Starting phenix.real_space_refine on Sun May 18 19:46:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g8b_51127/05_2025/9g8b_51127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g8b_51127/05_2025/9g8b_51127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9g8b_51127/05_2025/9g8b_51127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g8b_51127/05_2025/9g8b_51127.map" model { file = "/net/cci-nas-00/data/ceres_data/9g8b_51127/05_2025/9g8b_51127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g8b_51127/05_2025/9g8b_51127.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 10703 2.51 5 N 2849 2.21 5 O 3703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.05s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 17346 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2478 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 23, 'TRANS': 321} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.39, per 1000 atoms: 0.37 Number of scatterers: 17346 At special positions: 0 Unit cell: (101.175, 102.24, 185.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 3703 8.00 N 2849 7.00 C 10703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=28, symmetry=0 Simple disulfide: pdb=" SG CYS A2906 " - pdb=" SG CYS A3058 " distance=2.04 Simple disulfide: pdb=" SG CYS A2988 " - pdb=" SG CYS A3140 " distance=2.04 Simple disulfide: pdb=" SG CYS A3001 " - pdb=" SG CYS A3051 " distance=2.03 Simple disulfide: pdb=" SG CYS A3085 " - pdb=" SG CYS A3222 " distance=2.04 Simple disulfide: pdb=" SG CYS C2906 " - pdb=" SG CYS C3058 " distance=2.04 Simple disulfide: pdb=" SG CYS B2906 " - pdb=" SG CYS B3058 " distance=2.04 Simple disulfide: pdb=" SG CYS E2906 " - pdb=" SG CYS E3058 " distance=2.04 Simple disulfide: pdb=" SG CYS D2906 " - pdb=" SG CYS D3058 " distance=2.04 Simple disulfide: pdb=" SG CYS G2906 " - pdb=" SG CYS G3058 " distance=2.04 Simple disulfide: pdb=" SG CYS F2906 " - pdb=" SG CYS F3058 " distance=2.04 Simple disulfide: pdb=" SG CYS C2988 " - pdb=" SG CYS C3140 " distance=2.04 Simple disulfide: pdb=" SG CYS B2988 " - pdb=" SG CYS B3140 " distance=2.04 Simple disulfide: pdb=" SG CYS E2988 " - pdb=" SG CYS E3140 " distance=2.04 Simple disulfide: pdb=" SG CYS D2988 " - pdb=" SG CYS D3140 " distance=2.04 Simple disulfide: pdb=" SG CYS G2988 " - pdb=" SG CYS G3140 " distance=2.04 Simple disulfide: pdb=" SG CYS F2988 " - pdb=" SG CYS F3140 " distance=2.04 Simple disulfide: pdb=" SG CYS C3001 " - pdb=" SG CYS C3051 " distance=2.03 Simple disulfide: pdb=" SG CYS B3001 " - pdb=" SG CYS B3051 " distance=2.03 Simple disulfide: pdb=" SG CYS E3001 " - pdb=" SG CYS E3051 " distance=2.03 Simple disulfide: pdb=" SG CYS D3001 " - pdb=" SG CYS D3051 " distance=2.03 Simple disulfide: pdb=" SG CYS G3001 " - pdb=" SG CYS G3051 " distance=2.03 Simple disulfide: pdb=" SG CYS F3001 " - pdb=" SG CYS F3051 " distance=2.03 Simple disulfide: pdb=" SG CYS C3085 " - pdb=" SG CYS C3222 " distance=2.04 Simple disulfide: pdb=" SG CYS B3085 " - pdb=" SG CYS B3222 " distance=2.04 Simple disulfide: pdb=" SG CYS E3085 " - pdb=" SG CYS E3222 " distance=2.04 Simple disulfide: pdb=" SG CYS D3085 " - pdb=" SG CYS D3222 " distance=2.04 Simple disulfide: pdb=" SG CYS G3085 " - pdb=" SG CYS G3222 " distance=2.04 Simple disulfide: pdb=" SG CYS F3085 " - pdb=" SG CYS F3222 " 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: 4.21 Conformation dependent library (CDL) restraints added in 2.2 seconds 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4382 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 70 sheets defined 6.1% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.66 Creating SS restraints... Processing helix chain 'A' and resid 2927 through 2929 No H-bonds generated for 'chain 'A' and resid 2927 through 2929' Processing helix chain 'A' and resid 2944 through 2948 Processing helix chain 'A' and resid 3107 through 3111 removed outlier: 4.290A pdb=" N THR A3111 " --> pdb=" O SER A3108 " (cutoff:3.500A) Processing helix chain 'A' and resid 3188 through 3190 No H-bonds generated for 'chain 'A' and resid 3188 through 3190' Processing helix chain 'A' and resid 3205 through 3209 Processing helix chain 'B' and resid 2927 through 2929 No H-bonds generated for 'chain 'B' and resid 2927 through 2929' Processing helix chain 'B' and resid 2944 through 2948 Processing helix chain 'B' and resid 3107 through 3111 removed outlier: 4.290A pdb=" N THR B3111 " --> pdb=" O SER B3108 " (cutoff:3.500A) Processing helix chain 'B' and resid 3188 through 3190 No H-bonds generated for 'chain 'B' and resid 3188 through 3190' Processing helix chain 'B' and resid 3205 through 3209 Processing helix chain 'C' and resid 2927 through 2929 No H-bonds generated for 'chain 'C' and resid 2927 through 2929' Processing helix chain 'C' and resid 2944 through 2948 Processing helix chain 'C' and resid 3107 through 3111 removed outlier: 4.291A pdb=" N THR C3111 " --> pdb=" O SER C3108 " (cutoff:3.500A) Processing helix chain 'C' and resid 3188 through 3190 No H-bonds generated for 'chain 'C' and resid 3188 through 3190' Processing helix chain 'C' and resid 3205 through 3209 Processing helix chain 'D' and resid 2927 through 2929 No H-bonds generated for 'chain 'D' and resid 2927 through 2929' Processing helix chain 'D' and resid 2944 through 2948 Processing helix chain 'D' and resid 3107 through 3111 removed outlier: 4.290A pdb=" N THR D3111 " --> pdb=" O SER D3108 " (cutoff:3.500A) Processing helix chain 'D' and resid 3188 through 3190 No H-bonds generated for 'chain 'D' and resid 3188 through 3190' Processing helix chain 'D' and resid 3205 through 3209 Processing helix chain 'E' and resid 2927 through 2929 No H-bonds generated for 'chain 'E' and resid 2927 through 2929' Processing helix chain 'E' and resid 2944 through 2948 Processing helix chain 'E' and resid 3107 through 3111 removed outlier: 4.290A pdb=" N THR E3111 " --> pdb=" O SER E3108 " (cutoff:3.500A) Processing helix chain 'E' and resid 3188 through 3190 No H-bonds generated for 'chain 'E' and resid 3188 through 3190' Processing helix chain 'E' and resid 3205 through 3209 Processing helix chain 'F' and resid 2927 through 2929 No H-bonds generated for 'chain 'F' and resid 2927 through 2929' Processing helix chain 'F' and resid 2944 through 2948 Processing helix chain 'F' and resid 3107 through 3111 removed outlier: 4.290A pdb=" N THR F3111 " --> pdb=" O SER F3108 " (cutoff:3.500A) Processing helix chain 'F' and resid 3188 through 3190 No H-bonds generated for 'chain 'F' and resid 3188 through 3190' Processing helix chain 'F' and resid 3205 through 3209 Processing helix chain 'G' and resid 2927 through 2929 No H-bonds generated for 'chain 'G' and resid 2927 through 2929' Processing helix chain 'G' and resid 2944 through 2948 Processing helix chain 'G' and resid 3107 through 3111 removed outlier: 4.290A pdb=" N THR G3111 " --> pdb=" O SER G3108 " (cutoff:3.500A) Processing helix chain 'G' and resid 3188 through 3190 No H-bonds generated for 'chain 'G' and resid 3188 through 3190' Processing helix chain 'G' and resid 3205 through 3209 Processing sheet with id=AA1, first strand: chain 'A' and resid 2903 through 2906 removed outlier: 6.549A pdb=" N PHE A2903 " --> pdb=" O GLY A2971 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN A2973 " --> pdb=" O PHE A2903 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL A2905 " --> pdb=" O ASN A2973 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 2981 through 2982 Processing sheet with id=AA3, first strand: chain 'A' and resid 2987 through 2988 removed outlier: 7.051A pdb=" N ILE A2987 " --> pdb=" O ASN A3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 3027 through 3028 Processing sheet with id=AA5, first strand: chain 'A' and resid 3027 through 3028 Processing sheet with id=AA6, first strand: chain 'A' and resid 3078 through 3080 removed outlier: 5.901A pdb=" N GLY A3088 " --> pdb=" O ASN A3124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN A3124 " --> pdb=" O GLY A3088 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 3084 through 3085 removed outlier: 6.548A pdb=" N VAL A3084 " --> pdb=" O HIS A3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'A' and resid 3113 through 3115 Processing sheet with id=AA9, first strand: chain 'A' and resid 3113 through 3115 Processing sheet with id=AB1, first strand: chain 'A' and resid 3164 through 3167 removed outlier: 6.865A pdb=" N PHE A3164 " --> pdb=" O THR A3232 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP A3234 " --> pdb=" O PHE A3164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL A3166 " --> pdb=" O ASP A3234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER A3182 " --> pdb=" O ILE A3217 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 2903 through 2906 removed outlier: 6.549A pdb=" N PHE B2903 " --> pdb=" O GLY B2971 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN B2973 " --> pdb=" O PHE B2903 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL B2905 " --> pdb=" O ASN B2973 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 2981 through 2982 Processing sheet with id=AB4, first strand: chain 'B' and resid 2987 through 2988 removed outlier: 7.051A pdb=" N ILE B2987 " --> pdb=" O ASN B3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 3027 through 3028 Processing sheet with id=AB6, first strand: chain 'B' and resid 3027 through 3028 Processing sheet with id=AB7, first strand: chain 'B' and resid 3078 through 3080 removed outlier: 5.901A pdb=" N GLY B3088 " --> pdb=" O ASN B3124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN B3124 " --> pdb=" O GLY B3088 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 3084 through 3085 removed outlier: 6.548A pdb=" N VAL B3084 " --> pdb=" O HIS B3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB8 Processing sheet with id=AB9, first strand: chain 'B' and resid 3113 through 3115 Processing sheet with id=AC1, first strand: chain 'B' and resid 3113 through 3115 Processing sheet with id=AC2, first strand: chain 'B' and resid 3164 through 3167 removed outlier: 6.865A pdb=" N PHE B3164 " --> pdb=" O THR B3232 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP B3234 " --> pdb=" O PHE B3164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL B3166 " --> pdb=" O ASP B3234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER B3182 " --> pdb=" O ILE B3217 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'C' and resid 2903 through 2906 removed outlier: 6.549A pdb=" N PHE C2903 " --> pdb=" O GLY C2971 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN C2973 " --> pdb=" O PHE C2903 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL C2905 " --> pdb=" O ASN C2973 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'C' and resid 2981 through 2982 Processing sheet with id=AC5, first strand: chain 'C' and resid 2987 through 2988 removed outlier: 7.050A pdb=" N ILE C2987 " --> pdb=" O ASN C3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC5 Processing sheet with id=AC6, first strand: chain 'C' and resid 3027 through 3028 Processing sheet with id=AC7, first strand: chain 'C' and resid 3027 through 3028 Processing sheet with id=AC8, first strand: chain 'C' and resid 3078 through 3080 removed outlier: 5.902A pdb=" N GLY C3088 " --> pdb=" O ASN C3124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C3124 " --> pdb=" O GLY C3088 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 3084 through 3085 removed outlier: 6.548A pdb=" N VAL C3084 " --> pdb=" O HIS C3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC9 Processing sheet with id=AD1, first strand: chain 'C' and resid 3113 through 3115 Processing sheet with id=AD2, first strand: chain 'C' and resid 3113 through 3115 Processing sheet with id=AD3, first strand: chain 'C' and resid 3164 through 3167 removed outlier: 6.865A pdb=" N PHE C3164 " --> pdb=" O THR C3232 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP C3234 " --> pdb=" O PHE C3164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL C3166 " --> pdb=" O ASP C3234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER C3182 " --> pdb=" O ILE C3217 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 2903 through 2906 removed outlier: 6.549A pdb=" N PHE D2903 " --> pdb=" O GLY D2971 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN D2973 " --> pdb=" O PHE D2903 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N VAL D2905 " --> pdb=" O ASN D2973 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 2981 through 2982 Processing sheet with id=AD6, first strand: chain 'D' and resid 2987 through 2988 removed outlier: 7.051A pdb=" N ILE D2987 " --> pdb=" O ASN D3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD6 Processing sheet with id=AD7, first strand: chain 'D' and resid 3027 through 3028 Processing sheet with id=AD8, first strand: chain 'D' and resid 3027 through 3028 Processing sheet with id=AD9, first strand: chain 'D' and resid 3078 through 3080 removed outlier: 5.901A pdb=" N GLY D3088 " --> pdb=" O ASN D3124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN D3124 " --> pdb=" O GLY D3088 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 3084 through 3085 removed outlier: 6.549A pdb=" N VAL D3084 " --> pdb=" O HIS D3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'D' and resid 3113 through 3115 Processing sheet with id=AE3, first strand: chain 'D' and resid 3113 through 3115 Processing sheet with id=AE4, first strand: chain 'D' and resid 3164 through 3167 removed outlier: 6.866A pdb=" N PHE D3164 " --> pdb=" O THR D3232 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP D3234 " --> pdb=" O PHE D3164 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL D3166 " --> pdb=" O ASP D3234 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N SER D3182 " --> pdb=" O ILE D3217 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'E' and resid 2903 through 2906 removed outlier: 6.549A pdb=" N PHE E2903 " --> pdb=" O GLY E2971 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASN E2973 " --> pdb=" O PHE E2903 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL E2905 " --> pdb=" O ASN E2973 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'E' and resid 2981 through 2982 Processing sheet with id=AE7, first strand: chain 'E' and resid 2987 through 2988 removed outlier: 7.051A pdb=" N ILE E2987 " --> pdb=" O ASN E3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE7 Processing sheet with id=AE8, first strand: chain 'E' and resid 3027 through 3028 Processing sheet with id=AE9, first strand: chain 'E' and resid 3027 through 3028 Processing sheet with id=AF1, first strand: chain 'E' and resid 3078 through 3080 removed outlier: 