Starting phenix.real_space_refine on Sat Aug 23 08:40:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewv_50023/08_2025/9ewv_50023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewv_50023/08_2025/9ewv_50023.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ewv_50023/08_2025/9ewv_50023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewv_50023/08_2025/9ewv_50023.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ewv_50023/08_2025/9ewv_50023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewv_50023/08_2025/9ewv_50023.map" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians C 3360 2.51 5 N 936 2.21 5 O 1068 1.98 5 H 5676 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11040 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 920 Classifications: {'peptide': 64} Link IDs: {'TRANS': 63} Restraints were copied for chains: B, C, D, E, I, F, G, H, J, K, L Time building chain proxies: 0.95, per 1000 atoms: 0.09 Number of scatterers: 11040 At special positions: 0 Unit cell: (76.386, 138.724, 45.656, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) O 1068 8.00 N 936 7.00 C 3360 6.00 H 5676 1.00 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: 0.78 Conformation dependent library (CDL) restraints added in 238.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1296 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 15 sheets defined 0.0% alpha, 49.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'E' and resid 35 through 43 removed outlier: 6.566A pdb=" N GLY A 36 " --> pdb=" O VAL I 37 " (cutoff:3.500A) removed outlier: 8.395A pdb=" N TYR I 39 " --> pdb=" O GLY A 36 " (cutoff:3.500A) removed outlier: 6.457A pdb=" N LEU A 38 " --> pdb=" O TYR I 39 " (cutoff:3.500A) removed outlier: 8.361A pdb=" N GLY I 41 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N VAL A 40 " --> pdb=" O GLY I 41 " (cutoff:3.500A) removed outlier: 8.526A pdb=" N LYS I 43 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N SER A 42 " --> pdb=" O LYS I 43 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 47 through 50 removed outlier: 6.682A pdb=" N GLU C 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N VAL D 49 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N VAL C 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N GLY A 47 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.341A pdb=" N HIS I 50 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N VAL A 49 " --> pdb=" O HIS I 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 54 through 57 removed outlier: 6.504A pdb=" N VAL C 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N THR A 54 " --> pdb=" O VAL I 55 " (cutoff:3.500A) removed outlier: 8.261A pdb=" N GLU I 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.692A pdb=" N ALA A 56 " --> pdb=" O GLU I 57 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 61 through 65 removed outlier: 6.715A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 8.305A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU B 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 8.258A pdb=" N THR C 64 " --> pdb=" O GLU B 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL B 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 8.293A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 71 through 78 removed outlier: 8.857A pdb=" N THR D 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N THR E 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL E 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR C 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N THR D 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL D 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL C 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N VAL A 71 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 8.722A pdb=" N VAL B 74 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 71 through 78 removed outlier: 8.857A pdb=" N THR D 72 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 9.725A pdb=" N THR E 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL D 74 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL E 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ALA D 76 " --> pdb=" O VAL E 77 " (cutoff:3.500A) removed outlier: 8.937A pdb=" N THR C 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 9.807A pdb=" N THR D 75 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N VAL C 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N VAL D 77 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.276A pdb=" N ALA C 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.812A pdb=" N THR B 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 9.693A pdb=" N THR C 75 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N VAL B 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 7.983A pdb=" N VAL C 77 " --> pdb=" O VAL B 74 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ALA B 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N ALA A 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 89 through 90 removed outlier: 6.282A pdb=" N ALA A 89 " --> pdb=" O ALA I 90 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 93 through 96 removed outlier: 6.793A pdb=" N GLY A 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 8.326A pdb=" N LYS I 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N VAL A 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'K' and resid 35 through 43 removed outlier: 