Starting phenix.real_space_refine on Sun Dec 29 16:31:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ewv_50023/12_2024/9ewv_50023.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ewv_50023/12_2024/9ewv_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_50023/12_2024/9ewv_50023.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ewv_50023/12_2024/9ewv_50023.map" model { file = "/net/cci-nas-00/data/ceres_data/9ewv_50023/12_2024/9ewv_50023.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ewv_50023/12_2024/9ewv_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-5532/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: 3.63, per 1000 atoms: 0.33 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: 2.92 Conformation dependent library (CDL) restraints added in 826.9 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: 1.20 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: 4.00 Time building geometry restraints manager: 3.48 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: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.340 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: 0.220 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 25.120 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:14.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.230 ------------------------------------------------------------------------------- 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 : 0.857 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: 1.8860 time to fit residues: 263.7720 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 : 0.848 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6445 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 : 0.840 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: 0.7847 (tttt) cc_final: 0.7444 (mmtt) REVERT: C 45 LYS cc_start: 0.8292 (tttt) cc_final: 0.7518 (mmpt) REVERT: C 57 GLU cc_start: 0.5835 (mt-10) cc_final: 0.5513 (mp0) REVERT: D 45 LYS cc_start: 0.8298 (tttt) cc_final: 0.7458 (mmpt) REVERT: E 45 LYS cc_start: 0.8145 (tttt) cc_final: 0.7459 (tppt) REVERT: E 87 ASN cc_start: 0.7356 (OUTLIER) cc_final: 0.6646 (t0) REVERT: I 57 GLU cc_start: 0.6253 (mt-10) cc_final: 0.5979 (mt-10) REVERT: I 87 ASN cc_start: 0.6946 (m-40) cc_final: 0.6553 (t0) REVERT: F 57 GLU cc_start: 0.5972 (mt-10) cc_final: 0.5650 (mm-30) REVERT: G 45 LYS cc_start: 0.7949 (tttt) cc_final: 0.7480 (mmpt) REVERT: H 45 LYS cc_start: 0.8536 (tttt) cc_final: 0.7497 (mmpt) REVERT: J 45 LYS cc_start: 0.8129 (tttt) cc_final: 0.7333 (mptt) REVERT: J 57 GLU cc_start: 0.6108 (mt-10) cc_final: 0.5068 (mp0) REVERT: K 45 LYS cc_start: 0.8472 (tttt) cc_final: 0.8083 (ttpp) outliers start: 7 outliers final: 4 residues processed: 89 average time/residue: 1.6251 time to fit residues: 154.9451 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 : 0.763 ------------------------------------------------------------------------------- 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 36 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6555 moved from start: 0.3380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5388 Z= 0.229 Angle : 0.569 3.240 7272 Z= 0.341 Chirality : 0.052 0.148 948 Planarity : 0.003 0.010 900 Dihedral : 8.050 31.063 768 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.80 % Favored : 92.20 % Rotamer: Outliers : 1.09 % Allowed : 11.23 % Favored : 87.68 % 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: -3.52 (0.24), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 50 PHE 0.013 0.003 PHE D 94 TYR 0.005 0.002 TYR J 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 83 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 77 time to evaluate : 0.800 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: