Starting phenix.real_space_refine on Wed Mar 5 23:05:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cu7_7618/03_2025/6cu7_7618.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cu7_7618/03_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/6cu7_7618/03_2025/6cu7_7618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cu7_7618/03_2025/6cu7_7618.map" model { file = "/net/cci-nas-00/data/ceres_data/6cu7_7618/03_2025/6cu7_7618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cu7_7618/03_2025/6cu7_7618.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 ------------------------------------------------------------------------------- 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-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4140 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" 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: C, B, E, D, G, F, I, H, J Time building chain proxies: 1.67, per 1000 atoms: 0.40 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: 0.86 Conformation dependent library (CDL) restraints added in 606.8 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: 0.64 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: 0.94 Time building geometry restraints manager: 1.06 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: 0.04 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'B' selection = chain 'E' selection = chain 'D' selection = chain 'G' selection = chain 'F' selection = chain 'I' selection = chain 'H' 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: 0.490 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.910 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.690 ------------------------------------------------------------------------------- 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= 0.443 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 (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: -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 HIS 0.006 0.004 HIS H 50 PHE 0.017 0.005 PHE H 94 TYR 0.007 0.002 TYR H 39 *********************** 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 : 0.460 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: 0.1472 time to fit residues: 25.8705 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 : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 20.0000 chunk 45 optimal weight: 30.0000 chunk 25 optimal weight: 30.0000 chunk 15 optimal weight: 9.9990 chunk 30 optimal weight: 40.0000 chunk 24 optimal weight: 20.0000 chunk 47 optimal weight: 30.0000 chunk 18 optimal weight: 30.0000 chunk 28 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 40.0000 overall best weight: 12.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 50 HIS ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 50 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4412 r_free = 0.4412 target = 0.140569 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.130519 restraints weight = 11406.408| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4311 r_free = 0.4311 target = 0.132796 restraints weight = 6160.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4331 r_free = 0.4331 target = 0.134357 restraints weight = 3891.267| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2807 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 4160 Z= 0.399 Angle : 0.778 5.124 5620 Z= 0.460 Chirality : 0.056 0.142 740 Planarity : 0.003 0.012 690 Dihedral : 8.531 21.327 600 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 5.95 % Allowed : 9.76 % Favored : 84.29 % 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: -4.53 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.44 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS J 50 PHE 0.009 0.002 PHE J 94 TYR 0.007 0.001 TYR B 39 *********************** 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 94 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 69 time to evaluate : 0.417 Fit side-chains REVERT: E 59 THR cc_start: 0.8598 (m) cc_final: 0.7838 (p) REVERT: E 75 THR cc_start: 0.8218 (m) cc_final: 0.7865 (p) REVERT: C 59 THR cc_start: 0.8604 (m) cc_final: 0.8149 (p) REVERT: D 59 THR cc_start: 0.8519 (m) cc_final: 0.7551 (p) REVERT: F 59 THR cc_start: 0.8345 (m) cc_final: 0.7863 (p) REVERT: F 61 GLU cc_start: 0.8168 (mp0) cc_final: 0.7144 (mp0) REVERT: F 75 THR cc_start: 0.8202 (m) cc_final: 0.7851 (p) REVERT: F 77 VAL cc_start: 0.8169 (t) cc_final: 0.7937 (t) REVERT: H 59 THR cc_start: 0.8387 (m) cc_final: 0.7483 (p) REVERT: J 61 GLU cc_start: 0.8073 (mp0) cc_final: 0.7493 (mp0) outliers start: 25 outliers final: 9 residues processed: 87 average time/residue: 0.1267 time to fit residues: 14.6179 Evaluate side-chains 60 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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 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 C residue 65 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain J residue 66 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 0.3980 chunk 59 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 47 optimal weight: 30.0000 chunk 3 optimal weight: 10.0000 chunk 23 optimal weight: 20.0000 chunk 8 optimal weight: 0.0030 chunk 7 optimal weight: 10.0000 overall best weight: 5.6800 ------------------------------------------------------------------------------- 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 C 50 HIS ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS F 50 HIS G 50 HIS H 50 HIS I 50 HIS J 50 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.145249 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.135308 restraints weight = 11176.772| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.137655 restraints weight = 6091.