Starting phenix.real_space_refine on Fri Jan 17 14:30:37 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewv_50023/01_2025/9ewv_50023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewv_50023/01_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_50023/01_2025/9ewv_50023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewv_50023/01_2025/9ewv_50023.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewv_50023/01_2025/9ewv_50023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewv_50023/01_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-5571/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: 3.78, per 1000 atoms: 0.34 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: 3.06 Conformation dependent library (CDL) restraints added in 806.6 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: 1.18 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: 4.03 Time building geometry restraints manager: 3.58 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: 2.390 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: 0.410 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.210 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:13.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.700 ------------------------------------------------------------------------------- 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= 0.617 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 *********************** 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 : 0.861 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: 1.9204 time to fit residues: 268.1704 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 : 0.816 ------------------------------------------------------------------------------- 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 = 0.215770 restraints weight = 21568.184| |-----------------------------------------------------------------------------| 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= 0.196 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 *********************** 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 : 0.814 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: 0.7887 (tttt) cc_final: 0.7416 (mmtt) REVERT: C 45 LYS cc_start: 0.8315 (tttt) cc_final: 0.7511 (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: 0.7459 (mmpt) REVERT: E 45 LYS cc_start: 0.8144 (tttt) cc_final: 0.7519 (tppt) REVERT: E 87 ASN cc_start: 0.7399 (OUTLIER) cc_final: 0.6665 (t0) REVERT: I 57 GLU cc_start: 0.6266 (mt-10) cc_final: 0.6017 (mt-10) REVERT: I 87 ASN cc_start: 0.6926 (m-40) cc_final: 0.6547 (t0) REVERT: F 57 GLU cc_start: 0.6006 (mt-10) cc_final: 0.5677 (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: 0.5194 (mp0) REVERT: K 45 LYS cc_start: 0.8438 (tttt) cc_final: 0.8068 (ttpp) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 1.6338 time to fit residues: 155.8913 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 : 0.887 ------------------------------------------------------------------------------- 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: 0.1980 chunk 45 optimal weight: 1.9990 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: 1.5786 ------------------------------------------------------------------------------- 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 = 0.5058 r_free = 0.5058 target = 0.226672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.208892 restraints weight = 22025.736| |-----------------------------------------------------------------------------| r_work (start): 0.4911 rms_B_bonded: 2.75 r_work: 0.4835 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.4835 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6638 moved from start: 0.3570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 5388 Z= 0.303 Angle : 0.648 4.050 7272 Z= 0.389 Chirality : 0.053 0.153 948 Planarity : 0.004 0.013 900 Dihedral : 8.901 32.434 768 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 19.