A 46 GLU cc_start: 0.7615 (tt0) cc_final: 0.7414 (tt0) REVERT: B 45 LYS cc_start: 0.7999 (tttt) cc_final: 0.7586 (mmpt) REVERT: C 45 LYS cc_start: 0.8428 (tttt) cc_final: 0.7776 (mmpt) REVERT: C 46 GLU cc_start: 0.7627 (tt0) cc_final: 0.7412 (mt-10) REVERT: C 57 GLU cc_start: 0.5851 (mt-10) cc_final: 0.5264 (mm-30) REVERT: D 45 LYS cc_start: 0.8499 (tttt) cc_final: 0.7646 (mmpt) REVERT: E 45 LYS cc_start: 0.8312 (tttt) cc_final: 0.7602 (tppt) REVERT: E 87 ASN cc_start: 0.7299 (m110) cc_final: 0.6506 (t0) REVERT: G 45 LYS cc_start: 0.8043 (tttt) cc_final: 0.7562 (mmpt) REVERT: G 57 GLU cc_start: 0.5742 (mm-30) cc_final: 0.5451 (mm-30) REVERT: H 45 LYS cc_start: 0.8680 (tttt) cc_final: 0.7728 (mmpt) REVERT: H 57 GLU cc_start: 0.5845 (mt-10) cc_final: 0.5347 (mp0) REVERT: J 45 LYS cc_start: 0.8218 (tttt) cc_final: 0.7471 (mptt) REVERT: J 57 GLU cc_start: 0.6212 (mt-10) cc_final: 0.5135 (mp0) REVERT: K 45 LYS cc_start: 0.8557 (tttt) cc_final: 0.7762 (mptt) outliers start: 6 outliers final: 6 residues processed: 79 average time/residue: 1.6318 time to fit residues: 138.5262 Evaluate side-chains 79 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 64 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 0.3980 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 2.9990 chunk 69 optimal weight: 0.3980 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6501 moved from start: 0.3693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5388 Z= 0.168 Angle : 0.487 3.670 7272 Z= 0.289 Chirality : 0.052 0.148 948 Planarity : 0.002 0.008 900 Dihedral : 7.344 30.186 768 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.09 % Allowed : 13.59 % Favored : 85.33 % 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: -3.52 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.68 (0.18), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.009 0.002 PHE D 94 TYR 0.004 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: 6 poor density : 79 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: symmetry clash revert: symmetry clash REVERT: B 45 LYS cc_start: 0.7993 (tttt) cc_final: 0.7517 (mmtt) REVERT: C 45 LYS cc_start: 0.8453 (tttt) cc_final: 0.7804 (mmpt) REVERT: C 46 GLU cc_start: 0.7517 (tt0) cc_final: 0.7295 (mt-10) REVERT: C 57 GLU cc_start: 0.5767 (mt-10) cc_final: 0.5197 (mm-30) REVERT: D 45 LYS cc_start: 0.8511 (tttt) cc_final: 0.7669 (mmtm) REVERT: E 45 LYS cc_start: 0.8352 (tttt) cc_final: 0.7624 (tppt) REVERT: E 87 ASN cc_start: 0.6971 (m110) cc_final: 0.6321 (t0) REVERT: F 57 GLU cc_start: 0.5550 (mt-10) cc_final: 0.4404 (mp0) REVERT: G 45 LYS cc_start: 0.8122 (tttt) cc_final: 0.7623 (mmpt) REVERT: H 45 LYS cc_start: 0.8688 (tttt) cc_final: 0.7733 (mmpt) REVERT: H 57 GLU cc_start: 0.5808 (mt-10) cc_final: 0.5316 (mp0) REVERT: J 45 LYS cc_start: 0.8236 (tttt) cc_final: 0.7541 (mptt) REVERT: J 57 GLU cc_start: 0.6250 (mt-10) cc_final: 0.5189 (mp0) REVERT: K 45 LYS cc_start: 0.8584 (tttt) cc_final: 0.7769 (mptt) REVERT: L 57 GLU cc_start: 0.6171 (mt-10) cc_final: 0.4851 (mp0) outliers start: 6 outliers final: 5 residues processed: 82 average time/residue: 1.5884 time to fit residues: 139.8183 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 : 0.829 ------------------------------------------------------------------------------- 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 57 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 62 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6724 moved from start: 0.4317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5388 Z= 0.374 Angle : 0.705 4.066 7272 Z= 0.423 Chirality : 0.054 0.170 948 Planarity : 0.004 0.017 900 Dihedral : 9.463 32.855 768 Min Nonbonded Distance : 2.365 Molprobity Statistics. All-atom Clashscore : 22.