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.139268 restraints weight = 3837.540| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7188 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4160 Z= 0.224 Angle : 0.648 6.133 5620 Z= 0.380 Chirality : 0.053 0.140 740 Planarity : 0.002 0.010 690 Dihedral : 7.926 20.918 600 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.38 % Favored : 88.62 % Rotamer: Outliers : 3.81 % Allowed : 12.38 % Favored : 83.81 % 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: -4.45 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.003 0.001 PHE E 94 TYR 0.007 0.001 TYR C 39 *********************** 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 83 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 0.424 Fit side-chains REVERT: E 38 LEU cc_start: 0.7999 (OUTLIER) cc_final: 0.7650 (mt) REVERT: D 38 LEU cc_start: 0.8021 (OUTLIER) cc_final: 0.7362 (pp) REVERT: D 59 THR cc_start: 0.8127 (m) cc_final: 0.7919 (p) REVERT: D 61 GLU cc_start: 0.8362 (mp0) cc_final: 0.7977 (mp0) REVERT: D 75 THR cc_start: 0.8385 (m) cc_final: 0.8042 (p) REVERT: F 61 GLU cc_start: 0.8165 (mp0) cc_final: 0.7226 (mp0) REVERT: F 75 THR cc_start: 0.8272 (m) cc_final: 0.8051 (p) REVERT: F 77 VAL cc_start: 0.8078 (t) cc_final: 0.7875 (t) REVERT: G 59 THR cc_start: 0.8407 (m) cc_final: 0.7736 (p) outliers start: 16 outliers final: 5 residues processed: 78 average time/residue: 0.0988 time to fit residues: 10.9196 Evaluate side-chains 56 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 49 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 38 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 7.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 40.0000 chunk 59 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 18 optimal weight: 20.0000 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 4.9990 chunk 11 optimal weight: 9.9990 chunk 14 optimal weight: 10.0000 chunk 48 optimal weight: 30.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- 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 = 0.4518 r_free = 0.4518 target = 0.149103 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.138575 restraints weight = 10463.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.140881 restraints weight = 5568.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4439 r_free = 0.4439 target = 0.142602 restraints weight = 3603.253| |-----------------------------------------------------------------------------| r_work (final): 0.4424 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4160 Z= 0.210 Angle : 0.608 4.985 5620 Z= 0.357 Chirality : 0.052 0.140 740 Planarity : 0.002 0.011 690 Dihedral : 7.551 21.085 600 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.52 % Allowed : 13.10 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.38 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.21), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 50 PHE 0.003 0.001 PHE E 94 TYR 0.006 0.001 TYR C 39 *********************** 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 83 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.426 Fit side-chains REVERT: E 38 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7700 (mt) REVERT: A 77 VAL cc_start: 0.7647 (t) cc_final: 0.7437 (t) REVERT: D 38 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7325 (pp) REVERT: D 59 THR cc_start: 0.8055 (m) cc_final: 0.7724 (p) REVERT: D 61 GLU cc_start: 0.8422 (mp0) cc_final: 0.8019 (mp0) REVERT: D 75 THR cc_start: 0.8392 (m) cc_final: 0.8062 (p) REVERT: F 61 GLU cc_start: 0.7878 (mp0) cc_final: 0.7213 (mp0) REVERT: F 75 THR cc_start: 0.8232 (m) cc_final: 0.8031 (p) REVERT: J 61 GLU cc_start: 0.7973 (mp0) cc_final: 0.7705 (mp0) outliers start: 19 outliers final: 11 residues processed: 79 average time/residue: 0.0801 time to fit residues: 9.5057 Evaluate side-chains 62 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 49 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 38 LEU 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 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 92 THR 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 I residue 52 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 40.0000 chunk 17 optimal weight: 40.0000 chunk 46 optimal weight: 8.9990 chunk 1 optimal weight: 30.0000 chunk 21 optimal weight: 40.0000 chunk 19 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 54 optimal weight: 40.0000 chunk 30 optimal weight: 40.0000 chunk 13 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 overall best weight: 8.3992 ------------------------------------------------------------------------------- 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 = 0.4454 r_free = 0.4454 target = 0.143628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.133386 restraints weight = 11337.371| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.135688 restraints weight = 6310.