 (ppp) outliers start: 0 outliers final: 0 residues processed: 566 average time/residue: 0.4380 time to fit residues: 358.5862 Evaluate side-chains 480 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 480 time to evaluate : 1.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 49 optimal weight: 20.0000 chunk 19 optimal weight: 30.0000 chunk 225 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 38 optimal weight: 30.0000 chunk 186 optimal weight: 20.0000 chunk 165 optimal weight: 20.0000 chunk 201 optimal weight: 10.0000 chunk 156 optimal weight: 30.0000 chunk 123 optimal weight: 10.0000 chunk 78 optimal weight: 9.9990 overall best weight: 13.9998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 154 GLN B 154 GLN D 154 GLN F 154 GLN H 154 GLN J 154 GLN L 154 GLN N 154 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.062566 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.051784 restraints weight = 389796.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054357 restraints weight = 211707.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.056134 restraints weight = 130944.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.057607 restraints weight = 87744.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.058753 restraints weight = 61958.223| |-----------------------------------------------------------------------------| r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.9607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 22480 Z= 0.284 Angle : 0.753 5.500 30544 Z= 0.412 Chirality : 0.043 0.173 3216 Planarity : 0.006 0.034 3888 Dihedral : 7.149 34.669 2960 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 16.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.55 % Favored : 85.45 % Rotamer: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.39 (0.14), residues: 2640 helix: -3.83 (0.35), residues: 96 sheet: 0.56 (0.17), residues: 688 loop : -2.54 (0.12), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG B 213 TYR 0.013 0.002 TYR K 177 PHE 0.021 0.003 PHE E 176 TRP 0.024 0.002 TRP N 122 HIS 0.009 0.004 HIS C 207 Details of bonding type rmsd covalent geometry : bond 0.00588 (22448) covalent geometry : angle 0.75209 (30480) SS BOND : bond 0.00904 ( 32) SS BOND : angle 1.23264 ( 64) hydrogen bonds : bond 0.03944 ( 432) hydrogen bonds : angle 6.68911 ( 1632) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 412 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 214 MET cc_start: 0.9330 (ppp) cc_final: 0.9049 (ppp) REVERT: A 151 TYR cc_start: 0.7645 (m-80) cc_final: 0.7262 (m-10) REVERT: A 214 MET cc_start: 0.9268 (ppp) cc_final: 0.9004 (ppp) REVERT: B 214 MET cc_start: 0.9369 (ppp) cc_final: 0.9074 (ppp) REVERT: C 151 TYR cc_start: 0.7653 (m-80) cc_final: 0.7269 (m-10) REVERT: C 214 MET cc_start: 0.9280 (ppp) cc_final: 0.9013 (ppp) REVERT: D 214 MET cc_start: 0.9363 (ppp) cc_final: 0.9071 (ppp) REVERT: E 151 TYR cc_start: 0.7667 (m-80) cc_final: 0.7278 (m-10) REVERT: E 214 MET cc_start: 0.9283 (ppp) cc_final: 0.9014 (ppp) REVERT: F 214 MET cc_start: 0.9356 (ppp) cc_final: 0.9062 (ppp) REVERT: G 151 TYR cc_start: 0.7639 (m-80) cc_final: 0.7255 (m-10) REVERT: G 214 MET cc_start: 0.9341 (ppp) cc_final: 0.9033 (ppp) REVERT: H 214 MET cc_start: 0.9356 (ppp) cc_final: 0.9072 (ppp) REVERT: I 151 TYR cc_start: 0.7693 (m-80) cc_final: 0.7295 (m-10) REVERT: I 214 MET cc_start: 0.9315 (ppp) cc_final: 0.9039 (ppp) REVERT: J 214 MET cc_start: 0.9377 (ppp) cc_final: 0.9083 (ppp) REVERT: K 151 TYR cc_start: 0.7684 (m-80) cc_final: 0.7287 (m-10) REVERT: K 214 MET cc_start: 0.9316 (ppp) cc_final: 0.9040 (ppp) REVERT: L 214 MET cc_start: 0.9290 (ppp) cc_final: 0.8969 (ppp) REVERT: M 151 TYR cc_start: 0.7685 (m-80) cc_final: 0.7291 (m-10) REVERT: M 214 MET cc_start: 0.9304 (ppp) cc_final: 0.9030 (ppp) REVERT: N 214 MET cc_start: 0.9365 (ppp) cc_final: 0.9068 (ppp) REVERT: P 151 TYR cc_start: 0.7664 (m-80) cc_final: 0.7273 (m-10) REVERT: P 214 MET cc_start: 0.9363 (ppp) cc_final: 0.9048 (ppp) outliers start: 0 outliers final: 0 residues processed: 412 average time/residue: 0.5032 time to fit residues: 293.0168 Evaluate side-chains 335 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 335 time to evaluate : 1.