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.29 % Favored : 88.71 % Rotamer: Outliers : 2.17 % Allowed : 19.20 % Favored : 78.62 % 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: -3.93 (0.23), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS K 50 PHE 0.018 0.005 PHE D 94 TYR 0.011 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 96 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 84 time to evaluate : 0.855 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: 0.8056 (tttt) cc_final: 0.7524 (mmtt) REVERT: C 45 LYS cc_start: 0.8539 (tttt) cc_final: 0.7929 (mmpt) REVERT: C 57 GLU cc_start: 0.5842 (mt-10) cc_final: 0.5444 (mp0) REVERT: D 45 LYS cc_start: 0.8661 (tttt) cc_final: 0.7820 (mmtm) REVERT: D 57 GLU cc_start: 0.6476 (mt-10) cc_final: 0.5546 (mp0) REVERT: E 45 LYS cc_start: 0.8486 (tttt) cc_final: 0.7745 (tppt) REVERT: E 87 ASN cc_start: 0.7234 (m110) cc_final: 0.6362 (t0) REVERT: I 45 LYS cc_start: 0.8201 (tttt) cc_final: 0.7898 (mmtt) REVERT: F 57 GLU cc_start: 0.5722 (mt-10) cc_final: 0.5062 (mp0) REVERT: G 45 LYS cc_start: 0.8135 (tttt) cc_final: 0.7623 (mmpt) REVERT: H 45 LYS cc_start: 0.8822 (tttt) cc_final: 0.7811 (mmpt) REVERT: H 57 GLU cc_start: 0.6014 (mt-10) cc_final: 0.5448 (mp0) REVERT: J 45 LYS cc_start: 0.8386 (tttt) cc_final: 0.7712 (mptt) REVERT: J 57 GLU cc_start: 0.6493 (mt-10) cc_final: 0.5396 (mp0) REVERT: K 45 LYS cc_start: 0.8687 (tttt) cc_final: 0.7907 (mptt) REVERT: L 45 LYS cc_start: 0.8181 (tttt) cc_final: 0.7890 (mmtt) REVERT: L 57 GLU cc_start: 0.6219 (mt-10) cc_final: 0.5064 (mp0) outliers start: 12 outliers final: 8 residues processed: 88 average time/residue: 1.5085 time to fit residues: 144.4671 Evaluate side-chains 88 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.895 ------------------------------------------------------------------------------- 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 13 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 2.9990 chunk 57 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6738 moved from start: 0.4756 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= 0.345 Angle : 0.697 6.317 7272 Z= 0.410 Chirality : 0.054 0.173 948 Planarity : 0.004 0.014 900 Dihedral : 9.308 33.503 768 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.37 % Favored : 87.63 % Rotamer: Outliers : 2.36 % Allowed : 21.74 % Favored : 75.91 % 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: -4.15 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.014 0.004 PHE B 94 TYR 0.010 0.003 TYR J 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 98 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 85 time to evaluate : 0.763 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: 0.8053 (tttt) cc_final: 0.7535 (mmtt) REVERT: B 97 LYS cc_start: 0.7210 (OUTLIER) cc_final: 0.6407 (tmmt) REVERT: C 45 LYS cc_start: 0.8578 (tttt) cc_final: 0.7940 (mmpt) REVERT: C 57 GLU cc_start: 0.5987 (mt-10) cc_final: 0.5334 (mm-30) REVERT: D 45 LYS cc_start: 0.8627 (tttt) cc_final: 0.7806 (mmtt) REVERT: D 57 GLU cc_start: 0.6474 (mt-10) cc_final: 0.5525 (mp0) REVERT: E 45 LYS cc_start: 0.8512 (tttt) cc_final: 0.7744 (tppt) REVERT: E 83 GLU cc_start: 0.6878 (OUTLIER) cc_final: 0.6614 (tt0) REVERT: E 87 ASN cc_start: 0.7131 (m110) cc_final: 0.6284 (t0) REVERT: I 45 LYS cc_start: 0.8268 (tttt) cc_final: 0.7905 (mmtt) REVERT: I 87 ASN cc_start: 0.7110 (m-40) cc_final: 0.6695 (t0) REVERT: F 92 THR cc_start: 0.5471 (t) cc_final: 0.5156 (t) REVERT: G 45 LYS cc_start: 0.8140 (tttt) cc_final: 0.7604 (mmpt) REVERT: H 45 LYS cc_start: 0.8803 (tttt) cc_final: 0.7809 (mmpt) REVERT: H 57 GLU cc_start: 0.6034 (mt-10) cc_final: 0.5471 (mp0) REVERT: J 45 LYS cc_start: 