5.901A pdb=" N GLY E3088 " --> pdb=" O ASN E3124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN E3124 " --> pdb=" O GLY E3088 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 3084 through 3085 removed outlier: 6.548A pdb=" N VAL E3084 " --> pdb=" O HIS E3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF2 Processing sheet with id=AF3, first strand: chain 'E' and resid 3113 through 3115 Processing sheet with id=AF4, first strand: chain 'E' and resid 3113 through 3115 Processing sheet with id=AF5, first strand: chain 'E' and resid 3164 through 3167 removed outlier: 6.866A pdb=" N PHE E3164 " --> pdb=" O THR E3232 " (cutoff:3.500A) removed outlier: 8.043A pdb=" N ASP E3234 " --> pdb=" O PHE E3164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL E3166 " --> pdb=" O ASP E3234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER E3182 " --> pdb=" O ILE E3217 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'F' and resid 2903 through 2906 removed outlier: 6.548A pdb=" N PHE F2903 " --> pdb=" O GLY F2971 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N ASN F2973 " --> pdb=" O PHE F2903 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL F2905 " --> pdb=" O ASN F2973 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'F' and resid 2981 through 2982 Processing sheet with id=AF8, first strand: chain 'F' and resid 2987 through 2988 removed outlier: 7.050A pdb=" N ILE F2987 " --> pdb=" O ASN F3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AF8 Processing sheet with id=AF9, first strand: chain 'F' and resid 3027 through 3028 Processing sheet with id=AG1, first strand: chain 'F' and resid 3027 through 3028 Processing sheet with id=AG2, first strand: chain 'F' and resid 3078 through 3080 removed outlier: 5.900A pdb=" N GLY F3088 " --> pdb=" O ASN F3124 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ASN F3124 " --> pdb=" O GLY F3088 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 3084 through 3085 removed outlier: 6.548A pdb=" N VAL F3084 " --> pdb=" O HIS F3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG3 Processing sheet with id=AG4, first strand: chain 'F' and resid 3113 through 3115 Processing sheet with id=AG5, first strand: chain 'F' and resid 3113 through 3115 Processing sheet with id=AG6, first strand: chain 'F' and resid 3164 through 3167 removed outlier: 6.866A pdb=" N PHE F3164 " --> pdb=" O THR F3232 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP F3234 " --> pdb=" O PHE F3164 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL F3166 " --> pdb=" O ASP F3234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER F3182 " --> pdb=" O ILE F3217 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'G' and resid 2903 through 2906 removed outlier: 6.549A pdb=" N PHE G2903 " --> pdb=" O GLY G2971 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N ASN G2973 " --> pdb=" O PHE G2903 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL G2905 " --> pdb=" O ASN G2973 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'G' and resid 2981 through 2982 Processing sheet with id=AG9, first strand: chain 'G' and resid 2987 through 2988 removed outlier: 7.051A pdb=" N ILE G2987 " --> pdb=" O ASN G3070 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG9 Processing sheet with id=AH1, first strand: chain 'G' and resid 3027 through 3028 Processing sheet with id=AH2, first strand: chain 'G' and resid 3027 through 3028 Processing sheet with id=AH3, first strand: chain 'G' and resid 3078 through 3080 removed outlier: 5.901A pdb=" N GLY G3088 " --> pdb=" O ASN G3124 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN G3124 " --> pdb=" O GLY G3088 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 3084 through 3085 removed outlier: 6.548A pdb=" N VAL G3084 " --> pdb=" O HIS G3152 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH4 Processing sheet with id=AH5, first strand: chain 'G' and resid 3113 through 3115 Processing sheet with id=AH6, first strand: chain 'G' and resid 3113 through 3115 Processing sheet with id=AH7, first strand: chain 'G' and resid 3164 through 3167 removed outlier: 6.865A pdb=" N PHE G3164 " --> pdb=" O THR G3232 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N ASP G3234 " --> pdb=" O PHE G3164 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL G3166 " --> pdb=" O ASP G3234 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N SER G3182 " --> pdb=" O ILE G3217 " (cutoff:3.500A) 616 hydrogen bonds defined for protein. 1449 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 6.94 Time building geometry restraints manager: 4.93 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 3828 1.32 - 1.45: 4699 1.45 - 1.58: 9057 1.58 - 1.71: 21 1.71 - 1.84: 112 Bond restraints: 17717 Sorted by residual: bond pdb=" CA GLU D3061 " pdb=" C GLU D3061 " ideal model delta sigma weight residual 1.524 1.442 0.081 1.33e-02 5.65e+03 3.73e+01 bond pdb=" CA GLU E3061 " pdb=" C GLU E3061 " ideal model delta sigma weight residual 1.524 1.442 0.081 1.33e-02 5.65e+03 3.72e+01 bond pdb=" CA GLU B3061 " pdb=" C GLU B3061 " ideal model delta sigma weight residual 1.524 1.443 0.081 1.33e-02 5.65e+03 3.67e+01 bond pdb=" CA GLU C3061 " pdb=" C GLU C3061 " ideal model delta sigma weight residual 1.524 1.443 0.080 1.33e-02 5.65e+03 3.66e+01 bond pdb=" CA GLU A3061 " pdb=" C GLU A3061 " ideal model delta sigma weight residual 1.524 1.443 0.080 1.33e-02 5.65e+03 3.65e+01 ... (remaining 17712 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.39: 22164 2.39 - 4.79: 2026 4.79 - 7.18: 247 7.18 - 9.57: 28 9.57 - 11.97: 21 Bond angle restraints: 24486 Sorted by residual: angle pdb=" CA TYR E3048 " pdb=" CB TYR E3048 " pdb=" CG TYR E3048 " ideal model delta sigma weight residual 113.90 125.69 -11.79 1.80e+00 3.09e-01 4.29e+01 angle pdb=" CA TYR F3048 " pdb=" CB TYR F3048 " pdb=" CG TYR F3048 " ideal model delta sigma weight residual 113.90 125.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CA TYR D3048 " pdb=" CB TYR D3048 " pdb=" CG TYR D3048 " ideal model delta sigma weight residual 113.90 125.66 -11.76 1.80e+00 3.09e-01 4.27e+01 angle pdb=" CA TYR A3048 " pdb=" CB TYR A3048 " pdb=" CG TYR A3048 " ideal model delta sigma weight residual 113.90 125.65 -11.75 1.80e+00 3.09e-01 4.26e+01 angle pdb=" CA TYR C3048 " pdb=" CB TYR C3048 " pdb=" CG TYR C3048 " ideal model delta sigma weight residual 113.90 125.64 -11.74 1.80e+00 3.09e-01 4.25e+01 ... (remaining 24481 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.00: 9938 14.00 - 28.00: 380 28.00 - 42.00: 70 42.00 - 56.00: 14 56.00 - 70.00: 14 Dihedral angle restraints: 10416 sinusoidal: 3556 harmonic: 6860 Sorted by residual: dihedral pdb=" CB CYS G2906 " pdb=" SG CYS G2906 " pdb=" SG CYS G3058 " pdb=" CB CYS G3058 " ideal model delta sinusoidal sigma weight residual 93.00 126.97 -33.97 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CB CYS F2906 " pdb=" SG CYS F2906 " pdb=" SG CYS F3058 " pdb=" CB CYS F3058 " ideal model delta sinusoidal sigma weight residual 93.00 126.97 -33.97 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" CB CYS B2906 " pdb=" SG CYS B2906 " pdb=" SG CYS B3058 " pdb=" CB CYS B3058 " ideal model delta sinusoidal sigma weight residual 93.00 126.95 -33.95 1 1.00e+01 1.00e-02 1.64e+01 ... (remaining 10413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 