Starting phenix.real_space_refine on Tue Feb 11 03:50:13 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6cu7_7618/02_2025/6cu7_7618.cif Found real_map, /net/cci-nas-00/data/ceres_data/6cu7_7618/02_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_7618/02_2025/6cu7_7618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6cu7_7618/02_2025/6cu7_7618.map" model { file = "/net/cci-nas-00/data/ceres_data/6cu7_7618/02_2025/6cu7_7618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6cu7_7618/02_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-5592/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: 1.65, 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: 0.99 Conformation dependent library (CDL) restraints added in 569.9 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: 0.62 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: 0.95 Time building geometry restraints manager: 1.15 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: 0.300 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: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.000 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: 0.010 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.460 ------------------------------------------------------------------------------- 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 : 0.500 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: 0.1517 time to fit residues: 26.5616 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 : 0.476 ------------------------------------------------------------------------------- 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 = 0.4312 r_free = 0.4312 target = 0.132796 restraints weight = 6160.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.134350 restraints weight = 3890.774| |-----------------------------------------------------------------------------| r_work (final): 0.4346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7276 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 : 0.477 Fit side-chains REVERT: E 59 THR cc_start: 0.8599 (m) cc_final: 0.7838 (p) REVERT: E 75 THR cc_start: 0.8218 (m) cc_final: 0.7866 (p) REVERT: C 59 THR cc_start: 0.8605 (m) cc_final: 0.8152 (p) REVERT: D 59 THR cc_start: 0.8523 (m) cc_final: 0.7558 (p) REVERT: F 59 THR cc_start: 0.8349 (m) cc_final: 0.7870 (p) REVERT: F 61 GLU cc_start: 0.8167 (mp0) cc_final: 0.7151 (mp0) REVERT: F 75 THR cc_start: 0.8206 (m) cc_final: 0.7857 (p) REVERT: F 77 VAL cc_start: 0.8163 (t) cc_final: 0.7930 (t) REVERT: H 59 THR cc_start: 0.8390 (m) cc_final: 0.7486 (p) REVERT: J 61 GLU cc_start: 0.8073 (mp0) cc_final: 0.7495 (mp0) outliers start: 25 outliers final: 9 residues processed: 87 average time/residue: 0.1209 time to fit residues: 14.1560 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 : 0.476 ------------------------------------------------------------------------------- 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: 8.9990 chunk 19 optimal weight: 7.9990 chunk 16 optimal weight: 0.2980 chunk 59 optimal weight: 30.0000 chunk 14 optimal weight: 30.0000 chunk 47 optimal weight: 30.0000 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 8 optimal weight: 5.9990 chunk 7 optimal weight: 10.0000 overall best weight: 5.8588 ------------------------------------------------------------------------------- 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 = 0.4483 r_free = 0.4483 target = 0.145277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.135180 restraints weight = 11139.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.137550 restraints weight = 6125.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.139190 restraints weight = 3874.755| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.3609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4160 Z= 0.223 Angle : 0.646 6.166 5620 Z= 0.379 Chirality : 0.053 0.138 740 Planarity : 0.002 0.011 690 Dihedral : 7.863 20.870 600 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 15.