6.667A pdb=" N GLY F 36 " --> pdb=" O VAL L 37 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N TYR L 39 " --> pdb=" O GLY F 36 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N LEU F 38 " --> pdb=" O TYR L 39 " (cutoff:3.500A) removed outlier: 8.465A pdb=" N GLY L 41 " --> pdb=" O LEU F 38 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N VAL F 40 " --> pdb=" O GLY L 41 " (cutoff:3.500A) removed outlier: 8.623A pdb=" N LYS L 43 " --> pdb=" O VAL F 40 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N SER F 42 " --> pdb=" O LYS L 43 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 47 through 50 removed outlier: 6.483A pdb=" N VAL F 48 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N GLY F 47 " --> pdb=" O VAL L 48 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N HIS L 50 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL F 49 " --> pdb=" O HIS L 50 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 54 through 57 removed outlier: 6.494A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N VAL F 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 6.146A pdb=" N THR F 54 " --> pdb=" O VAL L 55 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N GLU L 57 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N ALA F 56 " --> pdb=" O GLU L 57 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 61 through 65 removed outlier: 6.578A pdb=" N GLU G 61 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 8.227A pdb=" N THR H 64 " --> pdb=" O GLU G 61 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N VAL G 63 " --> pdb=" O THR H 64 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 71 through 78 removed outlier: 8.863A pdb=" N THR J 72 " --> pdb=" O GLY K 73 " (cutoff:3.500A) removed outlier: 9.745A pdb=" N THR K 75 " --> pdb=" O THR J 72 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N VAL J 74 " --> pdb=" O THR K 75 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL K 77 " --> pdb=" O VAL J 74 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ALA J 76 " --> pdb=" O VAL K 77 " (cutoff:3.500A) removed outlier: 8.888A pdb=" N THR H 72 " --> pdb=" O GLY J 73 " (cutoff:3.500A) removed outlier: 9.782A pdb=" N THR J 75 " --> pdb=" O THR H 72 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N VAL H 74 " --> pdb=" O THR J 75 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N VAL J 77 " --> pdb=" O VAL H 74 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA H 76 " --> pdb=" O VAL J 77 " (cutoff:3.500A) removed outlier: 8.858A pdb=" N THR G 72 " --> pdb=" O GLY H 73 " (cutoff:3.500A) removed outlier: 9.732A pdb=" N THR H 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N VAL G 74 " --> pdb=" O THR H 75 " (cutoff:3.500A) removed outlier: 7.967A pdb=" N VAL H 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N ALA G 76 " --> pdb=" O VAL H 77 " (cutoff:3.500A) removed outlier: 9.269A pdb=" N VAL F 70 " --> pdb=" O VAL G 71 " (cutoff:3.500A) removed outlier: 10.383A pdb=" N GLY G 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 8.964A pdb=" N THR F 72 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 9.834A pdb=" N THR G 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N VAL F 74 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 7.763A pdb=" N VAL G 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.214A pdb=" N ALA F 76 " --> pdb=" O VAL G 77 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N VAL F 70 " --> pdb=" O VAL L 71 " (cutoff:3.500A) removed outlier: 8.254A pdb=" N GLY L 73 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N THR F 72 " --> pdb=" O GLY L 73 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N THR L 75 " --> pdb=" O THR F 72 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N VAL F 74 " --> pdb=" O THR L 75 " (cutoff:3.500A) removed outlier: 9.857A pdb=" N VAL L 77 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ALA F 76 " --> pdb=" O VAL L 77 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'K' and resid 89 through 90 removed outlier: 6.342A pdb=" N ALA F 89 " --> pdb=" O ALA L 90 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'K' and resid 93 through 96 removed outlier: 6.676A pdb=" N GLY F 93 " --> pdb=" O PHE L 94 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N LYS L 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.416A pdb=" N VAL F 95 " --> pdb=" O LYS L 96 " (cutoff:3.500A) 160 hydrogen bonds defined for protein. 477 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.01 Time building geometry restraints manager: 1.18 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 0.98: 5676 0.98 - 1.12: 0 1.12 - 1.26: 936 1.26 - 1.40: 1020 1.40 - 1.55: 3432 Bond restraints: 11064 Sorted by residual: bond pdb=" CE2 PHE E 94 " pdb=" CZ PHE E 94 " ideal model delta sigma weight residual 1.382 1.315 0.067 3.00e-02 1.11e+03 4.93e+00 bond pdb=" CE2 PHE L 94 " pdb=" CZ PHE L 94 " ideal model delta sigma weight residual 1.382 1.315 0.067 3.00e-02 1.11e+03 4.93e+00 bond pdb=" CE2 PHE D 94 " pdb=" CZ PHE D 94 " ideal model delta sigma weight residual 1.382 1.315 0.067 3.00e-02 1.11e+03 4.92e+00 bond pdb=" CE2 PHE I 94 " pdb=" CZ PHE I 94 " ideal model delta sigma weight residual 1.382 1.316 0.066 3.00e-02 1.11e+03 4.90e+00 bond pdb=" CE2 PHE J 94 " pdb=" CZ PHE J 94 " ideal model delta sigma weight residual 1.382 1.316 0.066 3.00e-02 1.11e+03 4.90e+00 ... (remaining 11059 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 