Starting phenix.real_space_refine on Mon Nov 17 14:01:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cu7_7618/11_2025/6cu7_7618.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cu7_7618/11_2025/6cu7_7618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6cu7_7618/11_2025/6cu7_7618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cu7_7618/11_2025/6cu7_7618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6cu7_7618/11_2025/6cu7_7618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cu7_7618/11_2025/6cu7_7618.map" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.001 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 2600 2.51 5 N 720 2.21 5 O 820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5881/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4140 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 414 Classifications: {'peptide': 60} Link IDs: {'TRANS': 59} Restraints were copied for chains: A, B, C, D, F, G, H, I, J Time building chain proxies: 0.63, per 1000 atoms: 0.15 Number of scatterers: 4140 At special positions: 0 Unit cell: (84.53, 103.79, 42.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 820 8.00 N 720 7.00 C 2600 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.33 Conformation dependent library (CDL) restraints added in 176.7 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 47.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 43 through 54 removed outlier: 6.896A pdb=" N THR A 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS C 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU A 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY C 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LYS E 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU C 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS E 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLY E 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N HIS C 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N VAL E 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY E 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.638A pdb=" N THR C 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ALA E 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 10.047A pdb=" N LYS C 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLU E 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N LYS C 60 " --> pdb=" O GLU E 57 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N THR E 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 8.519A pdb=" N GLN C 62 " --> pdb=" O THR E 59 " (cutoff:3.500A) removed outlier: 6.779A pdb=" N GLU E 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N THR C 64 " --> pdb=" O GLU E 61 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N VAL E 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LYS A 58 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLU C 61 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N LYS A 60 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N VAL C 63 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 43 through 54 removed outlier: 6.896A pdb=" N THR A 44 " --> pdb=" O LYS C 43 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N LYS C 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N GLU A 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N GLY C 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N VAL A 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N ALA C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR A 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 8.776A pdb=" N LYS E 43 " --> pdb=" O THR C 44 " (cutoff:3.500A) removed outlier: 9.694A pdb=" N GLU C 46 " --> pdb=" O LYS E 43 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N LYS E 45 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N VAL C 48 " --> pdb=" O LYS E 45 " (cutoff:3.500A) removed outlier: 5.742A pdb=" N GLY E 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N HIS C 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.625A pdb=" N VAL E 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N VAL C 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 8.828A pdb=" N GLY E 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 10.638A pdb=" N THR C 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 9.217A pdb=" N ALA E 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 9.221A pdb=" N THR E 44 " --> pdb=" O LYS G 45 " (cutoff:3.500A) removed outlier: 9.243A pdb=" N GLY G 47 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N GLU E 46 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N VAL G 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N VAL E 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 8.123A pdb=" N GLY G 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N HIS E 50 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 10.244A pdb=" N ALA G 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 8.747A pdb=" N VAL E 52 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 10.266A pdb=" N VAL G 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 9.100A pdb=" N THR E 54 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 9.861A pdb=" N GLU G 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N ALA E 56 " --> pdb=" O GLU G 57 " (cutoff:3.500A) removed outlier: 8.029A pdb=" N THR G 59 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LYS E 58 " --> pdb=" O THR G 59 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLU G 61 " --> pdb=" O LYS E 58 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LYS E 60 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N VAL G 63 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N GLN E 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N THR G 44 " --> pdb=" O LYS I 43 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N LYS I 45 " --> pdb=" O THR G 44 " (cutoff:3.500A) removed outlier: 6.821A pdb=" N GLU G 46 " --> pdb=" O LYS I 45 " (cutoff:3.500A) removed outlier: 6.920A pdb=" N GLY I 51 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL G 52 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA I 53 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N THR G 54 " --> pdb=" O ALA I 53 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N VAL I 55 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.751A pdb=" N ALA G 56 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N GLU I 57 " --> pdb=" O ALA G 56 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 70 through 73 removed outlier: 7.015A pdb=" N GLY A 73 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 5.748A pdb=" N VAL E 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 7.615A pdb=" N GLY C 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.214A pdb=" N THR E 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N GLY E 73 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLY G 73 " --> pdb=" O THR I 72 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 76 through 77 removed outlier: 6.082A pdb=" N ALA E 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 80 through 81 removed outlier: 5.940A pdb=" N LYS E 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 91 through 92 removed outlier: 6.328A pdb=" N ALA A 91 " --> pdb=" O THR C 92 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ALA E 91 " --> pdb=" O THR G 92 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ALA G 91 " --> pdb=" O THR I 92 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 43 through 54 removed outlier: 6.890A pdb=" N THR B 44 " --> pdb=" O LYS D 43 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N LYS D 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLU B 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLY D 51 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N VAL B 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA D 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N THR B 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N THR D 44 " --> pdb=" O LYS F 43 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LYS F 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N GLU D 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N GLY F 51 " --> pdb=" O HIS D 50 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL D 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N ALA F 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR D 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N THR F 44 " --> pdb=" O LYS H 43 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N LYS H 45 " --> pdb=" O THR F 44 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N GLU F 46 " --> pdb=" O LYS H 45 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N GLY H 51 " --> pdb=" O HIS F 50 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N VAL F 52 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ALA H 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N THR F 54 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N THR H 44 " --> pdb=" O LYS J 43 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LYS J 45 " --> pdb=" O THR H 44 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLU H 46 " --> pdb=" O LYS J 45 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N GLY J 51 " --> pdb=" O HIS H 50 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N VAL H 52 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ALA J 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N THR H 54 " --> pdb=" O ALA J 53 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 58 through 64 removed outlier: 6.318A pdb=" N LYS B 58 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 7.922A pdb=" N GLU D 61 " --> pdb=" O LYS B 58 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N LYS B 60 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL D 63 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N GLN B 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N LYS D 58 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLU F 61 " --> pdb=" O LYS D 58 " (cutoff:3.500A) removed outlier: 6.544A pdb=" N LYS D 60 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL F 63 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N GLN D 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N LYS F 58 " --> pdb=" O THR H 59 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N GLU H 61 " --> pdb=" O LYS F 58 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N LYS F 60 " --> pdb=" O GLU H 61 " (cutoff:3.500A) removed outlier: 7.507A pdb=" N VAL H 63 " --> pdb=" O LYS F 60 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N