Starting phenix.real_space_refine on Thu Sep 18 14:20:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9g8b_51127/09_2025/9g8b_51127.cif Found real_map, /net/cci-nas-00/data/ceres_data/9g8b_51127/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/9g8b_51127/09_2025/9g8b_51127.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9g8b_51127/09_2025/9g8b_51127.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9g8b_51127/09_2025/9g8b_51127.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9g8b_51127/09_2025/9g8b_51127.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: B, C, D, E, F, G Time building chain proxies: 2.43, per 1000 atoms: 0.14 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 B2906 " - pdb=" SG CYS B3058 " distance=2.04 Simple disulfide: pdb=" SG CYS C2906 " - pdb=" SG CYS C3058 " distance=2.04 Simple disulfide: pdb=" SG CYS D2906 " - pdb=" SG CYS D3058 " distance=2.04 Simple disulfide: pdb=" SG CYS E2906 " - pdb=" SG CYS E3058 " distance=2.04 Simple disulfide: pdb=" SG CYS F2906 " - pdb=" SG CYS F3058 " distance=2.04 Simple disulfide: pdb=" SG CYS G2906 " - pdb=" SG CYS G3058 " distance=2.04 Simple disulfide: pdb=" SG CYS B2988 " - pdb=" SG CYS B3140 " distance=2.04 Simple disulfide: pdb=" SG CYS C2988 " - pdb=" SG CYS C3140 " distance=2.04 Simple disulfide: pdb=" SG CYS D2988 " - pdb=" SG CYS D3140 " distance=2.04 Simple disulfide: pdb=" SG CYS E2988 " - pdb=" SG CYS E3140 " distance=2.04 Simple disulfide: pdb=" SG CYS F2988 " - pdb=" SG CYS F3140 " distance=2.04 Simple disulfide: pdb=" SG CYS G2988 " - pdb=" SG CYS G3140 " distance=2.04 Simple disulfide: pdb=" SG CYS B3001 " - pdb=" SG CYS B3051 " distance=2.03 Simple disulfide: pdb=" SG CYS C3001 " - pdb=" SG CYS C3051 " distance=2.03 Simple disulfide: pdb=" SG CYS D3001 " - pdb=" SG CYS D3051 " distance=2.03 Simple disulfide: pdb=" SG CYS E3001 " - pdb=" SG CYS E3051 " distance=2.03 Simple disulfide: pdb=" SG CYS F3001 " - pdb=" SG CYS F3051 " distance=2.03 Simple disulfide: pdb=" SG CYS G3001 " - pdb=" SG CYS G3051 " distance=2.03 Simple disulfide: pdb=" SG CYS B3085 " - pdb=" SG CYS B3222 " distance=2.04 Simple disulfide: pdb=" SG CYS C3085 " - pdb=" SG CYS C3222 " distance=2.04 Simple disulfide: pdb=" SG CYS D3085 " - pdb=" SG CYS D3222 " distance=2.04 Simple disulfide: pdb=" SG CYS E3085 " - pdb=" SG CYS E3222 " distance=2.04 Simple disulfide: pdb=" SG CYS F3085 " - pdb=" SG CYS F3222 " distance=2.04 Simple disulfide: pdb=" SG CYS G3085 " - pdb=" SG CYS G3222 " 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: 1.39 Conformation dependent library (CDL) restraints added in 899.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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: 1.02 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: 3.42 Time building geometry restraints manager: 1.90 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: 0.06 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 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: 0.010 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.250 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.59 (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 ARG 0.001 0.000 ARG F2969 TYR 0.049 0.007 TYR B3048 PHE 0.055 0.008 PHE B3164 TRP 0.024 0.006 TRP F3185 HIS 0.009 0.006 HIS B3152 Details of bonding type rmsd covalent geometry : bond 0.01795 (17717) covalent geometry : angle 1.48500 (24486) SS BOND : bond 0.00625 ( 28) SS BOND : angle 2.57364 ( 56) hydrogen bonds : bond 0.17405 ( 504) hydrogen bonds : angle 8.19665 ( 1449) *********************** 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 : 0.411 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: 0.0872 time to fit residues: 61.4060 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 : 0.636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 216 optimal weight: 0.7980 chunk 98 optimal weight: 1.9990 chunk 194 optimal weight: 3.9990 chunk 227 optimal weight: 0.8980 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 130 optimal weight: 0.9980 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 9.9990 chunk 235 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 G3063 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.111778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.093679 restraints weight = 21778.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.092855 restraints weight = 23514.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.094003 restraints weight = 24517.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.093905 restraints weight = 18986.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.095094 restraints weight = 17207.132| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8175 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 17745 Z= 0.160 Angle : 0.596 6.808 24542 Z= 0.332 Chirality : 0.049 0.150 3017 Planarity : 0.005 0.033 3213 Dihedral : 4.780 17.323 2499 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 2.45 % Allowed : 7.41 % Favored : 90.