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 251 optimal weight: 8.9990 chunk 177 optimal weight: 9.9990 chunk 165 optimal weight: 6.9990 chunk 88 optimal weight: 30.0000 chunk 152 optimal weight: 30.0000 chunk 86 optimal weight: 20.0000 chunk 25 optimal weight: 7.9990 chunk 21 optimal weight: 20.0000 chunk 35 optimal weight: 40.0000 chunk 17 optimal weight: 9.9990 chunk 137 optimal weight: 8.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.063468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.051602 restraints weight = 358914.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.054455 restraints weight = 189317.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.056590 restraints weight = 115583.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.058044 restraints weight = 76618.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.059250 restraints weight = 53776.201| |-----------------------------------------------------------------------------| r_work (final): 0.3585 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.9937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 22480 Z= 0.172 Angle : 0.614 4.783 30544 Z= 0.337 Chirality : 0.044 0.130 3216 Planarity : 0.005 0.037 3888 Dihedral : 6.756 34.313 2960 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.48 % Favored : 86.52 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.15), residues: 2640 helix: -4.16 (0.28), residues: 96 sheet: 0.67 (0.18), residues: 688 loop : -2.48 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 102 TYR 0.011 0.001 TYR H 89 PHE 0.010 0.001 PHE E 176 TRP 0.011 0.001 TRP A 122 HIS 0.004 0.002 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00353 (22448) covalent geometry : angle 0.60964 (30480) SS BOND : bond 0.00495 ( 32) SS BOND : angle 1.68171 ( 64) hydrogen bonds : bond 0.03435 ( 432) hydrogen bonds : angle 6.09744 ( 1632) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 414 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 414 time to evaluate : 1.235 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 214 MET cc_start: 0.9379 (ppp) cc_final: 0.9102 (ppp) REVERT: A 214 MET cc_start: 0.9458 (ppp) cc_final: 0.9162 (ppp) REVERT: B 214 MET cc_start: 0.9403 (ppp) cc_final: 0.9123 (ppp) REVERT: C 214 MET cc_start: 0.9451 (ppp) cc_final: 0.9159 (ppp) REVERT: D 214 MET cc_start: 0.9409 (ppp) cc_final: 0.9126 (ppp) REVERT: E 214 MET cc_start: 0.9451 (ppp) cc_final: 0.9157 (ppp) REVERT: F 214 MET cc_start: 0.9394 (ppp) cc_final: 0.9111 (ppp) REVERT: G 214 MET cc_start: 0.9478 (ppp) cc_final: 0.9133 (ppp) REVERT: H 214 MET cc_start: 0.9372 (ppp) cc_final: 0.9098 (ppp) REVERT: I 214 MET cc_start: 0.9452 (ppp) cc_final: 0.9156 (ppp) REVERT: J 214 MET cc_start: 0.9400 (ppp) cc_final: 0.9120 (ppp) REVERT: K 214 MET cc_start: 0.9450 (ppp) cc_final: 0.9154 (ppp) REVERT: L 214 MET cc_start: 0.9412 (ppp) cc_final: 0.9118 (ppp) REVERT: M 214 MET cc_start: 0.9448 (ppp) cc_final: 0.9153 (ppp) REVERT: N 214 MET cc_start: 0.9398 (ppp) cc_final: 0.9115 (ppp) REVERT: P 214 MET cc_start: 0.9467 (ppp) cc_final: 0.9123 (ppp) outliers start: 0 outliers final: 0 residues processed: 414 average time/residue: 0.5039 time to fit residues: 293.0460 Evaluate side-chains 322 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 322 time to evaluate : 1.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 159 optimal weight: 9.9990 chunk 172 optimal weight: 20.0000 chunk 202 optimal weight: 20.0000 chunk 208 optimal weight: 3.9990 chunk 84 optimal weight: 20.0000 chunk 183 optimal weight: 8.9990 chunk 77 optimal weight: 1.9990 chunk 166 optimal weight: 5.9990 chunk 204 optimal weight: 20.0000 chunk 37 optimal weight: 40.0000 chunk 14 optimal weight: 9.