Starting phenix.real_space_refine on Mon Jun 9 19:57:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewv_50023/06_2025/9ewv_50023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewv_50023/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9ewv_50023/06_2025/9ewv_50023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewv_50023/06_2025/9ewv_50023.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewv_50023/06_2025/9ewv_50023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewv_50023/06_2025/9ewv_50023.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 3.19, per 1000 atoms: 0.29 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: 2.63 Conformation dependent library (CDL) restraints added in 724.1 milliseconds 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: 1.14 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: 3.58 Time building geometry restraints manager: 3.23 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: 0.06 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 'K' selection = chain 'J' 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: 2.580 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: 0.200 Extract box with map and model: 0.390 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 23.160 Find NCS groups from input model: 0.160 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:12.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.050 ------------------------------------------------------------------------------- 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 (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: -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 HIS 0.004 0.002 HIS D 50 PHE 0.028 0.009 PHE L 94 TYR 0.005 0.002 TYR C 39 Details of bonding type rmsd hydrogen bonds : bond 0.14705 ( 160) hydrogen bonds : angle 5.93329 ( 477) covalent geometry : bond 0.00876 ( 5388) covalent geometry : angle 0.91843 ( 7272) *********************** 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 : 0.895 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: 1.8635 time to fit residues: 260.0990 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 : 0.765 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 42 optimal weight: 0.5980 chunk 65 optimal weight: 0.7980 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 = 37)----------------| | r_work = 0.4985 r_free = 0.4985 target = 0.215772 restraints weight = 21568.186| |-----------------------------------------------------------------------------| r_work (start): 0.4981 rms_B_bonded: 2.65 r_work: 0.4913 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work (final): 0.4913 ------------------------------------------------------------------------------- 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 (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: -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 HIS 0.001 0.000 HIS G 50 PHE 0.010 0.002 PHE B 94 TYR 0.005 0.001 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.01511 ( 160) hydrogen bonds : angle 3.66904 ( 477) covalent geometry : bond 0.00295 ( 5388) covalent geometry : angle 0.58296 ( 7272) *********************** 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 : 0.773 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: 0.7886 (tttt) cc_final: 0.7416 (mmtt) REVERT: C 45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7513 (mmpt) REVERT: C 57 GLU cc_start: 0.5885 (mt-10) cc_final: 0.5584 (mp0) REVERT: D 45 LYS cc_start: 0.8289 (tttt) cc_final: 0.7460 (mmpt) REVERT: E 45 LYS cc_start: 0.8144 (tttt) cc_final: 0.7520 (tppt) REVERT: E 87 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.6665 (t0) REVERT: I 57 GLU cc_start: 0.6267 (mt-10) cc_final: 0.6017 (mt-10) REVERT: I 87 ASN cc_start: 0.6927 (m-40) cc_final: 0.6548 (t0) REVERT: F 57 GLU cc_start: 0.6005 (mt-10) cc_final: 0.5678 (mm-30) REVERT: G 45 LYS cc_start: 0.7937 (tttt) cc_final: 0.7428 (mmpt) REVERT: H 45 LYS cc_start: 0.8510 (tttt) cc_final: 0.7470 (mmpt) REVERT: J 45 LYS cc_start: 0.8089 (tttt) cc_final: 0.7320 (mptt) REVERT: J 57 GLU cc_start: 0.6197 (mt-10) cc_final: 0.5195 (mp0) REVERT: K 45 LYS cc_start: 0.8438 (tttt) cc_final: 0.8069 (ttpp) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 1.5714 time to fit residues: 150.1724 