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 1.10 (0.16), residues: 840 loop : 1.14 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D2969 TYR 0.018 0.001 TYR F3048 PHE 0.010 0.001 PHE B3164 TRP 0.014 0.002 TRP A3047 HIS 0.003 0.002 HIS E3152 Details of bonding type rmsd covalent geometry : bond 0.00362 (17717) covalent geometry : angle 0.59340 (24486) SS BOND : bond 0.00122 ( 28) SS BOND : angle 1.33188 ( 56) hydrogen bonds : bond 0.04988 ( 504) hydrogen bonds : angle 6.24512 ( 1449) *********************** 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 281 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 231 time to evaluate : 0.773 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 3156 VAL cc_start: 0.8646 (t) cc_final: 0.8385 (m) REVERT: B 3007 ILE cc_start: 0.9088 (mm) cc_final: 0.8877 (mt) REVERT: B 3213 THR cc_start: 0.9113 (m) cc_final: 0.8818 (p) REVERT: C 3213 THR cc_start: 0.9260 (m) cc_final: 0.8900 (p) REVERT: D 3007 ILE cc_start: 0.9012 (mm) cc_final: 0.8787 (mt) REVERT: D 3093 SER cc_start: 0.8978 (p) cc_final: 0.8755 (p) REVERT: E 2987 ILE cc_start: 0.8321 (OUTLIER) cc_final: 0.8078 (tp) REVERT: E 3213 THR cc_start: 0.9153 (m) cc_final: 0.8832 (p) REVERT: F 3093 SER cc_start: 0.8946 (p) cc_final: 0.8729 (p) REVERT: F 3213 THR cc_start: 0.9156 (m) cc_final: 0.8765 (p) REVERT: G 3213 THR cc_start: 0.9230 (m) cc_final: 0.8895 (p) outliers start: 50 outliers final: 32 residues processed: 258 average time/residue: 0.0880 time to fit residues: 40.8582 Evaluate side-chains 189 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 156 time to evaluate : 0.641 ------------------------------------------------------------------------------- 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 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 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 3063 ASN 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 3037 MET Chi-restraints excluded: chain G residue 3063 ASN 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 62 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 195 optimal weight: 4.9990 chunk 106 optimal weight: 5.9990 chunk 214 optimal weight: 0.6980 chunk 234 optimal weight: 4.9990 chunk 176 optimal weight: 6.9990 chunk 184 optimal weight: 0.0870 chunk 169 optimal weight: 7.9990 chunk 144 optimal weight: 6.9990 chunk 13 optimal weight: 0.9990 overall best weight: 2.1564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3041 ASN A3063 ASN B2942 ASN B3041 ASN B3063 ASN C3063 ASN D2942 ASN D3041 ASN D3063 ASN E2942 ASN E3041 ASN E3063 ASN ** F3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G2942 ASN G3063 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.105441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.086733 restraints weight = 22349.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.086180 restraints weight = 21368.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.087019 restraints weight = 20872.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.087331 restraints weight = 17196.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.087507 restraints weight = 17317.483| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 17745 Z= 0.254 Angle : 0.606 5.069 24542 Z= 0.333 Chirality : 0.050 0.150 3017 Planarity : 0.005 0.044 3213 Dihedral : 4.620 17.827 2499 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 4.32 % Allowed : 9.23 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.96 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.66 (0.15), residues: 861 loop : 0.78 (0.16), residues: 1540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B2969 TYR 0.019 0.001 TYR E3048 PHE 0.011 0.002 PHE E3191 TRP 0.013 0.002 TRP A3047 HIS 0.003 0.002 HIS F3152 Details of bonding type rmsd covalent geometry : bond 0.00620 (17717) covalent geometry : angle 0.60465 (24486) SS BOND : bond 0.00292 ( 28) SS BOND : angle 1.06394 ( 56) hydrogen bonds : bond 0.04736 ( 504) hydrogen bonds : angle 5.71839 ( 1449) *********************** 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 256 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 168 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: A 3063 ASN cc_start: 0.8734 (OUTLIER) cc_final: 0.8429 (p0) REVERT: B 3063 ASN cc_start: 0.8673 (OUTLIER) cc_final: 0.8438 (p0) REVERT: C 3213 THR cc_start: 0.9335 (m) cc_final: 0.8950 (p) REVERT: D 3093 SER cc_start: 0.8984 (p) cc_final: 0.8751 (p) REVERT: E 2987 ILE cc_start: 0.8533 (OUTLIER) cc_final: 0.8288 (tp) REVERT: F 2959 ASN cc_start: 0.8335 (p0) cc_final: 0.8074 (p0) REVERT: F 3007 ILE cc_start: 0.9076 (mm) cc_final: 0.8815 (mt) REVERT: F 3093 SER cc_start: 0.8979 (p) cc_final: 0.8777 (p) REVERT: F 3213 THR cc_start: 0.9197 (m) cc_final: 0.8789 (p) outliers start: 88 outliers final: 60 residues processed: 236 average time/residue: 0.0839 time to fit residues: 