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN F 121 GLN I 172 ASN L 121 GLN M 121 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.063099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.051043 restraints weight = 354307.154| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.053970 restraints weight = 185294.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.056113 restraints weight = 112479.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.057642 restraints weight = 74952.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.058833 restraints weight = 52635.458| |-----------------------------------------------------------------------------| r_work (final): 0.3581 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 1.0225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 22480 Z= 0.140 Angle : 0.573 4.338 30544 Z= 0.316 Chirality : 0.044 0.146 3216 Planarity : 0.005 0.039 3888 Dihedral : 6.361 30.199 2960 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.94 % Favored : 86.06 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.63 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.31 (0.15), residues: 2640 helix: -4.29 (0.26), residues: 96 sheet: 0.38 (0.18), residues: 720 loop : -2.38 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG O 102 TYR 0.011 0.002 TYR I 165 PHE 0.010 0.001 PHE E 176 TRP 0.011 0.001 TRP O 122 HIS 0.004 0.002 HIS I 207 Details of bonding type rmsd covalent geometry : bond 0.00293 (22448) covalent geometry : angle 0.56718 (30480) SS BOND : bond 0.00303 ( 32) SS BOND : angle 1.86312 ( 64) hydrogen bonds : bond 0.03274 ( 432) hydrogen bonds : angle 5.58322 ( 1632) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 370 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 214 MET cc_start: 0.9423 (ppp) cc_final: 0.9119 (ppp) REVERT: A 214 MET cc_start: 0.9445 (ppp) cc_final: 0.9124 (ppp) REVERT: B 214 MET cc_start: 0.9445 (ppp) cc_final: 0.9131 (ppp) REVERT: C 214 MET cc_start: 0.9449 (ppp) cc_final: 0.9129 (ppp) REVERT: D 214 MET cc_start: 0.9454 (ppp) cc_final: 0.9139 (ppp) REVERT: E 214 MET cc_start: 0.9449 (ppp) cc_final: 0.9130 (ppp) REVERT: F 214 MET cc_start: 0.9439 (ppp) cc_final: 0.9126 (ppp) REVERT: G 214 MET cc_start: 0.9471 (ppp) cc_final: 0.9117 (ppp) REVERT: H 214 MET cc_start: 0.9425 (ppp) cc_final: 0.9122 (ppp) REVERT: I 214 MET cc_start: 0.9453 (ppp) cc_final: 0.9132 (ppp) REVERT: J 214 MET cc_start: 0.9452 (ppp) cc_final: 0.9139 (ppp) REVERT: K 214 MET cc_start: 0.9455 (ppp) cc_final: 0.9132 (ppp) REVERT: L 214 MET cc_start: 0.9458 (ppp) cc_final: 0.9129 (ppp) REVERT: M 214 MET cc_start: 0.9448 (ppp) cc_final: 0.9129 (ppp) REVERT: N 214 MET cc_start: 0.9445 (ppp) cc_final: 0.9127 (ppp) REVERT: P 214 MET cc_start: 0.9468 (ppp) cc_final: 0.9113 (ppp) outliers start: 0 outliers final: 0 residues processed: 370 average time/residue: 0.5139 time to fit residues: 265.1422 Evaluate side-chains 296 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 296 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 25 optimal weight: 20.0000 chunk 78 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 165 optimal weight: 20.0000 chunk 245 optimal weight: 30.0000 chunk 103 optimal weight: 9.9990 chunk 177 optimal weight: 20.0000 chunk 153 optimal weight: 20.0000 chunk 161 optimal weight: 20.0000 chunk 92 optimal weight: 30.0000 chunk 37 optimal weight: 20.0000 overall best weight: 11.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: O 121 GLN A 121 GLN B 121 GLN C 121 GLN D 121 GLN E 121 GLN G 121 GLN H 121 GLN I 121 GLN J 121 GLN K 121 GLN N 121 GLN P 121 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.060645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.049652 restraints weight = 380259.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.052278 restraints weight = 208661.555| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.054120 restraints weight = 128900.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.055557 restraints weight = 86815.