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.52 % Favored : 89.48 % Rotamer: Outliers : 4.29 % Allowed : 11.90 % 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: -4.43 (0.27), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (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 89 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 0.464 Fit side-chains REVERT: E 38 LEU cc_start: 0.7967 (OUTLIER) cc_final: 0.7607 (mt) REVERT: D 38 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7338 (pp) REVERT: D 61 GLU cc_start: 0.8366 (mp0) cc_final: 0.7745 (mp0) REVERT: D 75 THR cc_start: 0.8395 (m) cc_final: 0.8018 (p) REVERT: F 61 GLU cc_start: 0.8149 (mp0) cc_final: 0.7218 (mp0) REVERT: F 75 THR cc_start: 0.8253 (m) cc_final: 0.8030 (p) REVERT: G 59 THR cc_start: 0.8397 (m) cc_final: 0.7722 (p) outliers start: 18 outliers final: 6 residues processed: 83 average time/residue: 0.0981 time to fit residues: 11.5975 Evaluate side-chains 58 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 50 time to evaluate : 0.495 ------------------------------------------------------------------------------- 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 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 4 optimal weight: 6.9990 chunk 16 optimal weight: 4.9990 chunk 47 optimal weight: 40.0000 chunk 59 optimal weight: 10.0000 chunk 6 optimal weight: 20.0000 chunk 18 optimal weight: 30.0000 chunk 28 optimal weight: 5.9990 chunk 23 optimal weight: 30.0000 chunk 11 optimal weight: 0.6980 chunk 14 optimal weight: 30.0000 chunk 48 optimal weight: 30.0000 overall best weight: 5.7390 ------------------------------------------------------------------------------- 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 = 0.4516 r_free = 0.4516 target = 0.148811 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4378 r_free = 0.4378 target = 0.138204 restraints weight = 10541.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.140641 restraints weight = 5631.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4431 r_free = 0.4431 target = 0.142256 restraints weight = 3538.354| |-----------------------------------------------------------------------------| r_work (final): 0.4418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7152 moved from start: 0.3969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4160 Z= 0.213 Angle : 0.610 5.121 5620 Z= 0.359 Chirality : 0.052 0.138 740 Planarity : 0.002 0.011 690 Dihedral : 7.554 20.923 600 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.62 % Favored : 86.38 % Rotamer: Outliers : 4.76 % Allowed : 14.05 % Favored : 81.19 % 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: -4.38 (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 C 50 PHE 0.002 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 82 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.436 Fit side-chains REVERT: E 38 LEU cc_start: 0.8029 (OUTLIER) cc_final: 0.7696 (mt) REVERT: A 77 VAL cc_start: 0.7662 (t) cc_final: 0.7440 (t) REVERT: D 38 LEU cc_start: 0.7915 (OUTLIER) cc_final: 0.7303 (pp) REVERT: D 75 THR cc_start: 0.8392 (m) cc_final: 0.8064 (p) REVERT: F 61 GLU cc_start: 0.7908 (mp0) cc_final: 0.7058 (mp0) REVERT: J 61 GLU cc_start: 0.7898 (mp0) cc_final: 0.7567 (mp0) outliers start: 20 outliers final: 11 residues processed: 77 average time/residue: 0.0807 time to fit residues: 9.3126 Evaluate side-chains 64 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 H residue 52 VAL 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: 7.9990 chunk 19 optimal weight: 9.9990 chunk 33 optimal weight: 6.9990 chunk 54 optimal weight: 40.0000 chunk 30 optimal weight: 40.0000 chunk 13 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.4467 r_free = 0.4467 target = 0.144193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.134051 restraints weight = 11473.973| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.136345 restraints weight = 6542.300| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4379 r_free = 0.4379 target = 0.137885 restraints weight = 4207.710| |-----------------------------------------------------------------------------| r_work (final): 0.4380 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.4303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4160 Z= 0.268 Angle : 0.663 5.804 5620 Z= 0.389 Chirality : 0.054 0.139 740 Planarity : 0.002 0.014 690 Dihedral : 7.677 21.702 600 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.79 % Favored : 86.21 % Rotamer: Outliers : 5.24 % Allowed : 17.38 % 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 (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 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.005 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 74 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 52 time to evaluate : 0.450 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8072 (OUTLIER) cc_final: 0.7777 (mt) REVERT: C 46 GLU cc_start: 0.7455 (mm-30) cc_final: 0.6985 (mm-30) REVERT: D 38 LEU cc_start: 0.8134 (OUTLIER) cc_final: 0.7478 (pp) REVERT: D 61 GLU cc_start: 0.8005 (mp0) cc_final: 0.7570 (mp0) REVERT: F 61 GLU cc_start: 0.8018 (mp0) cc_final: 0.7386 (mp0) outliers start: 22 outliers final: 16 residues processed: 70 average time/residue: 0.0778 time to fit residues: 8.4751 Evaluate side-chains 66 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 