Starting phenix.real_space_refine on Fri Oct 10 12:49:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sel_40421/10_2025/8sel_40421_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sel_40421/10_2025/8sel_40421.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sel_40421/10_2025/8sel_40421.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sel_40421/10_2025/8sel_40421.map" model { file = "/net/cci-nas-00/data/ceres_data/8sel_40421/10_2025/8sel_40421_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sel_40421/10_2025/8sel_40421_neut.cif" } resolution = 3.8 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= 0.010 sd= 0.297 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 S 20 5.16 5 C 3510 2.51 5 N 940 2.21 5 O 1030 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 30 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5842/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 5500 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 244 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 244 Classifications: {'peptide': 33} Modifications used: {'COO': 1} Link IDs: {'TRANS': 32} Chain: "B" Number of atoms: 306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 306 Classifications: {'peptide': 40} Modifications used: {'COO': 1} Link IDs: {'TRANS': 39} Restraints were copied for chains: C, E, G, I, K, M, O, Q, S, D, F, H, J, L, N, P, R, T Time building chain proxies: 0.89, per 1000 atoms: 0.16 Number of scatterers: 5500 At special positions: 0 Unit cell: (152.83, 60.078, 41.106, 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) S 20 16.00 O 1030 8.00 N 940 7.00 C 3510 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: 0.46 Conformation dependent library (CDL) restraints added in 223.6 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 16 sheets defined 0.0% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.365A pdb=" N TYR A 10 " --> pdb=" O GLU E 11 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS E 13 " --> pdb=" O TYR A 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL A 12 " --> pdb=" O HIS E 13 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR E 10 " --> pdb=" O GLU I 11 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS I 13 " --> pdb=" O TYR E 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL E 12 " --> pdb=" O HIS I 13 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR I 10 " --> pdb=" O GLU M 11 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N HIS M 13 " --> pdb=" O TYR I 10 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL I 12 " --> pdb=" O HIS M 13 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N TYR M 10 " --> pdb=" O GLU Q 11 " (cutoff:3.500A) removed outlier: 7.798A pdb=" N HIS Q 13 " --> pdb=" O TYR M 10 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N VAL M 12 " --> pdb=" O HIS Q 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 16 through 21 Processing sheet with id=AA3, first strand: chain 'A' and resid 24 through 26 removed outlier: 7.972A pdb=" N VAL A 24 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N VAL E 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL I 24 " --> pdb=" O GLY M 25 " (cutoff:3.500A) removed outlier: 7.972A pdb=" N VAL M 24 " --> pdb=" O GLY Q 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.930A pdb=" N ILE E 31 " --> pdb=" O ALA A 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE A 32 " --> pdb=" O ILE E 31 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLY E 33 " --> pdb=" O ILE A 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE I 31 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE E 32 " --> pdb=" O ILE I 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY I 33 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE M 31 " --> pdb=" O ALA I 30 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ILE I 32 " --> pdb=" O ILE M 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY M 33 " --> pdb=" O ILE I 32 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ILE Q 31 " --> pdb=" O ALA M 30 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N ILE M 32 " --> pdb=" O ILE Q 31 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N GLY Q 33 " --> pdb=" O ILE M 32 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 3 through 6 Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 12 Processing sheet with id=AA7, first strand: chain 'B' and resid 15 through 21 Processing sheet with id=AA8, first strand: chain 'B' and resid 29 through 36 removed outlier: 6.896A pdb=" N ALA B 30 " --> pdb=" O GLY F 29 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE F 31 " --> pdb=" O ALA B 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE B 32 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY F 33 " --> pdb=" O ILE B 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA F 30 " --> pdb=" O GLY J 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE J 31 " --> pdb=" O ALA F 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE F 32 " --> pdb=" O ILE J 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY J 33 " --> pdb=" O ILE F 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA J 30 " --> pdb=" O GLY N 29 " (cutoff:3.500A) removed outlier: 6.822A pdb=" N ILE N 31 " --> pdb=" O ALA J 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE J 32 " --> pdb=" O ILE N 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY N 33 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA N 30 " --> pdb=" O GLY R 29 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N ILE R 31 " --> pdb=" O ALA N 30 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE N 32 " --> pdb=" O ILE R 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY R 33 " --> pdb=" O ILE N 32 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 9 through 13 removed outlier: 6.353A pdb=" N TYR C 10 " --> pdb=" O GLU G 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS G 13 " --> pdb=" O TYR C 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL C 12 " --> pdb=" O HIS G 13 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR G 10 " --> pdb=" O GLU K 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS K 13 " --> pdb=" O TYR G 10 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N VAL G 12 " --> pdb=" O HIS K 13 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N TYR K 10 " --> pdb=" O GLU O 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS O 13 " --> pdb=" O TYR K 10 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL K 12 " --> pdb=" O HIS O 13 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N TYR O 10 " --> pdb=" O GLU S 11 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N HIS S 13 " --> pdb=" O TYR O 10 " (cutoff:3.500A) removed outlier: 6.619A pdb=" N VAL O 12 " --> pdb=" O HIS S 13 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 16 through 21 Processing sheet with id=AB2, first strand: chain 'C' and resid 24 through 26 removed outlier: 7.962A pdb=" N VAL C 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.963A pdb=" N VAL G 24 " --> pdb=" O GLY K 25 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL K 24 " --> pdb=" O GLY O 25 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N VAL O 24 " --> pdb=" O GLY S 25 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 30 through 36 removed outlier: 6.914A pdb=" N ILE G 31 " --> pdb=" O ALA C 30 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE C 32 " --> pdb=" O ILE G 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY G 33 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE K 31 " --> pdb=" O ALA G 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE G 32 " --> pdb=" O ILE K 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY K 33 " --> pdb=" O ILE G 32 " (cutoff:3.500A) removed outlier: 6.914A pdb=" N ILE O 31 " --> pdb=" O ALA K 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE K 32 " --> pdb=" O ILE O 31 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N GLY O 33 " --> pdb=" O ILE K 32 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N ILE S 31 " --> pdb=" O ALA O 30 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ILE O 32 " --> pdb=" O ILE S 31 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N GLY S 33 " --> pdb=" O ILE O 32 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 3 through 6 Processing sheet with id=AB5, first strand: chain 'D' and resid 10 through 12 Processing sheet with id=AB6, first strand: chain 'D' and resid 15 through 21 Processing sheet with id=AB7, first strand: chain 'D' and resid 29 through 36 removed outlier: 6.884A pdb=" N ALA D 30 " --> pdb=" O GLY H 29 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE H 31 " --> pdb=" O ALA D 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE D 32 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N GLY H 33 " --> pdb=" O ILE D 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA H 30 " --> pdb=" O GLY L 29 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE L 31 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE H 32 " --> pdb=" O ILE L 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY L 33 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ALA L 30 " --> pdb=" O GLY P 29 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ILE P 31 " --> pdb=" O ALA L 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE L 32 " --> pdb=" O ILE P 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY P 33 " --> pdb=" O ILE L 32 " (cutoff:3.500A) removed outlier: 6.883A pdb=" N ALA P 30 " --> pdb=" O GLY T 29 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE T 31 " --> pdb=" O ALA P 30 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE P 32 " --> pdb=" O ILE T 31 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N GLY T 33 " --> pdb=" O ILE P 32 " (cutoff:3.500A) 176 hydrogen bonds defined for protein. 528 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: 0.71 Time building geometry restraints manager: 0.64 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.31: 1228 1.31 - 1.43: 1272 1.43 - 1.54: 2932 1.54 - 1.66: 128 1.66 - 1.78: 40 Bond restraints: 5600 Sorted by residual: bond pdb=" CG GLN N 15 " pdb=" CD GLN N 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.07e+01 bond pdb=" CG GLN R 15 " pdb=" CD GLN R 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.07e+01 bond pdb=" CG GLN F 15 " pdb=" CD GLN F 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.06e+01 bond pdb=" CG GLN B 15 " pdb=" CD GLN B 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.04e+01 bond pdb=" CG GLN D 15 " pdb=" CD GLN D 15 " ideal model delta sigma weight residual 1.516 1.357 0.159 2.50e-02 1.60e+03 4.04e+01 ... (remaining 5595 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.59: 6237 2.59 - 5.19: 975 5.19 - 7.78: 218 7.78 - 10.37: 70 10.37 - 12.96: 20 Bond angle restraints: 7520 Sorted by residual: angle pdb=" N HIS E 13 " pdb=" CA