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.41 % Favored : 90.59 % Rotamer: Outliers : 1.63 % Allowed : 13.59 % Favored : 84.78 % 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: -3.73 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.83 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 50 PHE 0.016 0.004 PHE B 94 TYR 0.008 0.002 TYR K 39 *********************** 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 92 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 83 time to evaluate : 0.801 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: 0.8075 (tttt) cc_final: 0.7539 (mmpt) REVERT: C 45 LYS cc_start: 0.8513 (tttt) cc_final: 0.7848 (mmpt) REVERT: C 46 GLU cc_start: 0.7741 (tt0) cc_final: 0.7529 (mt-10) REVERT: C 57 GLU cc_start: 0.5961 (mt-10) cc_final: 0.5508 (mp0) REVERT: D 45 LYS cc_start: 0.8545 (tttt) cc_final: 0.7734 (mmpt) REVERT: D 57 GLU cc_start: 0.6479 (mt-10) cc_final: 0.5613 (mp0) REVERT: E 45 LYS cc_start: 0.8360 (tttt) cc_final: 0.7674 (mptt) REVERT: I 45 LYS cc_start: 0.8060 (tttt) cc_final: 0.7731 (mmtt) REVERT: G 45 LYS cc_start: 0.8115 (tttt) cc_final: 0.7642 (mmpt) REVERT: H 45 LYS cc_start: 0.8702 (tttt) cc_final: 0.7810 (mmpt) REVERT: J 45 LYS cc_start: 0.8215 (tttt) cc_final: 0.7597 (mptt) REVERT: J 57 GLU cc_start: 0.6351 (mt-10) cc_final: 0.5314 (mp0) REVERT: K 45 LYS cc_start: 0.8558 (tttt) cc_final: 0.7892 (mptt) outliers start: 9 outliers final: 8 residues processed: 87 average time/residue: 1.6491 time to fit residues: 153.6264 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 : 0.874 ------------------------------------------------------------------------------- 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: 1.9990 chunk 34 optimal weight: 0.9990 chunk 59 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 0.0050 chunk 9 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 52 optimal weight: 2.9990 chunk 4 optimal weight: 0.6980 overall best weight: 0.9398 ------------------------------------------------------------------------------- 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 = 0.5090 r_free = 0.5090 target = 0.229532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.212284 restraints weight = 21498.691| |-----------------------------------------------------------------------------| r_work (start): 0.4946 rms_B_bonded: 2.61 r_work: 0.4892 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.4788 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.4788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6606 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5388 Z= 0.201 Angle : 0.539 4.067 7272 Z= 0.320 Chirality : 0.052 0.153 948 Planarity : 0.002 0.009 900 Dihedral : 7.945 31.198 768 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.91 % Allowed : 17.57 % Favored : 81.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -3.74 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.84 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS K 50 PHE 0.008 0.002 PHE E 94 TYR 0.005 0.001 TYR K 39 *********************** 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: 5 poor density : 80 time to evaluate : 0.830 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: 0.8178 (tttt) cc_final: 0.7550 (mmpt) REVERT: C 45 LYS cc_start: 0.8582 (tttt) cc_final: 0.7858 (mmpt) REVERT: C 46 GLU cc_start: 0.7754 (tt0) cc_final: 0.7552 (mt-10) REVERT: C 57 GLU cc_start: 0.5996 (mt-10) cc_final: 0.5444 (mp0) REVERT: D 45 LYS cc_start: 0.8586 (tttt) cc_final: 0.7669 (mmtm) REVERT: D 57 GLU cc_start: 0.6561 (mt-10) cc_final: 0.5588 (mp0) REVERT: E 45 LYS cc_start: 0.8444 (tttt) cc_final: 0.7711 (tppt) REVERT: E 87 ASN cc_start: 0.7380 (m110) cc_final: 0.6490 (t0) REVERT: I 45 LYS cc_start: 0.8212 (tttt) cc_final: 0.7853 (mmtt) REVERT: F 57 GLU cc_start: 0.5529 (mt-10) cc_final: 0.4864 (mp0) REVERT: G 45 LYS cc_start: 0.8168 (tttt) cc_final: 0.7491 (mmpt) REVERT: H 45 LYS cc_start: 0.8719 (tttt) cc_final: 0.7602 (mmpt) REVERT: H 57 GLU cc_start: 0.6036 (mt-10) cc_final: 0.5460 (mp0) REVERT: J 45 LYS cc_start: 0.8296 (tttt) cc_final: 0.7471 (mptt) REVERT: J 57 GLU cc_start: 0.6557 (mt-10) cc_final: 0.5394 (mp0) REVERT: K 45 LYS cc_start: 0.8640 (tttt) cc_final: 0.8188 (ttpp) REVERT: L 57 GLU cc_start: 0.6366 (mt-10) cc_final: 0.5015 (mp0) outliers start: 5 outliers final: 5 residues processed: 82 average time/residue: 1.6622 time to fit residues: 146.1590 Evaluate side-chains 80 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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: 3.9990 chunk 13 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 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: 5.9990 chunk 31 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.4997 r_free = 0.4997 target = 0.220516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4854 r_free = 0.4854 target = 0.203377 restraints weight = 22150.468| |-----------------------------------------------------------------------------| r_work (start): 0.4846 rms_B_bonded: 2.53 r_work: 0.4775 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.4655 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6781 moved from start: 0.4510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 5388 Z= 0.352 Angle : 0.689 4.215 7272 Z= 0.412 Chirality : 0.054 0.170 948 Planarity : 0.004 0.016 900 Dihedral : 9.318 33.267 768 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 23.