GLN F 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 6.477A pdb=" N LYS H 58 " --> pdb=" O THR J 59 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N GLU J 61 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N LYS H 60 " --> pdb=" O GLU J 61 " (cutoff:3.500A) removed outlier: 7.710A pdb=" N VAL J 63 " --> pdb=" O LYS H 60 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN H 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 70 through 73 removed outlier: 7.014A pdb=" N GLY B 73 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N GLY D 73 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N GLY F 73 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLY H 73 " --> pdb=" O THR J 72 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 76 through 77 Processing sheet with id=AB2, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AB3, first strand: chain 'B' and resid 91 through 92 removed outlier: 6.322A pdb=" N ALA B 91 " --> pdb=" O THR D 92 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ALA D 91 " --> pdb=" O THR F 92 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ALA F 91 " --> pdb=" O THR H 92 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ALA H 91 " --> pdb=" O THR J 92 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 64 hydrogen bonds defined for protein. 192 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: 0.53 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 710 1.28 - 1.35: 640 1.35 - 1.42: 180 1.42 - 1.49: 728 1.49 - 1.55: 1902 Bond restraints: 4160 Sorted by residual: bond pdb=" CB ASN B 65 " pdb=" CG ASN B 65 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CB ASN A 65 " pdb=" CG ASN A 65 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.76e+00 bond pdb=" CB ASN G 65 " pdb=" CG ASN G 65 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.73e+00 bond pdb=" CB ASN D 65 " pdb=" CG ASN D 65 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.70e+00 bond pdb=" CB ASN C 65 " pdb=" CG ASN C 65 " ideal model delta sigma weight residual 1.516 1.483 0.033 2.50e-02 1.60e+03 1.69e+00 ... (remaining 4155 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.25: 4690 1.25 - 2.51: 783 2.51 - 3.76: 117 3.76 - 5.01: 20 5.01 - 6.26: 10 Bond angle restraints: 5620 Sorted by residual: angle pdb=" N VAL D 40 " pdb=" CA VAL D 40 " pdb=" C VAL D 40 " ideal model delta sigma weight residual 113.42 110.46 2.96 1.17e+00 7.31e-01 6.39e+00 angle pdb=" N VAL C 40 " pdb=" CA VAL C 40 " pdb=" C VAL C 40 " ideal model delta sigma weight residual 113.42 110.46 2.96 1.17e+00 7.31e-01 6.38e+00 angle pdb=" N VAL J 40 " pdb=" CA VAL J 40 " pdb=" C VAL J 40 " ideal model delta sigma weight residual 113.42 110.48 2.94 1.17e+00 7.31e-01 6.33e+00 angle pdb=" N VAL F 40 " pdb=" CA VAL F 40 " pdb=" C VAL F 40 " ideal model delta sigma weight residual 113.42 110.48 2.94 1.17e+00 7.31e-01 6.30e+00 angle pdb=" N VAL G 40 " pdb=" CA VAL G 40 " pdb=" C VAL G 40 " ideal model delta sigma weight residual 113.42 110.49 2.93 1.17e+00 7.31e-01 6.27e+00 ... (remaining 5615 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 5.92: 1720 5.92 - 11.83: 450 11.83 - 17.75: 158 17.75 - 23.67: 82 23.67 - 29.58: 20 Dihedral angle restraints: 2430 sinusoidal: 810 harmonic: 1620 Sorted by residual: dihedral pdb=" CA TYR I 39 " pdb=" C TYR I 39 " pdb=" N VAL I 40 " pdb=" CA VAL I 40 " ideal model delta harmonic sigma weight residual 180.00 157.76 22.24 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA TYR H 39 " pdb=" C TYR H 39 " pdb=" N VAL H 40 " pdb=" CA VAL H 40 " ideal model delta harmonic sigma weight residual 180.00 157.79 22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA TYR A 39 " pdb=" C TYR A 39 " pdb=" N VAL A 40 " pdb=" CA VAL A 40 " ideal model delta harmonic sigma weight residual 180.00 157.80 22.20 0 5.00e+00 4.00e-02 1.97e+01 ... (remaining 2427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 370 0.041 - 0.082: 228 0.082 - 0.124: 98 0.124 - 0.165: 34 0.165 - 0.206: 10 Chirality restraints: 740 Sorted by residual: chirality pdb=" CB THR G 92 " pdb=" CA THR G 92 " pdb=" OG1 THR G 92 " pdb=" CG2 THR G 92 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CB THR E 92 " pdb=" CA THR E 92 " pdb=" OG1 THR E 92 " pdb=" CG2 THR E 92 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CB THR J 92 " pdb=" CA THR J 92 " pdb=" OG1 THR J 92 " pdb=" CG2 THR J 92 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 1.04e+00 ... (remaining 737 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL G 40 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.37e+00 pdb=" C VAL G 40 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL G 40 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY G 41 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 40 " 0.010 2.00e-02 2.50e+03 2.09e-02 4.35e+00 pdb=" C VAL A 40 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 40 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY A 41 " 0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL B 40 " 0.010 2.00e-02 2.50e+03 2.08e-02 4.32e+00 pdb=" C VAL B 40 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL B 40 " 0.013 2.00e-02 2.50e+03 pdb=" N GLY B 41 " 0.012 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1379 2.86 - 3.37: 