34.9676 Evaluate side-chains 196 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 133 time to evaluate : 0.620 ------------------------------------------------------------------------------- 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 2941 THR Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3063 ASN 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 2941 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 2994 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 2941 THR Chi-restraints excluded: chain D residue 2946 ILE Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 2994 VAL 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 2941 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 3015 SER 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 3205 THR Chi-restraints excluded: chain E residue 3216 ILE 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 2994 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 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 2941 THR 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 3121 MET 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 235 optimal weight: 5.9990 chunk 224 optimal weight: 0.9980 chunk 157 optimal weight: 0.5980 chunk 5 optimal weight: 0.3980 chunk 204 optimal weight: 6.9990 chunk 213 optimal weight: 0.0980 chunk 221 optimal weight: 0.7980 chunk 226 optimal weight: 0.0570 chunk 190 optimal weight: 0.5980 chunk 171 optimal weight: 7.9990 chunk 225 optimal weight: 0.8980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3063 ASN B2942 ASN B3063 ASN C3063 ASN F3063 ASN G3041 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.110294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.093805 restraints weight = 21805.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.092982 restraints weight = 28176.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.093668 restraints weight = 27316.914| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.094191 restraints weight = 20590.299| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.094292 restraints weight = 17721.681| |-----------------------------------------------------------------------------| r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.2900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 17745 Z= 0.093 Angle : 0.482 7.486 24542 Z= 0.263 Chirality : 0.047 0.146 3017 Planarity : 0.004 0.033 3213 Dihedral : 4.165 17.881 2499 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 2.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.29 % Favored : 98.71 % Rotamer: Outliers : 3.49 % Allowed : 11.54 % Favored : 84.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.14 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.69 (0.16), residues: 882 loop : 0.98 (0.17), residues: 1519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B2969 TYR 0.014 0.001 TYR C3048 PHE 0.005 0.001 PHE F3079 TRP 0.011 0.001 TRP G3185 HIS 0.002 0.001 HIS C3152 Details of bonding type rmsd covalent geometry : bond 0.00204 (17717) covalent geometry : angle 0.48121 (24486) SS BOND : bond 0.00209 ( 28) SS BOND : angle 0.66453 ( 56) hydrogen bonds : bond 0.03658 ( 504) hydrogen bonds : angle 5.44546 ( 1449) *********************** 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 266 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 195 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: A 3007 ILE cc_start: 0.8890 (mm) cc_final: 0.8608 (mt) REVERT: A 3186 SER cc_start: 0.8988 (p) cc_final: 0.8765 (m) REVERT: C 3093 SER cc_start: 0.8896 (p) cc_final: 0.8675 (p) REVERT: C 3213 THR cc_start: 0.9253 (m) cc_final: 0.8881 (p) REVERT: D 3093 SER cc_start: 0.8864 (p) cc_final: 0.8621 (m) REVERT: E 2987 ILE cc_start: 0.8552 (OUTLIER) cc_final: 0.8323 (tp) REVERT: E 3213 THR cc_start: 0.9005 (m) cc_final: 0.8643 (p) REVERT: F 3007 ILE cc_start: 0.8924 (mm) cc_final: 0.8670 (mt) REVERT: F 3093 SER cc_start: 0.8799 (p) cc_final: 0.8596 (m) REVERT: F 3213 THR cc_start: 0.9135 (m) cc_final: 0.8711 (p) outliers start: 71 outliers final: 43 residues processed: 257 average time/residue: 0.0825 time to fit residues: 37.5236 Evaluate side-chains 211 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 167 time to evaluate : 0.548 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 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 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 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 2982 VAL Chi-restraints excluded: chain E residue 2987 ILE Chi-restraints excluded: chain E residue 3019 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 E residue 3220 ASN Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3063 ASN Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3195 VAL 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 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 75 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 178 optimal weight: 0.0000 