Starting phenix.real_space_refine on Mon Nov 18 20:39:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g8b_51127/11_2024/9g8b_51127.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g8b_51127/11_2024/9g8b_51127.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g8b_51127/11_2024/9g8b_51127.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g8b_51127/11_2024/9g8b_51127.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g8b_51127/11_2024/9g8b_51127.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9g8b_51127/11_2024/9g8b_51127.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.141 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 91 5.16 5 C 10703 2.51 5 N 2849 2.21 5 O 3703 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 17346 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 2478 Number of conformers: 1 Conformer: "" Number of residues, atoms: 345, 2478 Classifications: {'peptide': 345} Link IDs: {'PTRANS': 23, 'TRANS': 321} Restraints were copied for chains: C, B, E, D, G, F Time building chain proxies: 6.39, per 1000 atoms: 0.37 Number of scatterers: 17346 At special positions: 0 Unit cell: (101.175, 102.24, 185.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 91 16.00 O 3703 8.00 N 2849 7.00 C 10703 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, 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 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 4.73 Conformation dependent library (CDL) restraints added in 2.7 seconds 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4382 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 70 sheets defined 6.1% alpha, 37.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 3.56 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: 7.01 Time building geometry restraints manager: 5.36 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: 9914 14.00 - 28.00: 362 28.00 - 42.00: 52 42.00 - 56.00: 8 56.00 - 70.00: 8 Dihedral angle restraints: 10344 sinusoidal: 3484 harmonic: 6860 Sorted by residual: dihedral pdb=" CB CYS A2906 " pdb=" SG CYS A2906 " pdb=" SG CYS A3058 " pdb=" CB CYS A3058 " ideal model delta sinusoidal sigma weight residual 93.00 126.94 -33.94 1 1.00e+01 1.00e-02 1.64e+01 dihedral pdb=" C HIS E3152 " pdb=" N HIS E3152 " pdb=" CA HIS E3152 " pdb=" CB HIS E3152 " ideal model delta harmonic sigma weight residual -122.60 -112.79 -9.81 0 2.50e+00 1.60e-01 1.54e+01 dihedral pdb=" C HIS G3152 " pdb=" N HIS G3152 " pdb=" CA HIS G3152 " pdb=" CB HIS G3152 " ideal model delta harmonic sigma weight residual -122.60 -112.80 -9.80 0 2.50e+00 1.60e-01 1.54e+01 ... (remaining 10341 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: 2.03 - 2.60: 213 2.60 - 3.18: 15424 3.18 - 3.75: 25794 3.75 - 4.33: 36105 4.33 - 4.90: 59186 Nonbonded interactions: 136722 Sorted by model distance: nonbonded pdb=" SG CYS E3001 " pdb=" SG CYS E3051 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS D3001 " pdb=" SG CYS D3051 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS G3001 " pdb=" SG CYS G3051 " model vdw 2.028 3.760 nonbonded pdb=" SG CYS C3001 " pdb=" SG CYS C3051 " model vdw 2.029 3.760 nonbonded pdb=" SG CYS B3001 " pdb=" SG CYS B3051 " model vdw 2.029 3.760 ... (remaining 136717 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: 0.00 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: 1.390 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: 0.670 Check model and map are aligned: 0.110 Set scattering table: 0.190 Process input model: 39.320 Find NCS groups from input model: 0.870 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.480 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.080 ------------------------------------------------------------------------------- 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 17717 Z= 1.195 Angle : 1.485 11.966 24486 Z= 0.970 Chirality : 0.080 0.417 3017 Planarity : 0.008 0.051 3213 Dihedral : 8.253 69.997 5950 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 3.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 1.03 (0.16), residues: 868 loop : 1.26 (0.16), residues: 1533 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.006 TRP F3185 HIS 0.009 0.006 HIS B3152 PHE 0.055 0.008 PHE B3164 TYR 0.049 0.007 TYR B3048 ARG 0.001 0.000 ARG F2969 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4802 Ramachandran restraints generated. 