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 : 0.846 ------------------------------------------------------------------------------- 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 58 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 45 optimal weight: 2.9990 chunk 14 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 48 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- 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 = 0.5049 r_free = 0.5049 target = 0.225680 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4919 r_free = 0.4919 target = 0.208564 restraints weight = 22061.855| |-----------------------------------------------------------------------------| r_work (start): 0.4901 rms_B_bonded: 2.61 r_work: 0.4834 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.4712 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.4712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6718 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 5388 Z= 0.258 Angle : 0.679 4.467 7272 Z= 0.408 Chirality : 0.053 0.155 948 Planarity : 0.004 0.014 900 Dihedral : 9.174 32.795 768 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.54 % Favored : 90.46 % Rotamer: Outliers : 1.81 % Allowed : 13.95 % Favored : 84.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.19 % 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: -3.78 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 PHE 0.017 0.004 PHE D 94 TYR 0.008 0.002 TYR J 39 Details of bonding type rmsd hydrogen bonds : bond 0.02655 ( 160) hydrogen bonds : angle 3.98478 ( 477) covalent geometry : bond 0.00484 ( 5388) covalent geometry : angle 0.67887 ( 7272) *********************** 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 94 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 84 time to evaluate : 0.825 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: 0.8182 (tttt) cc_final: 0.7462 (mmtt) REVERT: C 45 LYS cc_start: 0.8599 (tttt) cc_final: 0.7783 (mmpt) REVERT: C 46 GLU cc_start: 0.7885 (tt0) cc_final: 0.7645 (mt-10) REVERT: C 57 GLU cc_start: 0.6061 (mt-10) cc_final: 0.5501 (mp0) REVERT: D 45 LYS cc_start: 0.8621 (tttt) cc_final: 0.7672 (mmtm) REVERT: D 57 GLU cc_start: 0.6588 (mt-10) cc_final: 0.5638 (mp0) REVERT: E 45 LYS cc_start: 0.8493 (tttt) cc_final: 0.7656 (mptt) REVERT: I 45 LYS cc_start: 0.8211 (tttt) cc_final: 0.7772 (mmtt) REVERT: G 45 LYS cc_start: 0.8218 (tttt) cc_final: 0.7551 (mmpt) REVERT: G 57 GLU cc_start: 0.5875 (mm-30) cc_final: 0.5656 (mm-30) REVERT: H 45 LYS cc_start: 0.8779 (tttt) cc_final: 0.7757 (mmpt) REVERT: H 57 GLU cc_start: 0.6154 (mt-10) cc_final: 0.5571 (mp0) REVERT: J 45 LYS cc_start: 0.8332 (tttt) cc_final: 0.7562 (mptt) REVERT: J 57 GLU cc_start: 0.6460 (mt-10) cc_final: 0.5297 (mp0) REVERT: K 45 LYS cc_start: 0.8710 (tttt) cc_final: 0.7934 (mptt) REVERT: L 45 LYS cc_start: 0.8181 (tttt) cc_final: 0.7903 (mmtt) outliers start: 10 outliers final: 8 residues processed: 89 average time/residue: 1.6160 time to fit residues: 153.9906 Evaluate side-chains 81 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 73 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 THR 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 16 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 59 optimal weight: 5.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.0970 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 1.1182 ------------------------------------------------------------------------------- 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 = 0.5046 r_free = 0.5046 target = 0.226164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4905 r_free = 0.4905 target = 0.208902 restraints weight = 21951.620| |-----------------------------------------------------------------------------| r_work (start): 0.4900 rms_B_bonded: 2.58 r_work: 0.4849 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.4746 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.4746 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6636 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5388 Z= 0.180 Angle : 0.569 4.642 7272 Z= 0.337 Chirality : 0.053 0.160 948 Planarity : 0.003 0.010 900 Dihedral : 8.299 31.784 768 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 18.