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.137163 restraints weight = 4043.941| |-----------------------------------------------------------------------------| r_work (final): 0.4368 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7250 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4160 Z= 0.273 Angle : 0.674 5.731 5620 Z= 0.395 Chirality : 0.054 0.139 740 Planarity : 0.002 0.013 690 Dihedral : 7.722 21.804 600 Min Nonbonded Distance : 2.555 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 5.71 % Allowed : 15.71 % Favored : 78.57 % 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: -4.45 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.39 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.006 0.001 PHE I 94 TYR 0.005 0.001 TYR B 39 *********************** 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 79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 55 time to evaluate : 0.464 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8065 (OUTLIER) cc_final: 0.7767 (mt) REVERT: C 46 GLU cc_start: 0.7478 (mm-30) cc_final: 0.7002 (mm-30) REVERT: D 38 LEU cc_start: 0.8002 (OUTLIER) cc_final: 0.7361 (pp) REVERT: D 59 THR cc_start: 0.8119 (m) cc_final: 0.7710 (p) REVERT: D 61 GLU cc_start: 0.8541 (mp0) cc_final: 0.8321 (mp0) REVERT: D 75 THR cc_start: 0.8082 (m) cc_final: 0.7806 (p) REVERT: F 61 GLU cc_start: 0.8010 (mp0) cc_final: 0.7304 (mp0) outliers start: 24 outliers final: 21 residues processed: 77 average time/residue: 0.0761 time to fit residues: 9.0436 Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 50 time to evaluate : 0.469 ------------------------------------------------------------------------------- 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 B residue 95 VAL Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 38 LEU 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 65 ASN 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 30.0000 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 6.9990 chunk 6 optimal weight: 20.0000 chunk 24 optimal weight: 50.0000 chunk 31 optimal weight: 30.0000 chunk 9 optimal weight: 30.0000 chunk 11 optimal weight: 9.9990 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 7.9990 overall best weight: 9.1990 ------------------------------------------------------------------------------- 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 = 0.4452 r_free = 0.4452 target = 0.142960 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4315 r_free = 0.4315 target = 0.133220 restraints weight = 11177.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.135241 restraints weight = 6196.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.136873 restraints weight = 4080.127| |-----------------------------------------------------------------------------| r_work (final): 0.4366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7264 moved from start: 0.4523 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4160 Z= 0.290 Angle : 0.685 5.500 5620 Z= 0.403 Chirality : 0.054 0.140 740 Planarity : 0.002 0.009 690 Dihedral : 7.780 21.927 600 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.97 % Favored : 86.03 % Rotamer: Outliers : 5.48 % Allowed : 17.38 % 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 (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: -4.55 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 50 PHE 0.006 0.001 PHE I 94 TYR 0.005 0.001 TYR I 39 *********************** 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 80 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 57 time to evaluate : 0.480 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8035 (OUTLIER) cc_final: 0.7654 (pp) REVERT: C 46 GLU cc_start: 0.7508 (mm-30) cc_final: 0.7007 (mm-30) REVERT: C 77 VAL cc_start: 0.8259 (t) cc_final: 0.7967 (t) REVERT: D 38 LEU cc_start: 0.8268 (OUTLIER) cc_final: 0.7654 (pp) REVERT: D 59 THR cc_start: 0.8270 (m) cc_final: 0.7880 (p) REVERT: F 61 GLU cc_start: 0.8046 (mp0) cc_final: 0.7404 (mp0) outliers start: 23 outliers final: 19 residues processed: 79 average time/residue: 0.0833 time to fit residues: 9.8876 Evaluate side-chains 71 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 50 time to evaluate : 0.477 ------------------------------------------------------------------------------- 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 88 ILE Chi-restraints excluded: chain B residue 92 THR Chi-restraints excluded: chain C residue 65 ASN Chi-restraints excluded: chain C residue 80 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR 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 65 ASN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 22 optimal weight: 6.9990 chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 20.0000 chunk 18 optimal weight: 40.0000 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 0.9980 chunk 1 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 48 optimal weight: 40.0000 chunk 32 optimal weight: 40.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 = 0.4492 r_free = 0.4492 target = 0.146361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.136766 restraints weight = 11012.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.139003 restraints weight = 6213.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4408 r_free = 0.4408 target = 0.140534 restraints weight = 3992.149| |-----------------------------------------------------------------------------| r_work (final): 0.4409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4661 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= 0.212 Angle : 0.617 5.657 5620 Z= 0.362 Chirality : 0.053 0.139 740 Planarity : 0.002 0.011 690 Dihedral : 7.454 21.284 600 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 15.