2401 Oldfield, 0 Emsley, 2401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 396 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 396 time to evaluate : 1.954 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: 0.1920 time to fit residues: 133.1792 Evaluate side-chains 151 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 151 time to evaluate : 1.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 200 optimal weight: 1.9990 chunk 180 optimal weight: 3.9990 chunk 100 optimal weight: 0.8980 chunk 61 optimal weight: 0.9990 chunk 121 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 186 optimal weight: 0.7980 chunk 72 optimal weight: 2.9990 chunk 113 optimal weight: 0.9990 chunk 138 optimal weight: 0.9980 chunk 216 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3063 ASN B3063 ASN C2942 ASN D3063 ASN E3063 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7991 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 17717 Z= 0.244 Angle : 0.589 7.097 24486 Z= 0.325 Chirality : 0.050 0.146 3017 Planarity : 0.005 0.032 3213 Dihedral : 4.749 17.563 2499 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer: Outliers : 3.04 % Allowed : 7.27 % Favored : 89.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 1.07 (0.16), residues: 854 loop : 1.08 (0.17), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E3047 HIS 0.002 0.001 HIS F3152 PHE 0.007 0.001 PHE C2903 TYR 0.015 0.001 TYR F3048 ARG 0.003 0.001 ARG D2969 *********************** 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 306 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 244 time to evaluate : 2.026 Fit side-chains revert: symmetry clash REVERT: A 3156 VAL cc_start: 0.8624 (t) cc_final: 0.8365 (m) REVERT: B 3213 THR cc_start: 0.8976 (m) cc_final: 0.8758 (p) REVERT: C 3213 THR cc_start: 0.9148 (m) cc_final: 0.8880 (p) REVERT: D 3093 SER cc_start: 0.8843 (p) cc_final: 0.8637 (p) REVERT: E 3213 THR cc_start: 0.8962 (m) cc_final: 0.8712 (p) REVERT: F 3093 SER cc_start: 0.8832 (p) cc_final: 0.8617 (m) REVERT: F 3213 THR cc_start: 0.9055 (m) cc_final: 0.8722 (p) REVERT: G 3213 THR cc_start: 0.9061 (m) cc_final: 0.8825 (p) outliers start: 62 outliers final: 38 residues processed: 279 average time/residue: 0.2013 time to fit residues: 99.2763 Evaluate side-chains 198 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 160 time to evaluate : 2.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2941 THR Chi-restraints excluded: chain A residue 2967 THR Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3063 ASN Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3063 ASN Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 3023 SER Chi-restraints excluded: chain C residue 3037 MET Chi-restraints excluded: chain C residue 3081 ASP Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3063 ASN Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3023 SER Chi-restraints excluded: chain E residue 3063 ASN Chi-restraints excluded: chain F residue 2941 THR Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 120 optimal weight: 0.4980 chunk 67 optimal weight: 7.9990 chunk 179 optimal weight: 0.7980 chunk 147 optimal weight: 0.9980 chunk 59 optimal weight: 4.9990 chunk 216 optimal weight: 4.9990 chunk 233 optimal weight: 4.9990 chunk 192 optimal weight: 0.2980 chunk 214 optimal weight: 0.6980 chunk 73 optimal weight: 8.9990 chunk 173 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3063 ASN B2942 ASN B3041 ASN B3063 ASN ** C3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D2942 ASN D3041 ASN D3063 ASN E3041 ASN E3063 ASN G2942 ASN G3063 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.2573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 17717 Z= 0.185 Angle : 0.515 5.886 24486 Z= 0.282 Chirality : 0.047 0.143 3017 Planarity : 0.004 0.031 3213 Dihedral : 4.324 17.835 2499 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 3.09 % Allowed : 10.90 % Favored : 86.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 1.01 (0.16), residues: 854 loop : 1.12 (0.17), residues: 1547 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G3185 HIS 0.002 0.001 HIS C3152 PHE 0.006 0.001 PHE E3164 TYR 0.014 0.001 TYR E3048 ARG 0.005 0.000 ARG C3059 *********************** 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 229 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 166 time to evaluate : 1.932 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8735 (mm) cc_final: 0.8516 (mt) REVERT: A 3063 ASN cc_start: 0.8714 (OUTLIER) cc_final: 0.8394 (p0) REVERT: A 3156 VAL cc_start: 0.8679 (t) cc_final: 0.8449 (m) REVERT: B 3213 THR cc_start: 0.8942 (m) cc_final: 0.8713 (p) REVERT: C 3093 SER cc_start: 0.8852 (p) cc_final: 0.8643 (p) REVERT: C 3213 THR cc_start: 0.9138 (m) cc_final: 0.8894 (p) REVERT: E 3213 THR cc_start: 0.8976 (m) cc_final: 0.8747 (p) REVERT: F 3213 THR cc_start: 0.9076 (m) cc_final: 0.8786 (p) REVERT: G 2987 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8290 (tp) REVERT: G 3213 THR cc_start: 0.9074 (m) cc_final: 0.8842 (p) outliers start: 63 outliers final: 45 residues processed: 211 average time/residue: 0.1967 time to fit residues: 73.7995 Evaluate side-chains 189 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 142 time to evaluate : 1.924 ------------------------------------------------------------------------------- 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 3063 ASN Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain B residue 2934 LEU Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3121 MET Chi-restraints excluded: chain B residue 3156 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 3037 MET Chi-restraints excluded: chain C residue 3074 ASP 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 D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3123 VAL 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 2967 THR Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3074 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3216 ILE Chi-restraints excluded: chain G residue 2946 ILE Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 2987 ILE Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3195 VAL 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 213 optimal weight: 2.9990 chunk 162 optimal weight: 0.3980 chunk 112 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 103 optimal weight: 3.9990 chunk 145 optimal weight: 1.9990 chunk 217 optimal weight: 5.9990 chunk 230 optimal weight: 1.9990 chunk 113 optimal weight: 3.9990 chunk 205 optimal weight: 5.9990 chunk 61 optimal weight: 3.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A3041 ASN A3063 ASN C3063 ASN D2942 ASN F3063 ASN G3041 ASN ** G3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 17717 Z= 0.320 Angle : 0.538 4.992 24486 Z= 0.295 Chirality : 0.049 0.178 3017 Planarity : 0.005 0.045 3213 Dihedral : 4.275 17.357 2499 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 2.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.61 % Allowed : 10.21 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.74 (0.15), residues: 875 loop : 0.92 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP G3185 HIS 0.003 0.002 HIS F3152 PHE 0.009 0.002 PHE C3191 TYR 0.014 0.001 TYR A3048 ARG 0.002 0.000 ARG C3059 *********************** 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 262 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 168 time to evaluate : 2.278 Fit side-chains REVERT: A 3007 ILE cc_start: 0.8784 (mm) cc_final: 0.8547 (mt) REVERT: C 3093 SER cc_start: 0.8818 (p) cc_final: 0.8611 (p) REVERT: C 3213 THR cc_start: 0.9173 (m) cc_final: 0.8897 (p) REVERT: D 3074 ASP cc_start: 0.6943 (OUTLIER) cc_final: 0.6724 (m-30) REVERT: D 3093 SER cc_start: 0.8790 (p) cc_final: 0.8543 (m) REVERT: E 3213 THR cc_start: 0.8990 (m) cc_final: 0.8742 (p) REVERT: F 3213 THR cc_start: 0.9059 (m) cc_final: 0.8699 (p) REVERT: G 2955 VAL cc_start: 0.8214 (OUTLIER) cc_final: 0.7970 (t) outliers start: 94 outliers final: 54 residues processed: 236 average time/residue: 0.2197 time to fit residues: 91.6166 Evaluate side-chains 211 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 155 time to evaluate : 2.008 ------------------------------------------------------------------------------- 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 3093 SER Chi-restraints excluded: chain A residue 3157 THR Chi-restraints excluded: chain A residue 3205 THR 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 3216 ILE Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 2982 VAL 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 3157 THR Chi-restraints excluded: chain C residue 3205 THR Chi-restraints excluded: chain C residue 3216 ILE Chi-restraints excluded: chain D residue 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 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 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 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 2955 VAL Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 191 optimal weight: 0.7980 chunk 130 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 171 optimal weight: 2.9990 chunk 94 optimal weight: 0.0000 chunk 196 optimal weight: 4.9990 chunk 159 optimal weight: 0.8980 chunk 0 optimal weight: 6.9990 chunk 117 optimal weight: 1.9990 chunk 206 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 D2942 ASN ** F2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F3063 ASN ** G3063 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 17717 Z= 0.264 Angle : 0.505 5.179 24486 Z= 0.275 Chirality : 0.049 0.216 3017 Planarity : 0.005 0.050 3213 Dihedral : 4.166 17.463 2499 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 4.03 % Allowed : 11.09 % Favored : 84.