chunk 41 optimal weight: 4.9990 chunk 189 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 195 optimal weight: 5.9990 chunk 172 optimal weight: 6.9990 chunk 204 optimal weight: 7.9990 chunk 124 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 3.5992 ------------------------------------------------------------------------------- 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** C3041 ASN ** E2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3063 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.101306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.084006 restraints weight = 22701.647| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.082754 restraints weight = 31890.660| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.083859 restraints weight = 35643.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.083537 restraints weight = 24582.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.083828 restraints weight = 27852.823| |-----------------------------------------------------------------------------| r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.067 17745 Z= 0.388 Angle : 0.683 6.605 24542 Z= 0.376 Chirality : 0.055 0.228 3017 Planarity : 0.006 0.069 3213 Dihedral : 4.896 24.132 2499 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 4.71 % Allowed : 11.05 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.35 (0.16), residues: 2401 helix: None (None), residues: 0 sheet: 0.23 (0.15), residues: 875 loop : 0.36 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG E3059 TYR 0.021 0.002 TYR F3048 PHE 0.016 0.003 PHE C3191 TRP 0.015 0.003 TRP G3185 HIS 0.003 0.002 HIS F3152 Details of bonding type rmsd covalent geometry : bond 0.00955 (17717) covalent geometry : angle 0.67967 (24486) SS BOND : bond 0.00578 ( 28) SS BOND : angle 1.57123 ( 56) hydrogen bonds : bond 0.05155 ( 504) hydrogen bonds : angle 5.66587 ( 1449) *********************** 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 269 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 173 time to evaluate : 0.636 Fit side-chains REVERT: B 3183 TYR cc_start: 0.9216 (m-80) cc_final: 0.8945 (m-80) REVERT: D 3074 ASP cc_start: 0.7259 (OUTLIER) cc_final: 0.7024 (m-30) REVERT: D 3093 SER cc_start: 0.9057 (p) cc_final: 0.8826 (p) REVERT: E 2987 ILE cc_start: 0.8725 (OUTLIER) cc_final: 0.8461 (tp) REVERT: F 3063 ASN cc_start: 0.8720 (OUTLIER) cc_final: 0.8518 (p0) REVERT: F 3213 THR cc_start: 0.9211 (m) cc_final: 0.8799 (p) outliers start: 96 outliers final: 75 residues processed: 243 average time/residue: 0.0937 time to fit residues: 38.8454 Evaluate side-chains 236 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 158 time to evaluate : 0.639 ------------------------------------------------------------------------------- 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 3015 SER Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3156 VAL 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 3220 ASN Chi-restraints excluded: chain B residue 2967 THR 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 3213 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain B residue 3220 ASN Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 2994 VAL Chi-restraints excluded: chain C residue 3007 ILE Chi-restraints excluded: chain C residue 3015 SER Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3156 VAL Chi-restraints excluded: chain C residue 3157 THR 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 2994 VAL 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 3213 THR Chi-restraints excluded: chain D residue 3220 ASN 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 2994 VAL Chi-restraints excluded: chain E residue 3015 SER 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 3157 THR Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3213 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain E residue 3220 ASN Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 2994 VAL Chi-restraints excluded: chain F residue 3019 THR 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 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3220 ASN Chi-restraints excluded: chain G residue 2945 LEU Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3015 SER 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 Chi-restraints excluded: chain G residue 3236 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 24 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 227 optimal weight: 0.9980 chunk 146 optimal weight: 0.8980 chunk 217 optimal weight: 1.9990 chunk 195 optimal weight: 1.9990 chunk 97 optimal weight: 0.4980 chunk 39 optimal weight: 0.9980 chunk 83 optimal weight: 0.8980 chunk 145 optimal weight: 0.9980 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D2980 ASN E2980 ASN ** F2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3063 ASN ** G2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.106465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.089419 restraints weight = 22079.