2221 0.083 - 0.167: 704 0.167 - 0.250: 71 0.250 - 0.334: 14 0.334 - 0.417: 7 Chirality restraints: 3017 Sorted by residual: chirality pdb=" CA ASN C3012 " pdb=" N ASN C3012 " pdb=" C ASN C3012 " pdb=" CB ASN C3012 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.36e+00 chirality pdb=" CA ASN D3012 " pdb=" N ASN D3012 " pdb=" C ASN D3012 " pdb=" CB ASN D3012 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.35e+00 chirality pdb=" CA ASN F3012 " pdb=" N ASN F3012 " pdb=" C ASN F3012 " pdb=" CB ASN F3012 " both_signs ideal model delta sigma weight residual False 2.51 2.09 0.42 2.00e-01 2.50e+01 4.33e+00 ... (remaining 3014 not shown) Planarity restraints: 3213 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER B3062 " -0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C SER B3062 " 0.088 2.00e-02 2.50e+03 pdb=" O SER B3062 " -0.034 2.00e-02 2.50e+03 pdb=" N ASN B3063 " -0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E3062 " 0.025 2.00e-02 2.50e+03 5.07e-02 2.57e+01 pdb=" C SER E3062 " -0.088 2.00e-02 2.50e+03 pdb=" O SER E3062 " 0.034 2.00e-02 2.50e+03 pdb=" N ASN E3063 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER G3062 " -0.025 2.00e-02 2.50e+03 5.06e-02 2.56e+01 pdb=" C SER G3062 " 0.088 2.00e-02 2.50e+03 pdb=" O SER G3062 " -0.034 2.00e-02 2.50e+03 pdb=" N ASN G3063 " -0.029 2.00e-02 2.50e+03 ... (remaining 3210 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 5644 2.82 - 3.34: 15236 3.34 - 3.86: 28680 3.86 - 4.38: 31736 4.38 - 4.90: 55354 Nonbonded interactions: 136650 Sorted by model distance: nonbonded pdb=" OG SER C2998 " pdb=" OG SER D3013 " model vdw 2.304 3.040 nonbonded pdb=" OG SER A3013 " pdb=" OG SER G2998 " model vdw 2.316 3.040 nonbonded pdb=" OG SER B2998 " pdb=" OG SER C3013 " model vdw 2.317 3.040 nonbonded pdb=" OG SER D2998 " pdb=" OG SER E3013 " model vdw 2.318 3.040 nonbonded pdb=" OG SER F2998 " pdb=" OG SER G3013 " model vdw 2.320 3.040 ... (remaining 136645 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: 0.16 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.780 Check model and map are aligned: 0.140 Set scattering table: 0.190 Process input model: 37.870 Find NCS groups from input model: 0.370 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7957 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 : 0.018 0.135 17745 Z= 0.907 Angle : 1.488 11.966 24542 Z= 0.970 Chirality : 0.080 0.417 3017 Planarity : 0.008 0.051 3213 Dihedral : 8.253 69.997 5950 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 1.03 (0.16), residues: 868 loop : 1.26 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRP F3185 HIS 0.009 0.006 HIS B3152 PHE 0.055 0.008 PHE B3164 TYR 0.049 0.007 TYR B3048 ARG 0.001 0.000 ARG F2969 Details of bonding type rmsd hydrogen bonds : bond 0.17405 ( 504) hydrogen bonds : angle 8.19665 ( 1449) SS BOND : bond 0.00625 ( 28) SS BOND : angle 2.57364 ( 56) covalent geometry : bond 0.01795 (17717) covalent geometry : angle 1.48500 (24486) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.880 Fit side-chains REVERT: A 3156 VAL cc_start: 0.8355 (t) cc_final: 0.7996 (m) REVERT: B 3213 THR cc_start: 0.9127 (m) cc_final: 0.8838 (p) REVERT: C 3005 GLN cc_start: 0.8205 (tt0) cc_final: 0.7917 (tt0) REVERT: C 3156 VAL cc_start: 0.8226 (t) cc_final: 0.7939 (m) REVERT: C 3205 THR cc_start: 0.8601 (p) cc_final: 0.8334 (m) REVERT: C 3213 THR cc_start: 0.9192 (m) cc_final: 0.8911 (p) REVERT: D 3205 THR cc_start: 0.8507 (p) cc_final: 0.8289 (m) REVERT: E 3156 VAL cc_start: 0.8199 (t) cc_final: 0.7931 (m) REVERT: E 3205 THR cc_start: 0.8618 (p) cc_final: 0.8394 (m) REVERT: E 3213 THR cc_start: 0.9105 (m) cc_final: 0.8847 (p) REVERT: F 3205 THR cc_start: 0.8500 (p) cc_final: 0.8238 (m) REVERT: F 3213 THR cc_start: 0.9161 (m) cc_final: 0.8911 (p) REVERT: G 3205 THR cc_start: 0.8468 (p) cc_final: 0.8232 (m) REVERT: G 3213 THR cc_start: 0.9173 (m) cc_final: 0.8898 (p) outliers start: 0 outliers final: 0 residues processed: 396 average time/residue: 0.1913 time to fit residues: 133.3618 Evaluate side-chains 151 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 121 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 186 optimal weight: 6.9990 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 1.9990 chunk 138 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3063 ASN B3063 ASN C2942 ASN D3063 ASN E3063 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.111703 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.093319 restraints weight = 21751.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.092846 restraints weight = 25454.335| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2884 r_free = 0.2884 target = 0.094269 restraints weight = 26472.786| |-----------------------------------------------------------------------------| r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.2119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 17745 Z= 0.162 Angle : 0.586 7.225 24542 Z= 0.324 Chirality : 0.050 0.147 3017 Planarity : 0.005 0.034 3213 Dihedral : 4.758 17.351 2499 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.60 % Allowed : 7.31 % Favored : 90.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.42 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 1.00 (0.16), residues: 854 loop : 1.07 (0.17), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP F3131 HIS 0.002 0.001 HIS F3152 PHE 0.007 0.001 PHE C2903 TYR 0.017 0.001 TYR F3048 ARG 0.003 0.001 ARG D2969 Details of bonding type rmsd hydrogen bonds : bond 0.04736 ( 504) hydrogen bonds : angle 6.17743 ( 1449) SS BOND : bond 0.00123 ( 28) SS BOND : angle 1.36938 ( 56) covalent geometry : bond 0.00379 (17717) covalent geometry : angle 0.58278 (24486) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 236 time to evaluate : 1.809 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3156 VAL cc_start: 0.8666 (t) cc_final: 0.8413 (m) REVERT: B 3007 ILE cc_start: 0.9040 (mm) cc_final: 0.8829 (mt) REVERT: C 2987 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.8134 (tp) REVERT: C 3213 THR cc_start: 0.9249 (m) cc_final: 0.8911 (p) REVERT: D 3007 ILE cc_start: 0.8991 (mm) cc_final: 0.8775 (mt) REVERT: D 3093 SER cc_start: 0.8954 (p) cc_final: 0.8736 (p) REVERT: E 2987 ILE cc_start: 0.8340 (OUTLIER) cc_final: 0.8097 (tp) REVERT: E 3213 THR cc_start: 0.9122 (m) cc_final: 0.8808 (p) REVERT: F 3093 SER cc_start: 0.8925 (p) cc_final: 0.8709 (p) REVERT: F 3213 THR cc_start: 0.9131 (m) cc_final: 0.8764 (p) REVERT: G 3213 THR cc_start: 0.9199 (m) cc_final: 0.8878 (p) outliers start: 53 outliers final: 34 residues processed: 264 average time/residue: 0.1875 time to fit residues: 87.8136 Evaluate side-chains 196 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 160 time to evaluate : 1.