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.68 (0.15), residues: 875 loop : 0.84 (0.16), residues: 1526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G3185 HIS 0.002 0.001 HIS F3152 PHE 0.008 0.001 PHE A3191 TYR 0.014 0.001 TYR A3048 ARG 0.003 0.000 ARG B2969 *********************** 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 261 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 179 time to evaluate : 2.023 Fit side-chains REVERT: B 3186 SER cc_start: 0.8940 (t) cc_final: 0.8598 (m) REVERT: C 3093 SER cc_start: 0.8802 (p) cc_final: 0.8594 (p) REVERT: C 3213 THR cc_start: 0.9167 (m) cc_final: 0.8879 (p) REVERT: D 3074 ASP cc_start: 0.6952 (OUTLIER) cc_final: 0.6736 (m-30) REVERT: D 3093 SER cc_start: 0.8784 (p) cc_final: 0.8556 (m) REVERT: F 3213 THR cc_start: 0.9063 (m) cc_final: 0.8702 (p) outliers start: 82 outliers final: 59 residues processed: 238 average time/residue: 0.1971 time to fit residues: 82.1349 Evaluate side-chains 222 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 162 time to evaluate : 1.981 ------------------------------------------------------------------------------- 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 3093 SER 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 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 2982 VAL 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 3157 THR 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 2967 THR Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3074 ASP Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2982 VAL 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 3216 ILE Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain F residue 3216 ILE Chi-restraints excluded: chain G residue 2946 ILE Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3074 ASP Chi-restraints excluded: chain G residue 3110 LEU Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 77 optimal weight: 0.9980 chunk 207 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 135 optimal weight: 6.9990 chunk 56 optimal weight: 0.5980 chunk 230 optimal weight: 0.9980 chunk 191 optimal weight: 1.9990 chunk 106 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 120 optimal weight: 0.6980 overall best weight: 0.8582 ------------------------------------------------------------------------------- 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 G3063 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8056 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17717 Z= 0.190 Angle : 0.471 4.946 24486 Z= 0.255 Chirality : 0.047 0.165 3017 Planarity : 0.005 0.052 3213 Dihedral : 3.996 20.460 2499 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 3.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 3.98 % Allowed : 11.93 % Favored : 84.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.67 (0.15), residues: 903 loop : 0.92 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G3185 HIS 0.002 0.001 HIS C3152 PHE 0.007 0.001 PHE C3191 TYR 0.012 0.001 TYR A3048 ARG 0.005 0.000 ARG B2969 *********************** 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 258 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 177 time to evaluate : 2.692 Fit side-chains REVERT: B 3186 SER cc_start: 0.8930 (t) cc_final: 0.8592 (m) REVERT: C 3213 THR cc_start: 0.9128 (m) cc_final: 0.8807 (p) REVERT: F 3213 THR cc_start: 0.9036 (m) cc_final: 0.8661 (p) REVERT: G 3171 ASN cc_start: 0.8307 (m-40) cc_final: 0.8099 (m-40) outliers start: 81 outliers final: 56 residues processed: 233 average time/residue: 0.2249 time to fit residues: 92.7004 Evaluate side-chains 222 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 166 time to evaluate : 2.