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.056698 restraints weight = 61145.035| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8261 moved from start: 1.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22480 Z= 0.217 Angle : 0.634 4.206 30544 Z= 0.348 Chirality : 0.043 0.151 3216 Planarity : 0.005 0.036 3888 Dihedral : 6.661 29.456 2960 Min Nonbonded Distance : 2.395 Molprobity Statistics. All-atom Clashscore : 12.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.43 % Favored : 85.57 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.15), residues: 2640 helix: -4.48 (0.23), residues: 96 sheet: 0.46 (0.18), residues: 688 loop : -2.59 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG F 102 TYR 0.010 0.002 TYR O 166 PHE 0.014 0.002 PHE I 176 TRP 0.020 0.002 TRP O 122 HIS 0.005 0.003 HIS A 66 Details of bonding type rmsd covalent geometry : bond 0.00450 (22448) covalent geometry : angle 0.62672 (30480) SS BOND : bond 0.00486 ( 32) SS BOND : angle 2.12117 ( 64) hydrogen bonds : bond 0.03444 ( 432) hydrogen bonds : angle 5.78852 ( 1632) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 326 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 214 MET cc_start: 0.9371 (ppp) cc_final: 0.9094 (ppp) REVERT: A 214 MET cc_start: 0.9382 (ppp) cc_final: 0.9060 (ppp) REVERT: B 214 MET cc_start: 0.9422 (ppp) cc_final: 0.9117 (ppp) REVERT: C 214 MET cc_start: 0.9394 (ppp) cc_final: 0.9083 (ppp) REVERT: D 214 MET cc_start: 0.9413 (ppp) cc_final: 0.9115 (ppp) REVERT: E 214 MET cc_start: 0.9378 (ppp) cc_final: 0.9060 (ppp) REVERT: F 214 MET cc_start: 0.9408 (ppp) cc_final: 0.9109 (ppp) REVERT: G 214 MET cc_start: 0.9400 (ppp) cc_final: 0.9038 (ppp) REVERT: H 214 MET cc_start: 0.9379 (ppp) cc_final: 0.9099 (ppp) REVERT: I 214 MET cc_start: 0.9396 (ppp) cc_final: 0.9073 (ppp) REVERT: J 214 MET cc_start: 0.9418 (ppp) cc_final: 0.9116 (ppp) REVERT: K 214 MET cc_start: 0.9397 (ppp) cc_final: 0.9084 (ppp) REVERT: L 214 MET cc_start: 0.9376 (ppp) cc_final: 0.9045 (ppp) REVERT: M 214 MET cc_start: 0.9387 (ppp) cc_final: 0.9063 (ppp) REVERT: N 214 MET cc_start: 0.9405 (ppp) cc_final: 0.9105 (ppp) REVERT: P 214 MET cc_start: 0.9412 (ppp) cc_final: 0.9051 (ppp) outliers start: 0 outliers final: 0 residues processed: 326 average time/residue: 0.5597 time to fit residues: 249.6903 Evaluate side-chains 253 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 253 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 119 optimal weight: 7.9990 chunk 147 optimal weight: 40.0000 chunk 179 optimal weight: 40.0000 chunk 106 optimal weight: 9.9990 chunk 60 optimal weight: 40.0000 chunk 18 optimal weight: 6.9990 chunk 157 optimal weight: 0.2980 chunk 93 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 130 optimal weight: 20.0000 chunk 216 optimal weight: 40.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.061696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.049956 restraints weight = 364068.140| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.052846 restraints weight = 190774.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.054981 restraints weight = 116182.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.056511 restraints weight = 76767.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.057648 restraints weight = 53525.871| |-----------------------------------------------------------------------------| r_work (final): 0.3550 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 1.0901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22480 Z= 0.126 Angle : 0.588 4.629 30544 Z= 0.320 Chirality : 0.045 0.141 3216 Planarity : 0.005 0.037 3888 Dihedral : 6.412 27.029 2960 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.73 % Favored : 87.27 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.34 (0.15), residues: 2640 helix: -4.47 (0.22), residues: 96 sheet: 0.57 (0.18), residues: 688 loop : -2.44 (0.13), residues: 1856 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 102 TYR 0.008 0.001 TYR M 165 PHE 0.009 0.001 PHE B 198 TRP 0.012 0.001 TRP O 122 HIS 0.004 0.001 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00265 (22448) covalent geometry : angle 0.57764 (30480) SS BOND : bond 0.00351 ( 32) SS BOND : angle 2.43441 ( 64) hydrogen bonds : bond 0.03097 ( 432) hydrogen bonds : angle 5.48820 ( 1632) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5280 Ramachandran restraints generated. 