3314 3.37 - 3.88: 7138 3.88 - 4.39: 6647 4.39 - 4.90: 14750 Nonbonded interactions: 33228 Sorted by model distance: nonbonded pdb=" O LEU E 38 " pdb=" N LEU G 38 " model vdw 2.346 3.120 nonbonded pdb=" N ASN H 65 " pdb=" OD1 ASN H 65 " model vdw 2.374 3.120 nonbonded pdb=" N ASN B 65 " pdb=" OD1 ASN B 65 " model vdw 2.374 3.120 nonbonded pdb=" N ASN G 65 " pdb=" OD1 ASN G 65 " model vdw 2.374 3.120 nonbonded pdb=" N ASN D 65 " pdb=" OD1 ASN D 65 " model vdw 2.375 3.120 ... (remaining 33223 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: 0.02 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.650 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: 0.000 Extract box with map and model: 0.040 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.007 0.047 4160 Z= 0.297 Angle : 0.993 6.263 5620 Z= 0.571 Chirality : 0.065 0.206 740 Planarity : 0.004 0.021 690 Dihedral : 9.610 29.582 1410 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.52 % Favored : 84.48 % Rotamer: Outliers : 2.38 % Allowed : 4.76 % Favored : 92.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.74 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR H 39 PHE 0.017 0.005 PHE H 94 HIS 0.006 0.004 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00663 ( 4160) covalent geometry : angle 0.99260 ( 5620) hydrogen bonds : bond 0.19760 ( 60) hydrogen bonds : angle 11.92943 ( 192) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 140 time to evaluate : 0.161 Fit side-chains revert: symmetry clash REVERT: A 64 THR cc_start: 0.8549 (m) cc_final: 0.8217 (m) REVERT: A 80 LYS cc_start: 0.6865 (tttt) cc_final: 0.6520 (pttm) REVERT: B 38 LEU cc_start: 0.7694 (pp) cc_final: 0.7390 (mt) REVERT: B 52 VAL cc_start: 0.8818 (t) cc_final: 0.8567 (m) REVERT: B 75 THR cc_start: 0.8216 (m) cc_final: 0.7809 (p) REVERT: B 80 LYS cc_start: 0.7081 (tttt) cc_final: 0.6580 (pttp) REVERT: C 75 THR cc_start: 0.8433 (m) cc_final: 0.8050 (p) REVERT: D 75 THR cc_start: 0.8360 (m) cc_final: 0.8067 (p) REVERT: D 97 LYS cc_start: 0.8561 (mttt) cc_final: 0.8294 (mttp) REVERT: F 75 THR cc_start: 0.8307 (m) cc_final: 0.7995 (p) REVERT: G 75 THR cc_start: 0.8423 (m) cc_final: 0.8100 (p) REVERT: H 52 VAL cc_start: 0.9092 (t) cc_final: 0.8875 (m) REVERT: H 75 THR cc_start: 0.8233 (m) cc_final: 0.7924 (p) REVERT: I 52 VAL cc_start: 0.8900 (t) cc_final: 0.8533 (m) REVERT: I 95 VAL cc_start: 0.7914 (t) cc_final: 0.7603 (m) REVERT: J 38 LEU cc_start: 0.7576 (pp) cc_final: 0.7219 (mt) REVERT: J 52 VAL cc_start: 0.8887 (t) cc_final: 0.8680 (m) outliers start: 10 outliers final: 0 residues processed: 140 average time/residue: 0.0675 time to fit residues: 11.9036 Evaluate side-chains 76 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 40.0000 chunk 24 optimal weight: 40.0000 chunk 48 optimal weight: 40.0000 chunk 56 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 2 optimal weight: 40.0000 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 50 HIS A 50 HIS ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 50 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 50 HIS ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 50 HIS ** I 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4504 r_free = 0.4504 target = 0.149771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.137987 restraints weight = 10506.176| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.140692 restraints weight = 5435.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4430 r_free = 0.4430 target = 0.142516 restraints weight = 3336.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.143716 restraints weight = 2276.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.144525 restraints weight = 1681.671| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7181 moved from start: 0.2637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4160 Z= 0.179 Angle : 0.670 4.375 5620 Z= 0.396 Chirality : 0.054 0.142 740 Planarity : 0.003 0.012 690 Dihedral : 8.142 20.588 600 Min Nonbonded Distance : 2.623 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 3.57 % Allowed : 11.43 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.38 (0.28), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.22), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR B 39 PHE 0.003 0.001 PHE J 94 HIS 0.003 0.001 HIS J 50 Details of bonding type rmsd covalent geometry : bond 0.00399 ( 4160) covalent geometry : angle 0.66971 ( 5620) hydrogen bonds : bond 0.03435 ( 60) hydrogen bonds : angle 6.78258 ( 192) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 77 time to evaluate : 0.151 Fit side-chains REVERT: E 59 THR cc_start: 0.8532 (m) cc_final: 0.7601 (p) REVERT: E 75 THR cc_start: 0.8133 (m) cc_final: 0.7762 (p) REVERT: A 75 THR cc_start: 0.8264 (m) cc_final: 0.8040 (p) REVERT: B 75 THR cc_start: 0.8134 (m) cc_final: 0.7893 (p) REVERT: C 59 THR cc_start: 0.8581 (m) cc_final: 0.8206 (p) REVERT: D 59 THR cc_start: 0.8390 (m) cc_final: 0.7472 (p) REVERT: D 75 THR cc_start: 0.8215 (m) cc_final: 0.7965 (p) REVERT: F 59 THR cc_start: 0.8331 (m) cc_final: 0.7755 (p) REVERT: F 61 GLU cc_start: 0.7934 (mp0) cc_final: 0.7098 (mp0) REVERT: F 75 THR cc_start: 0.8260 (m) cc_final: 0.7968 (p) REVERT: G 59 THR cc_start: 0.8544 (m) cc_final: 0.7889 (p) REVERT: H 59 THR cc_start: 0.8362 (m) cc_final: 