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.09 % Allowed : 18.66 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % 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: -3.82 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 50 PHE 0.010 0.003 PHE E 94 TYR 0.005 0.001 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.01754 ( 160) hydrogen bonds : angle 3.74878 ( 477) covalent geometry : bond 0.00339 ( 5388) covalent geometry : angle 0.56875 ( 7272) *********************** 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 85 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8198 (tttt) cc_final: 0.7585 (mmpt) REVERT: C 45 LYS cc_start: 0.8610 (tttt) cc_final: 0.7884 (mmpt) REVERT: C 46 GLU cc_start: 0.7854 (tt0) cc_final: 0.7645 (mt-10) REVERT: C 57 GLU cc_start: 0.6014 (mt-10) cc_final: 0.5461 (mp0) REVERT: D 45 LYS cc_start: 0.8643 (tttt) cc_final: 0.7749 (mmtm) REVERT: D 57 GLU cc_start: 0.6585 (mt-10) cc_final: 0.5625 (mp0) REVERT: E 45 LYS cc_start: 0.8529 (tttt) cc_final: 0.7700 (mptt) REVERT: E 87 ASN cc_start: 0.7223 (m110) cc_final: 0.6398 (t0) REVERT: I 45 LYS cc_start: 0.8253 (tttt) cc_final: 0.7913 (mmtt) REVERT: G 45 LYS cc_start: 0.8222 (tttt) cc_final: 0.7594 (mmpt) REVERT: H 45 LYS cc_start: 0.8824 (tttt) cc_final: 0.7792 (mmpt) REVERT: H 57 GLU cc_start: 0.6106 (mt-10) cc_final: 0.5541 (mp0) REVERT: J 45 LYS cc_start: 0.8381 (tttt) cc_final: 0.7603 (mptt) REVERT: J 57 GLU cc_start: 0.6582 (mt-10) cc_final: 0.5443 (mp0) REVERT: K 45 LYS cc_start: 0.8692 (tttt) cc_final: 0.7896 (mptt) REVERT: L 45 LYS cc_start: 0.8100 (tttt) cc_final: 0.7893 (mmtt) REVERT: L 57 GLU cc_start: 0.6306 (mt-10) cc_final: 0.5332 (mp0) outliers start: 6 outliers final: 6 residues processed: 81 average time/residue: 1.4676 time to fit residues: 128.1885 Evaluate side-chains 82 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 H residue 64 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 92 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 47 optimal weight: 4.9990 chunk 13 optimal weight: 0.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 29 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- 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** ** 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 = 0.4945 r_free = 0.4945 target = 0.218560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.199493 restraints weight = 22180.925| |-----------------------------------------------------------------------------| r_work (start): 0.4800 rms_B_bonded: 2.65 r_work: 0.4713 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work (final): 0.4713 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6769 moved from start: 0.4600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.056 5388 Z= 0.335 Angle : 0.757 4.444 7272 Z= 0.452 Chirality : 0.055 0.176 948 Planarity : 0.004 0.018 900 Dihedral : 9.861 33.981 768 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 24.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.50 % Favored : 87.50 % Rotamer: Outliers : 3.26 % Allowed : 21.01 % Favored : 75.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.59 % 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: -4.13 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.14 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.019 0.005 PHE F 94 TYR 0.011 0.003 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.03031 ( 160) hydrogen bonds : angle 4.44894 ( 477) covalent geometry : bond 0.00624 ( 5388) covalent geometry : angle 0.75718 ( 7272) *********************** 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 99 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 81 time to evaluate : 0.771 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: 0.8113 (tttt) cc_final: 0.7605 (mmtt) REVERT: B 97 LYS cc_start: 0.7225 (OUTLIER) cc_final: 0.6348 (tmmt) REVERT: C 45 LYS cc_start: 0.8585 (tttt) cc_final: 0.7946 (mmpt) REVERT: C 57 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5622 (mp0) REVERT: D 45 LYS cc_start: 0.8693 (tttt) cc_final: 0.7928 (mmtm) REVERT: D 57 GLU cc_start: 0.6663 (mt-10) cc_final: 0.5677 (mp0) REVERT: E 45 LYS cc_start: 0.8483 (tttt) cc_final: 0.7868 (tppt) REVERT: E 83 GLU cc_start: 0.6889 (OUTLIER) cc_final: 0.6645 (tt0) REVERT: E 87 ASN cc_start: 0.7295 (m110) cc_final: 0.6441 (t0) REVERT: I 45 LYS cc_start: 0.8312 (tttt) cc_final: 0.8031 (mmtt) REVERT: F 57 GLU cc_start: 0.5817 (mt-10) cc_final: 0.5138 (mp0) REVERT: G 45 LYS cc_start: 0.8150 (tttt) cc_final: 0.7668 (mmpt) REVERT: H 45 LYS cc_start: 0.8812 (tttt) cc_final: 0.7889 (mmpt) REVERT: H 57 GLU cc_start: 0.6159 (mt-10) cc_final: 0.5609 (mp0) REVERT: J 45 LYS cc_start: 0.8383 (tttt) cc_final: 0.7816 (mptt) REVERT: J 57 GLU cc_start: 0.6735 (mt-10) cc_final: 0.5587 (mp0) REVERT: K 45 LYS cc_start: 0.8654 (tttt) cc_final: 0.8261 (ttpp) REVERT: L 57 GLU cc_start: 0.6350 (mt-10) cc_final: 0.5280 (mp0) REVERT: L 64 THR cc_start: 0.6822 (OUTLIER) cc_final: 0.6534 (m) outliers start: 18 outliers final: 10 residues processed: 91 average time/residue: 1.5252 time to fit residues: 149.2654 Evaluate side-chains 92 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 79 time to evaluate : 0.806 ------------------------------------------------------------------------------- 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 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 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 57 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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** ** 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 = 0.4990 r_free = 0.4990 target = 0.223213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4833 r_free = 0.4833 target = 0.204695 restraints weight = 21997.574| |-----------------------------------------------------------------------------| r_work (start): 0.4855 rms_B_bonded: 2.65 r_work: 0.4771 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work (final): 0.4771 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6663 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5388 Z= 0.192 Angle : 0.603 5.207 7272 Z= 0.356 Chirality : 0.053 0.161 948 Planarity : 0.003 0.010 900 Dihedral : 8.531 33.011 768 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.36 % Allowed : 23.01 % Favored : 74.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.79 % 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: -4.18 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.18 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.010 0.002 PHE B 94 TYR 0.007 0.002 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.01911 ( 160) hydrogen bonds : angle 4.04184 ( 477) covalent geometry : bond 0.00352 ( 5388) covalent geometry : angle 0.60342 ( 7272) *********************** 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 97 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.902 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: 0.8086 (tttt) cc_final: 0.7598 (mmtt) REVERT: B 97 LYS cc_start: 0.7206 (OUTLIER) cc_final: 0.6434 (tmmt) REVERT: C 45 LYS cc_start: 0.8621 (tttt) cc_final: 0.7957 (mmpt) REVERT: C 57 GLU cc_start: 0.6002 (mt-10) cc_final: 0.5504 (mp0) REVERT: D 45 LYS cc_start: 0.8636 (tttt) cc_final: 0.7872 (mmtt) REVERT: D 57 GLU cc_start: 0.6594 (mt-10) cc_final: 0.5611 (mp0) REVERT: E 45 LYS cc_start: 0.8460 (tttt) cc_final: 0.7820 (tppt) REVERT: E 87 ASN cc_start: 0.7039 (m110) cc_final: 0.6278 (t0) REVERT: I 45 LYS cc_start: 0.8219 (tttt) cc_final: 0.7992 (mmtt) REVERT: G 45 LYS cc_start: 0.8145 (tttt) cc_final: 0.7654 (mmpt) REVERT: H 45 LYS cc_start: 0.8730 (tttt) cc_final: 0.7801 (mmpt) REVERT: H 57 GLU cc_start: 0.6065 (mt-10) cc_final: 0.5538 (mp0) REVERT: J 45 LYS cc_start: 0.8308 (tttt) cc_final: 0.7753 (mptt) REVERT: J 57 GLU cc_start: 0.6699 (mt-10) cc_final: 0.5580 (mp0) REVERT: K 45 LYS cc_start: 0.8585 (tttt) cc_final: 0.8199 (ttpp) REVERT: L 57 GLU cc_start: 0.6246 (mt-10) cc_final: 0.5464 (mp0) outliers start: 13 outliers final: 9 residues processed: 91 average time/residue: 1.5223 time to fit residues: 149.5000 Evaluate side-chains 92 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 82 time to evaluate : 0.859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LYS 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 92 THR Chi-restraints excluded: chain I residue 83 GLU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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** ** K 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 = 0.4963 r_free = 0.4963 target = 0.219633 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4815 