48 time to evaluate : 0.444 ------------------------------------------------------------------------------- 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 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 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 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: 7.9990 chunk 59 optimal weight: 30.0000 chunk 2 optimal weight: 9.9990 chunk 6 optimal weight: 30.0000 chunk 24 optimal weight: 50.0000 chunk 31 optimal weight: 10.0000 chunk 9 optimal weight: 0.0030 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 50.0000 chunk 39 optimal weight: 30.0000 overall best weight: 7.2000 ------------------------------------------------------------------------------- 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 = 0.4482 r_free = 0.4482 target = 0.145600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.135971 restraints weight = 11139.343| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.138218 restraints weight = 6423.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4399 r_free = 0.4399 target = 0.139755 restraints weight = 4145.282| |-----------------------------------------------------------------------------| r_work (final): 0.4395 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7235 moved from start: 0.4494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4160 Z= 0.240 Angle : 0.633 5.034 5620 Z= 0.372 Chirality : 0.053 0.138 740 Planarity : 0.002 0.010 690 Dihedral : 7.519 21.687 600 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.76 % Favored : 87.24 % Rotamer: Outliers : 5.24 % Allowed : 17.86 % Favored : 76.90 % 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: -4.48 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS I 50 PHE 0.004 0.001 PHE I 94 TYR 0.005 0.001 TYR H 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 79 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 57 time to evaluate : 0.539 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8082 (OUTLIER) cc_final: 0.7805 (mt) REVERT: C 46 GLU cc_start: 0.7465 (mm-30) cc_final: 0.7020 (mm-30) REVERT: D 38 LEU cc_start: 0.8275 (OUTLIER) cc_final: 0.7654 (pp) REVERT: D 61 GLU cc_start: 0.8072 (mp0) cc_final: 0.7647 (mp0) REVERT: F 61 GLU cc_start: 0.8019 (mp0) cc_final: 0.7451 (mp0) outliers start: 22 outliers final: 18 residues processed: 76 average time/residue: 0.0890 time to fit residues: 10.0481 Evaluate side-chains 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 52 time to evaluate : 0.499 ------------------------------------------------------------------------------- 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 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 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: 4.9990 chunk 7 optimal weight: 20.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 30.0000 chunk 6 optimal weight: 5.9990 chunk 31 optimal weight: 6.9990 chunk 55 optimal weight: 40.0000 chunk 1 optimal weight: 30.0000 chunk 53 optimal weight: 30.0000 chunk 48 optimal weight: 40.0000 chunk 32 optimal weight: 20.0000 overall best weight: 9.5994 ------------------------------------------------------------------------------- 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 = 0.4465 r_free = 0.4465 target = 0.143084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4324 r_free = 0.4324 target = 0.133333 restraints weight = 11296.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.135318 restraints weight = 6415.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.136893 restraints weight = 4281.701| |-----------------------------------------------------------------------------| r_work (final): 0.4374 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 4160 Z= 0.301 Angle : 0.695 5.825 5620 Z= 0.408 Chirality : 0.055 0.144 740 Planarity : 0.002 0.012 690 Dihedral : 7.784 22.730 600 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.45 % Favored : 86.55 % Rotamer: Outliers : 5.95 % Allowed : 18.57 % 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: -4.59 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS I 50 PHE 0.007 0.002 PHE I 94 TYR 0.005 0.001 TYR I 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 78 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 53 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8044 (OUTLIER) cc_final: 0.7657 (pp) REVERT: C 46 GLU cc_start: 0.7511 (mm-30) cc_final: 0.7038 (mm-30) REVERT: D 38 LEU cc_start: 0.8192 (OUTLIER) cc_final: 0.7581 (pp) REVERT: D 61 GLU cc_start: 0.8225 (mp0) cc_final: 0.7725 (mp0) REVERT: F 61 GLU cc_start: 0.8087 (mp0) cc_final: 0.7478 (mp0) outliers start: 25 outliers final: 21 residues processed: 76 