HIS E 13 " pdb=" C HIS E 13 " ideal model delta sigma weight residual 108.79 120.11 -11.32 1.53e+00 4.27e-01 5.47e+01 angle pdb=" N HIS O 13 " pdb=" CA HIS O 13 " pdb=" C HIS O 13 " ideal model delta sigma weight residual 108.79 120.10 -11.31 1.53e+00 4.27e-01 5.47e+01 angle pdb=" N HIS S 13 " pdb=" CA HIS S 13 " pdb=" C HIS S 13 " ideal model delta sigma weight residual 108.79 120.09 -11.30 1.53e+00 4.27e-01 5.46e+01 angle pdb=" N HIS M 13 " pdb=" CA HIS M 13 " pdb=" C HIS M 13 " ideal model delta sigma weight residual 108.79 120.09 -11.30 1.53e+00 4.27e-01 5.45e+01 angle pdb=" N HIS Q 13 " pdb=" CA HIS Q 13 " pdb=" C HIS Q 13 " ideal model delta sigma weight residual 108.79 120.09 -11.30 1.53e+00 4.27e-01 5.45e+01 ... (remaining 7515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.47: 2970 17.47 - 34.93: 110 34.93 - 52.40: 30 52.40 - 69.87: 0 69.87 - 87.33: 20 Dihedral angle restraints: 3130 sinusoidal: 1180 harmonic: 1950 Sorted by residual: dihedral pdb=" N HIS F 13 " pdb=" C HIS F 13 " pdb=" CA HIS F 13 " pdb=" CB HIS F 13 " ideal model delta harmonic sigma weight residual 122.80 130.46 -7.66 0 2.50e+00 1.60e-01 9.38e+00 dihedral pdb=" N HIS H 13 " pdb=" C HIS H 13 " pdb=" CA HIS H 13 " pdb=" CB HIS H 13 " ideal model delta harmonic sigma weight residual 122.80 130.41 -7.61 0 2.50e+00 1.60e-01 9.26e+00 dihedral pdb=" N HIS B 13 " pdb=" C HIS B 13 " pdb=" CA HIS B 13 " pdb=" CB HIS B 13 " ideal model delta harmonic sigma weight residual 122.80 130.41 -7.61 0 2.50e+00 1.60e-01 9.26e+00 ... (remaining 3127 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.102: 518 0.102 - 0.203: 232 0.203 - 0.305: 26 0.305 - 0.406: 24 0.406 - 0.508: 10 Chirality restraints: 810 Sorted by residual: chirality pdb=" CA HIS F 13 " pdb=" N HIS F 13 " pdb=" C HIS F 13 " pdb=" CB HIS F 13 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.45e+00 chirality pdb=" CA HIS B 13 " pdb=" N HIS B 13 " pdb=" C HIS B 13 " pdb=" CB HIS B 13 " both_signs ideal model delta sigma weight residual False 2.51 2.00 0.51 2.00e-01 2.50e+01 6.40e+00 chirality pdb=" CA HIS J 13 " pdb=" N HIS J 13 " pdb=" C HIS J 13 " pdb=" CB HIS J 13 " both_signs ideal model delta sigma weight residual False 2.51 2.01 0.50 2.00e-01 2.50e+01 6.36e+00 ... (remaining 807 not shown) Planarity restraints: 990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL O 40 " -0.025 2.00e-02 2.50e+03 4.99e-02 2.49e+01 pdb=" C VAL O 40 " 0.086 2.00e-02 2.50e+03 pdb=" O VAL O 40 " -0.031 2.00e-02 2.50e+03 pdb=" OXT VAL O 40 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL K 40 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C VAL K 40 " 0.086 2.00e-02 2.50e+03 pdb=" O VAL K 40 " -0.031 2.00e-02 2.50e+03 pdb=" OXT VAL K 40 " -0.031 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL M 40 " -0.025 2.00e-02 2.50e+03 4.98e-02 2.48e+01 pdb=" C VAL M 40 " 0.086 2.00e-02 2.50e+03 pdb=" O VAL M 40 " -0.031 2.00e-02 2.50e+03 pdb=" OXT VAL M 40 " -0.031 2.00e-02 2.50e+03 ... (remaining 987 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.96: 3029 2.96 - 3.44: 5294 3.44 - 3.93: 8855 3.93 - 4.41: 11486 4.41 - 4.90: 20185 Nonbonded interactions: 48849 Sorted by model distance: nonbonded pdb=" O HIS N 13 " pdb=" N GLN N 15 " model vdw 2.474 3.120 nonbonded pdb=" O HIS D 13 " pdb=" N GLN D 15 " model vdw 2.475 3.120 nonbonded pdb=" O HIS T 13 " pdb=" N GLN T 15 " model vdw 2.475 3.120 nonbonded pdb=" O HIS L 13 " pdb=" N GLN L 15 " model vdw 2.475 3.120 nonbonded pdb=" O HIS B 13 " pdb=" N GLN B 15 " model vdw 2.475 3.120 ... (remaining 48844 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = chain 'I' selection = chain 'K' selection = chain 'M' selection = chain 'O' selection = chain 'Q' selection = chain 'S' } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' selection = chain 'T' } 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 group one per residue 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: 2.030 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: 0.100 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 6.590 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.010 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 10.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7121 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 : 0.026 0.159 5600 Z= 1.358 Angle : 2.245 12.963 7520 Z= 1.380 Chirality : 0.132 0.508 810 Planarity : 0.010 0.050 990 Dihedral : 12.887 87.332 1910 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 1.85 Ramachandran Plot: Outliers : 2.90 % Allowed : 4.35 % Favored : 92.75 % Rotamer: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % 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 aren not related in a simple way. whole: -1.59 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.21), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 5 TYR 0.029 0.010 TYR R 10 PHE 0.017 0.006 PHE R 19 HIS 0.003 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.02573 ( 5600) covalent geometry : angle 2.24532 ( 7520) hydrogen bonds : bond 0.07391 ( 176) hydrogen bonds : angle 8.42342 ( 528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 222 time to evaluate : 0.131 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 24 VAL cc_start: 0.8272 (t) cc_final: 0.8000 (m) REVERT: D 24 VAL cc_start: 0.8182 (t) cc_final: 0.7958 (m) REVERT: M 34 LEU cc_start: 0.8312 (tp) cc_final: 0.8065 (tp) REVERT: N 16 LYS cc_start: 0.7781 (tttt) cc_final: 0.7460 (mmtm) REVERT: Q 26 SER cc_start: 0.8867 (t) cc_final: 0.8561 (m) REVERT: S 26 SER cc_start: 0.8852 (t) cc_final: 0.8415 (m) REVERT: S 27 ASN cc_start: 0.7148 (t0) cc_final: 0.6548 (p0) outliers start: 0 outliers final: 0 residues processed: 222 average time/residue: 0.0640 time to fit residues: 19.1125 Evaluate side-chains 158 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 0.