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.088652 restraints weight = 30273.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.089237 restraints weight = 30179.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.089558 restraints weight = 24193.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.089583 restraints weight = 21606.686| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3429 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= 0.118 Angle : 0.496 5.317 24542 Z= 0.270 Chirality : 0.048 0.179 3017 Planarity : 0.005 0.047 3213 Dihedral : 4.329 23.004 2499 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer: Outliers : 3.53 % Allowed : 13.25 % Favored : 83.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.51 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.28 (0.15), residues: 903 loop : 0.51 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C3059 TYR 0.014 0.001 TYR F3048 PHE 0.008 0.001 PHE E2989 TRP 0.020 0.001 TRP G3185 HIS 0.001 0.001 HIS E3152 Details of bonding type rmsd covalent geometry : bond 0.00277 (17717) covalent geometry : angle 0.49254 (24486) SS BOND : bond 0.00531 ( 28) SS BOND : angle 1.31306 ( 56) hydrogen bonds : bond 0.03705 ( 504) hydrogen bonds : angle 5.44727 ( 1449) *********************** 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 245 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 173 time to evaluate : 0.667 Fit side-chains REVERT: B 3186 SER cc_start: 0.9102 (t) cc_final: 0.8695 (m) REVERT: C 3093 SER cc_start: 0.8977 (p) cc_final: 0.8776 (p) REVERT: C 3213 THR cc_start: 0.9286 (m) cc_final: 0.8884 (p) REVERT: D 3074 ASP cc_start: 0.7093 (OUTLIER) cc_final: 0.6859 (m-30) REVERT: D 3093 SER cc_start: 0.8940 (p) cc_final: 0.8648 (m) REVERT: E 2987 ILE cc_start: 0.8447 (OUTLIER) cc_final: 0.8205 (tp) REVERT: E 3213 THR cc_start: 0.9034 (m) cc_final: 0.8732 (p) REVERT: F 3007 ILE cc_start: 0.8971 (mm) cc_final: 0.8710 (mt) REVERT: F 3213 THR cc_start: 0.9092 (m) cc_final: 0.8636 (p) outliers start: 72 outliers final: 52 residues processed: 229 average time/residue: 0.0952 time to fit residues: 37.4917 Evaluate side-chains 217 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 163 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3081 ASP Chi-restraints excluded: chain A residue 3093 SER Chi-restraints excluded: chain A residue 3157 THR Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE 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 3220 ASN Chi-restraints excluded: chain C residue 3049 MET 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 3114 VAL 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 3220 ASN Chi-restraints excluded: chain E residue 2909 ASP 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 3110 LEU 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 3019 THR Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3121 MET Chi-restraints excluded: chain F residue 3123 VAL Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3220 ASN 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 204 optimal weight: 7.9990 chunk 156 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 93 optimal weight: 5.9990 chunk 99 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 190 optimal weight: 2.9990 chunk 108 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 chunk 177 optimal weight: 8.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- 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 F3063 ASN F3119 ASN G2980 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.101529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.084202 restraints weight = 22470.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.082927 restraints weight = 31559.110| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.084065 restraints weight = 34919.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.083784 restraints weight = 24092.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.084006 restraints weight = 28169.105| |-----------------------------------------------------------------------------| r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.057 17745 Z= 0.330 Angle : 0.633 6.238 24542 Z= 0.344 Chirality : 0.053 0.225 3017 Planarity : 0.006 0.072 3213 Dihedral : 4.825 28.621 2499 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.12 % Allowed : 13.11 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.06 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: -0.10 (0.15), residues: 917 loop : 0.26 (0.17), residues: 1484 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG D2969 TYR 0.019 0.002 TYR A3048 PHE 0.014 0.002 PHE G3191 TRP 0.014 0.002 TRP G3185 HIS 0.002 0.001 HIS G3152 Details of bonding type rmsd covalent geometry : bond 0.00811 (17717) covalent geometry : angle 0.62794 (24486) SS BOND : bond 0.00374 ( 28) SS BOND : angle 1.71820 ( 56) hydrogen bonds : bond 0.04776 ( 504) hydrogen bonds : angle 5.60452 ( 1449) *********************** 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 259 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 175 time to evaluate : 0.678 Fit side-chains REVERT: A 2931 THR cc_start: 0.9290 (t) cc_final: 0.8990 (m) REVERT: D 3093 SER cc_start: 0.9051 (p) cc_final: 0.8847 (p) REVERT: F 3213 THR cc_start: 0.9218 (m) cc_final: 0.8771 (p) outliers start: 84 outliers final: 59 residues processed: 235 average time/residue: 0.1074 time to fit residues: 41.6846 Evaluate side-chains 223 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 164 time to evaluate : 0.592 ------------------------------------------------------------------------------- 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 3081 ASP 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 3037 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 3213 THR Chi-restraints excluded: chain B residue 3216 ILE 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 3156 VAL Chi-restraints excluded: chain C residue 3195 VAL Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR 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 3156 VAL 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 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 3063 ASN Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3123 VAL 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 2967 THR Chi-restraints excluded: chain G residue 2982 VAL 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 196 optimal weight: 1.9990 chunk 188 optimal weight: 0.8980 chunk 140 optimal weight: 4.9990 chunk 112 optimal weight: 0.9990 chunk 40 optimal weight: 0.9990 chunk 175 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 104 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 F3063 ASN G2980 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.105571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.088054 restraints weight = 22341.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.086853 restraints weight = 33548.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.087929 restraints weight = 35116.085| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.088027 restraints weight = 23599.703| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2794 r_free = 0.2794 target = 0.088712 restraints weight = 21336.381| |-----------------------------------------------------------------------------| r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.3701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 17745 Z= 0.125 Angle : 0.502 6.631 24542 Z= 0.271 Chirality : 0.048 0.211 3017 Planarity : 0.005 0.053 3213 Dihedral : 4.386 26.018 2499 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 3.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 3.93 % Allowed : 13.84 % Favored : 82.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.16 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.22 (0.16), residues: 847 loop : 0.14 (0.16), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B3059 TYR 0.013 0.001 TYR F3048 PHE 0.006 0.001 PHE F3164 TRP 0.020 0.002 TRP G3185 HIS 0.001 0.001 HIS E3152 Details of bonding type rmsd covalent geometry : bond 0.00298 (17717) covalent geometry : angle 0.49932 (24486) SS BOND : bond 0.00233 ( 28) SS BOND : angle 1.24892 ( 56) hydrogen bonds : bond 0.03678 ( 504) hydrogen bonds : angle 5.42259 ( 1449) *********************** 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: 80 poor density : 171 time to evaluate : 0.635 Fit side-chains REVERT: A 2931 THR cc_start: 0.9219 (t) cc_final: 0.8913 (m) REVERT: B 3186 SER cc_start: 0.9098 (t) cc_final: 0.8680 (m) REVERT: C 3213 THR cc_start: 0.9311 (m) cc_final: 0.8871 (p) REVERT: D 3093 SER cc_start: 0.8981 (p) cc_final: 0.8655 (m) REVERT: E 2987 ILE cc_start: 0.8430 (OUTLIER) cc_final: 0.8151 (tp) REVERT: F 3007 ILE cc_start: 0.8916 (mm) cc_final: 0.8678 (mt) REVERT: F 3213 THR cc_start: 0.9145 (m) cc_final: 0.8559 (p) outliers start: 80 outliers final: 56 residues processed: 227 average time/residue: 0.0920 time to fit residues: 36.1221 Evaluate side-chains 219 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 162 time to evaluate : 0.660 ------------------------------------------------------------------------------- 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 3081 ASP 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 2945 LEU Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3037 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 C residue 3049 MET Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3156 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 2967 THR Chi-restraints excluded: chain D residue 3019 THR 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 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain D residue 3220 ASN 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 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 2967 THR Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3123 VAL 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 2967 THR Chi-restraints excluded: chain G residue 2982 VAL 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 45 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 1 optimal weight: 0.9990 chunk 152 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 234 optimal weight: 3.9990 chunk 226 optimal weight: 0.0170 chunk 80 optimal weight: 4.9990 chunk 174 optimal weight: 5.9990 chunk 10 optimal weight: 3.