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 2.36 % Allowed : 20.83 % Favored : 76.81 % 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: -4.03 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 50 PHE 0.017 0.004 PHE B 94 TYR 0.010 0.003 TYR K 39 *********************** 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 93 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 80 time to evaluate : 0.831 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: 0.8228 (tttt) cc_final: 0.7566 (mmpt) REVERT: C 45 LYS cc_start: 0.8676 (tttt) cc_final: 0.7941 (mmpt) REVERT: C 57 GLU cc_start: 0.6014 (mt-10) cc_final: 0.5550 (mp0) REVERT: D 45 LYS cc_start: 0.8764 (tttt) cc_final: 0.7893 (mmtm) REVERT: D 57 GLU cc_start: 0.6694 (mt-10) cc_final: 0.5694 (mp0) REVERT: E 45 LYS cc_start: 0.8632 (tttt) cc_final: 0.7893 (tppt) REVERT: E 87 ASN cc_start: 0.7353 (m110) cc_final: 0.6444 (t0) REVERT: I 45 LYS cc_start: 0.8423 (tttt) cc_final: 0.7975 (mmtt) REVERT: F 57 GLU cc_start: 0.5755 (mt-10) cc_final: 0.5077 (mp0) REVERT: G 45 LYS cc_start: 0.8316 (tttt) cc_final: 0.7687 (mmpt) REVERT: H 45 LYS cc_start: 0.8912 (tttt) cc_final: 0.7965 (mmpt) REVERT: H 57 GLU cc_start: 0.6242 (mt-10) cc_final: 0.5657 (mp0) REVERT: J 45 LYS cc_start: 0.8541 (tttt) cc_final: 0.7809 (mptt) REVERT: J 57 GLU cc_start: 0.6686 (mt-10) cc_final: 0.5597 (mp0) REVERT: K 45 LYS cc_start: 0.8795 (tttt) cc_final: 0.8056 (mptt) REVERT: L 57 GLU cc_start: 0.6338 (mt-10) cc_final: 0.5252 (mp0) outliers start: 13 outliers final: 9 residues processed: 85 average time/residue: 1.4420 time to fit residues: 132.5379 Evaluate side-chains 88 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 92 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 0.6980 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5062 r_free = 0.5062 target = 0.226733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.4926 r_free = 0.4926 target = 0.209595 restraints weight = 21738.637| |-----------------------------------------------------------------------------| r_work (start): 0.4923 rms_B_bonded: 2.65 r_work: 0.4851 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work (final): 0.4851 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4632 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= 0.208 Angle : 0.558 5.298 7272 Z= 0.328 Chirality : 0.052 0.155 948 Planarity : 0.002 0.009 900 Dihedral : 8.075 32.111 768 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 16.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 1.81 % Allowed : 21.38 % Favored : 76.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.40 % 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: -4.01 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.05 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.009 0.002 PHE E 94 TYR 0.005 0.001 TYR I 39 *********************** 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: 10 poor density : 87 time to evaluate : 0.888 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: 0.8046 (tttt) cc_final: 0.7465 (mmtt) REVERT: B 97 LYS cc_start: 0.7205 (OUTLIER) cc_final: 0.6349 (tmmt) REVERT: C 45 LYS cc_start: 0.8582 (tttt) cc_final: 0.7911 (mmpt) REVERT: C 57 GLU cc_start: 0.5842 (mt-10) cc_final: 0.5514 (mp0) REVERT: D 45 LYS cc_start: 0.8621 (tttt) cc_final: 0.7824 (mmtm) REVERT: D 57 GLU cc_start: 0.6567 (mt-10) cc_final: 0.5676 (mp0) REVERT: E 45 LYS cc_start: 0.8516 (tttt) cc_final: 0.7777 (tppt) REVERT: E 83 GLU cc_start: 0.6461 (OUTLIER) cc_final: 0.6103 (tt0) REVERT: E 87 ASN cc_start: 0.7049 (m110) cc_final: 0.6332 (t0) REVERT: I 45 LYS cc_start: 0.8187 (tttt) cc_final: 0.7856 (mmtt) REVERT: G 45 LYS cc_start: 0.8126 (tttt) cc_final: 0.7626 (mmpt) REVERT: H 45 LYS cc_start: 0.8740 (tttt) cc_final: 0.7779 (mmpt) REVERT: H 57 GLU cc_start: 0.5998 (mt-10) cc_final: 0.5582 (mp0) REVERT: J 45 LYS cc_start: 0.8326 (tttt) cc_final: 0.7672 (mptt) REVERT: J 57 GLU cc_start: 0.6491 (mt-10) cc_final: 0.5453 (mp0) REVERT: K 45 LYS cc_start: 0.8620 (tttt) cc_final: 0.8164 (ttpp) REVERT: L 57 GLU cc_start: 0.6257 (mt-10) cc_final: 0.5430 (mp0) outliers start: 10 outliers final: 7 residues processed: 91 average time/residue: 1.5054 time to fit residues: 147.9767 Evaluate side-chains 91 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 82 time to evaluate : 0.