0.8414 (tttt) cc_final: 0.7752 (mptt) REVERT: J 57 GLU cc_start: 0.6601 (mt-10) cc_final: 0.5446 (mp0) REVERT: K 45 LYS cc_start: 0.8680 (tttt) cc_final: 0.8194 (ttpp) REVERT: L 45 LYS cc_start: 0.8125 (tttt) cc_final: 0.7867 (mmtt) REVERT: L 57 GLU cc_start: 0.6120 (mt-10) cc_final: 0.5260 (mp0) outliers start: 13 outliers final: 8 residues processed: 91 average time/residue: 1.5575 time to fit residues: 152.2265 Evaluate side-chains 91 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 97 LYS Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 64 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain K residue 83 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 27 optimal weight: 1.9990 chunk 41 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6693 moved from start: 0.4884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 5388 Z= 0.262 Angle : 0.613 6.485 7272 Z= 0.362 Chirality : 0.053 0.165 948 Planarity : 0.003 0.011 900 Dihedral : 8.576 32.988 768 Min Nonbonded Distance : 2.368 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.77 % Favored : 87.23 % Rotamer: Outliers : 1.81 % Allowed : 23.37 % Favored : 74.82 % 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: -4.21 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.20 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 50 PHE 0.011 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 88 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 0.816 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: 0.8043 (tttt) cc_final: 0.7536 (mmtt) REVERT: C 45 LYS cc_start: 0.8585 (tttt) cc_final: 0.7928 (mmpt) REVERT: C 57 GLU cc_start: 0.5801 (mt-10) cc_final: 0.5246 (mm-30) REVERT: D 45 LYS cc_start: 0.8616 (tttt) cc_final: 0.7793 (mmtt) REVERT: D 57 GLU cc_start: 0.6462 (mt-10) cc_final: 0.5523 (mp0) REVERT: E 45 LYS cc_start: 0.8623 (tttt) cc_final: 0.7810 (tppt) REVERT: E 87 ASN cc_start: 0.7124 (m110) cc_final: 0.6266 (t0) REVERT: I 45 LYS cc_start: 0.8267 (tttt) cc_final: 0.7908 (mptt) REVERT: G 45 LYS cc_start: 0.8136 (tttt) cc_final: 0.7597 (mmpt) REVERT: H 45 LYS cc_start: 0.8782 (tttt) cc_final: 0.7782 (mmpt) REVERT: H 57 GLU cc_start: 0.5991 (mt-10) cc_final: 0.5434 (mp0) REVERT: J 45 LYS cc_start: 0.8405 (tttt) cc_final: 0.7698 (mptt) REVERT: J 57 GLU cc_start: 0.6591 (mt-10) cc_final: 0.5456 (mp0) REVERT: K 45 LYS cc_start: 0.8670 (tttt) cc_final: 0.8180 (ttpp) REVERT: L 57 GLU cc_start: 0.6098 (mt-10) cc_final: 0.5269 (mp0) REVERT: L 64 THR cc_start: 0.6773 (OUTLIER) cc_final: 0.6498 (m) outliers start: 10 outliers final: 7 residues processed: 83 average time/residue: 1.6164 time to fit residues: 143.9488 Evaluate side-chains 87 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 0.839 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain H residue 64 THR Chi-restraints excluded: chain K residue 64 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 20 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.9990 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** ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6763 moved from start: 0.5169 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= 0.340 Angle : 0.701 7.200 7272 Z= 0.413 Chirality : 0.053 0.175 948 Planarity : 0.004 0.015 900 Dihedral : 9.274 33.778 768 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 24.