Starting phenix.real_space_refine on Sat Apr 4 21:53:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9rb6_53885/04_2026/9rb6_53885.cif Found real_map, /net/cci-nas-00/data/ceres_data/9rb6_53885/04_2026/9rb6_53885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.02 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9rb6_53885/04_2026/9rb6_53885.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9rb6_53885/04_2026/9rb6_53885.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9rb6_53885/04_2026/9rb6_53885.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9rb6_53885/04_2026/9rb6_53885.map" } resolution = 3.02 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 3 Type Number sf(0) Gaussians C 2700 2.51 5 N 740 2.21 5 O 870 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4310 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 431 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Restraints were copied for chains: B, C, D, E, F, G, H, I, J Time building chain proxies: 0.39, per 1000 atoms: 0.09 Number of scatterers: 4310 At special positions: 0 Unit cell: (81.928, 89.452, 40.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 870 8.00 N 740 7.00 C 2700 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 138.8 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1060 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 33.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.23 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 40 Processing sheet with id=AA2, first strand: chain 'A' and resid 49 through 54 removed outlier: 6.806A pdb=" N VAL A 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N THR C 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR A 54 " --> pdb=" O THR C 53 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N VAL C 52 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N THR E 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N THR C 54 " --> pdb=" O THR E 53 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N VAL E 52 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N THR G 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.817A pdb=" N THR E 54 " --> pdb=" O THR G 53 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N VAL G 52 " --> pdb=" O GLY I 51 " (cutoff:3.500A) removed outlier: 6.862A pdb=" N THR I 53 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N THR G 54 " --> pdb=" O THR I 53 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 57 through 59 removed outlier: 6.364A pdb=" N GLU C 57 " --> pdb=" O LYS E 58 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 62 through 65 removed outlier: 6.607A pdb=" N GLN A 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.149A pdb=" N ASN C 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N THR A 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N GLN C 62 " --> pdb=" O VAL E 63 " (cutoff:3.500A) removed outlier: 8.148A pdb=" N ASN E 65 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR C 64 " --> pdb=" O ASN E 65 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N GLN E 62 " --> pdb=" O VAL G 63 " (cutoff:3.500A) removed outlier: 8.167A pdb=" N ASN G 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N THR E 64 " --> pdb=" O ASN G 65 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N GLN G 62 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN I 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N THR G 64 " --> pdb=" O ASN I 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 71 removed outlier: 6.189A pdb=" N ALA A 69 " --> pdb=" O VAL C 70 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ALA C 69 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA E 69 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N ALA G 69 " --> pdb=" O VAL I 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 75 through 77 Processing sheet with id=AA7, first strand: chain 'A' and resid 88 through 89 Processing sheet with id=AA8, first strand: chain 'A' and resid 92 through 96 removed outlier: 6.743A pdb=" N GLY A 93 " --> pdb=" O PHE C 94 " (cutoff:3.500A) removed outlier: 7.896A pdb=" N LYS C 96 " --> pdb=" O GLY A 93 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N GLY C 93 " --> pdb=" O PHE E 94 " (cutoff:3.500A) removed outlier: 7.885A pdb=" N LYS E 96 " --> pdb=" O GLY C 93 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N VAL C 95 " --> pdb=" O LYS E 96 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY E 93 " --> pdb=" O PHE G 94 " (cutoff:3.500A) removed outlier: 7.893A pdb=" N LYS G 96 " --> pdb=" O GLY E 93 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N VAL E 95 " --> pdb=" O LYS G 96 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N GLY G 93 " --> pdb=" O PHE I 94 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N LYS I 96 " --> pdb=" O GLY G 93 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N VAL G 95 " --> pdb=" O LYS I 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AB1, first strand: chain 'B' and resid 49 through 54 removed outlier: 6.816A pdb=" N VAL B 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR D 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N THR B 54 " --> pdb=" O THR D 53 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N VAL D 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR F 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N THR D 54 " --> pdb=" O THR F 53 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N VAL F 52 " --> pdb=" O GLY H 51 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N THR