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain J residue 81 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 92 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: 4.9990 chunk 48 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- 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 = 0.5032 r_free = 0.5032 target = 0.223271 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4894 r_free = 0.4894 target = 0.206610 restraints weight = 21930.113| |-----------------------------------------------------------------------------| r_work (start): 0.4893 rms_B_bonded: 2.52 r_work: 0.4824 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.4705 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.4705 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6748 moved from start: 0.4841 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= 0.283 Angle : 0.618 5.966 7272 Z= 0.366 Chirality : 0.053 0.169 948 Planarity : 0.003 0.013 900 Dihedral : 8.553 32.765 768 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.90 % Favored : 87.10 % Rotamer: Outliers : 2.90 % Allowed : 23.19 % Favored : 73.91 % 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: -4.15 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.013 0.003 PHE B 94 TYR 0.007 0.002 TYR K 39 *********************** 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 96 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 80 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: 0.8174 (tttt) cc_final: 0.7426 (mmtt) REVERT: B 97 LYS cc_start: 0.7223 (OUTLIER) cc_final: 0.6416 (tmmt) REVERT: C 45 LYS cc_start: 0.8645 (tttt) cc_final: 0.7871 (mmpt) REVERT: C 57 GLU cc_start: 0.6087 (mt-10) cc_final: 0.5351 (mm-30) REVERT: D 45 LYS cc_start: 0.8731 (tttt) cc_final: 0.7754 (mmtt) REVERT: D 57 GLU cc_start: 0.6735 (mt-10) cc_final: 0.5709 (mp0) REVERT: E 45 LYS cc_start: 0.8670 (tttt) cc_final: 0.7810 (tppt) REVERT: E 83 GLU cc_start: 0.6973 (OUTLIER) cc_final: 0.6728 (tt0) REVERT: E 87 ASN cc_start: 0.7276 (m110) cc_final: 0.6395 (t0) REVERT: I 45 LYS cc_start: 0.8420 (tttt) cc_final: 0.7877 (mmtt) REVERT: F 57 GLU cc_start: 0.5621 (mt-10) cc_final: 0.5106 (mp0) REVERT: G 45 LYS cc_start: 0.8267 (tttt) cc_final: 0.7629 (mmpt) REVERT: H 45 LYS cc_start: 0.8868 (tttt) cc_final: 0.7847 (mmpt) REVERT: H 57 GLU cc_start: 0.6134 (mt-10) cc_final: 0.5591 (mp0) REVERT: J 45 LYS cc_start: 0.8498 (tttt) cc_final: 0.7771 (mptt) REVERT: J 57 GLU cc_start: 0.6778 (mt-10) cc_final: 0.5656 (mp0) REVERT: K 45 LYS cc_start: 0.8749 (tttt) cc_final: 0.8282 (ttpp) REVERT: L 43 LYS cc_start: 0.7134 (ttpt) cc_final: 0.6481 (tttp) REVERT: L 57 GLU cc_start: 0.6358 (mt-10) cc_final: 0.5217 (mp0) REVERT: L 64 THR cc_start: 0.6909 (OUTLIER) cc_final: 0.6603 (m) outliers start: 16 outliers final: 11 residues processed: 89 average time/residue: 1.5481 time to fit residues: 148.3827 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 : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LYS 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 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 64 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 64 THR 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: 0.6980 chunk 56 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 20 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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 = 0.5034 r_free = 0.5034 target = 0.223138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.206553 restraints weight = 21596.396| |-----------------------------------------------------------------------------| r_work (start): 0.4891 rms_B_bonded: 2.52 r_work: 0.4834 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.4730 rms_B_bonded: 4.70 restraints_weight: 0.2500 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6737 moved from start: 0.4997 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= 0.275 Angle : 0.620 5.984 7272 Z= 0.366 Chirality : 0.053 0.167 948 Planarity : 0.003 0.012 900 Dihedral : 8.581 32.348 768 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 20.