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.07 % Favored : 87.93 % Rotamer: Outliers : 5.71 % Allowed : 18.10 % Favored : 76.19 % 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: -4.47 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS I 50 PHE 0.003 0.001 PHE I 94 TYR 0.005 0.001 TYR J 39 *********************** 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 77 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 53 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7756 (mt) REVERT: C 46 GLU cc_start: 0.7565 (mm-30) cc_final: 0.7052 (mm-30) REVERT: C 77 VAL cc_start: 0.8134 (t) cc_final: 0.7853 (t) REVERT: D 38 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7700 (pp) REVERT: D 59 THR cc_start: 0.8135 (m) cc_final: 0.7924 (p) REVERT: F 61 GLU cc_start: 0.8049 (mp0) cc_final: 0.7265 (mp0) outliers start: 24 outliers final: 18 residues processed: 75 average time/residue: 0.0806 time to fit residues: 9.0646 Evaluate side-chains 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 50 time to evaluate : 0.421 ------------------------------------------------------------------------------- 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 80 LYS Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 30.0000 chunk 5 optimal weight: 30.0000 chunk 27 optimal weight: 40.0000 chunk 15 optimal weight: 9.9990 chunk 51 optimal weight: 20.0000 chunk 46 optimal weight: 9.9990 chunk 37 optimal weight: 8.9990 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 8.9990 chunk 57 optimal weight: 40.0000 chunk 50 optimal weight: 6.9990 overall best weight: 8.9990 ------------------------------------------------------------------------------- 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 = 0.4458 r_free = 0.4458 target = 0.143580 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.134092 restraints weight = 11146.251| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.136153 restraints weight = 6289.088| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.137506 restraints weight = 4060.773| |-----------------------------------------------------------------------------| r_work (final): 0.4377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7272 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 4160 Z= 0.284 Angle : 0.682 5.907 5620 Z= 0.400 Chirality : 0.054 0.143 740 Planarity : 0.002 0.015 690 Dihedral : 7.725 22.368 600 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 16.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.48 % Favored : 85.52 % Rotamer: Outliers : 5.48 % Allowed : 19.05 % Favored : 75.48 % 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: -4.54 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 PHE 0.007 0.002 PHE I 94 TYR 0.005 0.001 TYR I 39 *********************** 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 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 51 time to evaluate : 0.418 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8049 (OUTLIER) cc_final: 0.7714 (mt) REVERT: A 61 GLU cc_start: 0.4414 (pm20) cc_final: 0.4187 (pm20) REVERT: B 59 THR cc_start: 0.8324 (p) cc_final: 0.7898 (p) REVERT: B 61 GLU cc_start: 0.4239 (pm20) cc_final: 0.4009 (pm20) REVERT: C 46 GLU cc_start: 0.7517 (mm-30) cc_final: 0.7048 (mm-30) REVERT: C 77 VAL cc_start: 0.8139 (OUTLIER) cc_final: 0.7856 (t) REVERT: D 38 LEU cc_start: 0.8221 (OUTLIER) cc_final: 0.7621 (pp) REVERT: F 61 GLU cc_start: 0.8019 (mp0) cc_final: 0.7507 (mp0) outliers start: 23 outliers final: 20 residues processed: 72 average time/residue: 0.0822 time to fit residues: 9.0492 Evaluate side-chains 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 47 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR 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 65 ASN 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 Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 0.0050 chunk 16 optimal weight: 8.9990 chunk 0 optimal weight: 50.0000 chunk 34 optimal weight: 6.9990 chunk 12 optimal weight: 30.0000 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 10.0000 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 30.0000 overall best weight: 5.0002 ------------------------------------------------------------------------------- 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 = 0.4513 r_free = 0.4513 target = 0.147823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.137919 restraints weight = 10912.819| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.139901 restraints weight = 6395.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.141461 restraints weight = 4289.161| |-----------------------------------------------------------------------------| r_work (final): 0.4414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.4839 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= 0.191 Angle : 0.609 6.092 5620 Z= 0.356 Chirality : 0.052 0.139 740 Planarity : 0.002 0.014 690 Dihedral : 7.306 21.157 600 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.72 % Favored : 88.28 % Rotamer: Outliers : 5.71 % Allowed : 19.05 % Favored : 75.