average time/residue: 0.0851 time to fit residues: 9.6797 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 : 0.485 ------------------------------------------------------------------------------- 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 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 30.0000 chunk 5 optimal weight: 20.0000 chunk 27 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 51 optimal weight: 20.0000 chunk 46 optimal weight: 7.9990 chunk 37 optimal weight: 9.9990 chunk 9 optimal weight: 30.0000 chunk 14 optimal weight: 10.0000 chunk 57 optimal weight: 40.0000 chunk 50 optimal weight: 8.9990 overall best weight: 9.1992 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.150098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4419 r_free = 0.4419 target = 0.140769 restraints weight = 11554.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.142639 restraints weight = 6861.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4466 r_free = 0.4466 target = 0.143904 restraints weight = 4662.230| |-----------------------------------------------------------------------------| r_work (final): 0.4398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.4843 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= 0.284 Angle : 0.675 5.707 5620 Z= 0.397 Chirality : 0.054 0.140 740 Planarity : 0.002 0.013 690 Dihedral : 7.718 22.310 600 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 16.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.59 % Favored : 87.41 % Rotamer: Outliers : 5.95 % Allowed : 19.29 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (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 0.006 0.001 TYR H 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: 25 poor density : 49 time to evaluate : 0.448 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.7988 (OUTLIER) cc_final: 0.7640 (pp) REVERT: C 46 GLU cc_start: 0.7538 (mm-30) cc_final: 0.7068 (mm-30) REVERT: D 38 LEU cc_start: 0.8179 (OUTLIER) cc_final: 0.7617 (pp) REVERT: D 61 GLU cc_start: 0.8218 (mp0) cc_final: 0.7757 (mp0) REVERT: F 61 GLU cc_start: 0.8108 (mp0) cc_final: 0.7498 (mp0) REVERT: F 77 VAL cc_start: 0.8137 (OUTLIER) cc_final: 0.7808 (t) outliers start: 25 outliers final: 21 residues processed: 72 average time/residue: 0.0887 time to fit residues: 9.5360 Evaluate side-chains 73 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 49 time to evaluate : 0.519 ------------------------------------------------------------------------------- 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 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 77 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 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 34 optimal weight: 9.9990 chunk 12 optimal weight: 30.0000 chunk 46 optimal weight: 8.9990 chunk 15 optimal weight: 0.3980 chunk 36 optimal weight: 4.9990 chunk 10 optimal weight: 8.9990 chunk 25 optimal weight: 20.0000 chunk 24 optimal weight: 20.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- 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 = 0.4534 r_free = 0.4534 target = 0.147310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.137212 restraints weight = 10772.281| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.139385 restraints weight = 6146.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4448 r_free = 0.4448 target = 0.140933 restraints weight = 4002.463| |-----------------------------------------------------------------------------| r_work (final): 0.4446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7209 moved from start: 0.4895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 4160 Z= 0.198 Angle : 0.595 4.834 5620 Z= 0.350 Chirality : 0.053 0.140 740 Planarity : 0.002 0.009 690 Dihedral : 7.318 21.110 600 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 13.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.41 % Favored : 87.59 % Rotamer: Outliers : 5.71 % Allowed : 19.52 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.50 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.003 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 78 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 54 time to evaluate : 0.481 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 38 LEU cc_start: 0.7997 (OUTLIER) cc_final: 0.7650 (pp) REVERT: C 46 GLU cc_start: 0.7643 (mm-30) cc_final: 0.7168 (mm-30) REVERT: D 38 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7664 (pp) REVERT: D 61 GLU cc_start: 0.8296 (mp0) cc_final: 0.7870 (mp0) REVERT: F 61 GLU cc_start: 0.8121 (mp0) cc_final: 0.7453 (mp0) outliers start: 24 outliers final: 19 residues processed: 75 average time/residue: 0.0869 time to fit residues: 9.7656 Evaluate side-chains 70 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 49 time to evaluate : 0.440 ------------------------------------------------------------------------------- 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 38 LEU Chi-restraints excluded: chain D residue 65 ASN Chi-restraints excluded: chain D residue 92 THR Chi-restraints excluded: chain F residue 77 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 6.9990 chunk 43 optimal weight: 30.0000 chunk 25 optimal weight: 20.0000 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 8.