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.04 % Favored : 86.96 % Rotamer: Outliers : 2.17 % Allowed : 24.09 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % 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: -4.25 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.23 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.012 0.003 PHE B 94 TYR 0.008 0.002 TYR I 39 *********************** 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 93 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 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: 0.8199 (tttt) cc_final: 0.7434 (mmtt) REVERT: B 97 LYS cc_start: 0.7212 (OUTLIER) cc_final: 0.6444 (tmmt) REVERT: C 45 LYS cc_start: 0.8645 (tttt) cc_final: 0.7825 (mmpt) REVERT: C 57 GLU cc_start: 0.6067 (mt-10) cc_final: 0.5293 (mm-30) REVERT: D 45 LYS cc_start: 0.8668 (tttt) cc_final: 0.7736 (mmtm) REVERT: D 57 GLU cc_start: 0.6683 (mt-10) cc_final: 0.5682 (mp0) REVERT: E 45 LYS cc_start: 0.8730 (tttt) cc_final: 0.7811 (tppt) REVERT: E 83 GLU cc_start: 0.6990 (OUTLIER) cc_final: 0.6755 (tt0) REVERT: E 87 ASN cc_start: 0.7241 (m110) cc_final: 0.6345 (t0) REVERT: I 45 LYS cc_start: 0.8432 (tttt) cc_final: 0.7857 (mptt) REVERT: G 45 LYS cc_start: 0.8243 (tttt) cc_final: 0.7634 (mmpt) REVERT: H 45 LYS cc_start: 0.8833 (tttt) cc_final: 0.7851 (mmpt) REVERT: H 57 GLU cc_start: 0.6168 (mt-10) cc_final: 0.5588 (mp0) REVERT: J 45 LYS cc_start: 0.8465 (tttt) cc_final: 0.7745 (mptt) REVERT: J 57 GLU cc_start: 0.6754 (mt-10) cc_final: 0.5609 (mp0) REVERT: K 45 LYS cc_start: 0.8726 (tttt) cc_final: 0.8229 (ttpp) REVERT: L 43 LYS cc_start: 0.7145 (ttpt) cc_final: 0.6478 (tttp) REVERT: L 57 GLU cc_start: 0.6312 (mt-10) cc_final: 0.5351 (mp0) REVERT: L 64 THR cc_start: 0.6743 (OUTLIER) cc_final: 0.6429 (m) outliers start: 12 outliers final: 7 residues processed: 88 average time/residue: 1.5409 time to fit residues: 146.1828 Evaluate side-chains 90 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G 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: 2.9990 chunk 6 optimal weight: 4.9990 chunk 56 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 50 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 68 optimal weight: 0.0770 chunk 62 optimal weight: 0.6980 overall best weight: 1.1340 ------------------------------------------------------------------------------- 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 = 0.5055 r_free = 0.5055 target = 0.224889 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.208445 restraints weight = 21653.319| |-----------------------------------------------------------------------------| r_work (start): 0.4923 rms_B_bonded: 2.53 r_work: 0.4871 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.4772 rms_B_bonded: 4.63 restraints_weight: 0.2500 r_work (final): 0.4772 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5388 Z= 0.223 Angle : 0.569 6.461 7272 Z= 0.334 Chirality : 0.052 0.162 948 Planarity : 0.002 0.010 900 Dihedral : 7.989 31.354 768 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 19.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 1.63 % Allowed : 24.46 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.26 % 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: -4.26 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.24 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 PHE 0.009 0.002 PHE B 94 TYR 0.006 0.001 TYR I 39 *********************** 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 83 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 0.829 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: 0.8182 (tttt) cc_final: 0.7498 (mmtt) REVERT: C 45 LYS cc_start: 0.8677 (tttt) cc_final: 0.7859 (mmpt) REVERT: C 57 GLU cc_start: 0.5917 (mt-10) cc_final: 0.5469 (mm-30) REVERT: D 45 LYS cc_start: 0.8657 (tttt) cc_final: 0.7733 (mmtm) REVERT: E 45 LYS cc_start: 0.8687 (tttt) cc_final: 0.7757 (tppt) REVERT: E 83 GLU cc_start: 0.6869 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: E 87 ASN cc_start: 0.7221 (m110) cc_final: 0.6310 (t0) REVERT: I 45 LYS cc_start: 0.8440 (tttt) cc_final: 0.7916 (mptt) REVERT: G 45 LYS cc_start: 0.8242 (tttt) cc_final: 0.7618 (mmpt) REVERT: H 45 LYS cc_start: 0.8797 (tttt) cc_final: 0.7787 (mmpt) REVERT: H 57 GLU cc_start: 0.6164 (mt-10) cc_final: 0.5604 (mp0) REVERT: J 45 LYS cc_start: 0.8429 (tttt) cc_final: 0.7708 (mptt) REVERT: J 57 GLU cc_start: 0.6759 (mt-10) cc_final: 0.5641 (mp0) REVERT: K 45 LYS cc_start: 0.8696 (tttt) cc_final: 0.8205 (ttpp) REVERT: L 43 LYS cc_start: 0.7116 (ttpt) cc_final: 0.6486 (tttp) REVERT: L 57 GLU cc_start: 0.6342 (mt-10) cc_final: 0.5456 (mp0) REVERT: L 64 THR cc_start: 0.6665 (OUTLIER) cc_final: 0.6352 (m) outliers start: 9 outliers final: 6 residues processed: 80 average time/residue: 1.6803 time to fit residues: 143.9618 Evaluate side-chains 82 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.843 ------------------------------------------------------------------------------- 