0.7838 (p) REVERT: J 38 LEU cc_start: 0.7714 (pp) cc_final: 0.7478 (mt) outliers start: 15 outliers final: 5 residues processed: 87 average time/residue: 0.0544 time to fit residues: 6.3225 Evaluate side-chains 59 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 54 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 65 ASN Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 65 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 25 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 19 optimal weight: 20.0000 chunk 34 optimal weight: 5.9990 chunk 2 optimal weight: 40.0000 chunk 10 optimal weight: 4.9990 chunk 30 optimal weight: 40.0000 chunk 57 optimal weight: 7.9990 chunk 6 optimal weight: 20.0000 chunk 42 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS F 50 HIS H 50 HIS J 50 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4539 r_free = 0.4539 target = 0.150565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.139346 restraints weight = 10334.131| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.141852 restraints weight = 5329.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.143642 restraints weight = 3361.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.144811 restraints weight = 2315.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.145577 restraints weight = 1719.175| |-----------------------------------------------------------------------------| r_work (final): 0.4433 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4160 Z= 0.173 Angle : 0.658 6.758 5620 Z= 0.387 Chirality : 0.053 0.147 740 Planarity : 0.002 0.011 690 Dihedral : 7.867 21.226 600 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 4.52 % Allowed : 12.86 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.41 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR C 39 PHE 0.003 0.001 PHE J 94 HIS 0.004 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00386 ( 4160) covalent geometry : angle 0.65751 ( 5620) hydrogen bonds : bond 0.04004 ( 60) hydrogen bonds : angle 6.41039 ( 192) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 66 time to evaluate : 0.165 Fit side-chains REVERT: E 38 LEU cc_start: 0.7879 (OUTLIER) cc_final: 0.7440 (pp) REVERT: B 75 THR cc_start: 0.8186 (m) cc_final: 0.7911 (p) REVERT: D 38 LEU cc_start: 0.7822 (OUTLIER) cc_final: 0.7177 (pp) REVERT: D 59 THR cc_start: 0.8208 (m) cc_final: 0.7798 (p) REVERT: D 61 GLU cc_start: 0.8476 (mp0) cc_final: 0.8224 (mp0) REVERT: D 75 THR cc_start: 0.8437 (m) cc_final: 0.8095 (p) REVERT: F 61 GLU cc_start: 0.8081 (mp0) cc_final: 0.6866 (mp0) REVERT: F 75 THR cc_start: 0.8179 (m) cc_final: 0.7937 (p) outliers start: 19 outliers final: 8 residues processed: 82 average time/residue: 0.0327 time to fit residues: 4.2261 Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 50 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 56 optimal weight: 30.0000 chunk 24 optimal weight: 40.0000 chunk 20 optimal weight: 20.0000 chunk 34 optimal weight: 0.9980 chunk 47 optimal weight: 40.0000 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 40.0000 chunk 6 optimal weight: 20.0000 chunk 49 optimal weight: 0.0970 overall best weight: 2.5982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4573 r_free = 0.4573 target = 0.153039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.142129 restraints weight = 10502.784| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4464 r_free = 0.4464 target = 0.144550 restraints weight = 5960.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.146162 restraints weight = 3931.817| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.147429 restraints weight = 2818.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.148144 restraints weight = 2109.819| |-----------------------------------------------------------------------------| r_work (final): 0.4518 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7073 moved from start: 0.4047 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 4160 Z= 0.103 Angle : 0.543 4.511 5620 Z= 0.318 Chirality : 0.052 0.148 740 Planarity : 0.002 0.011 690 Dihedral : 6.963 20.718 600 Min Nonbonded Distance : 2.627 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.00 % Favored : 90.00 % Rotamer: Outliers : 2.86 % Allowed : 16.43 % Favored : 80.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.24 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR C 39 PHE 0.005 0.001 PHE E 94 HIS 0.002 0.001 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.00224 ( 4160) covalent geometry : angle 0.54320 ( 5620) hydrogen bonds : bond 0.02840 ( 60) hydrogen bonds : angle 5.82234 ( 192) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.169 Fit side-chains REVERT: E 38 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7617 (mt) REVERT: D 38 LEU cc_start: 0.7840 (OUTLIER) cc_final: 0.7281 (pp) REVERT: D 61 GLU cc_start: 0.8404 (mp0) cc_final: 0.8149 (mp0) REVERT: D 75 THR cc_start: 0.8461 (m) cc_final: 0.8109 (p) REVERT: F 75 THR cc_start: 0.8279 (m) cc_final: 0.7979 (p) outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 0.0405 time to fit residues: 5.5684 Evaluate side-chains 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 60 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain G residue 38 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 24 optimal weight: 20.0000 chunk 15 optimal weight: 6.9990 chunk 6 optimal weight: 30.0000 chunk 51 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 3 optimal weight: 40.0000 chunk 4 optimal weight: 3.9990 chunk 52 optimal weight: 6.9990 chunk 20 optimal weight: 40.0000 chunk 21 optimal weight: 10.0000 chunk 19 optimal weight: 20.0000 overall best weight: 7.