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3063 ASN Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3063 ASN Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 2987 ILE Chi-restraints excluded: chain C residue 3023 SER Chi-restraints excluded: chain C residue 3037 MET Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3063 ASN Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3023 SER Chi-restraints excluded: chain E residue 3063 ASN Chi-restraints excluded: chain F residue 2941 THR Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 2987 ILE Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 138 optimal weight: 0.7980 chunk 88 optimal weight: 0.7980 chunk 152 optimal weight: 3.9990 chunk 215 optimal weight: 0.9990 chunk 167 optimal weight: 3.9990 chunk 126 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 79 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 148 optimal weight: 0.8980 chunk 221 optimal weight: 0.0970 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3063 ASN B2942 ASN B3041 ASN B3063 ASN ** C3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2942 ASN D3041 ASN D3063 ASN E2942 ASN E3041 ASN E3063 ASN G2942 ASN G3063 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.112257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.097966 restraints weight = 21404.106| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2913 r_free = 0.2913 target = 0.096366 restraints weight = 33125.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.097015 restraints weight = 31364.047| |-----------------------------------------------------------------------------| r_work (final): 0.2897 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.2499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 17745 Z= 0.114 Angle : 0.516 5.948 24542 Z= 0.282 Chirality : 0.047 0.145 3017 Planarity : 0.004 0.032 3213 Dihedral : 4.330 17.895 2499 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 2.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.24 % Allowed : 10.46 % Favored : 86.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.38 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.86 (0.15), residues: 875 loop : 1.14 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G3185 HIS 0.002 0.001 HIS E3152 PHE 0.007 0.001 PHE E3164 TYR 0.014 0.001 TYR E3048 ARG 0.004 0.000 ARG B2969 Details of bonding type rmsd hydrogen bonds : bond 0.04086 ( 504) hydrogen bonds : angle 5.69678 ( 1449) SS BOND : bond 0.00212 ( 28) SS BOND : angle 0.83073 ( 56) covalent geometry : bond 0.00263 (17717) covalent geometry : angle 0.51488 (24486) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 176 time to evaluate : 1.848 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8850 (mm) cc_final: 0.8601 (mt) REVERT: A 3156 VAL cc_start: 0.8736 (t) cc_final: 0.8505 (m) REVERT: B 3213 THR cc_start: 0.9036 (m) cc_final: 0.8761 (p) REVERT: C 3093 SER cc_start: 0.8957 (p) cc_final: 0.8731 (p) REVERT: C 3110 LEU cc_start: 0.8706 (mp) cc_final: 0.8462 (mt) REVERT: C 3213 THR cc_start: 0.9246 (m) cc_final: 0.8919 (p) REVERT: E 2987 ILE cc_start: 0.8511 (OUTLIER) cc_final: 0.8270 (tp) REVERT: E 3213 THR cc_start: 0.9128 (m) cc_final: 0.8876 (p) REVERT: F 3007 ILE cc_start: 0.8932 (mm) cc_final: 0.8704 (mt) REVERT: F 3093 SER cc_start: 0.8822 (p) cc_final: 0.8596 (m) REVERT: F 3213 THR cc_start: 0.9208 (m) cc_final: 0.8857 (p) REVERT: G 3213 THR cc_start: 0.9197 (m) cc_final: 0.8894 (p) outliers start: 66 outliers final: 46 residues processed: 222 average time/residue: 0.1893 time to fit residues: 74.5575 Evaluate side-chains 197 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 150 time to evaluate : 1.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain B residue 2934 LEU Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3121 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 3074 ASP Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3123 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3216 ILE Chi-restraints excluded: chain G residue 2946 ILE Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 164 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 0.0270 chunk 210 optimal weight: 5.9990 chunk 92 optimal weight: 0.1980 chunk 86 optimal weight: 0.9990 chunk 211 optimal weight: 3.9990 chunk 175 optimal weight: 7.9990 chunk 204 optimal weight: 0.6980 chunk 109 optimal weight: 6.9990 chunk 18 optimal weight: 4.9990 overall best weight: 0.9842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3041 ASN C3063 ASN D2942 ASN F3063 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.108941 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.092274 restraints weight = 21780.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.091637 restraints weight = 29209.678| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.092278 restraints weight = 28759.896| |-----------------------------------------------------------------------------| r_work (final): 0.2841 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.2851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17745 Z= 0.132 Angle : 0.493 5.471 24542 Z= 0.269 Chirality : 0.048 0.164 3017 Planarity : 0.004 0.043 3213 Dihedral : 4.126 17.211 2499 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % Rotamer: Outliers : 4.12 % Allowed : 10.11 % Favored : 85.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.78 (0.15), residues: 875 loop : 1.06 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E3185 HIS 0.002 0.002 HIS E3152 PHE 0.007 0.001 PHE G3191 TYR 0.014 0.001 TYR F3048 ARG 0.001 0.000 ARG F2969 Details of bonding type rmsd hydrogen bonds : bond 0.03772 ( 504) hydrogen bonds : angle 5.32603 ( 1449) SS BOND : bond 0.00498 ( 28) SS BOND : angle 0.74619 ( 56) covalent geometry : bond 0.00316 (17717) covalent geometry : angle 0.49270 (24486) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 180 time to evaluate : 1.872 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8873 (mm) cc_final: 0.8625 (mt) REVERT: B 3058 CYS cc_start: 0.5632 (m) cc_final: 0.5188 (m) REVERT: B 3213 THR cc_start: 0.9002 (m) cc_final: 0.8739 (p) REVERT: C 3063 ASN cc_start: 0.8427 (OUTLIER) cc_final: 0.8221 (p0) REVERT: C 3093 SER cc_start: 0.8908 (p) cc_final: 0.8685 (p) REVERT: C 3213 THR cc_start: 0.9284 (m) cc_final: 0.8907 (p) REVERT: D 3074 ASP cc_start: 0.7105 (OUTLIER) cc_final: 0.6874 (m-30) REVERT: D 3093 SER cc_start: 0.8823 (p) cc_final: 0.8589 (m) REVERT: E 2987 ILE cc_start: 0.8550 (OUTLIER) cc_final: 0.8318 (tp) REVERT: E 3213 THR cc_start: 0.9150 (m) cc_final: 0.8833 (p) REVERT: F 3007 ILE cc_start: 0.8975 (mm) cc_final: 0.8728 (mt) REVERT: F 3093 SER cc_start: 0.8830 (p) cc_final: 0.8595 (m) REVERT: F 3213 THR cc_start: 0.9185 (m) cc_final: 0.8769 (p) outliers start: 84 outliers final: 52 residues processed: 241 average time/residue: 0.1851 time to fit residues: 79.1977 Evaluate side-chains 217 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 162 time to evaluate : 1.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3121 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 2982 VAL Chi-restraints excluded: chain C residue 3063 ASN Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3157 THR Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3157 THR Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3049 MET Chi-restraints excluded: chain F residue 3063 ASN Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3216 ILE Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 4 optimal weight: 0.9990 chunk 226 optimal weight: 0.0970 chunk 34 optimal weight: 7.9990 chunk 81 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 76 optimal weight: 0.0670 chunk 55 optimal weight: 0.9980 chunk 218 optimal weight: 0.1980 chunk 130 optimal weight: 3.9990 chunk 84 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 overall best weight: 0.4718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C3063 ASN D2942 ASN F3063 ASN ** G2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3063 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.110708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.093888 restraints weight = 21930.