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 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 2909 ASP 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 3216 ILE Chi-restraints excluded: chain C residue 2982 VAL 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 D residue 2934 LEU Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3114 VAL Chi-restraints excluded: chain D residue 3121 MET Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3157 THR Chi-restraints excluded: chain D residue 3195 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain E residue 2967 THR Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3121 MET Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3063 ASN Chi-restraints excluded: chain G residue 3110 LEU Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 222 optimal weight: 0.0980 chunk 25 optimal weight: 2.9990 chunk 131 optimal weight: 0.5980 chunk 168 optimal weight: 3.9990 chunk 130 optimal weight: 0.9990 chunk 193 optimal weight: 0.4980 chunk 128 optimal weight: 0.0040 chunk 229 optimal weight: 1.9990 chunk 143 optimal weight: 7.9990 chunk 139 optimal weight: 1.9990 chunk 105 optimal weight: 5.9990 overall best weight: 0.4394 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** G3063 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.3500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 17717 Z= 0.140 Angle : 0.462 6.394 24486 Z= 0.246 Chirality : 0.047 0.206 3017 Planarity : 0.004 0.043 3213 Dihedral : 3.854 22.783 2499 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 3.39 % Allowed : 13.30 % Favored : 83.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.82 (0.16), residues: 847 loop : 0.80 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP G3185 HIS 0.001 0.001 HIS C3152 PHE 0.005 0.001 PHE E3079 TYR 0.011 0.001 TYR A3048 ARG 0.004 0.001 ARG D2969 *********************** 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 245 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 176 time to evaluate : 2.135 Fit side-chains REVERT: B 3186 SER cc_start: 0.8899 (t) cc_final: 0.8573 (m) REVERT: C 3213 THR cc_start: 0.9096 (m) cc_final: 0.8789 (p) REVERT: F 3213 THR cc_start: 0.9017 (m) cc_final: 0.8621 (p) outliers start: 69 outliers final: 49 residues processed: 223 average time/residue: 0.2116 time to fit residues: 82.6385 Evaluate side-chains 215 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 166 time to evaluate : 1.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 2982 VAL Chi-restraints excluded: chain A residue 3037 MET Chi-restraints excluded: chain A residue 3110 LEU Chi-restraints excluded: chain A residue 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 2909 ASP Chi-restraints excluded: chain B residue 3029 ILE 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 2982 VAL 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 3216 ILE Chi-restraints excluded: chain D residue 2934 LEU Chi-restraints excluded: chain D residue 3019 THR 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 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 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 G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 141 optimal weight: 0.7980 chunk 91 optimal weight: 0.8980 chunk 137 optimal weight: 4.9990 chunk 69 optimal weight: 6.9990 chunk 45 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 145 optimal weight: 3.9990 chunk 156 optimal weight: 0.6980 chunk 113 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 180 optimal weight: 4.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ** G2980 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 17717 Z= 0.312 Angle : 0.520 5.531 24486 Z= 0.281 Chirality : 0.049 0.223 3017 Planarity : 0.005 0.052 3213 Dihedral : 4.130 24.580 2499 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 2.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.73 % Allowed : 13.21 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.58 (0.15), residues: 903 loop : 0.79 (0.17), residues: 1498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B2924 HIS 0.002 0.001 HIS D3152 PHE 0.010 0.002 PHE C3191 TYR 0.018 0.001 TYR A3048 ARG 0.004 0.000 ARG B2969 *********************** 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 243 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 167 time to evaluate : 2.075 Fit side-chains REVERT: B 3186 SER cc_start: 0.8935 (t) cc_final: 0.8577 (m) REVERT: F 3213 THR cc_start: 0.9023 (m) cc_final: 0.8661 (p) outliers start: 76 outliers final: 57 residues processed: 220 average time/residue: 0.2074 time to fit residues: 79.1601 Evaluate side-chains 217 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 160 time to evaluate : 1.968 ------------------------------------------------------------------------------- 