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4488 r_free = 0.4488 target = 0.146246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.135912 restraints weight = 11048.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.138150 restraints weight = 6303.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.139723 restraints weight = 4126.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.140743 restraints weight = 2927.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.141492 restraints weight = 2243.800| |-----------------------------------------------------------------------------| r_work (final): 0.4423 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4160 Z= 0.173 Angle : 0.641 6.056 5620 Z= 0.375 Chirality : 0.053 0.144 740 Planarity : 0.002 0.013 690 Dihedral : 7.298 20.747 600 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 4.76 % Allowed : 18.10 % Favored : 77.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.21 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR C 39 PHE 0.004 0.001 PHE J 94 HIS 0.004 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00377 ( 4160) covalent geometry : angle 0.64139 ( 5620) hydrogen bonds : bond 0.04082 ( 60) hydrogen bonds : angle 6.19437 ( 192) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 54 time to evaluate : 0.168 Fit side-chains REVERT: E 38 LEU cc_start: 0.7916 (OUTLIER) cc_final: 0.7666 (mt) REVERT: C 46 GLU cc_start: 0.7550 (mm-30) cc_final: 0.7032 (mm-30) REVERT: D 38 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7306 (pp) REVERT: D 61 GLU cc_start: 0.8364 (mp0) cc_final: 0.8127 (mp0) REVERT: D 75 THR cc_start: 0.8429 (m) cc_final: 0.8115 (p) REVERT: F 61 GLU cc_start: 0.7970 (mp0) cc_final: 0.7087 (mp0) REVERT: F 75 THR cc_start: 0.8229 (m) cc_final: 0.8011 (p) outliers start: 20 outliers final: 15 residues processed: 72 average time/residue: 0.0364 time to fit residues: 4.0789 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 47 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 38 LEU Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 8.9990 chunk 18 optimal weight: 40.0000 chunk 35 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 48 optimal weight: 40.0000 chunk 53 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.152768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4425 r_free = 0.4425 target = 0.143212 restraints weight = 11917.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4452 r_free = 0.4452 target = 0.145098 restraints weight = 7025.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4472 r_free = 0.4472 target = 0.146387 restraints weight = 4754.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.147230 restraints weight = 3546.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.147946 restraints weight = 2839.073| |-----------------------------------------------------------------------------| r_work (final): 0.4426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4160 Z= 0.176 Angle : 0.648 5.066 5620 Z= 0.382 Chirality : 0.053 0.139 740 Planarity : 0.002 0.010 690 Dihedral : 7.425 21.433 600 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 5.00 % Allowed : 18.57 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.26 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR J 39 PHE 0.005 0.001 PHE I 94 HIS 0.004 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00385 ( 4160) covalent geometry : angle 0.64778 ( 5620) hydrogen bonds : bond 0.04213 ( 60) hydrogen bonds : angle 6.52091 ( 192) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 54 time to evaluate : 0.172 Fit side-chains REVERT: E 38 LEU cc_start: 0.8077 (OUTLIER) cc_final: 0.7761 (mt) REVERT: C 46 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6909 (mm-30) REVERT: D 38 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7516 (pp) REVERT: D 61 GLU cc_start: 0.8222 (mp0) cc_final: 0.7704 (mp0) REVERT: D 75 THR cc_start: 0.8464 (m) cc_final: 0.8153 (p) REVERT: F 61 GLU cc_start: 0.8001 (mp0) cc_final: 0.7502 (mp0) REVERT: F 75 THR cc_start: 0.8196 (m) cc_final: 0.7972 (p) outliers start: 21 outliers final: 16 residues processed: 73 average time/residue: 0.0338 time to fit residues: 3.8737 Evaluate side-chains 68 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 50 time to evaluate : 0.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 34 optimal weight: 20.0000 chunk 19 optimal weight: 8.9990 chunk 7 optimal weight: 40.0000 chunk 37 optimal weight: 30.0000 chunk 54 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 44 optimal weight: 30.0000 chunk 11 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 40.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.150031 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.139268 restraints weight = 10397.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.141708 restraints weight = 5593.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.143406 restraints weight = 3504.