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.093174 restraints weight = 29597.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.093853 restraints weight = 27478.658| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.3037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 17745 Z= 0.094 Angle : 0.466 6.423 24542 Z= 0.253 Chirality : 0.047 0.147 3017 Planarity : 0.004 0.048 3213 Dihedral : 3.932 17.096 2499 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 3.24 % Allowed : 11.49 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.81 (0.15), residues: 875 loop : 1.06 (0.17), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E3185 HIS 0.002 0.001 HIS F3152 PHE 0.005 0.001 PHE A3191 TYR 0.013 0.001 TYR F3048 ARG 0.003 0.000 ARG B2969 Details of bonding type rmsd hydrogen bonds : bond 0.03432 ( 504) hydrogen bonds : angle 5.24521 ( 1449) SS BOND : bond 0.00188 ( 28) SS BOND : angle 0.66673 ( 56) covalent geometry : bond 0.00216 (17717) covalent geometry : angle 0.46533 (24486) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 192 time to evaluate : 1.839 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8863 (mm) cc_final: 0.8565 (mt) REVERT: B 3213 THR cc_start: 0.8975 (m) cc_final: 0.8544 (p) REVERT: C 3063 ASN cc_start: 0.8527 (OUTLIER) cc_final: 0.8191 (p0) REVERT: C 3093 SER cc_start: 0.8803 (p) cc_final: 0.8600 (m) REVERT: C 3213 THR cc_start: 0.9257 (m) cc_final: 0.8873 (p) REVERT: D 3074 ASP cc_start: 0.7096 (OUTLIER) cc_final: 0.6862 (m-30) REVERT: D 3093 SER cc_start: 0.8725 (p) cc_final: 0.8514 (m) REVERT: E 2987 ILE cc_start: 0.8523 (OUTLIER) cc_final: 0.8300 (tp) REVERT: E 3213 THR cc_start: 0.9138 (m) cc_final: 0.8813 (p) REVERT: F 3007 ILE cc_start: 0.8956 (mm) cc_final: 0.8738 (mt) REVERT: F 3093 SER cc_start: 0.8767 (p) cc_final: 0.8562 (m) REVERT: F 3213 THR cc_start: 0.9124 (m) cc_final: 0.8679 (p) outliers start: 66 outliers final: 47 residues processed: 243 average time/residue: 0.1874 time to fit residues: 81.4307 Evaluate side-chains 218 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 168 time to evaluate : 1.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain C residue 2982 VAL Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3063 ASN Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 2934 LEU Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3157 THR Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3216 ILE Chi-restraints excluded: chain G residue 2902 ASP Chi-restraints excluded: chain G residue 2946 ILE Chi-restraints excluded: chain G residue 3063 ASN Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 88 optimal weight: 2.9990 chunk 53 optimal weight: 3.9990 chunk 49 optimal weight: 4.9990 chunk 189 optimal weight: 3.9990 chunk 97 optimal weight: 0.0370 chunk 126 optimal weight: 3.9990 chunk 212 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 87 optimal weight: 0.9990 chunk 59 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 overall best weight: 2.4066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2980 ASN ** C2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C3063 ASN D2942 ASN D2980 ASN E2980 ASN ** F2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3063 ASN ** G2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G3063 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.104655 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.087921 restraints weight = 22489.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2771 r_free = 0.2771 target = 0.086981 restraints weight = 30625.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.087581 restraints weight = 28876.562| |-----------------------------------------------------------------------------| r_work (final): 0.2772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8315 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 17745 Z= 0.269 Angle : 0.587 5.416 24542 Z= 0.321 Chirality : 0.051 0.251 3017 Planarity : 0.005 0.052 3213 Dihedral : 4.419 24.485 2499 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 4.52 % Allowed : 11.14 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.16), residues: 2401 helix: None (None), residues: 0 sheet: 0.53 (0.15), residues: 875 loop : 0.69 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A3047 HIS 0.003 0.001 HIS F3152 PHE 0.013 0.002 PHE G3191 TYR 0.018 0.002 TYR C3048 ARG 0.004 0.001 ARG B2969 Details of bonding type rmsd hydrogen bonds : bond 0.04365 ( 504) hydrogen bonds : angle 5.35185 ( 1449) SS BOND : bond 0.00386 ( 28) SS BOND : angle 1.16810 ( 56) covalent geometry : bond 0.00660 (17717) covalent geometry : angle 0.58476 (24486) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 179 time to evaluate : 1.830 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8892 (mm) cc_final: 0.8628 (mt) REVERT: B 3232 THR cc_start: 0.8305 (OUTLIER) cc_final: 0.8101 (t) REVERT: C 3007 ILE cc_start: 0.8755 (OUTLIER) cc_final: 0.8480 (mt) REVERT: C 3063 ASN cc_start: 0.8710 (OUTLIER) cc_final: 0.8248 (p0) REVERT: D 3074 ASP cc_start: 0.7186 (OUTLIER) cc_final: 0.6942 (m-30) REVERT: D 3093 SER cc_start: 0.8900 (p) cc_final: 0.8591 (m) REVERT: E 2987 ILE cc_start: 0.8682 (OUTLIER) cc_final: 0.8469 (tp) REVERT: F 3007 ILE cc_start: 0.9038 (mm) cc_final: 0.8830 (mt) REVERT: F 3093 SER cc_start: 0.8889 (p) cc_final: 0.8680 (p) REVERT: F 3213 THR cc_start: 0.9184 (m) cc_final: 0.8770 (p) outliers start: 92 outliers final: 57 residues processed: 247 average time/residue: 0.2010 time to fit residues: 85.0113 Evaluate side-chains 227 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 165 time to evaluate : 2.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3157 THR Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3121 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain B residue 3220 ASN Chi-restraints excluded: chain B residue 3232 THR Chi-restraints excluded: chain C residue 3007 ILE Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3063 ASN Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3195 VAL Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 2934 LEU Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain D residue 3220 ASN Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3157 THR Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3063 ASN Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3216 ILE Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3121 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Chi-restraints excluded: chain G residue 3220 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 9 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 223 optimal weight: 0.8980 chunk 78 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 192 optimal weight: 0.6980 chunk 55 optimal weight: 0.5980 chunk 138 optimal weight: 1.9990 chunk 164 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2980 ASN B2980 ASN C2980 ASN C3063 ASN D2980 ASN E2980 ASN F2980 ASN F3063 ASN G2980 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.107872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2825 r_free = 0.2825 target = 0.090855 restraints weight = 21967.319| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.090040 restraints weight = 30320.