H 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N THR F 54 " --> pdb=" O THR H 53 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N VAL H 52 " --> pdb=" O GLY J 51 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N THR J 53 " --> pdb=" O VAL H 52 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N THR H 54 " --> pdb=" O THR J 53 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 57 through 59 Processing sheet with id=AB3, first strand: chain 'B' and resid 62 through 65 removed outlier: 6.615A pdb=" N GLN B 62 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N ASN D 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR B 64 " --> pdb=" O ASN D 65 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN D 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN F 65 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N THR D 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) removed outlier: 6.627A pdb=" N GLN F 62 " --> pdb=" O VAL H 63 " (cutoff:3.500A) removed outlier: 8.169A pdb=" N ASN H 65 " --> pdb=" O GLN F 62 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N THR F 64 " --> pdb=" O ASN H 65 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLN H 62 " --> pdb=" O VAL J 63 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N ASN J 65 " --> pdb=" O GLN H 62 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N THR H 64 " --> pdb=" O ASN J 65 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'B' and resid 69 through 71 removed outlier: 6.188A pdb=" N ALA B 69 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ALA D 69 " --> pdb=" O VAL F 70 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N ALA F 69 " --> pdb=" O VAL H 70 " (cutoff:3.500A) removed outlier: 6.162A pdb=" N ALA H 69 " --> pdb=" O VAL J 70 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'B' and resid 75 through 77 Processing sheet with id=AB6, first strand: chain 'B' and resid 88 through 89 Processing sheet with id=AB7, first strand: chain 'B' and resid 92 through 96 removed outlier: 6.736A pdb=" N GLY B 93 " --> pdb=" O PHE D 94 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N LYS D 96 " --> pdb=" O GLY B 93 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL B 95 " --> pdb=" O LYS D 96 " (cutoff:3.500A) removed outlier: 6.733A pdb=" N GLY D 93 " --> pdb=" O PHE F 94 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N LYS F 96 " --> pdb=" O GLY D 93 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N GLY F 93 " --> pdb=" O PHE H 94 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N LYS H 96 " --> pdb=" O GLY F 93 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N VAL F 95 " --> pdb=" O LYS H 96 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N GLY H 93 " --> pdb=" O PHE J 94 " (cutoff:3.500A) removed outlier: 7.910A pdb=" N LYS J 96 " --> pdb=" O GLY H 93 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 95 " --> pdb=" O LYS J 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 70 hydrogen bonds defined for protein. 210 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.60 Time building geometry restraints manager: 0.46 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.28: 750 1.28 - 1.36: 670 1.36 - 1.44: 220 1.44 - 1.52: 1057 1.52 - 1.61: 1633 Bond restraints: 4330 Sorted by residual: bond pdb=" N GLU G 46 " pdb=" CA GLU G 46 " ideal model delta sigma weight residual 1.457 1.520 -0.064 1.32e-02 5.74e+03 2.33e+01 bond pdb=" N GLU B 46 " pdb=" CA GLU B 46 " ideal model delta sigma weight residual 1.457 1.520 -0.064 1.32e-02 5.74e+03 2.32e+01 bond pdb=" N GLU F 46 " pdb=" CA GLU F 46 " ideal model delta sigma weight residual 1.457 1.520 -0.064 1.32e-02 5.74e+03 2.32e+01 bond pdb=" N GLU C 46 " pdb=" CA GLU C 46 " ideal model delta sigma weight residual 1.457 1.520 -0.064 1.32e-02 5.74e+03 2.31e+01 bond pdb=" N GLU J 46 " pdb=" CA GLU J 46 " ideal model delta sigma weight residual 1.457 1.520 -0.063 1.32e-02 5.74e+03 2.31e+01 ... (remaining 4325 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 4873 2.88 - 5.75: 837 5.75 - 8.63: 90 8.63 - 11.50: 40 11.50 - 14.38: 20 Bond angle restraints: 5860 Sorted by residual: angle pdb=" N GLU I 46 " pdb=" CA GLU I 46 " pdb=" C GLU I 46 " ideal model delta sigma weight residual 110.35 124.73 -14.38 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N GLU D 46 " pdb=" CA GLU D 46 " pdb=" C GLU D 46 " ideal model delta sigma weight residual 110.35 124.72 -14.37 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N GLU F 46 " pdb=" CA GLU F 46 " pdb=" C GLU F 46 " ideal model delta sigma weight residual 110.35 124.71 -14.36 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N GLU A 46 " pdb=" CA GLU A 46 " pdb=" C GLU A 46 " ideal model delta sigma weight residual 110.35 124.70 -14.35 1.40e+00 5.10e-01 1.05e+02 angle pdb=" N GLU H 46 " pdb=" CA GLU H 46 " pdb=" C GLU H 46 " ideal model delta sigma weight residual 110.35 124.70 -14.35 1.40e+00 5.10e-01 1.05e+02 ... (remaining 5855 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 14.95: 2170 14.95 - 29.88: 250 29.88 - 44.82: 50 44.82 - 59.75: 50 59.75 - 74.68: 10 Dihedral angle restraints: 2530 sinusoidal: 850 harmonic: 1680 Sorted by residual: dihedral pdb=" CB LYS B 45 " pdb=" CG LYS B 45 " pdb=" CD LYS B 45 " pdb=" CE LYS B 45 " ideal model delta sinusoidal sigma weight residual -180.00 -123.28 -56.72 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS C 45 " pdb=" CG LYS C 45 " pdb=" CD LYS C 45 " pdb=" CE LYS C 45 " ideal model delta sinusoidal sigma weight residual -180.00 -123.29 -56.71 