17679 1.04 - 2.09: 2075 2.09 - 3.13: 322 3.13 - 4.18: 49 4.18 - 5.22: 23 Bond angle restraints: 20148 Sorted by residual: angle pdb=" N ALA F 91 " pdb=" CA ALA F 91 " pdb=" C ALA F 91 " ideal model delta sigma weight residual 108.38 112.65 -4.27 1.35e+00 5.49e-01 9.98e+00 angle pdb=" N ALA H 91 " pdb=" CA ALA H 91 " pdb=" C ALA H 91 " ideal model delta sigma weight residual 108.38 112.61 -4.23 1.35e+00 5.49e-01 9.80e+00 angle pdb=" N ALA D 91 " pdb=" CA ALA D 91 " pdb=" C ALA D 91 " ideal model delta sigma weight residual 108.38 112.61 -4.23 1.35e+00 5.49e-01 9.80e+00 angle pdb=" N ALA G 91 " pdb=" CA ALA G 91 " pdb=" C ALA G 91 " ideal model delta sigma weight residual 108.38 112.60 -4.22 1.35e+00 5.49e-01 9.78e+00 angle pdb=" N ALA B 91 " pdb=" CA ALA B 91 " pdb=" C ALA B 91 " ideal model delta sigma weight residual 108.38 112.59 -4.21 1.35e+00 5.49e-01 9.74e+00 ... (remaining 20143 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 4370 17.83 - 35.66: 289 35.66 - 53.50: 213 53.50 - 71.33: 168 71.33 - 89.16: 12 Dihedral angle restraints: 5052 sinusoidal: 2844 harmonic: 2208 Sorted by residual: dihedral pdb=" CA ASN B 65 " pdb=" C ASN B 65 " pdb=" N VAL B 66 " pdb=" CA VAL B 66 " ideal model delta harmonic sigma weight residual 180.00 149.84 30.16 0 5.00e+00 4.00e-02 3.64e+01 dihedral pdb=" CA ASN E 65 " pdb=" C ASN E 65 " pdb=" N VAL E 66 " pdb=" CA VAL E 66 " ideal model delta harmonic sigma weight residual 180.00 149.87 30.13 0 5.00e+00 4.00e-02 3.63e+01 dihedral pdb=" CA ASN H 65 " pdb=" C ASN H 65 " pdb=" N VAL H 66 " pdb=" CA VAL H 66 " ideal model delta harmonic sigma weight residual 180.00 149.87 30.13 0 5.00e+00 4.00e-02 3.63e+01 ... (remaining 5049 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 459 0.029 - 0.059: 237 0.059 - 0.088: 75 0.088 - 0.118: 126 0.118 - 0.147: 51 Chirality restraints: 948 Sorted by residual: chirality pdb=" CA VAL L 70 " pdb=" N VAL L 70 " pdb=" C VAL L 70 " pdb=" CB VAL L 70 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.43e-01 chirality pdb=" CA VAL E 70 " pdb=" N VAL E 70 " pdb=" C VAL E 70 " pdb=" CB VAL E 70 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.41e-01 chirality pdb=" CA VAL F 70 " pdb=" N VAL F 70 " pdb=" C VAL F 70 " pdb=" CB VAL F 70 " both_signs ideal model delta sigma weight residual False 2.44 2.59 -0.15 2.00e-01 2.50e+01 5.40e-01 ... (remaining 945 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE J 94 " 0.023 2.00e-02 2.50e+03 1.06e-02 3.36e+00 pdb=" CG PHE J 94 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE J 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE J 94 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE J 94 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE J 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE J 94 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE J 94 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE J 94 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE J 94 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE J 94 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE J 94 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE L 94 " 0.022 2.00e-02 2.50e+03 1.05e-02 3.31e+00 pdb=" CG PHE L 94 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 PHE L 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE L 94 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE L 94 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE L 94 " 0.000 2.00e-02 2.50e+03 pdb=" CZ PHE L 94 " 0.001 2.00e-02 2.50e+03 pdb=" HD1 PHE L 94 " -0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE L 94 " -0.001 2.00e-02 2.50e+03 pdb=" HE1 PHE L 94 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE L 94 " 0.004 2.00e-02 2.50e+03 pdb=" HZ PHE L 94 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE K 94 " 0.023 2.00e-02 2.50e+03 1.05e-02 3.30e+00 pdb=" CG PHE K 94 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 PHE K 94 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE K 94 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 PHE K 94 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 PHE K 94 " -0.000 2.00e-02 2.50e+03 pdb=" CZ PHE K 94 " 0.002 2.00e-02 2.50e+03 pdb=" HD1 PHE K 94 " -0.003 2.00e-02 2.50e+03 pdb=" HD2 PHE K 94 " -0.002 2.00e-02 2.50e+03 pdb=" HE1 PHE K 94 " 0.002 2.00e-02 2.50e+03 pdb=" HE2 PHE K 94 " 0.005 2.00e-02 2.50e+03 pdb=" HZ PHE K 94 " 0.002 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 1.76 - 2.30: 2731 2.30 - 2.85: 25446 2.85 - 3.40: 24981 3.40 - 3.95: 36863 3.95 - 4.50: 52123 Nonbonded interactions: 142144 Sorted by model distance: nonbonded pdb=" HZ3 LYS C 34 " pdb=" OE1 GLU C 83 " model vdw 1.755 2.450 nonbonded pdb=" HZ3 LYS L 34 " pdb=" OE1 GLU L 83 " model vdw 1.755 2.450 nonbonded pdb=" HZ3 LYS D 34 " pdb=" OE1 GLU D 83 " model vdw 1.755 2.450 nonbonded pdb=" HZ3 LYS H 34 " pdb=" OE1 GLU H 83 " model vdw 1.755 2.450 nonbonded pdb=" HZ3 LYS E 34 " pdb=" OE1 GLU E 83 " model vdw 1.756 2.450 ... (remaining 142139 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: 0.03 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'I' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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 individual isotropic 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: 3.110 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.070 Extract box with map and model: 0.180 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.510 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6407 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 : 0.009 0.067 5388 Z= 0.349 Angle : 0.918 5.222 7272 Z= 0.560 Chirality : 0.058 0.147 948 Planarity : 0.003 0.013 900 Dihedral : 15.090 89.162 1860 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 7.