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.46 % Favored : 84.54 % Rotamer: Outliers : 2.54 % Allowed : 23.37 % Favored : 74.09 % 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: -4.37 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS D 50 PHE 0.015 0.004 PHE F 94 TYR 0.011 0.003 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 96 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 82 time to evaluate : 0.876 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: 0.8109 (tttt) cc_final: 0.7569 (mmtt) REVERT: C 45 LYS cc_start: 0.8601 (tttt) cc_final: 0.7920 (mmpt) REVERT: C 57 GLU cc_start: 0.5936 (mt-10) cc_final: 0.5392 (mm-30) REVERT: D 45 LYS cc_start: 0.8613 (tttt) cc_final: 0.7862 (mmtm) REVERT: D 57 GLU cc_start: 0.6524 (mt-10) cc_final: 0.5579 (mp0) REVERT: E 45 LYS cc_start: 0.8632 (tttt) cc_final: 0.7823 (tppt) REVERT: E 87 ASN cc_start: 0.7141 (m110) cc_final: 0.6257 (t0) REVERT: I 45 LYS cc_start: 0.8358 (tttt) cc_final: 0.7942 (mptt) REVERT: I 87 ASN cc_start: 0.7188 (m-40) cc_final: 0.6631 (t0) REVERT: G 45 LYS cc_start: 0.8224 (tttt) cc_final: 0.7600 (mmpt) REVERT: H 45 LYS cc_start: 0.8806 (tttt) cc_final: 0.7802 (mmpt) REVERT: H 57 GLU cc_start: 0.6065 (mt-10) cc_final: 0.5501 (mp0) REVERT: J 45 LYS cc_start: 0.8423 (tttt) cc_final: 0.7728 (mptt) REVERT: J 57 GLU cc_start: 0.6607 (mt-10) cc_final: 0.5494 (mp0) REVERT: K 45 LYS cc_start: 0.8702 (tttt) cc_final: 0.8192 (ttpp) REVERT: L 43 LYS cc_start: 0.7040 (ttpt) cc_final: 0.6320 (tttp) REVERT: L 57 GLU cc_start: 0.6146 (mt-10) cc_final: 0.5306 (mp0) REVERT: L 64 THR cc_start: 0.6769 (OUTLIER) cc_final: 0.6496 (m) outliers start: 14 outliers final: 11 residues processed: 88 average time/residue: 1.5199 time to fit residues: 144.1748 Evaluate side-chains 91 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR 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 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 L residue 64 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 68 optimal weight: 0.5980 chunk 41 optimal weight: 3.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5388 Z= 0.244 Angle : 0.609 6.868 7272 Z= 0.357 Chirality : 0.053 0.166 948 Planarity : 0.003 0.011 900 Dihedral : 8.452 32.702 768 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 20.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.23 % Favored : 87.77 % Rotamer: Outliers : 1.81 % Allowed : 24.46 % Favored : 73.73 % 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: -4.38 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (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 0.008 0.002 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 86 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 76 time to evaluate : 0.876 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: 0.8084 (tttt) cc_final: 0.7561 (mmtt) REVERT: C 45 LYS cc_start: 0.8611 (tttt) cc_final: 0.7933 (mmpt) REVERT: C 57 GLU cc_start: 0.5856 (mt-10) cc_final: 0.5463 (mm-30) REVERT: D 45 LYS cc_start: 0.8607 (tttt) cc_final: 0.7815 (mmtm) REVERT: E 45 LYS cc_start: 0.8633 (tttt) cc_final: 0.7794 (tppt) REVERT: E 83 GLU cc_start: 0.6825 (OUTLIER) cc_final: 0.6568 (tt0) REVERT: I 45 LYS cc_start: 0.8324 (tttt) cc_final: 0.7913 (mptt) REVERT: G 45 LYS cc_start: 0.8217 (tttt) cc_final: 0.7585 (mmpt) REVERT: H 45 LYS cc_start: 0.8771 (tttt) cc_final: 0.7773 (mmpt) REVERT: H 57 GLU cc_start: 0.5988 (mt-10) cc_final: 0.5421 (mp0) REVERT: J 45 LYS cc_start: 0.8407 (tttt) cc_final: 0.7696 (mptt) REVERT: J 57 GLU cc_start: 0.6563 (mt-10) cc_final: 0.5473 (mp0) REVERT: K 45 LYS cc_start: 0.8699 (tttt) cc_final: 0.8188 (ttpp) REVERT: L 43 LYS cc_start: 0.6946 (ttpt) cc_final: 0.6286 (tttp) REVERT: L 57 GLU cc_start: 0.5994 (mt-10) cc_final: 0.5241 (mp0) REVERT: L 64 THR cc_start: 0.6640 (OUTLIER) cc_final: 0.6362 (m) outliers start: 10 outliers final: 7 residues processed: 81 average time/residue: 1.4996 time to fit residues: 130.8019 Evaluate side-chains 82 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 0.4980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6696 moved from start: 0.5282 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= 0.246 Angle : 0.604 7.055 7272 Z= 0.355 Chirality : 0.052 0.168 948 Planarity : 0.003 0.011 900 Dihedral : 8.321 30.482 768 Min Nonbonded Distance : 2.358 Molprobity Statistics. All-atom Clashscore : 20.