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 3049 MET Chi-restraints excluded: chain A residue 3157 THR Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain A residue 3220 ASN Chi-restraints excluded: chain B residue 2909 ASP 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 B residue 3220 ASN Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 2982 VAL 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 3216 ILE Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 3019 THR 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 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3156 VAL Chi-restraints excluded: chain E residue 3195 VAL Chi-restraints excluded: chain E residue 3205 THR Chi-restraints excluded: chain E residue 3216 ILE Chi-restraints excluded: chain E residue 3220 ASN Chi-restraints excluded: chain F residue 2967 THR Chi-restraints excluded: chain F residue 2982 VAL Chi-restraints excluded: chain F residue 3019 THR Chi-restraints excluded: chain F residue 3037 MET Chi-restraints excluded: chain F residue 3128 ASP Chi-restraints excluded: chain F residue 3156 VAL Chi-restraints excluded: chain F residue 3157 THR Chi-restraints excluded: chain F residue 3195 VAL Chi-restraints excluded: chain F residue 3205 THR Chi-restraints excluded: chain G residue 2967 THR Chi-restraints excluded: chain G residue 2982 VAL Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 208 optimal weight: 7.9990 chunk 219 optimal weight: 0.7980 chunk 200 optimal weight: 0.8980 chunk 213 optimal weight: 2.9990 chunk 128 optimal weight: 0.0030 chunk 93 optimal weight: 1.9990 chunk 167 optimal weight: 7.9990 chunk 65 optimal weight: 7.9990 chunk 193 optimal weight: 0.5980 chunk 202 optimal weight: 0.9990 chunk 140 optimal weight: 0.0060 overall best weight: 0.4606 ------------------------------------------------------------------------------- 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 G2980 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8037 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 17717 Z= 0.142 Angle : 0.458 6.861 24486 Z= 0.245 Chirality : 0.047 0.145 3017 Planarity : 0.004 0.056 3213 Dihedral : 3.857 23.385 2499 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 3.29 % Allowed : 13.99 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.94 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.73 (0.16), residues: 847 loop : 0.71 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B2924 HIS 0.001 0.001 HIS F3152 PHE 0.005 0.001 PHE E3079 TYR 0.011 0.001 TYR C3048 ARG 0.004 0.000 ARG B2969 *********************** 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 240 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 173 time to evaluate : 2.191 Fit side-chains REVERT: B 3186 SER cc_start: 0.8876 (t) cc_final: 0.8556 (m) REVERT: C 3213 THR cc_start: 0.8951 (m) cc_final: 0.8646 (p) REVERT: F 3213 THR cc_start: 0.8988 (m) cc_final: 0.8588 (p) outliers start: 67 outliers final: 50 residues processed: 216 average time/residue: 0.2057 time to fit residues: 76.7099 Evaluate side-chains 214 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 164 time to evaluate : 2.001 ------------------------------------------------------------------------------- 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 3110 LEU Chi-restraints excluded: chain A residue 3157 THR Chi-restraints excluded: chain A residue 3195 VAL Chi-restraints excluded: chain A residue 3205 THR Chi-restraints excluded: chain A residue 3216 ILE Chi-restraints excluded: chain A residue 3220 ASN Chi-restraints excluded: chain B residue 2967 THR Chi-restraints excluded: chain B residue 3037 MET Chi-restraints excluded: chain B residue 3156 VAL Chi-restraints excluded: chain B residue 3157 THR Chi-restraints excluded: chain B residue 3195 VAL Chi-restraints excluded: chain B residue 3205 THR Chi-restraints excluded: chain B residue 3216 ILE Chi-restraints excluded: chain C residue 2967 THR Chi-restraints excluded: chain C residue 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 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 3205 THR Chi-restraints excluded: chain D residue 3216 ILE Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET Chi-restraints excluded: chain E residue 3121 MET Chi-restraints excluded: chain E residue 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 3037 MET 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 G residue 2967 THR Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR Chi-restraints excluded: chain G residue 3236 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 238 random chunks: chunk 226 optimal weight: 0.7980 chunk 137 optimal weight: 6.9990 chunk 107 optimal weight: 0.6980 chunk 157 optimal weight: 2.9990 chunk 237 optimal weight: 4.9990 chunk 218 optimal weight: 1.9990 chunk 188 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 145 optimal weight: 0.8980 chunk 115 optimal weight: 2.9990 chunk 149 optimal weight: 5.