r_free = 0.4815 target = 0.201935 restraints weight = 22130.757| |-----------------------------------------------------------------------------| r_work (start): 0.4837 rms_B_bonded: 2.56 r_work: 0.4752 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4637 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.4637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6825 moved from start: 0.5043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5388 Z= 0.279 Angle : 0.698 7.035 7272 Z= 0.412 Chirality : 0.053 0.174 948 Planarity : 0.004 0.015 900 Dihedral : 9.234 33.816 768 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 23.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.78 % Favored : 85.22 % Rotamer: Outliers : 3.08 % Allowed : 24.28 % Favored : 72.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.06 % 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: -4.33 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.29 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.016 0.004 PHE D 94 TYR 0.009 0.002 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02639 ( 160) hydrogen bonds : angle 4.29168 ( 477) covalent geometry : bond 0.00515 ( 5388) covalent geometry : angle 0.69765 ( 7272) *********************** 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: 17 poor density : 77 time to evaluate : 0.886 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: 0.8247 (tttt) cc_final: 0.7539 (mmtt) REVERT: C 45 LYS cc_start: 0.8702 (tttt) cc_final: 0.7972 (mmpt) REVERT: C 57 GLU cc_start: 0.6118 (mt-10) cc_final: 0.5407 (mm-30) REVERT: D 45 LYS cc_start: 0.8768 (tttt) cc_final: 0.7919 (mmtm) REVERT: D 57 GLU cc_start: 0.6770 (mt-10) cc_final: 0.5745 (mp0) REVERT: E 45 LYS cc_start: 0.8759 (tttt) cc_final: 0.7994 (tppt) REVERT: E 87 ASN cc_start: 0.7084 (m110) cc_final: 0.6279 (t0) REVERT: I 45 LYS cc_start: 0.8437 (tttt) cc_final: 0.7996 (mmtm) REVERT: G 45 LYS cc_start: 0.8323 (tttt) cc_final: 0.7682 (mmpt) REVERT: H 45 LYS cc_start: 0.8899 (tttt) cc_final: 0.7871 (mmpt) REVERT: H 57 GLU cc_start: 0.6322 (mt-10) cc_final: 0.5711 (mp0) REVERT: J 45 LYS cc_start: 0.8487 (tttt) cc_final: 0.7834 (mptt) REVERT: J 57 GLU cc_start: 0.6893 (mt-10) cc_final: 0.5761 (mp0) REVERT: K 45 LYS cc_start: 0.8706 (tttt) cc_final: 0.8274 (ttpp) REVERT: L 57 GLU cc_start: 0.6442 (mt-10) cc_final: 0.5609 (mp0) outliers start: 17 outliers final: 12 residues processed: 86 average time/residue: 1.5725 time to fit residues: 145.8257 Evaluate side-chains 89 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 63 VAL 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 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** ** 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 = 0.4964 r_free = 0.4964 target = 0.219450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4816 r_free = 0.4816 target = 0.201784 restraints weight = 21809.233| |-----------------------------------------------------------------------------| r_work (start): 0.4835 rms_B_bonded: 2.57 r_work: 0.4755 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4639 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.4639 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6834 moved from start: 0.5196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5388 Z= 0.277 Angle : 0.705 7.888 7272 Z= 0.415 Chirality : 0.054 0.176 948 Planarity : 0.004 0.015 900 Dihedral : 9.335 33.719 768 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 23.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.84 % Favored : 86.16 % Rotamer: Outliers : 2.90 % Allowed : 24.09 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.93 % 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: -4.44 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.38 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.015 0.004 PHE B 94 TYR 0.009 0.002 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02611 ( 160) hydrogen bonds : angle 4.31866 ( 477) covalent geometry : bond 0.00513 ( 5388) covalent geometry : angle 0.70522 ( 7272) *********************** 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: 16 poor density : 81 time to evaluate : 0.740 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: 0.8263 (tttt) cc_final: 0.7575 (mmtt) REVERT: C 45 