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.11 % Favored : 94.89 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.24), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.57 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR C 39 PHE 0.028 0.009 PHE L 94 HIS 0.004 0.002 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00876 ( 5388) covalent geometry : angle 0.91843 ( 7272) hydrogen bonds : bond 0.14705 ( 160) hydrogen bonds : angle 5.93329 ( 477) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 132 time to evaluate : 0.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7388 (tttt) cc_final: 0.7177 (mmpt) REVERT: C 45 LYS cc_start: 0.8176 (tttt) cc_final: 0.7397 (mmpt) REVERT: C 57 GLU cc_start: 0.5517 (mt-10) cc_final: 0.5217 (mm-30) REVERT: D 45 LYS cc_start: 0.8113 (tttt) cc_final: 0.7289 (mmpt) REVERT: I 57 GLU cc_start: 0.5537 (mt-10) cc_final: 0.5185 (mm-30) REVERT: I 87 ASN cc_start: 0.7032 (m-40) cc_final: 0.6763 (t0) REVERT: F 57 GLU cc_start: 0.5616 (mt-10) cc_final: 0.5209 (mm-30) REVERT: H 45 LYS cc_start: 0.8445 (tttt) cc_final: 0.7414 (mmpt) REVERT: J 45 LYS cc_start: 0.8043 (tttt) cc_final: 0.7272 (mmpt) REVERT: J 57 GLU cc_start: 0.5838 (mt-10) cc_final: 0.5148 (mp0) REVERT: K 45 LYS cc_start: 0.8462 (tttt) cc_final: 0.8166 (ttpp) outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.9980 time to fit residues: 139.0006 Evaluate side-chains 75 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.5120 r_free = 0.5120 target = 0.232848 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4984 r_free = 0.4984 target = 0.215723 restraints weight = 21779.377| |-----------------------------------------------------------------------------| r_work (start): 0.4981 rms_B_bonded: 2.66 r_work: 0.4912 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5388 Z= 0.154 Angle : 0.583 3.981 7272 Z= 0.342 Chirality : 0.054 0.153 948 Planarity : 0.003 0.009 900 Dihedral : 8.093 32.038 768 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 1.27 % Allowed : 9.42 % Favored : 89.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.37 (0.24), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR K 39 PHE 0.010 0.002 PHE B 94 HIS 0.001 0.000 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 5388) covalent geometry : angle 0.58296 ( 7272) hydrogen bonds : bond 0.01511 ( 160) hydrogen bonds : angle 3.66904 ( 477) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 87 time to evaluate : 0.358 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7888 (tttt) cc_final: 0.7412 (mmtt) REVERT: C 45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7507 (mmpt) REVERT: C 57 GLU cc_start: 0.5889 (mt-10) cc_final: 0.5573 (mp0) REVERT: D 45 LYS cc_start: 0.8287 (tttt) cc_final: 0.7452 (mmpt) REVERT: E 45 LYS cc_start: 0.8142 (tttt) cc_final: 0.7516 (tppt) REVERT: E 87 ASN cc_start: 0.7400 (OUTLIER) cc_final: 0.6655 (t0) REVERT: I 57 GLU cc_start: 0.6277 (mt-10) cc_final: 0.6023 (mt-10) REVERT: I 87 ASN cc_start: 0.6946 (m-40) cc_final: 0.6546 (t0) REVERT: F 57 GLU cc_start: 0.6005 (mt-10) cc_final: 0.5667 (mm-30) REVERT: G 45 LYS cc_start: 0.7937 (tttt) cc_final: 0.7414 (mmpt) REVERT: H 45 LYS cc_start: 0.8510 (tttt) cc_final: 0.7458 (mmpt) REVERT: J 45 LYS cc_start: 0.8089 (tttt) cc_final: 0.7308 (mptt) REVERT: J 57 GLU cc_start: 0.6197 (mt-10) cc_final: 0.5175 (mp0) REVERT: K 45 LYS cc_start: 0.8444 (tttt) cc_final: 0.8068 (ttpp) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 0.8512 time to fit residues: 80.9478 Evaluate side-chains 83 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 78 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 87 ASN Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain K residue 92 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 3 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 37 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 32 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.5065 r_free = 0.5065 target = 0.227546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4933 r_free = 0.4933 target = 0.210086 restraints weight = 22141.775| |-----------------------------------------------------------------------------| r_work (start): 0.4920 rms_B_bonded: 2.70 r_work: 0.4844 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work (final): 0.4844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.3555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5388 Z= 0.223 Angle : 0.630 3.879 7272 Z= 0.378 Chirality : 0.053 0.150 948 Planarity : 0.003 0.012 900 Dihedral : 8.683 31.956 768 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.45 % Allowed : 13.04 % Favored : 85.