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.7980 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 HIS D 14 HIS F 14 HIS H 14 HIS J 14 HIS L 14 HIS N 14 HIS P 14 HIS Q 15 GLN R 14 HIS ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 15 GLN T 14 HIS ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5344 r_free = 0.5344 target = 0.269722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.5336 r_free = 0.5336 target = 0.217164 restraints weight = 7055.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.5404 r_free = 0.5404 target = 0.223357 restraints weight = 3207.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5435 r_free = 0.5435 target = 0.226998 restraints weight = 1752.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5465 r_free = 0.5465 target = 0.229498 restraints weight = 1117.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.5480 r_free = 0.5480 target = 0.231066 restraints weight = 790.686| |-----------------------------------------------------------------------------| r_work (final): 0.5286 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6614 moved from start: 0.4484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5600 Z= 0.194 Angle : 0.897 7.837 7520 Z= 0.488 Chirality : 0.063 0.206 810 Planarity : 0.004 0.018 990 Dihedral : 12.988 86.715 760 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.67 Ramachandran Plot: Outliers : 1.16 % Allowed : 10.29 % Favored : 88.55 % Rotamer: Outliers : 4.46 % Allowed : 13.93 % Favored : 81.61 % 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 aren not related in a simple way. whole: -2.21 (0.27), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.68 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG L 5 TYR 0.013 0.002 TYR J 10 PHE 0.017 0.003 PHE O 19 HIS 0.006 0.001 HIS R 14 Details of bonding type rmsd covalent geometry : bond 0.00445 ( 5600) covalent geometry : angle 0.89684 ( 7520) hydrogen bonds : bond 0.03419 ( 176) hydrogen bonds : angle 6.28929 ( 528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 189 time to evaluate : 0.214 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: A 13 HIS cc_start: 0.7640 (p90) cc_final: 0.7278 (p90) REVERT: B 10 TYR cc_start: 0.8280 (OUTLIER) cc_final: 0.6026 (p90) REVERT: C 13 HIS cc_start: 0.7667 (p90) cc_final: 0.7272 (p90) REVERT: D 10 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.5862 (p90) REVERT: E 34 LEU cc_start: 0.8017 (tp) cc_final: 0.7635 (tp) REVERT: F 10 TYR cc_start: 0.7973 (OUTLIER) cc_final: 0.5611 (p90) REVERT: F 16 LYS cc_start: 0.6660 (mmtm) cc_final: 0.6341 (mmtm) REVERT: H 10 TYR cc_start: 0.7955 (OUTLIER) cc_final: 0.5621 (p90) REVERT: H 16 LYS cc_start: 0.6623 (mmtm) cc_final: 0.6303 (mmtm) REVERT: I 24 VAL cc_start: 0.8934 (t) cc_final: 0.8717 (t) REVERT: J 10 TYR cc_start: 0.8254 (OUTLIER) cc_final: 0.6308 (p90) REVERT: L 10 TYR cc_start: 0.8223 (OUTLIER) cc_final: 0.6200 (p90) REVERT: M 34 LEU cc_start: 0.7816 (tp) cc_final: 0.7551 (tp) REVERT: N 16 LYS cc_start: 0.7017 (tttt) cc_final: 0.6429 (mmtm) REVERT: Q 26 SER cc_start: 0.8860 (t) cc_final: 0.8542 (m) REVERT: R 5 ARG cc_start: 0.8075 (mtp180) cc_final: 0.6715 (tpp-160) REVERT: R 7 ASP cc_start: 0.7796 (t0) cc_final: 0.7554 (t0) REVERT: S 26 SER cc_start: 0.8730 (t) cc_final: 0.8315 (m) REVERT: T 5 ARG cc_start: 0.8007 (mtp180) cc_final: 0.6685 (tpp-160) REVERT: T 7 ASP cc_start: 0.7775 (t0) cc_final: 0.7515 (t0) REVERT: T 27 ASN cc_start: 0.7295 (t0) cc_final: 0.5317 (p0) outliers start: 25 outliers final: 6 residues processed: 190 average time/residue: 0.0775 time to fit residues: 18.9736 Evaluate side-chains 171 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 159 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain P residue 36 VAL Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 17 LEU Chi-restraints excluded: chain T residue 10 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 37 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 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 = 0.5147 r_free = 0.5147 target = 0.202836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4947 r_free = 0.4947 target = 0.180007 restraints weight = 6674.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4997 r_free = 0.4997 target = 0.185167 restraints weight = 3188.768| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.5029 r_free = 0.5029 target = 0.188649 restraints weight = 1883.428| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.5051 r_free = 0.5051 target = 0.191241 restraints weight = 1279.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5068 r_free = 0.5068 target = 0.193030 restraints weight = 940.231| |-----------------------------------------------------------------------------| r_work (final): 0.5099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6755 moved from start: 0.5346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5600 Z= 0.175 Angle : 0.823 7.753 7520 Z= 0.452 Chirality : 0.062 0.192 810 Planarity : 0.003 0.018 990 Dihedral : 11.782 89.409 760 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 17.