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CB LYS D 45 " pdb=" CG LYS D 45 " pdb=" CD LYS D 45 " pdb=" CE LYS D 45 " ideal model delta sinusoidal sigma weight residual -180.00 -123.29 -56.71 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 2527 not shown) Histogram of chiral volume deviations from ideal: 0.003 - 0.056: 215 0.056 - 0.109: 196 0.109 - 0.162: 243 0.162 - 0.215: 66 0.215 - 0.268: 60 Chirality restraints: 780 Sorted by residual: chirality pdb=" CA VAL G 49 " pdb=" N VAL G 49 " pdb=" C VAL G 49 " pdb=" CB VAL G 49 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.71 -0.27 2.00e-01 2.50e+01 1.77e+00 ... (remaining 777 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY F 84 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY F 84 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY F 84 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA F 85 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY J 84 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY J 84 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY J 84 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA J 85 " 0.025 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY H 84 " 0.021 2.00e-02 2.50e+03 4.23e-02 1.79e+01 pdb=" C GLY H 84 " -0.073 2.00e-02 2.50e+03 pdb=" O GLY H 84 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA H 85 " 0.025 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 2054 2.96 - 3.44: 3605 3.44 - 3.93: 7469 3.93 - 4.41: 7577 4.41 - 4.90: 15366 Nonbonded interactions: 36071 Sorted by model distance: nonbonded pdb=" N THR E 72 " pdb=" O THR E 72 " model vdw 2.474 2.496 nonbonded pdb=" N THR A 72 " pdb=" O THR A 72 " model vdw 2.474 2.496 nonbonded pdb=" N THR D 72 " pdb=" O THR D 72 " model vdw 2.474 2.496 nonbonded pdb=" N THR H 72 " pdb=" O THR H 72 " model vdw 2.475 2.496 nonbonded pdb=" N THR G 72 " pdb=" O THR G 72 " model vdw 2.475 2.496 ... (remaining 36066 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: 0.01 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' } 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: 2.120 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: 0.000 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.090 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 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 : 0.022 0.084 4330 Z= 1.264 Angle : 2.359 14.379 5860 Z= 1.698 Chirality : 0.124 0.268 780 Planarity : 0.009 0.042 720 Dihedral : 17.308 74.681 1470 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 8.89 % Allowed : 8.89 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.32), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : 0.45 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR J 39 PHE 0.018 0.006 PHE G 94 HIS 0.007 0.004 HIS C 50 Details of bonding type rmsd covalent geometry : bond 0.02225 ( 4330) covalent geometry : angle 2.35950 ( 5860) hydrogen bonds : bond 0.13561 ( 70) hydrogen bonds : angle 7.89793 ( 210) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 158 time to evaluate : 0.122 Fit side-chains REVERT: A 43 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7936 (tptp) REVERT: B 43 LYS cc_start: 0.8130 (ttmt) cc_final: 0.7782 (tptp) REVERT: C 43 LYS cc_start: 0.7903 (ttmt) cc_final: 0.7625 (tptp) REVERT: D 43 LYS cc_start: 0.7841 (ttmt) cc_final: 0.7540 (tptp) REVERT: E 43 LYS cc_start: 0.7932 (ttmt) cc_final: 0.7677 (tptp) REVERT: F 43 LYS cc_start: 0.7878 (ttmt) cc_final: 0.7411 (tptm) REVERT: G 43 LYS cc_start: 0.8012 (ttmt) cc_final: 0.7749 (tptp) REVERT: H 43 LYS cc_start: 0.7838 (ttmt) cc_final: 0.7455 (tptp) REVERT: I 43 LYS cc_start: 0.7970 (ttmt) cc_final: 0.7717 (tptp) REVERT: J 43 LYS cc_start: 0.7952 (ttmt) cc_final: 0.7669 (tptp) outliers start: 40 outliers final: 20 residues processed: 178 average time/residue: 0.1167 time to fit residues: 23.7326 Evaluate side-chains 151 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 131 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 75 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 75 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 4.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 62 GLN B 79 GLN H 62 GLN H 79 GLN I 62 GLN I 79 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.122805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.105120 restraints weight = 5627.630| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 2.78 r_work: 0.3581 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3460 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.3460 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8365 moved from start: 0.2963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4330 Z= 0.147 Angle : 0.635 8.825 5860 Z= 0.340 Chirality : 0.051 0.146 780 Planarity : 0.002 0.009 720 Dihedral : 6.886 22.362 640 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 3.11 % Allowed : 14.22 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.93 (0.28), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.70 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.002 TYR H 39 PHE 0.011 0.003 PHE C 94 HIS 0.002 0.001 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00321 ( 4330) covalent geometry : angle 0.63537 ( 5860) hydrogen bonds : bond 0.02153 ( 70) hydrogen bonds : angle 5.48254 ( 210) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.142 Fit side-chains REVERT: A 43 LYS cc_start: 0.8087 (ttmt) cc_final: 0.7761 (tptp) REVERT: B 43 LYS cc_start: 0.8063 (ttmt) cc_final: 0.7641 (tptp) REVERT: B 45 LYS cc_start: 0.8165 (tptm) cc_final: 0.7708 (tppt) REVERT: B 97 LYS cc_start: 0.8835 (mmtp) cc_final: 0.8617 (mmtt) REVERT: C 43 LYS cc_start: 0.7712 (ttmt) cc_final: 0.7297 (tptp) REVERT: C 45 LYS cc_start: 0.8208 (tptm) cc_final: 0.7792 (tppt) REVERT: D 43 LYS cc_start: 0.7821 (ttmt) cc_final: 0.7285 (tptp) REVERT: D 97 LYS cc_start: 0.8729 (mmtp) cc_final: 0.8470 (mmtt) REVERT: E 38 LEU cc_start: 0.7749 (mp) cc_final: 0.7402 (tt) REVERT: E 43 LYS cc_start: 0.7809 (ttmt) cc_final: 0.7386 (tptp) REVERT: E 45 LYS cc_start: 0.8223 (tppp) cc_final: 0.7922 (tptm) REVERT: F 43 LYS cc_start: 0.7746 (ttmt) cc_final: 0.7295 (tptp) REVERT: F 45 LYS cc_start: 0.8085 (tppp) cc_final: 0.7597 (tppp) REVERT: G 43 LYS cc_start: 0.7961 (ttmt) cc_final: 0.7528 (tptp) REVERT: G 45 LYS cc_start: 0.8214 (tptm) cc_final: 0.8012 (tptm) REVERT: H 43 LYS cc_start: 0.7882 (ttmt) cc_final: 0.7407 (tptp) REVERT: I 43 LYS cc_start: 0.8067 (ttmt) cc_final: 0.7649 (tptp) REVERT: I 79 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8643 (mt0) REVERT: J 43 LYS cc_start: 0.7851 (ttmt) cc_final: 0.7453 (tptp) outliers start: 14 outliers final: 11 residues processed: 102 average time/residue: 0.1283 time to fit residues: 15.0088 Evaluate side-chains 104 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 95 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 8.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 49 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN E 79 GLN I 62 GLN I 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3761 r_free = 0.3761 target = 0.115711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.097982 restraints weight = 5540.672| |-----------------------------------------------------------------------------| r_work (start): 0.3585 rms_B_bonded: 2.76 r_work: 0.3468 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3340 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4330 Z= 0.252 Angle : 0.684 6.385 5860 Z= 0.372 Chirality : 0.051 0.141 780 Planarity : 0.002 0.008 720 Dihedral : 6.191 15.837 620 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 5.11 % Allowed : 17.78 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.34 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.01 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR C 39 PHE 0.012 0.003 PHE C 94 HIS 0.004 0.002 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00580 ( 4330) covalent geometry : angle 0.68445 ( 5860) hydrogen bonds : bond 0.02409 ( 70) hydrogen bonds : angle 5.40099 ( 210) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 95 time to evaluate : 0.101 Fit side-chains REVERT: A 43 LYS cc_start: 0.8252 (ttmt) cc_final: 0.7851 (tttp) REVERT: A 58 LYS cc_start: 0.8901 (mtpp) cc_final: 0.8692 (mtpt) REVERT: B 43 LYS cc_start: 0.8195 (ttmt) cc_final: 0.7755 (tptp) REVERT: B 45 LYS cc_start: 0.8443 (tptm) cc_final: 0.7979 (tppt) REVERT: C 43 LYS cc_start: 0.7822 (ttmt) cc_final: 0.7415 (tptp) REVERT: C 45 LYS cc_start: 0.8379 (tptm) cc_final: 0.7947 (tppt) REVERT: D 43 LYS cc_start: 0.7938 (ttmt) cc_final: 0.7385 (tptp) REVERT: E 43 LYS cc_start: 0.7868 (ttmt) cc_final: 0.7370 (tptp) REVERT: E 45 LYS cc_start: 0.8313 (tppp) cc_final: 0.7912 (tptm) REVERT: F 43 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7367 (tttm) REVERT: F 46 GLU cc_start: 0.7727 (pt0) cc_final: 0.7478 (mt-10) REVERT: G 43 LYS cc_start: 0.7967 (ttmt) cc_final: 0.7511 (tptp) REVERT: H 43 LYS cc_start: 0.7982 (ttmt) cc_final: 0.7480 (tptp) REVERT: I 43 LYS cc_start: 0.8149 (ttmt) cc_final: 0.7639 (tptp) REVERT: I 45 LYS cc_start: 0.8743 (tptm) cc_final: 0.8262 (tppt) REVERT: I 79 GLN cc_start: 0.9040 (OUTLIER) cc_final: 0.8657 (mt0) REVERT: I 81 THR cc_start: 0.8628 (m) cc_final: 0.8388 (t) REVERT: J 43 LYS cc_start: 0.8044 (ttmt) cc_final: 0.7499 (tptp) REVERT: J 79 GLN cc_start: 0.9036 (mt0) cc_final: 0.8803 (mt0) outliers start: 23 outliers final: 16 residues processed: 107 average time/residue: 0.1216 time to fit residues: 14.9944 Evaluate side-chains 108 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 91 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 95 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 2 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 16 optimal weight: 2.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 33 optimal weight: 10.0000 chunk 59 optimal weight: 8.9990 chunk 45 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 62 GLN I 79 GLN J 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3762 r_free = 0.3762 target = 0.113019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.095526 restraints weight = 5288.224| |-----------------------------------------------------------------------------| r_work (start): 0.3564 rms_B_bonded: 2.78 r_work: 0.3429 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.3294 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8476 moved from start: 0.4084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.037 4330 Z= 0.374 Angle : 0.749 6.687 5860 Z= 0.416 Chirality : 0.053 0.131 780 Planarity : 0.003 0.008 720 Dihedral : 6.465 18.060 620 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 7.11 % Allowed : 16.22 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.69 (0.29), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.22), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR I 39 PHE 0.015 0.004 PHE C 94 HIS 0.006 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00856 ( 4330) covalent geometry : angle 0.74919 ( 5860) hydrogen bonds : bond 0.02544 ( 70) hydrogen bonds : angle 5.37383 ( 210) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 96 time to evaluate : 0.151 Fit side-chains REVERT: A 43 LYS cc_start: 0.8231 (ttmt) cc_final: 0.7798 (tttm) REVERT: A 46 GLU cc_start: 0.8382 (pt0) cc_final: 0.7957 (mp0) REVERT: A 58 LYS cc_start: 0.8941 (mtpp) cc_final: 0.8717 (mtpt) REVERT: B 43 LYS cc_start: 0.8142 (ttmt) cc_final: 0.7665 (tttp) REVERT: B 45 LYS cc_start: 0.8434 (tptm) cc_final: 0.8185 (tttm) REVERT: B 46 GLU cc_start: 0.8308 (pt0) cc_final: 0.7988 (mp0) REVERT: C 43 LYS cc_start: 0.7859 (ttmt) cc_final: 0.7305 (tptp) REVERT: D 43 LYS cc_start: 0.7805 (ttmt) cc_final: 0.7172 (tptp) REVERT: D 46 GLU cc_start: 0.8035 (pt0) cc_final: 0.7516 (mp0) REVERT: E 43 LYS cc_start: 0.7832 (ttmt) cc_final: 0.7318 (tptp) REVERT: E 46 GLU cc_start: 0.7926 (pt0) cc_final: 0.7555 (mp0) REVERT: F 43 LYS cc_start: 0.7769 (ttmt) cc_final: 0.7388 (tttm) REVERT: F 45 LYS cc_start: 0.8411 (OUTLIER) cc_final: 0.8204 (tptt) REVERT: F 46 GLU cc_start: 0.7994 (pt0) cc_final: 0.7402 (mp0) REVERT: G 43 LYS cc_start: 0.7933 (ttmt) cc_final: 0.7450 (tttm) REVERT: G 46 GLU cc_start: 0.7867 (pt0) cc_final: 0.7319 (mp0) REVERT: H 43 LYS cc_start: 0.7986 (ttmt) cc_final: 0.7455 (tttp) REVERT: I 43 LYS cc_start: 0.8172 (ttmt) cc_final: 0.7646 (tptp) REVERT: I 45 LYS cc_start: 0.8814 (tptm) cc_final: 0.8538 (tptt) REVERT: I 79 GLN cc_start: 0.9213 (OUTLIER) cc_final: 0.8845 (mt0) REVERT: J 43 LYS cc_start: 0.8062 (ttmt) cc_final: 0.7608 (tttm) outliers start: 32 outliers final: 24 residues processed: 114 average time/residue: 0.1125 time to fit residues: 14.9392 Evaluate side-chains 122 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 96 time to evaluate : 0.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 79 GLN Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 58 LYS Chi-restraints excluded: chain J residue 95 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 37 optimal weight: 2.9990 chunk 16 optimal weight: 0.7980 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 10.0000 chunk 47 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 20 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN C 79 GLN D 62 GLN D 79 GLN E 79 GLN I 62 GLN I 79 GLN J 62 GLN J 79 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3801 r_free = 0.3801 target = 0.117686 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.099861 restraints weight = 5493.981| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 2.90 r_work: 0.3505 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.3505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.4166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4330 Z= 0.126 Angle : 0.534 6.887 5860 Z= 0.293 Chirality : 0.050 0.128 780 Planarity : 0.001 0.006 720 Dihedral : 5.580 15.741 620 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.67 % Favored : 98.33 % Rotamer: Outliers : 7.33 % Allowed : 16.00 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.30), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR I 39 PHE 0.008 0.002 PHE C 94 HIS 0.002 0.001 HIS B 50 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 4330) covalent geometry : angle 0.53393 ( 5860) hydrogen bonds : bond 0.01359 ( 70) hydrogen bonds : angle 4.80774 ( 210) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 90 time to evaluate : 0.097 Fit side-chains REVERT: A 43 LYS cc_start: 0.8226 (ttmt) cc_final: 0.7860 (tttp) REVERT: B 43 LYS cc_start: 0.8143 (ttmt) cc_final: 0.7758 (tptp) REVERT: C 43 LYS cc_start: 0.7823 (ttmt) cc_final: 0.7406 (tptp) REVERT: D 43 LYS cc_start: 0.7771 (ttmt) cc_final: 0.7292 (tptp) REVERT: D 45 LYS cc_start: 0.8285 (tptm) cc_final: 0.8050 (tttt) REVERT: E 43 LYS cc_start: 0.7737 (ttmt) cc_final: 0.7330 (tttm) REVERT: F 43 LYS cc_start: 0.7685 (ttmt) cc_final: 0.7348 (tttm) REVERT: F 45 LYS cc_start: 0.8363 (OUTLIER) cc_final: 0.8102 (tppt) REVERT: F 46 GLU cc_start: 0.7800 (pt0) cc_final: 0.7482 (mp0) REVERT: G 43 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7448 (tttm) REVERT: G 45 LYS cc_start: 0.8195 (tptm) cc_final: 0.7715 (tppt) REVERT: H 43 LYS cc_start: 0.7985 (ttmt) cc_final: 0.7531 (tttp) REVERT: H 45 LYS cc_start: 0.8256 (tttt) cc_final: 0.7849 (tttt) REVERT: I 43 LYS cc_start: 0.8140 (ttmt) cc_final: 0.7668 (tttm) REVERT: I 83 GLU cc_start: 0.8177 (mt-10) cc_final: 0.7860 (mt-10) REVERT: J 43 LYS cc_start: 0.7971 (ttmt) cc_final: 0.7551 (tttm) REVERT: J 45 LYS cc_start: 0.8446 (tppp) cc_final: 0.8159 (tppt) REVERT: J 83 GLU cc_start: 0.7992 (mt-10) cc_final: 0.7308 (mt-10) outliers start: 33 outliers final: 21 residues processed: 113 average time/residue: 0.1158 time to fit residues: 15.1445 Evaluate side-chains 107 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 85 time to evaluate : 0.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 95 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 31 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 15 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 59 optimal weight: 10.0000 chunk 51 optimal weight: 9.9990 chunk 52 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 overall best weight: 6.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 50 HIS ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN D 79 GLN E 79 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.109802 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3481 r_free = 0.3481 target = 0.092130 restraints weight = 5751.537| |-----------------------------------------------------------------------------| r_work (start): 0.3506 rms_B_bonded: 2.88 r_work: 0.3370 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 moved from start: 0.4487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.043 4330 Z= 0.355 Angle : 0.684 5.928 5860 Z= 0.386 Chirality : 0.053 0.145 780 Planarity : 0.002 0.007 720 Dihedral : 6.247 18.390 620 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.11 % Allowed : 15.78 % Favored : 77.