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.090769 restraints weight = 28472.563| |-----------------------------------------------------------------------------| r_work (final): 0.2818 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.3371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 17745 Z= 0.113 Angle : 0.482 5.107 24542 Z= 0.262 Chirality : 0.048 0.151 3017 Planarity : 0.005 0.048 3213 Dihedral : 4.149 23.174 2499 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.73 % Allowed : 12.86 % Favored : 83.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.51 (0.15), residues: 903 loop : 0.74 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G3185 HIS 0.002 0.001 HIS F3152 PHE 0.006 0.001 PHE A3191 TYR 0.014 0.001 TYR F3048 ARG 0.007 0.001 ARG C3059 Details of bonding type rmsd hydrogen bonds : bond 0.03553 ( 504) hydrogen bonds : angle 5.27529 ( 1449) SS BOND : bond 0.00132 ( 28) SS BOND : angle 1.14101 ( 56) covalent geometry : bond 0.00263 (17717) covalent geometry : angle 0.47985 (24486) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 174 time to evaluate : 1.906 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8863 (mm) cc_final: 0.8571 (mt) REVERT: B 3232 THR cc_start: 0.8306 (OUTLIER) cc_final: 0.8087 (t) REVERT: C 3063 ASN cc_start: 0.8583 (OUTLIER) cc_final: 0.8254 (p0) REVERT: C 3213 THR cc_start: 0.9073 (m) cc_final: 0.8662 (p) REVERT: D 3093 SER cc_start: 0.8853 (p) cc_final: 0.8568 (m) REVERT: E 2987 ILE cc_start: 0.8560 (OUTLIER) cc_final: 0.8347 (tp) REVERT: F 3007 ILE cc_start: 0.8970 (mm) cc_final: 0.8745 (mt) REVERT: F 3093 SER cc_start: 0.8840 (p) cc_final: 0.8581 (m) REVERT: F 3213 THR cc_start: 0.9146 (m) cc_final: 0.8695 (p) outliers start: 76 outliers final: 52 residues processed: 227 average time/residue: 0.2066 time to fit residues: 81.8995 Evaluate side-chains 220 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 1.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2912 ILE Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain B residue 3232 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 3007 ILE Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3063 ASN Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 2934 LEU Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3121 MET Chi-restraints excluded: chain E residue 3156 VAL Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain E residue 3220 ASN Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 131 optimal weight: 0.4980 chunk 228 optimal weight: 1.9990 chunk 163 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 206 optimal weight: 6.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 230 optimal weight: 3.9990 chunk 161 optimal weight: 0.8980 chunk 229 optimal weight: 2.9990 chunk 71 optimal weight: 4.9990 overall best weight: 1.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2980 ASN B2980 ASN C2980 ASN C3063 ASN D2980 ASN E2980 ASN F2980 ASN G2980 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.105969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.088718 restraints weight = 22141.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.087853 restraints weight = 29693.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2790 r_free = 0.2790 target = 0.088320 restraints weight = 28726.003| |-----------------------------------------------------------------------------| r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.3456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17745 Z= 0.193 Angle : 0.526 5.447 24542 Z= 0.285 Chirality : 0.049 0.165 3017 Planarity : 0.005 0.047 3213 Dihedral : 4.281 30.373 2499 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 4.07 % Allowed : 12.81 % Favored : 83.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.65 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.37 (0.15), residues: 903 loop : 0.61 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G3185 HIS 0.002 0.001 HIS F3152 PHE 0.009 0.002 PHE C3191 TYR 0.015 0.001 TYR F3048 ARG 0.005 0.001 ARG C3059 Details of bonding type rmsd hydrogen bonds : bond 0.03862 ( 504) hydrogen bonds : angle 5.25882 ( 1449) SS BOND : bond 0.00223 ( 28) SS BOND : angle 1.55382 ( 56) covalent geometry : bond 0.00470 (17717) covalent geometry : angle 0.52105 (24486) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 168 time to evaluate : 1.845 Fit side-chains REVERT: B 3232 THR cc_start: 0.8300 (OUTLIER) cc_final: 0.8082 (t) REVERT: C 3063 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8298 (p0) REVERT: C 3213 THR cc_start: 0.9067 (m) cc_final: 0.8662 (p) REVERT: D 3093 SER cc_start: 0.8893 (p) cc_final: 0.8610 (m) REVERT: E 2987 ILE cc_start: 0.8603 (OUTLIER) cc_final: 0.8386 (tp) REVERT: F 3007 ILE cc_start: 0.9001 (mm) cc_final: 0.8788 (mt) REVERT: F 3093 SER cc_start: 0.8849 (p) cc_final: 0.8577 (m) REVERT: F 3213 THR cc_start: 0.9159 (m) cc_final: 0.8698 (p) outliers start: 83 outliers final: 60 residues processed: 225 average time/residue: 0.2131 time to fit residues: 82.1558 Evaluate side-chains 228 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 165 time to evaluate : 1.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2912 ILE Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3157 THR Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain A residue 3220 ASN Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3037 MET Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3213 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain B residue 3232 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 3007 ILE Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3063 ASN Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3156 VAL Chi-restraints excluded: chain C residue 3195 VAL Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 2934 LEU Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3156 VAL Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain E residue 3220 ASN Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Chi-restraints excluded: chain G residue 3220 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 1 optimal weight: 1.9990 chunk 42 optimal weight: 0.0970 chunk 171 optimal weight: 6.9990 chunk 165 optimal weight: 1.9990 chunk 213 optimal weight: 0.8980 chunk 184 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 68 optimal weight: 7.9990 chunk 118 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2980 ASN B2980 ASN C2980 ASN C3063 ASN D2980 ASN E2980 ASN F2980 ASN F3063 ASN G2980 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.108440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.091116 restraints weight = 22106.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.090163 restraints weight = 31092.