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.38 % Favored : 85.62 % Rotamer: Outliers : 1.81 % Allowed : 25.18 % Favored : 73.01 % 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: -4.40 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS D 50 PHE 0.010 0.003 PHE B 94 TYR 0.008 0.002 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: 10 poor density : 73 time to evaluate : 0.757 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: 0.8096 (tttt) cc_final: 0.7560 (mmtt) REVERT: C 45 LYS cc_start: 0.8620 (tttt) cc_final: 0.7939 (mmpt) REVERT: C 57 GLU cc_start: 0.5944 (mt-10) cc_final: 0.5539 (mm-30) REVERT: D 45 LYS cc_start: 0.8605 (tttt) cc_final: 0.7778 (mmtm) REVERT: E 45 LYS cc_start: 0.8639 (tttt) cc_final: 0.7773 (tppt) REVERT: E 83 GLU cc_start: 0.6893 (OUTLIER) cc_final: 0.6621 (tt0) REVERT: I 45 LYS cc_start: 0.8383 (tttt) cc_final: 0.7966 (mptt) REVERT: I 87 ASN cc_start: 0.6910 (m-40) cc_final: 0.6464 (t0) REVERT: G 45 LYS cc_start: 0.8209 (tttt) cc_final: 0.7585 (mmpt) REVERT: H 45 LYS cc_start: 0.8801 (tttt) cc_final: 0.7780 (mmpt) REVERT: H 57 GLU cc_start: 0.6004 (mt-10) cc_final: 0.5441 (mp0) REVERT: J 45 LYS cc_start: 0.8417 (tttt) cc_final: 0.7694 (mptt) REVERT: J 57 GLU cc_start: 0.6553 (mt-10) cc_final: 0.5468 (mp0) REVERT: K 45 LYS cc_start: 0.8716 (tttt) cc_final: 0.8206 (ttpp) REVERT: L 43 LYS cc_start: 0.6964 (ttpt) cc_final: 0.6308 (tttp) REVERT: L 57 GLU cc_start: 0.5932 (mt-10) cc_final: 0.5194 (mp0) REVERT: L 64 THR cc_start: 0.6694 (OUTLIER) cc_final: 0.6409 (m) outliers start: 10 outliers final: 7 residues processed: 78 average time/residue: 1.5502 time to fit residues: 130.0697 Evaluate side-chains 82 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 73 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 81 THR Chi-restraints excluded: chain D residue 64 THR Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain G residue 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 52 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 50 optimal weight: 0.0270 chunk 3 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.9240 ------------------------------------------------------------------------------- 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 = 0.5030 r_free = 0.5030 target = 0.226427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.208750 restraints weight = 21359.480| |-----------------------------------------------------------------------------| r_work (start): 0.4893 rms_B_bonded: 2.65 r_work: 0.4830 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.4730 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.4730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6688 moved from start: 0.5304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5388 Z= 0.196 Angle : 0.552 6.216 7272 Z= 0.322 Chirality : 0.052 0.160 948 Planarity : 0.002 0.009 900 Dihedral : 7.695 29.418 768 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 18.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.69 % Favored : 88.31 % Rotamer: Outliers : 1.27 % Allowed : 25.91 % Favored : 72.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -4.36 (0.22), residues: 744 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.17), residues: 744 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS L 50 PHE 0.008 0.002 PHE B 94 TYR 0.006 0.001 TYR I 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4515.35 seconds wall clock time: 80 minutes 57.66 seconds (4857.66 seconds total)