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.144584 restraints weight = 2418.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4492 r_free = 0.4492 target = 0.145406 restraints weight = 1790.024| |-----------------------------------------------------------------------------| r_work (final): 0.4461 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7117 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4160 Z= 0.138 Angle : 0.591 5.444 5620 Z= 0.346 Chirality : 0.052 0.141 740 Planarity : 0.002 0.013 690 Dihedral : 7.117 20.191 600 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 5.48 % Allowed : 18.10 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.20 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR J 39 PHE 0.003 0.001 PHE I 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00303 ( 4160) covalent geometry : angle 0.59128 ( 5620) hydrogen bonds : bond 0.03576 ( 60) hydrogen bonds : angle 6.16975 ( 192) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.100 Fit side-chains REVERT: E 38 LEU cc_start: 0.7837 (OUTLIER) cc_final: 0.7574 (mt) REVERT: C 46 GLU cc_start: 0.7650 (mm-30) cc_final: 0.6910 (mm-30) REVERT: D 61 GLU cc_start: 0.8330 (mp0) cc_final: 0.7719 (mp0) REVERT: D 75 THR cc_start: 0.8417 (m) cc_final: 0.8084 (p) REVERT: F 61 GLU cc_start: 0.7934 (mp0) cc_final: 0.7464 (mp0) REVERT: F 75 THR cc_start: 0.8083 (m) cc_final: 0.7822 (p) outliers start: 23 outliers final: 17 residues processed: 72 average time/residue: 0.0269 time to fit residues: 3.1074 Evaluate side-chains 65 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 30.0000 chunk 35 optimal weight: 8.9990 chunk 3 optimal weight: 40.0000 chunk 15 optimal weight: 20.0000 chunk 2 optimal weight: 20.0000 chunk 23 optimal weight: 30.0000 chunk 14 optimal weight: 9.9990 chunk 25 optimal weight: 8.9990 chunk 29 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 30.0000 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.144578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.134462 restraints weight = 11342.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.136617 restraints weight = 6455.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.138144 restraints weight = 4190.316| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.139219 restraints weight = 2977.322| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.139939 restraints weight = 2246.698| |-----------------------------------------------------------------------------| r_work (final): 0.4410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7214 moved from start: 0.4786 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 4160 Z= 0.196 Angle : 0.674 5.782 5620 Z= 0.396 Chirality : 0.054 0.144 740 Planarity : 0.002 0.009 690 Dihedral : 7.495 21.715 600 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 5.48 % Allowed : 18.10 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.39 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR D 39 PHE 0.007 0.002 PHE I 94 HIS 0.005 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 4160) covalent geometry : angle 0.67447 ( 5620) hydrogen bonds : bond 0.04783 ( 60) hydrogen bonds : angle 6.71876 ( 192) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 46 time to evaluate : 0.171 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8052 (OUTLIER) cc_final: 0.7745 (mt) REVERT: C 46 GLU cc_start: 0.7570 (mm-30) cc_final: 0.6879 (mm-30) REVERT: D 61 GLU cc_start: 0.8327 (mp0) cc_final: 0.7856 (mp0) REVERT: D 75 THR cc_start: 0.8297 (m) cc_final: 0.7984 (p) REVERT: F 61 GLU cc_start: 0.7989 (mp0) cc_final: 0.7489 (mp0) outliers start: 23 outliers final: 21 residues processed: 67 average time/residue: 0.0343 time to fit residues: 3.6267 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 46 optimal weight: 2.9990 chunk 58 optimal weight: 7.9990 chunk 55 optimal weight: 40.0000 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 32 optimal weight: 40.0000 chunk 9 optimal weight: 30.0000 chunk 45 optimal weight: 7.9990 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 15 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4599 r_free = 0.4599 target = 0.153539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.144204 restraints weight = 11629.083| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.146028 restraints weight = 6840.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.4507 r_free = 0.4507 target = 0.147436 restraints weight = 4636.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.148330 restraints weight = 3362.766| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4532 r_free = 0.4532 target = 0.148943 restraints weight = 2624.665| |-----------------------------------------------------------------------------| r_work (final): 0.4462 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7182 moved from start: 0.4874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4160 Z= 0.157 Angle : 0.610 4.949 5620 Z= 0.360 Chirality : 0.053 0.141 740 Planarity : 0.002 0.014 690 Dihedral : 7.257 20.988 600 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 5.00 % Allowed : 18.33 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.37 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.005 0.001 PHE I 94 HIS 