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -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 HIS 0.003 0.001 HIS H 50 PHE 0.004 0.001 PHE E 94 TYR 0.005 0.001 TYR J 39 *********************** 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 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 50 time to evaluate : 0.471 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7763 (mt) REVERT: C 46 GLU cc_start: 0.7581 (mm-30) cc_final: 0.7092 (mm-30) REVERT: C 77 VAL cc_start: 0.8100 (OUTLIER) cc_final: 0.7824 (t) REVERT: D 38 LEU cc_start: 0.8239 (OUTLIER) cc_final: 0.7658 (pp) REVERT: D 59 THR cc_start: 0.8324 (p) cc_final: 0.8095 (p) REVERT: F 61 GLU cc_start: 0.8149 (mp0) cc_final: 0.7506 (mp0) outliers start: 24 outliers final: 17 residues processed: 71 average time/residue: 0.0793 time to fit residues: 8.6202 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 46 time to evaluate : 0.466 ------------------------------------------------------------------------------- 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 40 VAL 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 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 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 88 ILE 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 Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 8.9990 chunk 43 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 30.0000 chunk 10 optimal weight: 4.9990 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 30.0000 chunk 16 optimal weight: 10.0000 chunk 0 optimal weight: 50.0000 chunk 59 optimal weight: 30.0000 overall best weight: 9.9994 ------------------------------------------------------------------------------- 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 = 0.4556 r_free = 0.4556 target = 0.149763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.140533 restraints weight = 11676.026| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.142254 restraints weight = 6811.364| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.4465 r_free = 0.4465 target = 0.143610 restraints weight = 4692.106| |-----------------------------------------------------------------------------| r_work (final): 0.4396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4160 Z= 0.310 Angle : 0.697 6.118 5620 Z= 0.409 Chirality : 0.055 0.143 740 Planarity : 0.002 0.014 690 Dihedral : 7.701 22.361 600 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.31 % Favored : 85.69 % Rotamer: Outliers : 5.48 % Allowed : 18.81 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.60 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 PHE 0.008 0.002 PHE I 94 TYR 0.006 0.001 TYR J 39 ********************** 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 67 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 44 time to evaluate : 0.443 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.7976 (OUTLIER) cc_final: 0.7562 (pp) REVERT: C 46 GLU cc_start: 0.7584 (mm-30) cc_final: 0.7075 (mm-30) REVERT: C 77 VAL cc_start: 0.8146 (OUTLIER) cc_final: 0.7848 (t) REVERT: D 38 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7639 (pp) REVERT: F 61 GLU cc_start: 0.8090 (mp0) cc_final: 0.7519 (mp0) outliers start: 23 outliers final: 20 residues processed: 66 average time/residue: 0.0772 time to fit residues: 7.9798 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 43 time to evaluate : 0.551 ------------------------------------------------------------------------------- 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 40 VAL 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 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 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR 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 65 ASN Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 59 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 2 optimal weight: 8.9990 chunk 31 optimal weight: 8.9990 chunk 37 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 10.0000 chunk 38 optimal weight: 10.0000 chunk 59 optimal weight: 20.0000 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 7.9990 overall best weight: 7.1988 ------------------------------------------------------------------------------- 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 = 0.4569 r_free = 0.4569 target = 0.151369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.141797 restraints weight = 11734.246| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.143680 restraints weight = 7005.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.144989 restraints weight = 4758.485| |-----------------------------------------------------------------------------| r_work (final): 0.4477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.4956 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= 0.238 Angle : 0.644 6.087 5620 Z= 0.377 Chirality : 0.053 0.143 740 Planarity : 0.002 0.013 690 Dihedral : 7.488 21.833 600 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 14.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.93 % Favored : 87.07 % Rotamer: Outliers : 5.24 % Allowed : 18.81 % Favored : 75.95 % 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: -4.57 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS H 50 PHE 0.004 0.001 PHE I 94 TYR 0.005 0.001 TYR H 39 =============================================================================== Job complete usr+sys time: 1186.67 seconds wall clock time: 22 minutes 17.00 seconds (1337.00 seconds total)