2640 Oldfield, 0 Emsley, 2640 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: O 214 MET cc_start: 0.9446 (ppp) cc_final: 0.9142 (ppp) REVERT: A 214 MET cc_start: 0.9462 (ppp) cc_final: 0.9145 (ppp) REVERT: B 214 MET cc_start: 0.9476 (ppp) cc_final: 0.9151 (ppp) REVERT: C 214 MET cc_start: 0.9466 (ppp) cc_final: 0.9150 (ppp) REVERT: D 214 MET cc_start: 0.9476 (ppp) cc_final: 0.9152 (ppp) REVERT: E 214 MET cc_start: 0.9458 (ppp) cc_final: 0.9142 (ppp) REVERT: F 214 MET cc_start: 0.9471 (ppp) cc_final: 0.9146 (ppp) REVERT: G 214 MET cc_start: 0.9479 (ppp) cc_final: 0.9125 (ppp) REVERT: H 214 MET cc_start: 0.9455 (ppp) cc_final: 0.9150 (ppp) REVERT: I 214 MET cc_start: 0.9462 (ppp) cc_final: 0.9148 (ppp) REVERT: J 214 MET cc_start: 0.9484 (ppp) cc_final: 0.9158 (ppp) REVERT: K 214 MET cc_start: 0.9467 (ppp) cc_final: 0.9150 (ppp) REVERT: L 214 MET cc_start: 0.9491 (ppp) cc_final: 0.9153 (ppp) REVERT: M 214 MET cc_start: 0.9456 (ppp) cc_final: 0.9138 (ppp) REVERT: N 214 MET cc_start: 0.9476 (ppp) cc_final: 0.9148 (ppp) REVERT: P 214 MET cc_start: 0.9482 (ppp) cc_final: 0.9128 (ppp) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.5728 time to fit residues: 249.7585 Evaluate side-chains 269 residues out of total 2432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 269 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 256 random chunks: chunk 27 optimal weight: 0.9980 chunk 107 optimal weight: 9.9990 chunk 88 optimal weight: 50.0000 chunk 100 optimal weight: 20.0000 chunk 241 optimal weight: 9.9990 chunk 150 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 chunk 89 optimal weight: 5.9990 chunk 231 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 72 optimal weight: 3.9990 overall best weight: 4.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 ASN L 172 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.062012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.050052 restraints weight = 358520.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.052968 restraints weight = 186307.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.055109 restraints weight = 112996.292| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.056647 restraints weight = 74425.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.057804 restraints weight = 52346.881| |-----------------------------------------------------------------------------| r_work (final): 0.3555 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 1.1019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22480 Z= 0.120 Angle : 0.563 4.285 30544 Z= 0.309 Chirality : 0.044 0.138 3216 Planarity : 0.005 0.039 3888 Dihedral : 6.275 26.818 2960 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 8.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 12.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.21 (0.15), residues: 2640 helix: -4.31 (0.27), residues: 96 sheet: 0.45 (0.19), residues: 720 loop : -2.29 (0.13), residues: 1824 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG M 102 TYR 0.013 0.001 TYR M 165 PHE 0.025 0.002 PHE D 198 TRP 0.011 0.001 TRP A 122 HIS 0.003 0.002 HIS A 207 Details of bonding type rmsd covalent geometry : bond 0.00256 (22448) covalent geometry : angle 0.55733 (30480) SS BOND : bond 0.00254 ( 32) SS BOND : angle 1.88550 ( 64) hydrogen bonds : bond 0.03012 ( 432) hydrogen bonds : angle 5.46769 ( 1632) =============================================================================== Job complete usr+sys time: 7425.43 seconds wall clock time: 127 minutes 56.32 seconds (7676.32 seconds total)