LYS cc_start: 0.8717 (tttt) cc_final: 0.7984 (mmpt) REVERT: C 57 GLU cc_start: 0.6158 (mt-10) cc_final: 0.5524 (mm-30) REVERT: D 45 LYS cc_start: 0.8763 (tttt) cc_final: 0.7910 (mmtm) REVERT: D 57 GLU cc_start: 0.6783 (mt-10) cc_final: 0.5766 (mp0) REVERT: E 45 LYS cc_start: 0.8749 (tttt) cc_final: 0.7937 (tppt) REVERT: E 83 GLU cc_start: 0.7136 (OUTLIER) cc_final: 0.6931 (tt0) REVERT: E 87 ASN cc_start: 0.7221 (m110) cc_final: 0.6340 (t0) REVERT: I 45 LYS cc_start: 0.8478 (tttt) cc_final: 0.8031 (mptt) REVERT: G 45 LYS cc_start: 0.8306 (tttt) cc_final: 0.7663 (mmpt) REVERT: H 45 LYS cc_start: 0.8881 (tttt) cc_final: 0.7896 (mmpt) REVERT: H 57 GLU cc_start: 0.6297 (mt-10) cc_final: 0.5706 (mp0) REVERT: J 45 LYS cc_start: 0.8489 (tttt) cc_final: 0.7857 (mptt) REVERT: J 57 GLU cc_start: 0.6870 (mt-10) cc_final: 0.5749 (mp0) REVERT: K 45 LYS cc_start: 0.8700 (tttt) cc_final: 0.8268 (ttpp) REVERT: L 57 GLU cc_start: 0.6380 (mt-10) cc_final: 0.5507 (mp0) REVERT: L 64 THR cc_start: 0.6784 (OUTLIER) cc_final: 0.6479 (m) outliers start: 16 outliers final: 13 residues processed: 91 average time/residue: 1.4735 time to fit residues: 144.2700 Evaluate side-chains 95 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 80 time to evaluate : 0.751 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 63 VAL 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 H residue 81 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 0.0770 chunk 6 optimal weight: 3.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 50 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.0970 chunk 62 optimal weight: 0.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5093 r_free = 0.5093 target = 0.228753 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4958 r_free = 0.4958 target = 0.212043 restraints weight = 21328.564| |-----------------------------------------------------------------------------| r_work (start): 0.4959 rms_B_bonded: 2.61 r_work: 0.4901 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4798 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.4798 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6625 moved from start: 0.5141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5388 Z= 0.125 Angle : 0.526 5.776 7272 Z= 0.306 Chirality : 0.053 0.151 948 Planarity : 0.002 0.008 900 Dihedral : 7.434 31.162 768 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.22 % Favored : 89.78 % Rotamer: Outliers : 0.72 % Allowed : 26.27 % Favored : 73.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.005 0.001 PHE E 94 TYR 0.002 0.001 TYR H 39 Details of bonding type rmsd hydrogen bonds : bond 0.01577 ( 160) hydrogen bonds : angle 3.74075 ( 477) covalent geometry : bond 0.00243 ( 5388) covalent geometry : angle 0.52598 ( 7272) *********************** 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 85 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.823 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8194 (tttt) cc_final: 0.7487 (mmtt) REVERT: C 45 LYS cc_start: 0.8650 (tttt) cc_final: 0.7823 (mmpt) REVERT: C 57 GLU cc_start: 0.5811 (mt-10) cc_final: 0.5352 (mm-30) REVERT: D 45 LYS cc_start: 0.8630 (tttt) cc_final: 0.7679 (mmtm) REVERT: E 45 LYS cc_start: 0.8657 (tttt) cc_final: 0.7731 (tppt) REVERT: E 83 GLU cc_start: 0.6763 (OUTLIER) cc_final: 0.6492 (tt0) REVERT: E 87 ASN cc_start: 0.7128 (m110) cc_final: 0.6257 (t0) REVERT: I 45 LYS cc_start: 0.8360 (tttt) cc_final: 0.7832 (mmtt) REVERT: I 87 ASN cc_start: 0.7126 (m-40) cc_final: 0.6448 (t0) REVERT: G 45 LYS cc_start: 0.8269 (tttt) cc_final: 0.7598 (mmpt) REVERT: H 45 LYS cc_start: 0.8776 (tttt) cc_final: 0.7746 (mmpt) REVERT: J 45 LYS cc_start: 0.8396 (tttt) cc_final: 0.7658 (mptt) REVERT: J 57 GLU cc_start: 0.6737 (mt-10) cc_final: 0.5672 (mp0) REVERT: K 45 LYS cc_start: 0.8699 (tttt) cc_final: 0.8206 (ttpp) REVERT: L 57 GLU cc_start: 0.6232 (mt-10) cc_final: 0.5362 (mp0) outliers start: 4 outliers final: 3 residues processed: 83 average time/residue: 1.4586 time to fit residues: 130.8216 Evaluate side-chains 84 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.743 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 66 optimal weight: 0.7980 chunk 61 optimal weight: 2.