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.06 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.68 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR K 39 PHE 0.016 0.004 PHE D 94 HIS 0.001 0.000 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00423 ( 5388) covalent geometry : angle 0.63026 ( 7272) hydrogen bonds : bond 0.02490 ( 160) hydrogen bonds : angle 3.81308 ( 477) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 82 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8069 (tttt) cc_final: 0.7509 (mmpt) REVERT: C 45 LYS cc_start: 0.8508 (tttt) cc_final: 0.7852 (mmpt) REVERT: C 46 GLU cc_start: 0.7722 (tt0) cc_final: 0.7505 (mt-10) REVERT: C 57 GLU cc_start: 0.5936 (mt-10) cc_final: 0.5489 (mp0) REVERT: D 45 LYS cc_start: 0.8541 (tttt) cc_final: 0.7723 (mmpt) REVERT: D 57 GLU cc_start: 0.6467 (mt-10) cc_final: 0.5602 (mp0) REVERT: E 45 LYS cc_start: 0.8340 (tttt) cc_final: 0.7657 (mptt) REVERT: I 45 LYS cc_start: 0.8049 (tttt) cc_final: 0.7711 (mmtt) REVERT: G 45 LYS cc_start: 0.8108 (tttt) cc_final: 0.7636 (mmpt) REVERT: H 45 LYS cc_start: 0.8692 (tttt) cc_final: 0.7844 (mmpt) REVERT: J 45 LYS cc_start: 0.8212 (tttt) cc_final: 0.7594 (mptt) REVERT: J 57 GLU cc_start: 0.6346 (mt-10) cc_final: 0.5285 (mp0) REVERT: K 45 LYS cc_start: 0.8545 (tttt) cc_final: 0.7888 (mptt) outliers start: 8 outliers final: 7 residues processed: 85 average time/residue: 0.8863 time to fit residues: 80.1903 Evaluate side-chains 79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 72 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain K residue 92 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 25 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 22 optimal weight: 2.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 62 GLN ** 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 = 0.5012 r_free = 0.5012 target = 0.221325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4866 r_free = 0.4866 target = 0.203770 restraints weight = 22025.534| |-----------------------------------------------------------------------------| r_work (start): 0.4857 rms_B_bonded: 2.62 r_work: 0.4798 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.4693 rms_B_bonded: 4.84 restraints_weight: 0.2500 r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6809 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.057 5388 Z= 0.322 Angle : 0.752 4.876 7272 Z= 0.448 Chirality : 0.055 0.176 948 Planarity : 0.004 0.017 900 Dihedral : 9.882 33.425 768 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.17 % Favored : 86.83 % Rotamer: Outliers : 2.54 % Allowed : 20.29 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.02 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.003 TYR K 39 PHE 0.019 0.005 PHE D 94 HIS 0.003 0.001 HIS K 50 Details of bonding type rmsd covalent geometry : bond 0.00603 ( 5388) covalent geometry : angle 0.75169 ( 7272) hydrogen bonds : bond 0.02839 ( 160) hydrogen bonds : angle 4.38942 ( 477) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 86 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8188 (tttt) cc_final: 0.7460 (mmtt) REVERT: B 97 LYS cc_start: 0.7063 (OUTLIER) cc_final: 0.6227 (tmmt) REVERT: C 45 LYS cc_start: 0.8623 (tttt) cc_final: 0.7838 (mmpt) REVERT: C 57 GLU cc_start: 0.6131 (mt-10) cc_final: 0.5660 (mp0) REVERT: D 45 LYS cc_start: 0.8690 (tttt) cc_final: 0.7737 (mmtm) REVERT: D 57 GLU cc_start: 0.6753 (mt-10) cc_final: 0.5760 (mp0) REVERT: E 45 LYS cc_start: 0.8578 (tttt) cc_final: 0.7731 (tppt) REVERT: I 45 LYS cc_start: 0.8348 (tttt) cc_final: 0.7866 (mmtt) REVERT: F 57 GLU cc_start: 0.5823 (mt-10) cc_final: 0.5252 (mp0) REVERT: G 45 LYS cc_start: 0.8227 (tttt) cc_final: 0.7648 (mmpt) REVERT: H 45 LYS cc_start: 0.8830 (tttt) cc_final: 0.7850 (mmpt) REVERT: H 57 GLU cc_start: 0.6299 (mt-10) cc_final: 0.5739 (mp0) REVERT: J 45 LYS cc_start: 0.8453 (tttt) cc_final: 0.7760 (mptt) REVERT: J 57 GLU cc_start: 0.6680 (mt-10) cc_final: 0.5560 (mp0) REVERT: K 45 LYS cc_start: 0.8789 (tttt) cc_final: 0.8030 (mptt) REVERT: L 57 GLU cc_start: 0.6465 (mt-10) cc_final: 0.5359 (mp0) outliers start: 14 outliers final: 8 residues processed: 94 average time/residue: 0.8007 time to fit residues: 80.5920 Evaluate side-chains 89 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 80 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain J residue 81 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 42 optimal weight: 0.6980 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 65 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 62 GLN ** 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 = 0.4963 r_free = 0.4963 target = 0.220226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.201520 restraints weight = 21696.897| |-----------------------------------------------------------------------------| r_work (start): 0.4824 rms_B_bonded: 2.62 r_work: 0.4736 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6740 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5388 Z= 0.270 Angle : 0.694 5.897 7272 Z= 0.410 Chirality : 0.054 0.170 948 Planarity : 0.003 0.014 900 Dihedral : 9.382 33.746 768 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 23.