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 30.0000 chunk 33 optimal weight: 40.0000 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 50.0000 chunk 59 optimal weight: 0.0570 overall best weight: 3.7904 ------------------------------------------------------------------------------- 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 = 0.4587 r_free = 0.4587 target = 0.154140 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.4457 r_free = 0.4457 target = 0.143417 restraints weight = 10451.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4487 r_free = 0.4487 target = 0.145785 restraints weight = 5742.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.147325 restraints weight = 3652.585| |-----------------------------------------------------------------------------| r_work (final): 0.4502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7144 moved from start: 0.5014 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= 0.158 Angle : 0.555 4.480 5620 Z= 0.326 Chirality : 0.052 0.140 740 Planarity : 0.002 0.011 690 Dihedral : 6.945 20.624 600 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.21 % Favored : 88.79 % Rotamer: Outliers : 4.76 % Allowed : 20.48 % Favored : 74.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.31 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS H 50 PHE 0.005 0.001 PHE E 94 TYR 0.005 0.001 TYR H 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 82 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 62 time to evaluate : 0.495 Fit side-chains revert: symmetry clash REVERT: E 38 LEU cc_start: 0.8015 (OUTLIER) cc_final: 0.7799 (mt) REVERT: C 46 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7156 (mm-30) REVERT: D 38 LEU cc_start: 0.8308 (OUTLIER) cc_final: 0.7768 (pp) REVERT: D 61 GLU cc_start: 0.8367 (mp0) cc_final: 0.7966 (mp0) REVERT: F 61 GLU cc_start: 0.8100 (mp0) cc_final: 0.7552 (mp0) outliers start: 20 outliers final: 14 residues processed: 78 average time/residue: 0.0796 time to fit residues: 9.4905 Evaluate side-chains 72 residues out of total 420 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 56 time to evaluate : 0.527 ------------------------------------------------------------------------------- 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 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 D residue 38 LEU 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 7.9990 chunk 2 optimal weight: 9.9990 chunk 31 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 21 optimal weight: 40.0000 chunk 11 optimal weight: 30.0000 chunk 38 optimal weight: 8.9990 chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 40.0000 chunk 49 optimal weight: 20.0000 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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 = 0.4558 r_free = 0.4558 target = 0.150503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.140819 restraints weight = 11764.750| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.142669 restraints weight = 6974.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4458 r_free = 0.4458 target = 0.143901 restraints weight = 4773.710| |-----------------------------------------------------------------------------| r_work (final): 0.4439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 moved from start: 0.5017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4160 Z= 0.262 Angle : 0.668 5.722 5620 Z= 0.391 Chirality : 0.054 0.157 740 Planarity : 0.002 0.012 690 Dihedral : 7.401 21.712 600 Min Nonbonded Distance : 2.565 Molprobity Statistics. All-atom Clashscore : 14.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.14 % Favored : 85.86 % Rotamer: Outliers : 4.29 % Allowed : 21.19 % Favored : 74.52 % 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: -4.43 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS H 50 PHE 0.006 0.001 PHE I 94 TYR 0.006 0.001 TYR J 39 =============================================================================== Job complete usr+sys time: 1209.18 seconds wall clock time: 23 minutes 9.22 seconds (1389.22 seconds total)