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.17 % Favored : 87.83 % Rotamer: Outliers : 5.36 % Allowed : 16.43 % Favored : 78.21 % 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 aren not related in a simple way. whole: -2.56 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.94 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 5 TYR 0.011 0.002 TYR J 10 PHE 0.024 0.003 PHE S 19 HIS 0.005 0.001 HIS J 13 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 5600) covalent geometry : angle 0.82282 ( 7520) hydrogen bonds : bond 0.03378 ( 176) hydrogen bonds : angle 5.88211 ( 528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 183 time to evaluate : 0.196 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: A 13 HIS cc_start: 0.7591 (p90) cc_final: 0.7063 (p90) REVERT: B 10 TYR cc_start: 0.8387 (OUTLIER) cc_final: 0.6203 (p90) REVERT: C 13 HIS cc_start: 0.7609 (p90) cc_final: 0.7024 (p90) REVERT: D 10 TYR cc_start: 0.8424 (OUTLIER) cc_final: 0.6249 (p90) REVERT: E 34 LEU cc_start: 0.8198 (tp) cc_final: 0.7905 (tp) REVERT: F 10 TYR cc_start: 0.8092 (OUTLIER) cc_final: 0.5856 (p90) REVERT: G 28 LYS cc_start: 0.8184 (mmtp) cc_final: 0.7587 (mmmt) REVERT: H 10 TYR cc_start: 0.7762 (OUTLIER) cc_final: 0.5890 (p90) REVERT: H 36 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8254 (p) REVERT: I 35 MET cc_start: 0.7347 (mmm) cc_final: 0.6996 (mmm) REVERT: J 10 TYR cc_start: 0.8136 (OUTLIER) cc_final: 0.6779 (p90) REVERT: J 27 ASN cc_start: 0.8376 (t0) cc_final: 0.8144 (t0) REVERT: K 22 GLU cc_start: 0.7883 (mm-30) cc_final: 0.7574 (mm-30) REVERT: K 35 MET cc_start: 0.7406 (mmm) cc_final: 0.7022 (mmm) REVERT: L 27 ASN cc_start: 0.8399 (t0) cc_final: 0.8141 (t0) REVERT: M 28 LYS cc_start: 0.8527 (mmmt) cc_final: 0.8243 (mmmt) REVERT: M 34 LEU cc_start: 0.7902 (tp) cc_final: 0.7611 (tp) REVERT: N 16 LYS cc_start: 0.7062 (tttt) cc_final: 0.6457 (mmtm) REVERT: O 28 LYS cc_start: 0.8557 (mmmt) cc_final: 0.8293 (mmmt) REVERT: Q 26 SER cc_start: 0.8788 (t) cc_final: 0.8464 (m) REVERT: Q 35 MET cc_start: 0.7705 (mmm) cc_final: 0.7424 (mmm) REVERT: R 5 ARG cc_start: 0.8132 (mtp180) cc_final: 0.6876 (tpp-160) REVERT: R 7 ASP cc_start: 0.7832 (t0) cc_final: 0.7590 (t0) REVERT: R 34 LEU cc_start: 0.8924 (tp) cc_final: 0.8607 (tp) REVERT: S 23 ASP cc_start: 0.7924 (p0) cc_final: 0.6040 (m-30) REVERT: S 26 SER cc_start: 0.8888 (t) cc_final: 0.8460 (m) REVERT: S 35 MET cc_start: 0.7470 (mmm) cc_final: 0.7021 (mmm) REVERT: T 5 ARG cc_start: 0.8107 (mtp180) cc_final: 0.6865 (tpp-160) outliers start: 30 outliers final: 13 residues processed: 198 average time/residue: 0.0827 time to fit residues: 20.9697 Evaluate side-chains 190 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 0.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain T residue 10 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.9980 chunk 49 optimal weight: 7.9990 chunk 66 optimal weight: 0.0370 chunk 44 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 26 optimal weight: 5.9990 chunk 55 optimal weight: 0.4980 chunk 11 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.8860 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 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 = 0.5128 r_free = 0.5128 target = 0.196531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4920 r_free = 0.4920 target = 0.174776 restraints weight = 6801.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4969 r_free = 0.4969 target = 0.179593 restraints weight = 3269.946| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5005 r_free = 0.5005 target = 0.182962 restraints weight = 1938.417| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5024 r_free = 0.5024 target = 0.185185 restraints weight = 1310.828| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5036 r_free = 0.5036 target = 0.186855 restraints weight = 981.716| |-----------------------------------------------------------------------------| r_work (final): 0.5064 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6833 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5600 Z= 0.180 Angle : 0.800 7.739 7520 Z= 0.437 Chirality : 0.062 0.188 810 Planarity : 0.003 0.016 990 Dihedral : 11.661 89.670 760 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.33 % Favored : 86.67 % Rotamer: Outliers : 7.32 % Allowed : 18.04 % Favored : 74.64 % 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 aren not related in a simple way. whole: -2.74 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.08 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 5 TYR 0.010 0.001 TYR J 10 PHE 0.021 0.003 PHE K 19 HIS 0.004 0.001 HIS P 13 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 5600) covalent geometry : angle 0.79992 ( 7520) hydrogen bonds : bond 0.03014 ( 176) hydrogen bonds : angle 5.52878 ( 528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 189 time to evaluate : 0.129 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: A 13 HIS cc_start: 0.7637 (p90) cc_final: 0.7140 (p-80) REVERT: C 11 GLU cc_start: 0.7613 (mp0) cc_final: 0.7351 (mp0) REVERT: C 13 HIS cc_start: 0.7628 (p90) cc_final: 0.6899 (p-80) REVERT: C 24 VAL cc_start: 0.9029 (OUTLIER) cc_final: 0.8815 (m) REVERT: D 10 TYR cc_start: 0.8394 (OUTLIER) cc_final: 0.6201 (p90) REVERT: E 34 LEU cc_start: 0.8173 (tp) cc_final: 0.7959 (tp) REVERT: F 10 TYR cc_start: 0.7980 (OUTLIER) cc_final: 0.5875 (p90) REVERT: G 13 HIS