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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 F3063 ASN G2980 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.106744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.089452 restraints weight = 22196.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.088175 restraints weight = 29687.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2796 r_free = 0.2796 target = 0.088838 restraints weight = 31630.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2799 r_free = 0.2799 target = 0.089034 restraints weight = 22381.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.089346 restraints weight = 20234.915| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.3792 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= 0.124 Angle : 0.495 7.022 24542 Z= 0.265 Chirality : 0.048 0.181 3017 Planarity : 0.005 0.044 3213 Dihedral : 4.174 30.475 2499 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 3.49 % Allowed : 14.48 % Favored : 82.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.31 (0.16), residues: 847 loop : 0.22 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG E3059 TYR 0.012 0.001 TYR C3048 PHE 0.007 0.001 PHE E3191 TRP 0.018 0.001 TRP G3185 HIS 0.001 0.001 HIS F3152 Details of bonding type rmsd covalent geometry : bond 0.00301 (17717) covalent geometry : angle 0.49240 (24486) SS BOND : bond 0.00186 ( 28) SS BOND : angle 1.17841 ( 56) hydrogen bonds : bond 0.03507 ( 504) hydrogen bonds : angle 5.20143 ( 1449) *********************** 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 249 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 178 time to evaluate : 0.491 Fit side-chains REVERT: A 2931 THR cc_start: 0.9211 (t) cc_final: 0.8937 (m) REVERT: B 3186 SER cc_start: 0.9073 (t) cc_final: 0.8669 (m) REVERT: D 3093 SER cc_start: 0.8923 (p) cc_final: 0.8640 (m) REVERT: E 2987 ILE cc_start: 0.8390 (OUTLIER) cc_final: 0.8118 (tp) REVERT: F 3007 ILE cc_start: 0.8840 (mm) cc_final: 0.8639 (mt) REVERT: F 3093 SER cc_start: 0.8515 (p) cc_final: 0.8314 (m) REVERT: F 3213 THR cc_start: 0.9072 (m) cc_final: 0.8551 (p) outliers start: 71 outliers final: 55 residues processed: 224 average time/residue: 0.0961 time to fit residues: 36.3691 Evaluate side-chains 221 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 165 time to evaluate : 0.630 ------------------------------------------------------------------------------- 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 3081 ASP 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 2945 LEU Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3037 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 C residue 2967 THR Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3121 MET Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 2967 THR 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 3220 ASN Chi-restraints excluded: chain E residue 2909 ASP 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 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 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3063 ASN Chi-restraints excluded: chain F residue 3123 VAL Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL 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 2967 THR Chi-restraints excluded: chain G residue 2982 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 129 optimal weight: 0.9990 chunk 52 optimal weight: 0.7980 chunk 62 optimal weight: 0.8980 chunk 213 optimal weight: 0.8980 chunk 177 optimal weight: 9.9990 chunk 83 optimal weight: 3.9990 chunk 86 optimal weight: 0.7980 chunk 74 optimal weight: 5.9990 chunk 140 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 7.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- 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 = 0.3041 r_free = 0.3041 target = 0.106732 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.089502 restraints weight = 22143.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2788 r_free = 0.2788 target = 0.088309 restraints weight = 29747.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2806 r_free = 0.2806 target = 0.089417 restraints weight = 31893.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.089239 restraints weight = 22915.