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 3.62 % Allowed : 23.01 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.19 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.19 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.19 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR J 39 PHE 0.014 0.004 PHE A 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00500 ( 5388) covalent geometry : angle 0.69430 ( 7272) hydrogen bonds : bond 0.02514 ( 160) hydrogen bonds : angle 4.34162 ( 477) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 85 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8105 (tttt) cc_final: 0.7642 (mmtt) REVERT: C 45 LYS cc_start: 0.8610 (tttt) cc_final: 0.8029 (mmpt) REVERT: C 57 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5454 (mm-30) REVERT: D 45 LYS cc_start: 0.8663 (tttt) cc_final: 0.7970 (mmtm) REVERT: D 57 GLU cc_start: 0.6643 (mt-10) cc_final: 0.5659 (mp0) REVERT: E 45 LYS cc_start: 0.8494 (tttt) cc_final: 0.7897 (tppt) REVERT: E 83 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6571 (tt0) REVERT: I 45 LYS cc_start: 0.8272 (tttt) cc_final: 0.8042 (mmtt) REVERT: I 87 ASN cc_start: 0.7177 (m-40) cc_final: 0.6785 (t0) REVERT: F 57 GLU cc_start: 0.5709 (mt-10) cc_final: 0.5253 (mp0) REVERT: G 45 LYS cc_start: 0.8147 (tttt) cc_final: 0.7714 (mmpt) REVERT: H 45 LYS cc_start: 0.8784 (tttt) cc_final: 0.7916 (mmpt) REVERT: H 57 GLU cc_start: 0.6186 (mt-10) cc_final: 0.5673 (mp0) REVERT: J 45 LYS cc_start: 0.8351 (tttt) cc_final: 0.7858 (mptt) REVERT: J 57 GLU cc_start: 0.6707 (mt-10) cc_final: 0.5601 (mp0) REVERT: K 45 LYS cc_start: 0.8588 (tttt) cc_final: 0.8225 (ttpp) REVERT: L 57 GLU cc_start: 0.6330 (mt-10) cc_final: 0.5354 (mp0) REVERT: L 64 THR cc_start: 0.6735 (OUTLIER) cc_final: 0.6435 (m) outliers start: 20 outliers final: 11 residues processed: 97 average time/residue: 0.7005 time to fit residues: 73.5129 Evaluate side-chains 96 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** 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 = 0.4968 r_free = 0.4968 target = 0.220330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.201544 restraints weight = 21854.451| |-----------------------------------------------------------------------------| r_work (start): 0.4829 rms_B_bonded: 2.65 r_work: 0.4744 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 5388 Z= 0.252 Angle : 0.673 7.188 7272 Z= 0.398 Chirality : 0.054 0.170 948 Planarity : 0.003 0.014 900 Dihedral : 9.123 33.957 768 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.19 % Favored : 84.81 % Rotamer: Outliers : 3.99 % Allowed : 23.37 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.93 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.30 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.27 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.008 0.002 TYR K 39 PHE 0.013 0.003 PHE F 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00467 ( 5388) covalent geometry : angle 0.67327 ( 7272) hydrogen bonds : bond 0.02423 ( 160) hydrogen bonds : angle 4.29742 ( 477) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 80 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8125 (tttt) cc_final: 0.7609 (mmtt) REVERT: B 97 LYS cc_start: 0.7204 (OUTLIER) cc_final: 0.6529 (tmmt) REVERT: C 45 LYS cc_start: 0.8600 (tttt) cc_final: 0.7954 (mmpt) REVERT: C 57 GLU cc_start: 0.6003 (mt-10) cc_final: 0.5384 (mm-30) REVERT: D 45 LYS cc_start: 0.8629 (tttt) cc_final: 0.7890 (mmtt) REVERT: D 57 GLU cc_start: 0.6620 (mt-10) cc_final: 0.5637 (mp0) REVERT: D 88 ILE cc_start: 0.6668 (OUTLIER) cc_final: 0.6445 (mp) REVERT: E 45 LYS cc_start: 0.8624 (tttt) cc_final: 0.7929 (tppt) REVERT: E 83 GLU cc_start: 0.6933 (OUTLIER) cc_final: 0.6666 (tt0) REVERT: I 45 LYS cc_start: 0.8294 (tttt) cc_final: 0.8014 (mmtt) REVERT: I 87 ASN cc_start: 0.7235 (m-40) cc_final: 0.6770 (t0) REVERT: F 57 GLU cc_start: 0.5697 (mt-10) cc_final: 0.5238 (mp0) REVERT: G 45 LYS cc_start: 0.8183 (tttt) cc_final: 0.7694 (mmpt) REVERT: H 45 LYS cc_start: 0.8784 (tttt) cc_final: 0.7893 (mmpt) REVERT: H 57 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5596 (mp0) REVERT: J 45 LYS cc_start: 0.8366 (tttt) cc_final: 0.7834 (mptt) REVERT: J 57 GLU cc_start: 0.6721 (mt-10) cc_final: 0.5627 (mp0) REVERT: K 45 LYS cc_start: 0.8597 (tttt) cc_final: 0.8215 (ttpp) REVERT: L 57 GLU cc_start: 0.6298 (mt-10) cc_final: 0.5362 (mp0) REVERT: L 64 THR cc_start: 0.6720 (OUTLIER) cc_final: 0.6420 (m) outliers start: 22 outliers final: 14 residues processed: 95 average time/residue: 0.7541 time to fit residues: 76.7316 Evaluate side-chains 96 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 78 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 68 optimal weight: 2.9990 chunk 32 optimal weight: 0.2980 chunk 5 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** 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 = 0.4980 r_free = 0.4980 target = 0.221570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.203781 restraints weight = 21602.500| |-----------------------------------------------------------------------------| r_work (start): 0.4854 rms_B_bonded: 2.62 r_work: 0.4769 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work (final): 0.4769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 moved from start: 0.5088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5388 Z= 0.220 Angle : 0.634 6.780 7272 Z= 0.375 Chirality : 0.053 0.168 948 Planarity : 0.003 0.012 900 Dihedral : 8.767 33.599 768 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.63 % Favored : 87.37 % Rotamer: Outliers : 2.54 % Allowed : 24.28 % Favored : 73.