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 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 81 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain L residue 64 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 0.0980 chunk 49 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 0 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.5090 r_free = 0.5090 target = 0.228777 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4953 r_free = 0.4953 target = 0.211856 restraints weight = 21416.597| |-----------------------------------------------------------------------------| r_work (start): 0.4955 rms_B_bonded: 2.67 r_work: 0.4880 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work (final): 0.4880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6567 moved from start: 0.5101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.020 5388 Z= 0.161 Angle : 0.510 5.563 7272 Z= 0.297 Chirality : 0.052 0.152 948 Planarity : 0.002 0.009 900 Dihedral : 7.295 29.714 768 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 15.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Rotamer: Outliers : 1.09 % Allowed : 25.18 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.16 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.16 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 PHE 0.006 0.001 PHE C 94 TYR 0.005 0.001 TYR I 39 ********************** 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 83 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.879 Fit side-chains 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: 0.7502 (mmtt) REVERT: C 45 LYS cc_start: 0.8614 (tttt) cc_final: 0.7847 (mmpt) REVERT: C 57 GLU cc_start: 0.5728 (mt-10) cc_final: 0.5386 (mm-30) REVERT: D 45 LYS cc_start: 0.8598 (tttt) cc_final: 0.7744 (mmtm) REVERT: E 45 LYS cc_start: 0.8622 (tttt) cc_final: 0.7759 (tppt) REVERT: I 45 LYS cc_start: 0.8271 (tttt) cc_final: 0.7811 (mmtt) REVERT: I 87 ASN cc_start: 0.6995 (m-40) cc_final: 0.6426 (t0) REVERT: G 45 LYS cc_start: 0.8162 (tttt) cc_final: 0.7581 (mmpt) REVERT: H 45 LYS cc_start: 0.8748 (tttt) cc_final: 0.7733 (mmpt) REVERT: J 45 LYS cc_start: 0.8358 (tttt) cc_final: 0.7635 (mptt) REVERT: J 57 GLU cc_start: 0.6556 (mt-10) cc_final: 0.5524 (mp0) REVERT: K 45 LYS cc_start: 0.8696 (tttt) cc_final: 0.8180 (ttpp) REVERT: L 43 LYS cc_start: 0.7033 (ttpt) cc_final: 0.6433 (tttp) REVERT: L 57 GLU cc_start: 0.6037 (mt-10) cc_final: 0.5297 (mp0) REVERT: L 64 THR cc_start: 0.6498 (OUTLIER) cc_final: 0.6191 (m) outliers start: 6 outliers final: 5 residues processed: 80 average time/residue: 1.4846 time to fit residues: 128.3746 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 : 0.785 ------------------------------------------------------------------------------- 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 92 THR Chi-restraints excluded: chain K residue 83 GLU Chi-restraints excluded: chain K residue 92 THR Chi-restraints excluded: chain L residue 64 THR 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: 0.0980 chunk 58 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 14 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 66 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 overall best weight: 1.2186 ------------------------------------------------------------------------------- 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 = 0.5061 r_free = 0.5061 target = 0.225361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4918 r_free = 0.4918 target = 0.208274 restraints weight = 21608.224| |-----------------------------------------------------------------------------| r_work (start): 0.4917 rms_B_bonded: 2.67 r_work: 0.4839 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work (final): 0.4839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6637 moved from start: 0.5187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5388 Z= 0.228 Angle : 0.566 6.177 7272 Z= 0.333 Chirality : 0.052 0.165 948 Planarity : 0.003 0.011 900 Dihedral : 7.755 30.068 768 Min Nonbonded Distance : 2.382 Molprobity Statistics. All-atom Clashscore : 19.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.98 % Favored : 86.02 % Rotamer: Outliers : 1.27 % Allowed : 25.54 % Favored : 73.19 % 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: -4.23 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.22 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.011 0.003 PHE B 94 TYR 0.007 0.002 TYR K 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6865.06 seconds wall clock time: 121 minutes 49.67 seconds (7309.67 seconds total)