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.089393 restraints weight = 19943.993| |-----------------------------------------------------------------------------| r_work (final): 0.2801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.3804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.156 17745 Z= 0.163 Angle : 0.722 59.181 24542 Z= 0.411 Chirality : 0.049 0.363 3017 Planarity : 0.005 0.043 3213 Dihedral : 4.225 32.401 2499 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 3.24 % Allowed : 15.12 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.29 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.32 (0.16), residues: 847 loop : 0.22 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B3059 TYR 0.012 0.001 TYR E3048 PHE 0.006 0.001 PHE E3191 TRP 0.017 0.001 TRP G3185 HIS 0.001 0.001 HIS F3152 Details of bonding type rmsd covalent geometry : bond 0.00378 (17717) covalent geometry : angle 0.69630 (24486) SS BOND : bond 0.01061 ( 28) SS BOND : angle 4.05659 ( 56) hydrogen bonds : bond 0.03491 ( 504) hydrogen bonds : angle 5.20136 ( 1449) ********************** 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 229 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 163 time to evaluate : 0.632 Fit side-chains revert: symmetry clash REVERT: A 2931 THR cc_start: 0.9210 (t) cc_final: 0.8927 (m) REVERT: B 3186 SER cc_start: 0.9071 (t) cc_final: 0.8668 (m) REVERT: D 3093 SER cc_start: 0.8926 (p) cc_final: 0.8636 (m) REVERT: E 2987 ILE cc_start: 0.8392 (OUTLIER) cc_final: 0.8124 (tp) REVERT: F 3213 THR cc_start: 0.9074 (m) cc_final: 0.8553 (p) outliers start: 66 outliers final: 58 residues processed: 205 average time/residue: 0.0970 time to fit residues: 33.4667 Evaluate side-chains 219 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 160 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2980 ASN Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3029 ILE Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3081 ASP 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 2945 LEU Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3037 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 C residue 2967 THR Chi-restraints excluded: chain C residue 3049 MET Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3156 VAL Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 2980 ASN Chi-restraints excluded: chain D residue 3019 THR 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 D residue 3220 ASN Chi-restraints excluded: chain E residue 2909 ASP 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 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 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3123 VAL Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL 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 2967 THR Chi-restraints excluded: chain G residue 2982 VAL 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 27 optimal weight: 0.9990 chunk 69 optimal weight: 5.9990 chunk 178 optimal weight: 0.7980 chunk 224 optimal weight: 0.9990 chunk 200 optimal weight: 3.9990 chunk 119 optimal weight: 0.0980 chunk 220 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 163 optimal weight: 1.9990 chunk 130 optimal weight: 3.9990 chunk 226 optimal weight: 0.2980 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A2980 ASN B2980 ASN B3063 ASN C2980 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 = 0.3044 r_free = 0.3044 target = 0.106915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2808 r_free = 0.2808 target = 0.089661 restraints weight = 22175.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.088480 restraints weight = 29641.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2807 r_free = 0.2807 target = 0.089482 restraints weight = 31833.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.089311 restraints weight = 24272.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.089939 restraints weight = 20976.135| |-----------------------------------------------------------------------------| r_work (final): 0.2811 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8291 moved from start: 0.3799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 17745 Z= 0.186 Angle : 0.958 59.198 24542 Z= 0.585 Chirality : 0.050 0.581 3017 Planarity : 0.005 0.111 3213 Dihedral : 4.270 32.219 2499 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 3.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.44 % Allowed : 14.97 % Favored : 81.59 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.31 (0.16), residues: 847 loop : 0.21 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B3059 TYR 0.012 0.001 TYR D3048 PHE 0.006 0.001 PHE E3191 TRP 0.016 0.001 TRP G3185 HIS 0.001 0.001 HIS F3152 Details of bonding type rmsd covalent geometry : bond 0.00380 (17717) covalent geometry : angle 0.94357 (24486) SS BOND : bond 0.00585 ( 28) SS BOND : angle 3.59383 ( 56) hydrogen bonds : bond 0.03470 ( 504) hydrogen bonds : angle 5.20219 ( 1449) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2258.45 seconds wall clock time: 39 minutes 56.61 seconds (2396.61 seconds total)