0.004 0.002 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00340 ( 4160) covalent geometry : angle 0.61044 ( 5620) hydrogen bonds : bond 0.04069 ( 60) hydrogen bonds : angle 6.45975 ( 192) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 45 time to evaluate : 0.161 Fit side-chains REVERT: E 38 LEU cc_start: 0.8031 (OUTLIER) cc_final: 0.7730 (mt) REVERT: C 46 GLU cc_start: 0.7591 (mm-30) cc_final: 0.6927 (mm-30) REVERT: D 61 GLU cc_start: 0.8236 (mp0) cc_final: 0.7779 (mp0) REVERT: D 75 THR cc_start: 0.8519 (m) cc_final: 0.8260 (p) REVERT: F 61 GLU cc_start: 0.8040 (mp0) cc_final: 0.7655 (mp0) outliers start: 21 outliers final: 19 residues processed: 64 average time/residue: 0.0300 time to fit residues: 3.1632 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 44 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 65 ASN Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 10 optimal weight: 8.9990 chunk 50 optimal weight: 30.0000 chunk 8 optimal weight: 7.9990 chunk 52 optimal weight: 20.0000 chunk 38 optimal weight: 20.0000 chunk 19 optimal weight: 20.0000 chunk 55 optimal weight: 0.9990 chunk 47 optimal weight: 40.0000 chunk 18 optimal weight: 50.0000 chunk 4 optimal weight: 6.9990 chunk 28 optimal weight: 0.8980 overall best weight: 5.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4630 r_free = 0.4630 target = 0.155766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.146514 restraints weight = 11312.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4519 r_free = 0.4519 target = 0.148469 restraints weight = 6687.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.149742 restraints weight = 4448.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.150670 restraints weight = 3242.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.4563 r_free = 0.4563 target = 0.151271 restraints weight = 2508.240| |-----------------------------------------------------------------------------| r_work (final): 0.4487 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7149 moved from start: 0.4969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4160 Z= 0.132 Angle : 0.581 5.556 5620 Z= 0.341 Chirality : 0.052 0.143 740 Planarity : 0.002 0.014 690 Dihedral : 7.000 20.242 600 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.28 % Favored : 86.72 % Rotamer: Outliers : 5.48 % Allowed : 17.86 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR D 39 PHE 0.003 0.001 PHE E 94 HIS 0.003 0.001 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 4160) covalent geometry : angle 0.58098 ( 5620) hydrogen bonds : bond 0.03594 ( 60) hydrogen bonds : angle 6.20244 ( 192) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 52 time to evaluate : 0.174 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8018 (OUTLIER) cc_final: 0.7730 (mt) REVERT: C 46 GLU cc_start: 0.7584 (mm-30) cc_final: 0.6941 (mm-30) REVERT: D 61 GLU cc_start: 0.8222 (mp0) cc_final: 0.7765 (mp0) REVERT: D 75 THR cc_start: 0.8424 (m) cc_final: 0.8155 (p) REVERT: F 61 GLU cc_start: 0.7992 (mp0) cc_final: 0.7655 (mp0) outliers start: 23 outliers final: 18 residues processed: 72 average time/residue: 0.0365 time to fit residues: 4.0418 Evaluate side-chains 69 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 50 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain A residue 92 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 88 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 77 VAL Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 88 ILE Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 8.9990 chunk 9 optimal weight: 0.0970 chunk 12 optimal weight: 30.0000 chunk 15 optimal weight: 0.8980 chunk 52 optimal weight: 20.0000 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 54 optimal weight: 0.8980 chunk 23 optimal weight: 30.0000 chunk 57 optimal weight: 10.0000 overall best weight: 3.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4640 r_free = 0.4640 target = 0.157414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4500 r_free = 0.4500 target = 0.148065 restraints weight = 11156.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.150020 restraints weight = 6456.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4552 r_free = 0.4552 target = 0.151393 restraints weight = 4292.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.152337 restraints weight = 3114.477| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4577 r_free = 0.4577 target = 0.152967 restraints weight = 2402.037| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7071 moved from start: 0.5092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 4160 Z= 0.112 Angle : 0.549 5.485 5620 Z= 0.322 Chirality : 0.052 0.141 740 Planarity : 0.002 0.013 690 Dihedral : 6.740 20.030 600 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 4.05 % Allowed : 18.57 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 39 PHE 0.004 0.001 PHE E 94 HIS 0.003 0.001 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00246 ( 4160) covalent geometry : angle 0.54941 ( 5620) hydrogen bonds : bond 0.03166 ( 60) hydrogen bonds : angle 6.00212 ( 192) =============================================================================== Job complete usr+sys time: 721.88 seconds wall clock time: 13 minutes 34.05 seconds (814.05 seconds total)