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8063 moved from start: 0.3739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 17717 Z= 0.215 Angle : 0.476 6.079 24486 Z= 0.255 Chirality : 0.047 0.165 3017 Planarity : 0.004 0.049 3213 Dihedral : 3.899 28.746 2499 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.04 % Allowed : 14.48 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.78 (0.16), residues: 847 loop : 0.66 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B2924 HIS 0.002 0.001 HIS F3152 PHE 0.007 0.001 PHE C3191 TYR 0.012 0.001 TYR C3048 ARG 0.004 0.000 ARG B2969 ********************** 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 228 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 166 time to evaluate : 1.941 Fit side-chains REVERT: A 2931 THR cc_start: 0.8899 (t) cc_final: 0.8679 (m) REVERT: B 3186 SER cc_start: 0.8897 (t) cc_final: 0.8558 (m) REVERT: C 3213 THR cc_start: 0.8960 (m) cc_final: 0.8656 (p) REVERT: F 3213 THR cc_start: 0.8996 (m) cc_final: 0.8616 (p) outliers start: 62 outliers final: 47 residues processed: 207 average time/residue: 0.2272 time to fit residues: 81.4310 Evaluate side-chains 209 residues out of total 2037 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 162 time to evaluate : 1.999 ------------------------------------------------------------------------------- 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 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 2909 ASP 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 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 3216 ILE Chi-restraints excluded: chain C residue 3220 ASN Chi-restraints excluded: chain D residue 3019 THR Chi-restraints excluded: chain D residue 3123 VAL Chi-restraints excluded: chain D residue 3128 ASP Chi-restraints excluded: chain D residue 3156 VAL Chi-restraints excluded: chain D residue 3205 THR Chi-restraints excluded: chain D residue 3216 ILE Chi-restraints excluded: chain E residue 2982 VAL Chi-restraints excluded: chain E residue 3019 THR Chi-restraints excluded: chain E residue 3037 MET 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 3037 MET 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 G residue 2967 THR Chi-restraints excluded: chain G residue 3049 MET Chi-restraints excluded: chain G residue 3156 VAL Chi-restraints excluded: chain G residue 3157 THR Chi-restraints excluded: chain G residue 3195 VAL Chi-restraints excluded: chain G residue 3205 THR 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 201 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 174 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 52 optimal weight: 0.6980 chunk 189 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 194 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 34 optimal weight: 6.9990 chunk 166 optimal weight: 0.5980 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 F3171 ASN G2980 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3033 r_free = 0.3033 target = 0.106144 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.089407 restraints weight = 22939.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.088279 restraints weight = 32340.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.089275 restraints weight = 34341.177| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8266 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 : 0.003 0.032 17717 Z= 0.213 Angle : 0.475 6.119 24486 Z= 0.254 Chirality : 0.048 0.156 3017 Planarity : 0.004 0.049 3213 Dihedral : 3.908 28.581 2499 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.04 % Allowed : 14.83 % Favored : 82.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.17), residues: 2401 helix: None (None), residues: 0 sheet: 0.75 (0.16), residues: 847 loop : 0.63 (0.17), residues: 1554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B2924 HIS 0.002 0.001 HIS F3152 PHE 0.007 0.001 PHE C3191 TYR 0.012 0.001 TYR C3048 ARG 0.004 0.000 ARG B2969 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3034.45 seconds wall clock time: 57 minutes 7.83 seconds (3427.83 seconds total)