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.34 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR I 39 PHE 0.012 0.003 PHE B 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 5388) covalent geometry : angle 0.63444 ( 7272) hydrogen bonds : bond 0.02226 ( 160) hydrogen bonds : angle 4.16999 ( 477) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.309 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8129 (tttt) cc_final: 0.7565 (mmtt) REVERT: C 45 LYS cc_start: 0.8594 (tttt) cc_final: 0.7918 (mmpt) REVERT: C 57 GLU cc_start: 0.6025 (mt-10) cc_final: 0.5532 (mm-30) REVERT: D 45 LYS cc_start: 0.8630 (tttt) cc_final: 0.7886 (mmtm) REVERT: E 45 LYS cc_start: 0.8636 (tttt) cc_final: 0.7901 (tppt) REVERT: E 83 GLU cc_start: 0.6927 (OUTLIER) cc_final: 0.6678 (tt0) REVERT: I 45 LYS cc_start: 0.8294 (tttt) cc_final: 0.7962 (mptt) REVERT: I 87 ASN cc_start: 0.7153 (m-40) cc_final: 0.6709 (t0) REVERT: G 45 LYS cc_start: 0.8214 (tttt) cc_final: 0.7640 (mmpt) REVERT: H 45 LYS cc_start: 0.8771 (tttt) cc_final: 0.7848 (mmpt) REVERT: H 57 GLU cc_start: 0.6133 (mt-10) cc_final: 0.5638 (mp0) REVERT: J 45 LYS cc_start: 0.8356 (tttt) cc_final: 0.7793 (mptt) REVERT: J 57 GLU cc_start: 0.6698 (mt-10) cc_final: 0.5643 (mp0) REVERT: K 45 LYS cc_start: 0.8570 (tttt) cc_final: 0.8158 (ttpp) REVERT: L 43 LYS cc_start: 0.7177 (ttpt) cc_final: 0.6530 (tttp) REVERT: L 57 GLU cc_start: 0.6227 (mt-10) cc_final: 0.5487 (mp0) outliers start: 14 outliers final: 10 residues processed: 88 average time/residue: 0.8011 time to fit residues: 75.6017 Evaluate side-chains 90 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 79 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 83 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 30 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 41 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** 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 = 0.4974 r_free = 0.4974 target = 0.220510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4827 r_free = 0.4827 target = 0.202641 restraints weight = 21768.255| |-----------------------------------------------------------------------------| r_work (start): 0.4857 rms_B_bonded: 2.63 r_work: 0.4772 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5388 Z= 0.230 Angle : 0.644 6.911 7272 Z= 0.380 Chirality : 0.053 0.171 948 Planarity : 0.003 0.013 900 Dihedral : 8.792 33.495 768 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 22.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.46 % Favored : 84.54 % Rotamer: Outliers : 3.26 % Allowed : 23.91 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.009 0.002 TYR I 39 PHE 0.012 0.003 PHE B 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 5388) covalent geometry : angle 0.64406 ( 7272) hydrogen bonds : bond 0.02308 ( 160) hydrogen bonds : angle 4.16569 ( 477) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 79 time to evaluate : 0.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8131 (tttt) cc_final: 0.7614 (mmtt) REVERT: C 45 LYS cc_start: 0.8609 (tttt) cc_final: 0.7960 (mmpt) REVERT: C 57 GLU cc_start: 0.6030 (mt-10) cc_final: 0.5519 (mm-30) REVERT: D 45 LYS cc_start: 0.8634 (tttt) cc_final: 0.7900 (mmtm) REVERT: D 57 GLU cc_start: 0.6669 (mt-10) cc_final: 0.5733 (mp0) REVERT: E 45 LYS cc_start: 0.8609 (tttt) cc_final: 0.7882 (tppt) REVERT: E 83 GLU cc_start: 0.7067 (OUTLIER) cc_final: 0.6822 (tt0) REVERT: I 45 LYS cc_start: 0.8363 (tttt) cc_final: 0.8038 (mptt) REVERT: I 87 ASN cc_start: 0.7199 (m-40) cc_final: 0.6684 (t0) REVERT: G 45 LYS cc_start: 0.8211 (tttt) cc_final: 0.7680 (mmpt) REVERT: H 45 LYS cc_start: 0.8751 (tttt) cc_final: 0.7879 (mmpt) REVERT: H 57 GLU cc_start: 0.6119 (mt-10) cc_final: 0.5638 (mp0) REVERT: J 45 LYS cc_start: 0.8363 (tttt) cc_final: 0.7834 (mptt) REVERT: J 57 GLU cc_start: 0.6679 (mt-10) cc_final: 0.5665 (mp0) REVERT: K 45 LYS cc_start: 0.8582 (tttt) cc_final: 0.8174 (ttpp) REVERT: L 43 LYS cc_start: 0.7182 (ttpt) cc_final: 0.6561 (tttp) REVERT: L 57 GLU cc_start: 0.6233 (mt-10) cc_final: 0.5524 (mp0) REVERT: L 64 THR cc_start: 0.6596 (OUTLIER) cc_final: 0.6307 (m) outliers start: 18 outliers final: 14 residues processed: 89 average time/residue: 0.8165 time to fit residues: 77.7465 Evaluate side-chains 93 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 77 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain J residue 83 GLU Chi-restraints excluded: chain K residue 64 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 19 optimal weight: 0.0270 chunk 65 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 54 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 overall best weight: 1.3644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 62 GLN ** 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 = 0.4990 r_free = 0.4990 target = 0.222361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.204255 restraints weight = 21612.707| |-----------------------------------------------------------------------------| r_work (start): 0.4863 rms_B_bonded: 2.69 r_work: 0.4777 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.4777 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6717 moved from start: 0.5292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5388 Z= 0.206 Angle : 0.617 6.696 7272 Z= 0.363 Chirality : 0.053 0.167 948 Planarity : 0.003 0.012 900 Dihedral : 8.520 32.817 768 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 21.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.31 % Favored : 86.69 % Rotamer: Outliers : 2.72 % Allowed : 25.00 % Favored : 72.