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.82 (0.30), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.38 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR I 39 PHE 0.016 0.004 PHE C 94 HIS 0.005 0.003 HIS H 50 Details of bonding type rmsd covalent geometry : bond 0.00811 ( 4330) covalent geometry : angle 0.68407 ( 5860) hydrogen bonds : bond 0.02417 ( 70) hydrogen bonds : angle 4.94087 ( 210) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 97 time to evaluate : 0.156 Fit side-chains REVERT: A 43 LYS cc_start: 0.8209 (ttmt) cc_final: 0.7834 (tttm) REVERT: A 46 GLU cc_start: 0.8376 (pt0) cc_final: 0.8037 (mp0) REVERT: B 43 LYS cc_start: 0.8156 (ttmt) cc_final: 0.7711 (tttp) REVERT: B 46 GLU cc_start: 0.8250 (pt0) cc_final: 0.7955 (mp0) REVERT: C 43 LYS cc_start: 0.7860 (ttmt) cc_final: 0.7434 (tptp) REVERT: C 44 THR cc_start: 0.8888 (m) cc_final: 0.8624 (p) REVERT: D 43 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7381 (tptp) REVERT: D 46 GLU cc_start: 0.8125 (pt0) cc_final: 0.7791 (pt0) REVERT: E 43 LYS cc_start: 0.7812 (ttmt) cc_final: 0.7374 (tttm) REVERT: E 45 LYS cc_start: 0.8342 (tttt) cc_final: 0.7948 (tttt) REVERT: F 43 LYS cc_start: 0.7761 (ttmt) cc_final: 0.7389 (tttm) REVERT: F 45 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8143 (tptt) REVERT: F 46 GLU cc_start: 0.7865 (pt0) cc_final: 0.7522 (mp0) REVERT: G 43 LYS cc_start: 0.7920 (ttmt) cc_final: 0.7503 (tttm) REVERT: G 45 LYS cc_start: 0.8338 (OUTLIER) cc_final: 0.7944 (tptt) REVERT: H 43 LYS cc_start: 0.8035 (ttmt) cc_final: 0.7573 (tttm) REVERT: I 43 LYS cc_start: 0.8187 (ttmt) cc_final: 0.7732 (tttm) REVERT: I 83 GLU cc_start: 0.8233 (mt-10) cc_final: 0.7509 (mt-10) REVERT: J 43 LYS cc_start: 0.8026 (ttmt) cc_final: 0.7585 (tttm) REVERT: J 79 GLN cc_start: 0.9105 (mt0) cc_final: 0.8890 (mt0) REVERT: J 83 GLU cc_start: 0.8005 (mt-10) cc_final: 0.7351 (mt-10) outliers start: 32 outliers final: 28 residues processed: 114 average time/residue: 0.1143 time to fit residues: 15.0554 Evaluate side-chains 125 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 95 time to evaluate : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 GLN Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain I residue 95 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 95 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 51 optimal weight: 6.9990 chunk 15 optimal weight: 6.9990 chunk 25 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 44 optimal weight: 5.9990 chunk 14 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN C 79 GLN D 62 GLN F 79 GLN I 79 GLN J 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.112175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.094522 restraints weight = 5600.601| |-----------------------------------------------------------------------------| r_work (start): 0.3547 rms_B_bonded: 2.87 r_work: 0.3411 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8481 moved from start: 0.4536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4330 Z= 0.237 Angle : 0.587 5.793 5860 Z= 0.329 Chirality : 0.051 0.125 780 Planarity : 0.002 0.006 720 Dihedral : 5.940 16.846 620 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 6.89 % Allowed : 16.67 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.84 (0.31), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.23), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR C 39 PHE 0.011 0.003 PHE C 94 HIS 0.003 0.002 HIS A 50 Details of bonding type rmsd covalent geometry : bond 0.00539 ( 4330) covalent geometry : angle 0.58667 ( 5860) hydrogen bonds : bond 0.01926 ( 70) hydrogen bonds : angle 4.61183 ( 210) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 94 time to evaluate : 0.157 Fit side-chains REVERT: A 43 LYS cc_start: 0.8230 (ttmt) cc_final: 0.7870 (tttm) REVERT: B 43 LYS cc_start: 0.8160 (ttmt) cc_final: 0.7719 (tptp) REVERT: B 46 GLU cc_start: 0.8179 (OUTLIER) cc_final: 0.7887 (mp0) REVERT: C 43 LYS cc_start: 0.7792 (ttmt) cc_final: 0.7368 (tttp) REVERT: C 97 LYS cc_start: 0.8867 (mmtt) cc_final: 0.8660 (mmtt) REVERT: D 43 LYS cc_start: 0.7828 (ttmt) cc_final: 0.7346 (tptp) REVERT: D 46 GLU cc_start: 0.8071 (pt0) cc_final: 0.7726 (pt0) REVERT: E 43 LYS cc_start: 0.7770 (ttmt) cc_final: 0.7371 (tttm) REVERT: E 45 LYS cc_start: 0.8319 (tttt) cc_final: 0.7836 (tttt) REVERT: E 46 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7604 (mp0) REVERT: F 43 LYS cc_start: 0.7756 (ttmt) cc_final: 0.7374 (tttm) REVERT: F 45 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8045 (tptt) REVERT: F 46 GLU cc_start: 0.7787 (pt0) cc_final: 0.7526 (mp0) REVERT: G 43 LYS cc_start: 0.7906 (ttmt) cc_final: 0.7470 (tttm) REVERT: G 45 LYS cc_start: 0.8272 (OUTLIER) cc_final: 0.7774 (tppt) REVERT: G 46 GLU cc_start: 0.7567 (pt0) cc_final: 0.7366 (mp0) REVERT: H 43 LYS cc_start: 0.8011 (ttmt) cc_final: 0.7548 (tttm) REVERT: I 43 LYS cc_start: 0.8174 (ttmt) cc_final: 0.7729 (tttm) REVERT: I 83 GLU cc_start: 0.8292 (mt-10) cc_final: 0.7605 (mt-10) REVERT: J 43 LYS cc_start: 0.8010 (ttmt) cc_final: 0.7570 (tttm) REVERT: J 83 GLU cc_start: 0.8038 (mt-10) cc_final: 0.7419 (mt-10) outliers start: 31 outliers final: 24 residues