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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** ** 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 = 0.4975 r_free = 0.4975 target = 0.220650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4830 r_free = 0.4830 target = 0.203295 restraints weight = 21932.918| |-----------------------------------------------------------------------------| r_work (start): 0.4848 rms_B_bonded: 2.57 r_work: 0.4767 rms_B_bonded: 2.76 restraints_weight: 0.5000 r_work: 0.4650 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.4650 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6799 moved from start: 0.5322 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5388 Z= 0.244 Angle : 0.659 7.236 7272 Z= 0.387 Chirality : 0.053 0.175 948 Planarity : 0.003 0.014 900 Dihedral : 8.671 31.583 768 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 21.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.86 % Favored : 84.14 % Rotamer: Outliers : 0.91 % Allowed : 26.99 % 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 (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: -4.44 (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 HIS 0.002 0.000 HIS D 50 PHE 0.015 0.004 PHE B 94 TYR 0.009 0.002 TYR K 39 Details of bonding type rmsd hydrogen bonds : bond 0.02435 ( 160) hydrogen bonds : angle 4.10497 ( 477) covalent geometry : bond 0.00452 ( 5388) covalent geometry : angle 0.65925 ( 7272) ********************** 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 82 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.896 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.8251 (tttt) cc_final: 0.7578 (mmtt) REVERT: C 45 LYS cc_start: 0.8752 (tttt) cc_final: 0.7964 (mmpt) REVERT: C 57 GLU cc_start: 0.6094 (mt-10) cc_final: 0.5562 (mm-30) REVERT: D 45 LYS cc_start: 0.8752 (tttt) cc_final: 0.7904 (mmtm) REVERT: E 45 LYS cc_start: 0.8765 (tttt) cc_final: 0.7931 (tppt) REVERT: E 83 GLU cc_start: 0.7098 (OUTLIER) cc_final: 0.6881 (tt0) REVERT: E 87 ASN cc_start: 0.7106 (m110) cc_final: 0.6206 (t0) REVERT: I 45 LYS cc_start: 0.8552 (tttt) cc_final: 0.8076 (mptt) REVERT: G 45 LYS cc_start: 0.8360 (tttt) cc_final: 0.7665 (mmpt) REVERT: H 45 LYS cc_start: 0.8880 (tttt) cc_final: 0.7901 (mmpt) REVERT: H 57 GLU cc_start: 0.6276 (mt-10) cc_final: 0.5668 (mp0) REVERT: J 45 LYS cc_start: 0.8487 (tttt) cc_final: 0.7817 (mptt) REVERT: J 57 GLU cc_start: 0.6899 (mt-10) cc_final: 0.5732 (mp0) REVERT: K 45 LYS cc_start: 0.8705 (tttt) cc_final: 0.8268 (ttpp) REVERT: L 57 GLU cc_start: 0.6270 (mt-10) cc_final: 0.5416 (mp0) outliers start: 5 outliers final: 4 residues processed: 79 average time/residue: 1.6114 time to fit residues: 136.6274 Evaluate side-chains 79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 81 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 K residue 83 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 0.1980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.1980 overall best weight: 0.6382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5038 r_free = 0.5038 target = 0.227754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4895 r_free = 0.4895 target = 0.210373 restraints weight = 21366.417| |-----------------------------------------------------------------------------| r_work (start): 0.4902 rms_B_bonded: 2.63 r_work: 0.4840 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work (final): 0.4840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6588 moved from start: 0.5318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 5388 Z= 0.130 Angle : 0.528 5.927 7272 Z= 0.307 Chirality : 0.053 0.156 948 Planarity : 0.002 0.009 900 Dihedral : 7.409 30.067 768 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 0.91 % Allowed : 26.99 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % 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 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.28 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 50 PHE 0.005 0.001 PHE E 94 TYR 0.003 0.001 TYR I 39 Details of bonding type rmsd hydrogen bonds : bond 0.01563 ( 160) hydrogen bonds : angle 3.74924 ( 477) covalent geometry : bond 0.00245 ( 5388) covalent geometry : angle 0.52838 ( 7272) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7310.32 seconds wall clock time: 124 minutes 45.98 seconds (7485.98 seconds total)