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.090879 restraints weight = 30004.454| |-----------------------------------------------------------------------------| r_work (final): 0.2819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 17745 Z= 0.106 Angle : 0.474 5.062 24542 Z= 0.256 Chirality : 0.047 0.149 3017 Planarity : 0.004 0.042 3213 Dihedral : 4.094 30.106 2499 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.58 % Allowed : 13.35 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.56 (0.16), residues: 847 loop : 0.51 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F3185 HIS 0.001 0.001 HIS A3152 PHE 0.005 0.001 PHE A3191 TYR 0.012 0.001 TYR F3048 ARG 0.007 0.001 ARG C3059 Details of bonding type rmsd hydrogen bonds : bond 0.03396 ( 504) hydrogen bonds : angle 5.17935 ( 1449) SS BOND : bond 0.00121 ( 28) SS BOND : angle 1.22016 ( 56) covalent geometry : bond 0.00251 (17717) covalent geometry : angle 0.47128 (24486) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 177 time to evaluate : 2.045 Fit side-chains revert: symmetry clash REVERT: A 3007 ILE cc_start: 0.8868 (mm) cc_final: 0.8560 (mt) REVERT: B 3186 SER cc_start: 0.9076 (t) cc_final: 0.8676 (m) REVERT: B 3232 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8084 (t) REVERT: C 3063 ASN cc_start: 0.8528 (OUTLIER) cc_final: 0.8183 (p0) REVERT: C 3213 THR cc_start: 0.9030 (m) cc_final: 0.8637 (p) REVERT: D 3093 SER cc_start: 0.8825 (p) cc_final: 0.8551 (m) REVERT: E 2987 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8342 (tp) REVERT: F 3007 ILE cc_start: 0.8901 (mm) cc_final: 0.8687 (mt) REVERT: F 3093 SER cc_start: 0.8819 (p) cc_final: 0.8565 (m) REVERT: F 3213 THR cc_start: 0.9131 (m) cc_final: 0.8534 (p) outliers start: 73 outliers final: 52 residues processed: 227 average time/residue: 0.2142 time to fit residues: 83.7945 Evaluate side-chains 220 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 165 time to evaluate : 1.803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3037 MET Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain B residue 3232 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 3007 ILE Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3063 ASN Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain D residue 3216 ILE Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2980 ASN Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3156 VAL Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain E residue 3220 ASN Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3063 ASN Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3220 ASN Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 99 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 62 optimal weight: 0.0470 chunk 193 optimal weight: 0.3980 chunk 195 optimal weight: 4.9990 chunk 88 optimal weight: 0.9980 chunk 97 optimal weight: 0.0970 chunk 5 optimal weight: 3.9990 chunk 156 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.5076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2980 ASN B2980 ASN C2980 ASN D2980 ASN E2980 ASN F2980 ASN G2980 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.108548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.091284 restraints weight = 21982.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2818 r_free = 0.2818 target = 0.090338 restraints weight = 31102.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.090990 restraints weight = 30150.767| |-----------------------------------------------------------------------------| r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8257 moved from start: 0.3568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.147 17745 Z= 0.158 Angle : 0.823 59.200 24542 Z= 0.491 Chirality : 0.049 0.445 3017 Planarity : 0.005 0.118 3213 Dihedral : 4.194 32.925 2499 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.24 % Allowed : 14.14 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.56 (0.16), residues: 847 loop : 0.51 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F3185 HIS 0.001 0.001 HIS A3152 PHE 0.005 0.001 PHE E3079 TYR 0.013 0.001 TYR F3048 ARG 0.005 0.001 ARG C3059 Details of bonding type rmsd hydrogen bonds : bond 0.03376 ( 504) hydrogen bonds : angle 5.17723 ( 1449) SS BOND : bond 0.01029 ( 28) SS BOND : angle 5.16905 ( 56) covalent geometry : bond 0.00365 (17717) covalent geometry : angle 0.78635 (24486) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 1.788 Fit side-chains revert: symmetry clash REVERT: A 3007 ILE cc_start: 0.8872 (mm) cc_final: 0.8564 (mt) REVERT: B 3186 SER cc_start: 0.9071 (t) cc_final: 0.8673 (m) REVERT: B 3232 THR cc_start: 0.8319 (OUTLIER) cc_final: 0.8085 (t) REVERT: C 3213 THR cc_start: 0.9023 (m) cc_final: 0.8634 (p) REVERT: D 3093 SER cc_start: 0.8824 (p) cc_final: 0.8549 (m) REVERT: E 2987 ILE cc_start: 0.8554 (OUTLIER) cc_final: 0.8331 (tp) REVERT: F 3093 SER cc_start: 0.8831 (p) cc_final: 0.8573 (m) REVERT: F 3213 THR cc_start: 0.9065 (m) cc_final: 0.8531 (p) outliers start: 66 outliers final: 54 residues processed: 209 average time/residue: 0.2005 time to fit residues: 72.2997 Evaluate side-chains 220 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 164 time to evaluate : 1.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 2980 ASN Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 2980 ASN Chi-restraints excluded: chain B residue 3037 MET Chi-restraints excluded: chain B residue 3049 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain B residue 3232 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 3007 ILE Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 2980 ASN Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain D residue 3216 ILE Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3156 VAL Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain E residue 3220 ASN Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3220 ASN Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 164 optimal weight: 3.9990 chunk 146 optimal weight: 0.9980 chunk 109 optimal weight: 8.9990 chunk 96 optimal weight: 2.9990 chunk 201 optimal weight: 0.7980 chunk 194 optimal weight: 0.2980 chunk 91 optimal weight: 0.9980 chunk 158 optimal weight: 2.9990 chunk 180 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 162 optimal weight: 2.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B2975 ASN B2980 ASN C2980 ASN D2980 ASN ** E2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F2980 ASN G2980 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.108543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2830 r_free = 0.2830 target = 0.091238 restraints weight = 21952.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.090007 restraints weight = 29147.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2828 r_free = 0.2828 target = 0.091029 restraints weight = 31210.430| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.163 17745 Z= 0.308 Angle : 1.154 59.200 24542 Z= 0.740 Chirality : 0.054 0.703 3017 Planarity : 0.006 0.116 3213 Dihedral : 4.228 31.086 2499 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.44 % Allowed : 13.84 % Favored : 82.72 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.67 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.56 (0.16), residues: 847 loop : 0.50 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A3185 HIS 0.001 0.001 HIS A3152 PHE 0.005 0.001 PHE A3191 TYR 0.013 0.001 TYR F3048 ARG 0.005 0.001 ARG C3059 Details of bonding type rmsd hydrogen bonds : bond 0.03394 ( 504) hydrogen bonds : angle 5.17283 ( 1449) SS BOND : bond 0.00553 ( 28) SS BOND : angle 4.78293 ( 56) covalent geometry : bond 0.00560 (17717) covalent geometry : angle 1.13284 (24486) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4638.07 seconds wall clock time: 82 minutes 27.42 seconds (4947.42 seconds total)