processed: 110 average time/residue: 0.1233 time to fit residues: 15.6049 Evaluate side-chains 123 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 62 GLN Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 79 GLN Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 55 optimal weight: 7.9990 chunk 49 optimal weight: 6.9990 chunk 30 optimal weight: 10.0000 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 79 GLN D 62 GLN D 79 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.112701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.095110 restraints weight = 5584.607| |-----------------------------------------------------------------------------| r_work (start): 0.3555 rms_B_bonded: 2.82 r_work: 0.3421 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3289 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3289 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.4611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4330 Z= 0.229 Angle : 0.580 7.581 5860 Z= 0.324 Chirality : 0.051 0.126 780 Planarity : 0.002 0.007 720 Dihedral : 5.844 16.717 620 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 6.89 % Allowed : 16.67 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.80 (0.31), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.36 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.002 TYR C 39 PHE 0.011 0.002 PHE C 94 HIS 0.003 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00522 ( 4330) covalent geometry : angle 0.57975 ( 5860) hydrogen bonds : bond 0.01874 ( 70) hydrogen bonds : angle 4.53340 ( 210) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 97 time to evaluate : 0.119 Fit side-chains REVERT: A 43 LYS cc_start: 0.8336 (ttmt) cc_final: 0.8004 (tttm) REVERT: A 46 GLU cc_start: 0.8433 (pt0) cc_final: 0.8217 (mp0) REVERT: B 43 LYS cc_start: 0.8182 (ttmt) cc_final: 0.7740 (tptp) REVERT: B 46 GLU cc_start: 0.8382 (OUTLIER) cc_final: 0.8037 (mp0) REVERT: C 43 LYS cc_start: 0.7861 (ttmt) cc_final: 0.7449 (tttp) REVERT: D 43 LYS cc_start: 0.7875 (ttmt) cc_final: 0.7382 (tptp) REVERT: D 46 GLU cc_start: 0.8288 (pt0) cc_final: 0.7948 (pt0) REVERT: E 43 LYS cc_start: 0.7897 (ttmt) cc_final: 0.7463 (tttm) REVERT: E 45 LYS cc_start: 0.8352 (tttt) cc_final: 0.7944 (tttt) REVERT: E 46 GLU cc_start: 0.8279 (OUTLIER) cc_final: 0.7781 (mp0) REVERT: F 43 LYS cc_start: 0.7816 (ttmt) cc_final: 0.7411 (tttm) REVERT: F 45 LYS cc_start: 0.8287 (OUTLIER) cc_final: 0.8061 (tptt) REVERT: F 46 GLU cc_start: 0.7962 (pt0) cc_final: 0.7672 (mp0) REVERT: G 43 LYS cc_start: 0.7930 (ttmt) cc_final: 0.7499 (tttm) REVERT: G 45 LYS cc_start: 0.8250 (OUTLIER) cc_final: 0.7774 (tppt) REVERT: G 46 GLU cc_start: 0.7675 (pt0) cc_final: 0.7442 (mp0) REVERT: H 43 LYS cc_start: 0.8020 (ttmt) cc_final: 0.7542 (tttm) REVERT: I 43 LYS cc_start: 0.8247 (ttmt) cc_final: 0.7767 (tttm) REVERT: I 83 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7688 (mt-10) REVERT: J 43 LYS cc_start: 0.8090 (ttmt) cc_final: 0.7621 (tttm) outliers start: 31 outliers final: 24 residues processed: 112 average time/residue: 0.1110 time to fit residues: 14.3406 Evaluate side-chains 123 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 95 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 46 GLU Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 45 LYS Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 12 optimal weight: 0.3980 chunk 3 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 38 optimal weight: 9.9990 chunk 22 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 41 optimal weight: 9.9990 chunk 5 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 79 GLN D 62 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.114158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.096398 restraints weight = 5596.323| |-----------------------------------------------------------------------------| r_work (start): 0.3588 rms_B_bonded: 2.86 r_work: 0.3452 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.4651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4330 Z= 0.181 Angle : 0.538 5.957 5860 Z= 0.301 Chirality : 0.050 0.125 780 Planarity : 0.002 0.012 720 Dihedral : 5.639 15.743 620 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 6.44 % Allowed : 16.67 % Favored : 76.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.73 (0.32), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.31 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.009 0.002 PHE C 94 HIS 0.003 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00412 ( 4330) covalent geometry : angle 0.53801 ( 5860) hydrogen bonds : bond 0.01557 ( 70) hydrogen bonds : angle 4.39942 ( 210) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 90 time to evaluate : 0.137 Fit side-chains REVERT: A 43 LYS cc_start: 0.8217 (ttmt) cc_final: 0.7932 (tttm) REVERT: B 43 LYS cc_start: 0.8109 (ttmt) cc_final: 0.7746 (tptp) REVERT: B 45 LYS cc_start: 0.8473 (tttt) cc_final: 0.8157 (tttt) REVERT: C 43 LYS cc_start: 0.7720 (ttmt) cc_final: 0.7355 (tttm) REVERT: D 43 LYS cc_start: 0.7791 (ttmt) cc_final: 0.7345 (tttm) REVERT: D 45 LYS cc_start: 0.8372 (tttt) cc_final: 0.8003 (tttt) REVERT: D 46 GLU cc_start: 0.8061 (pt0) cc_final: 0.7673 (mp0) REVERT: E 43 LYS cc_start: 0.7780 (ttmt) cc_final: 0.7356 (tttp) REVERT: E 45 LYS cc_start: 0.8270 (tttt) cc_final: 0.7806 (tttt) REVERT: E 46 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7691 (mp0) REVERT: F 43 LYS cc_start: 0.7724 (ttmt) cc_final: 0.7365 (tttm) REVERT: F 46 GLU cc_start: 0.7806 (pt0) cc_final: 0.7187 (mp0) REVERT: G 43 LYS cc_start: 