cc_start: 0.7125 (OUTLIER) cc_final: 0.6343 (p90) REVERT: I 19 PHE cc_start: 0.6082 (OUTLIER) cc_final: 0.5405 (p90) REVERT: J 10 TYR cc_start: 0.8220 (OUTLIER) cc_final: 0.6747 (p90) REVERT: J 27 ASN cc_start: 0.8549 (t0) cc_final: 0.8208 (t0) REVERT: K 19 PHE cc_start: 0.6042 (OUTLIER) cc_final: 0.5453 (p90) REVERT: L 10 TYR cc_start: 0.8124 (OUTLIER) cc_final: 0.6948 (p90) REVERT: L 27 ASN cc_start: 0.8638 (t0) cc_final: 0.8084 (t0) REVERT: L 34 LEU cc_start: 0.9440 (tp) cc_final: 0.9217 (tt) REVERT: M 13 HIS cc_start: 0.6842 (OUTLIER) cc_final: 0.6253 (p90) REVERT: M 34 LEU cc_start: 0.7934 (tp) cc_final: 0.7641 (tp) REVERT: N 16 LYS cc_start: 0.7194 (tttt) cc_final: 0.6498 (mmtm) REVERT: P 10 TYR cc_start: 0.7993 (OUTLIER) cc_final: 0.6939 (p90) REVERT: Q 26 SER cc_start: 0.8802 (t) cc_final: 0.8490 (m) REVERT: Q 35 MET cc_start: 0.7649 (mmm) cc_final: 0.7297 (mmm) REVERT: R 35 MET cc_start: 0.6590 (OUTLIER) cc_final: 0.6182 (ttm) REVERT: S 23 ASP cc_start: 0.7640 (p0) cc_final: 0.5676 (m-30) REVERT: S 26 SER cc_start: 0.8974 (t) cc_final: 0.8606 (m) REVERT: S 35 MET cc_start: 0.7391 (mmm) cc_final: 0.6996 (mmm) outliers start: 41 outliers final: 22 residues processed: 211 average time/residue: 0.0697 time to fit residues: 19.4013 Evaluate side-chains 205 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 172 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 6 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 chunk 58 optimal weight: 4.9990 chunk 52 optimal weight: 10.0000 chunk 30 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 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 = 0.5104 r_free = 0.5104 target = 0.191092 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4888 r_free = 0.4888 target = 0.169863 restraints weight = 7087.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.174636 restraints weight = 3310.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.177822 restraints weight = 1929.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4999 r_free = 0.4999 target = 0.179973 restraints weight = 1303.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5012 r_free = 0.5012 target = 0.181349 restraints weight = 975.522| |-----------------------------------------------------------------------------| r_work (final): 0.5035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6924 moved from start: 0.6273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5600 Z= 0.207 Angle : 0.828 7.663 7520 Z= 0.454 Chirality : 0.062 0.194 810 Planarity : 0.003 0.015 990 Dihedral : 11.950 89.931 760 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 22.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 8.93 % Allowed : 19.64 % Favored : 71.43 % 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 aren not related in a simple way. whole: -2.86 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.17 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 5 TYR 0.010 0.002 TYR J 10 PHE 0.021 0.003 PHE K 19 HIS 0.004 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00479 ( 5600) covalent geometry : angle 0.82789 ( 7520) hydrogen bonds : bond 0.02867 ( 176) hydrogen bonds : angle 5.40913 ( 528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 188 time to evaluate : 0.235 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: A 13 HIS cc_start: 0.7681 (p90) cc_final: 0.7104 (p-80) REVERT: B 10 TYR cc_start: 0.8513 (OUTLIER) cc_final: 0.6372 (p90) REVERT: B 35 MET cc_start: 0.8332 (tpp) cc_final: 0.8044 (tpp) REVERT: C 11 GLU cc_start: 0.7640 (mp0) cc_final: 0.6635 (mp0) REVERT: D 35 MET cc_start: 0.8205 (tpp) cc_final: 0.7848 (tpp) REVERT: F 10 TYR cc_start: 0.8074 (OUTLIER) cc_final: 0.5771 (p90) REVERT: G 13 HIS cc_start: 0.7119 (OUTLIER) cc_final: 0.6291 (p90) REVERT: H 7 ASP cc_start: 0.7897 (OUTLIER) cc_final: 0.7411 (m-30) REVERT: H 10 TYR cc_start: 0.8117 (OUTLIER) cc_final: 0.6209 (p90) REVERT: H 16 LYS cc_start: 0.7041 (mmtm) cc_final: 0.6545 (mmtm) REVERT: H 34 LEU cc_start: 0.9629 (tt) cc_final: 0.9405 (tp) REVERT: I 19 PHE cc_start: 0.6526 (OUTLIER) cc_final: 0.5721 (p90) REVERT: I 35 MET cc_start: 0.7445 (mmm) cc_final: 0.7062 (mmm) REVERT: J 10 TYR cc_start: 0.8370 (OUTLIER) cc_final: 0.6852 (p90) REVERT: J 27 ASN cc_start: 0.8585 (t0) cc_final: 0.7974 (t0) REVERT: K 19 PHE cc_start: 0.6387 (OUTLIER) cc_final: 0.5679 (p90) REVERT: K 34 LEU cc_start: 0.7915 (tp) cc_final: 0.7687 (tp) REVERT: K 35 MET cc_start: 0.7535 (mmm) cc_final: 0.7102 (mmm) REVERT: L 10 TYR cc_start: 0.8259 (OUTLIER) cc_final: 0.7335 (p90) REVERT: L 27 ASN cc_start: 0.8585 (t0) cc_final: 0.8142 (t0) REVERT: M 13 HIS cc_start: 0.6888 (OUTLIER) cc_final: 0.6221 (p90) REVERT: M 34 LEU cc_start: 0.8054 (tp) cc_final: 0.7622 (tp) REVERT: N 16 LYS cc_start: 0.7135 (tttt) cc_final: 0.6478 (mmtm) REVERT: N 22 GLU cc_start: 0.7899 (tp30) cc_final: 0.7511 (tp30) REVERT: N 35 MET cc_start: 0.7773 (ttm) cc_final: 0.7350 (ttm) REVERT: P 10 TYR cc_start: 0.8224 (OUTLIER) cc_final: 0.7283 (p90) REVERT: P 22 GLU cc_start: 0.7927 (tp30) cc_final: 0.7565 (tp30) REVERT: Q 26 SER cc_start: 0.8835 (t) cc_final: 0.8544 (m) REVERT: Q 35 MET cc_start: 0.7504 (mmm) cc_final: 0.6982 (mmm) REVERT: R 1 ASP cc_start: 0.4548 (m-30) cc_final: 0.3573 (t70) REVERT: S 26 SER cc_start: 0.8998 (t) cc_final: 0.8576 (m) REVERT: S 35 MET cc_start: 0.7433 (mmm) cc_final: 0.6703 (mpp) REVERT: T 1 ASP cc_start: 0.4602 (m-30) cc_final: 0.3667 (t70) REVERT: T 14 HIS cc_start: 0.7409 (OUTLIER) cc_final: 0.7095 (t-90) REVERT: T 35 MET cc_start: 0.5725 (OUTLIER) cc_final: 0.5316 (ttm) outliers start: 50 outliers final: 26 residues processed: 212 average time/residue: 0.0628 time to fit residues: 18.0321 Evaluate side-chains 216 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 177 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 1 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 20 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 24 optimal weight: 9.9990 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 overall best weight: 1.4384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5041 r_free = 0.5041 target = 0.184672 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4838 r_free = 0.4838 target = 0.164865 restraints weight = 7169.