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.44 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR K 39 PHE 0.011 0.003 PHE B 94 HIS 0.001 0.000 HIS D 50 Details of bonding type rmsd covalent geometry : bond 0.00378 ( 5388) covalent geometry : angle 0.61706 ( 7272) hydrogen bonds : bond 0.02123 ( 160) hydrogen bonds : angle 4.08691 ( 477) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 78 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8127 (tttt) cc_final: 0.7676 (mmtt) REVERT: C 45 LYS cc_start: 0.8617 (tttt) cc_final: 0.7974 (mmpt) REVERT: C 57 GLU cc_start: 0.6115 (mt-10) cc_final: 0.5687 (mm-30) REVERT: D 45 LYS cc_start: 0.8648 (tttt) cc_final: 0.7918 (mmtm) REVERT: E 45 LYS cc_start: 0.8599 (tttt) cc_final: 0.7896 (tppt) REVERT: E 83 GLU cc_start: 0.7043 (OUTLIER) cc_final: 0.6810 (tt0) REVERT: I 45 LYS cc_start: 0.8361 (tttt) cc_final: 0.8073 (mptt) REVERT: I 87 ASN cc_start: 0.7042 (m-40) cc_final: 0.6598 (t0) REVERT: G 45 LYS cc_start: 0.8213 (tttt) cc_final: 0.7698 (mmpt) REVERT: H 45 LYS cc_start: 0.8784 (tttt) cc_final: 0.7920 (mmpt) REVERT: H 57 GLU cc_start: 0.6084 (mt-10) cc_final: 0.5629 (mp0) REVERT: J 45 LYS cc_start: 0.8354 (tttt) cc_final: 0.7840 (mptt) REVERT: J 57 GLU cc_start: 0.6720 (mt-10) cc_final: 0.5674 (mp0) REVERT: K 45 LYS cc_start: 0.8564 (tttt) cc_final: 0.8174 (ttpp) REVERT: L 43 LYS cc_start: 0.7156 (ttpt) cc_final: 0.6560 (tttp) REVERT: L 57 GLU cc_start: 0.6150 (mt-10) cc_final: 0.5477 (mp0) outliers start: 15 outliers final: 11 residues processed: 86 average time/residue: 0.8162 time to fit residues: 75.1982 Evaluate side-chains 88 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 76 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** 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 = 0.5010 r_free = 0.5010 target = 0.224507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4859 r_free = 0.4859 target = 0.206166 restraints weight = 21672.182| |-----------------------------------------------------------------------------| r_work (start): 0.4880 rms_B_bonded: 2.76 r_work: 0.4792 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work (final): 0.4792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.5323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5388 Z= 0.164 Angle : 0.568 6.914 7272 Z= 0.333 Chirality : 0.052 0.160 948 Planarity : 0.002 0.010 900 Dihedral : 8.002 32.243 768 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 1.45 % Allowed : 26.09 % Favored : 72.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.41 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR K 39 PHE 0.009 0.002 PHE B 94 HIS 0.001 0.000 HIS I 50 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 5388) covalent geometry : angle 0.56806 ( 7272) hydrogen bonds : bond 0.01846 ( 160) hydrogen bonds : angle 3.94239 ( 477) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1488 Ramachandran restraints generated. 744 Oldfield, 0 Emsley, 744 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8128 (tttt) cc_final: 0.7603 (mmtt) REVERT: C 45 LYS cc_start: 0.8646 (tttt) cc_final: 0.7947 (mmpt) REVERT: C 57 GLU cc_start: 0.5999 (mt-10) cc_final: 0.5519 (mm-30) REVERT: D 45 LYS cc_start: 0.8657 (tttt) cc_final: 0.7819 (mmtm) REVERT: E 45 LYS cc_start: 0.8642 (tttt) cc_final: 0.7856 (tppt) REVERT: I 45 LYS cc_start: 0.8376 (tttt) cc_final: 0.8002 (mptt) REVERT: I 87 ASN cc_start: 0.7043 (m-40) cc_final: 0.6520 (t0) REVERT: G 45 LYS cc_start: 0.8228 (tttt) cc_final: 0.7643 (mmpt) REVERT: H 45 LYS cc_start: 0.8793 (tttt) cc_final: 0.7852 (mmpt) REVERT: H 57 GLU cc_start: 0.6057 (mt-10) cc_final: 0.5539 (mp0) REVERT: J 45 LYS cc_start: 0.8376 (tttt) cc_final: 0.7765 (mptt) REVERT: J 57 GLU cc_start: 0.6720 (mt-10) cc_final: 0.5601 (mp0) REVERT: K 45 LYS cc_start: 0.8604 (tttt) cc_final: 0.8173 (ttpp) REVERT: L 43 LYS cc_start: 0.7120 (ttpt) cc_final: 0.6500 (tttp) REVERT: L 57 GLU cc_start: 0.5988 (mt-10) cc_final: 0.5315 (mp0) outliers start: 8 outliers final: 8 residues processed: 80 average time/residue: 0.7754 time to fit residues: 66.6133 Evaluate side-chains 84 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 76 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain I residue 83 GLU Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain J residue 63 VAL Chi-restraints excluded: chain K residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 68 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 4 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 62 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 62 GLN ** 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 = 0.4999 r_free = 0.4999 target = 0.223304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.205416 restraints weight = 21817.613| |-----------------------------------------------------------------------------| r_work (start): 0.4870 rms_B_bonded: 2.66 r_work: 0.4789 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6686 moved from start: 0.5408 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5388 Z= 0.194 Angle : 0.602 6.916 7272 Z= 0.351 Chirality : 0.053 0.165 948 Planarity : 0.003 0.011 900 Dihedral : 8.179 32.239 768 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 20.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.58 % Favored : 86.42 % Rotamer: Outliers : 1.45 % Allowed : 26.45 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.66 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.42 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR K 39 PHE 0.011 0.003 PHE B 94 HIS 0.001 0.000 HIS E 50 Details of bonding type rmsd covalent geometry : bond 0.00357 ( 5388) covalent geometry : angle 0.60152 ( 7272) hydrogen bonds : bond 0.02078 ( 160) hydrogen bonds : angle 4.01304 ( 477) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3673.85 seconds wall clock time: 63 minutes 19.46 seconds (3799.46 seconds total)