0.7803 (ttmt) cc_final: 0.7415 (tttm) REVERT: G 45 LYS cc_start: 0.8179 (OUTLIER) cc_final: 0.7729 (tppt) REVERT: H 43 LYS cc_start: 0.7948 (ttmt) cc_final: 0.7505 (tttm) REVERT: I 43 LYS cc_start: 0.8155 (ttmt) cc_final: 0.7677 (tttm) REVERT: I 83 GLU cc_start: 0.8225 (mt-10) cc_final: 0.7865 (mt-10) REVERT: J 43 LYS cc_start: 0.8009 (ttmt) cc_final: 0.7558 (tttm) outliers start: 29 outliers final: 22 residues processed: 108 average time/residue: 0.1140 time to fit residues: 14.2127 Evaluate side-chains 114 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 90 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 45 LYS Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 59 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 12 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 30 optimal weight: 9.9990 chunk 58 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 9.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 50 HIS D 62 GLN ** I 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.112120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.094305 restraints weight = 5583.496| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 2.90 r_work: 0.3426 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 4330 Z= 0.243 Angle : 0.598 7.121 5860 Z= 0.335 Chirality : 0.051 0.134 780 Planarity : 0.002 0.012 720 Dihedral : 5.854 16.706 620 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 5.56 % Allowed : 16.89 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.32), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.32 (0.24), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.002 TYR C 39 PHE 0.011 0.003 PHE C 94 HIS 0.003 0.002 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00557 ( 4330) covalent geometry : angle 0.59840 ( 5860) hydrogen bonds : bond 0.01904 ( 70) hydrogen bonds : angle 4.48872 ( 210) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 92 time to evaluate : 0.148 Fit side-chains REVERT: A 43 LYS cc_start: 0.8168 (ttmt) cc_final: 0.7796 (tttp) REVERT: B 43 LYS cc_start: 0.8113 (ttmt) cc_final: 0.7686 (tptp) REVERT: C 43 LYS cc_start: 0.7625 (ttmt) cc_final: 0.7252 (tttm) REVERT: D 43 LYS cc_start: 0.7716 (ttmt) cc_final: 0.7253 (tttp) REVERT: D 45 LYS cc_start: 0.8282 (tttt) cc_final: 0.7903 (tttt) REVERT: E 43 LYS cc_start: 0.7689 (ttmt) cc_final: 0.7228 (tttm) REVERT: E 45 LYS cc_start: 0.8085 (tttt) cc_final: 0.7626 (tttt) REVERT: E 46 GLU cc_start: 0.8276 (OUTLIER) cc_final: 0.7667 (mp0) REVERT: F 43 LYS cc_start: 0.7639 (ttmt) cc_final: 0.7247 (tttm) REVERT: F 46 GLU cc_start: 0.7883 (pt0) cc_final: 0.7578 (mp0) REVERT: G 43 LYS cc_start: 0.7802 (ttmt) cc_final: 0.7372 (tttp) REVERT: H 43 LYS cc_start: 0.7825 (ttmt) cc_final: 0.7359 (tttm) REVERT: I 43 LYS cc_start: 0.8108 (ttmt) cc_final: 0.7623 (tttm) REVERT: I 83 GLU cc_start: 0.8250 (mt-10) cc_final: 0.7866 (mt-10) REVERT: J 43 LYS cc_start: 0.7951 (ttmt) cc_final: 0.7477 (tttm) outliers start: 25 outliers final: 23 residues processed: 106 average time/residue: 0.1207 time to fit residues: 14.8499 Evaluate side-chains 117 residues out of total 450 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 93 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 75 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 75 THR Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain C residue 95 VAL Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain D residue 75 THR Chi-restraints excluded: chain D residue 81 THR Chi-restraints excluded: chain D residue 95 VAL Chi-restraints excluded: chain E residue 46 GLU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 75 THR Chi-restraints excluded: chain E residue 95 VAL Chi-restraints excluded: chain F residue 75 THR Chi-restraints excluded: chain F residue 95 VAL Chi-restraints excluded: chain G residue 75 THR Chi-restraints excluded: chain G residue 95 VAL Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain I residue 75 THR Chi-restraints excluded: chain J residue 75 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 38 optimal weight: 3.9990 chunk 43 optimal weight: 10.0000 chunk 56 optimal weight: 0.7980 chunk 28 optimal weight: 9.9990 chunk 8 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 25 optimal weight: 9.9990 chunk 26 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 62 GLN I 79 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.117309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.100157 restraints weight = 5233.220| |-----------------------------------------------------------------------------| r_work (start): 0.3668 rms_B_bonded: 2.79 r_work: 0.3541 rms_B_bonded: 2.98 restraints_weight: 0.5000 r_work: 0.3405 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 4330 Z= 0.135 Angle : 0.515 7.063 5860 Z= 0.284 Chirality : 0.050 0.130 780 Planarity : 0.001 0.006 720 Dihedral : 5.410 18.027 620 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 5.33 % Allowed : 17.33 % Favored : 77.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.32), residues: 600 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.23 (0.25), residues: 600 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.003 0.001 TYR C 39 PHE 0.009 0.002 PHE H 94 HIS 0.002 0.001 HIS G 50 Details of bonding type rmsd covalent geometry : bond 0.00307 ( 4330) covalent geometry : angle 0.51547 ( 5860) hydrogen bonds : bond 0.01244 ( 70) hydrogen bonds : angle 4.28505 ( 210) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1116.86 seconds wall clock time: 19 minutes 53.89 seconds (1193.89 seconds total)