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4886 r_free = 0.4886 target = 0.169413 restraints weight = 3248.413| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4922 r_free = 0.4922 target = 0.172474 restraints weight = 1859.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.174396 restraints weight = 1238.850| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4956 r_free = 0.4956 target = 0.175811 restraints weight = 927.399| |-----------------------------------------------------------------------------| r_work (final): 0.4983 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.6587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 5600 Z= 0.255 Angle : 0.890 8.488 7520 Z= 0.487 Chirality : 0.064 0.208 810 Planarity : 0.003 0.017 990 Dihedral : 12.141 89.945 760 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 10.00 % Allowed : 20.36 % Favored : 69.64 % 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 aren not related in a simple way. whole: -3.08 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.34 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 5 TYR 0.009 0.002 TYR O 10 PHE 0.021 0.003 PHE I 19 HIS 0.005 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00599 ( 5600) covalent geometry : angle 0.89036 ( 7520) hydrogen bonds : bond 0.03054 ( 176) hydrogen bonds : angle 5.22096 ( 528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 188 time to evaluate : 0.233 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 10 TYR cc_start: 0.8579 (OUTLIER) cc_final: 0.6421 (p90) REVERT: B 16 LYS cc_start: 0.7577 (mmtm) cc_final: 0.7270 (mmtm) REVERT: C 11 GLU cc_start: 0.7646 (mp0) cc_final: 0.6697 (mp0) REVERT: C 19 PHE cc_start: 0.6728 (OUTLIER) cc_final: 0.6421 (p90) REVERT: D 10 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.6448 (p90) REVERT: E 13 HIS cc_start: 0.6884 (OUTLIER) cc_final: 0.6116 (p90) REVERT: F 10 TYR cc_start: 0.8323 (OUTLIER) cc_final: 0.5833 (p90) REVERT: F 22 GLU cc_start: 0.8166 (tp30) cc_final: 0.7588 (tp30) REVERT: G 13 HIS cc_start: 0.7044 (OUTLIER) cc_final: 0.6243 (p90) REVERT: H 7 ASP cc_start: 0.7739 (OUTLIER) cc_final: 0.7503 (m-30) REVERT: H 10 TYR cc_start: 0.8145 (OUTLIER) cc_final: 0.6060 (p90) REVERT: H 22 GLU cc_start: 0.8109 (tp30) cc_final: 0.7545 (tp30) REVERT: I 19 PHE cc_start: 0.6734 (OUTLIER) cc_final: 0.6075 (p90) REVERT: I 35 MET cc_start: 0.7535 (mmm) cc_final: 0.7130 (mmm) REVERT: J 5 ARG cc_start: 0.8626 (mtp85) cc_final: 0.8060 (mtp85) REVERT: J 10 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.6752 (p90) REVERT: K 19 PHE cc_start: 0.6704 (OUTLIER) cc_final: 0.6189 (p90) REVERT: K 35 MET cc_start: 0.7586 (mmm) cc_final: 0.7131 (mmm) REVERT: L 10 TYR cc_start: 0.8367 (OUTLIER) cc_final: 0.7402 (p90) REVERT: L 27 ASN cc_start: 0.8635 (t0) cc_final: 0.8115 (t0) REVERT: M 13 HIS cc_start: 0.7008 (OUTLIER) cc_final: 0.6220 (p90) REVERT: M 34 LEU cc_start: 0.8163 (tp) cc_final: 0.7740 (tp) REVERT: N 10 TYR cc_start: 0.8182 (OUTLIER) cc_final: 0.7112 (p90) REVERT: N 16 LYS cc_start: 0.7068 (tttt) cc_final: 0.6488 (mmtm) REVERT: N 35 MET cc_start: 0.7686 (ttm) cc_final: 0.7122 (ttm) REVERT: O 31 ILE cc_start: 0.8232 (mp) cc_final: 0.8000 (tt) REVERT: P 10 TYR cc_start: 0.8195 (OUTLIER) cc_final: 0.7217 (p90) REVERT: P 22 GLU cc_start: 0.8033 (tp30) cc_final: 0.7564 (tp30) REVERT: Q 26 SER cc_start: 0.8872 (t) cc_final: 0.8571 (m) REVERT: Q 35 MET cc_start: 0.7482 (mmm) cc_final: 0.6913 (mmm) REVERT: S 26 SER cc_start: 0.9002 (t) cc_final: 0.8567 (m) REVERT: S 35 MET cc_start: 0.7391 (mmm) cc_final: 0.6666 (mpp) REVERT: T 14 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7119 (t-90) REVERT: T 16 LYS cc_start: 0.4206 (tppt) cc_final: 0.3712 (tppt) REVERT: T 35 MET cc_start: 0.5306 (OUTLIER) cc_final: 0.4750 (ttm) outliers start: 56 outliers final: 29 residues processed: 214 average time/residue: 0.0667 time to fit residues: 19.2177 Evaluate side-chains 227 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 181 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 7 ASP Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 7 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 26 SER Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain S residue 40 VAL Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 2 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 63 optimal weight: 5.9990 chunk 30 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 52 optimal weight: 7.9990 chunk 57 optimal weight: 0.0470 chunk 8 optimal weight: 1.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5050 r_free = 0.5050 target = 0.183499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.4849 r_free = 0.4849 target = 0.163970 restraints weight = 7159.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4899 r_free = 0.4899 target = 0.168440 restraints weight = 3183.474| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.171497 restraints weight = 1802.602| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.4946 r_free = 0.4946 target = 0.173390 restraints weight = 1190.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4963 r_free = 0.4963 target = 0.174751 restraints weight = 890.658| |-----------------------------------------------------------------------------| r_work (final): 0.4989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7021 moved from start: 0.6883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 5600 Z= 0.251 Angle : 0.899 8.515 7520 Z= 0.489 Chirality : 0.065 0.234 810 Planarity : 0.003 0.015 990 Dihedral : 12.148 89.526 760 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 26.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 10.18 % Allowed : 23.93 % Favored : 65.89 % 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 aren not related in a simple way. whole: -3.23 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG D 5 TYR 0.010 0.002 TYR J 10 PHE 0.027 0.003 PHE A 19 HIS 0.004 0.001 HIS P 13 Details of bonding type rmsd covalent geometry : bond 0.00594 ( 5600) covalent geometry : angle 0.89937 ( 7520) hydrogen bonds : bond 0.03178 ( 176) hydrogen bonds : angle 5.19998 ( 528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 184 time to evaluate : 0.248 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 10 TYR cc_start: 0.8607 (OUTLIER) cc_final: 0.6510 (p90) REVERT: B 16 LYS cc_start: 0.7544 (mmtm) cc_final: 0.7299 (mmtm) REVERT: C 11 GLU cc_start: 0.7534 (mp0) cc_final: 0.6584 (mp0) REVERT: C 19 PHE cc_start: 0.6756 (OUTLIER) cc_final: 0.6385 (p90) REVERT: D 10 TYR cc_start: 0.8564 (OUTLIER) cc_final: 0.6481 (p90) REVERT: D 16 LYS cc_start: 0.7612 (mmtm) cc_final: 0.7304 (mmtm) REVERT: D 35 MET cc_start: 0.8413 (tpp) cc_final: 0.7981 (tpp) REVERT: E 13 HIS cc_start: 0.6955 (OUTLIER) cc_final: 0.5873 (p90) REVERT: F 10 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.5870 (p90) REVERT: F 22 GLU cc_start: 0.8037 (tp30) cc_final: 0.7527 (tp30) REVERT: G 13 HIS cc_start: 0.6897 (OUTLIER) cc_final: 0.5823 (p90) REVERT: H 7 ASP cc_start: 0.7862 (t0) cc_final: 0.7628 (m-30) REVERT: H 10 TYR cc_start: 0.8243 (OUTLIER) cc_final: 0.6213 (p90) REVERT: H 22 GLU cc_start: 0.8018 (tp30) cc_final: 0.7530 (tp30) REVERT: H 34 LEU cc_start: 0.9619 (OUTLIER) cc_final: 0.9401 (tp) REVERT: I 13 HIS cc_start: 0.7215 (OUTLIER) cc_final: 0.6297 (p90) REVERT: I 19 PHE cc_start: 0.6774 (OUTLIER) cc_final: 0.6200 (p90) REVERT: I 35 MET cc_start: 0.7561 (mmm) cc_final: 0.7186 (mmm) REVERT: J 10 TYR cc_start: 0.8467 (OUTLIER) cc_final: 0.6901 (p90) REVERT: K 13 HIS cc_start: 0.7093 (OUTLIER) cc_final: 0.6458 (p90) REVERT: K 19 PHE cc_start: 0.6814 (OUTLIER) cc_final: 0.6330 (p90) REVERT: K 35 MET cc_start: 0.7466 (mmm) cc_final: 0.6954 (mmm) REVERT: L 10 TYR cc_start: 0.8488 (OUTLIER) cc_final: 0.7439 (p90) REVERT: M 13 HIS cc_start: 0.7009 (OUTLIER) cc_final: 0.6308 (p90) REVERT: M 34 LEU cc_start: 0.8214 (tp) cc_final: 0.7831 (tp) REVERT: N 10 TYR cc_start: 0.8214 (OUTLIER) cc_final: 0.7038 (p90) REVERT: N 16 LYS cc_start: 0.7134 (tttt) cc_final: 0.6410 (mmtm) REVERT: N 22 GLU cc_start: 0.7947 (tp30) cc_final: 0.7520 (tp30) REVERT: N 34 LEU cc_start: 0.9320 (tt) cc_final: 0.9044 (tt) REVERT: N 35 MET cc_start: 0.7638 (ttm) cc_final: 0.7198 (ttm) REVERT: O 31 ILE cc_start: 0.8277 (mp) cc_final: 0.8050 (tt) REVERT: P 10 TYR cc_start: 0.8233 (OUTLIER) cc_final: 0.7190 (p90) REVERT: P 22 GLU cc_start: 0.8056 (tp30) cc_final: 0.7591 (tp30) REVERT: Q 26 SER cc_start: 0.8828 (t) cc_final: 0.8536 (m) REVERT: Q 35 MET cc_start: 0.7485 (mmm) cc_final: 0.6839 (mmt) REVERT: S 26 SER cc_start: 0.8980 (t) cc_final: 0.8549 (m) REVERT: S 35 MET cc_start: 0.7411 (mmm) cc_final: 0.6826 (mmt) REVERT: T 14 HIS cc_start: 0.7343 (OUTLIER) cc_final: 0.6983 (t-90) REVERT: T 35 MET cc_start: 0.5919 (OUTLIER) cc_final: 0.5409 (ttm) outliers start: 57 outliers final: 30 residues processed: 209 average time/residue: 0.0665 time to fit residues: 18.8606 Evaluate side-chains 224 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 175 time to evaluate : 0.229 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 34 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 24 VAL Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 5 optimal weight: 3.9990 chunk 59 optimal weight: 8.9990 chunk 1 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 chunk 3 optimal weight: 6.9990 chunk 20 optimal weight: 0.2980 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 33 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 overall best weight: 0.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 27 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5179 r_free = 0.5179 target = 0.190530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4978 r_free = 0.4978 target = 0.171352 restraints weight = 7086.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.5030 r_free = 0.5030 target = 0.175826 restraints weight = 3282.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.5063 r_free = 0.5063 target = 0.178792 restraints weight = 1875.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.5085 r_free = 0.5085 target = 0.180787 restraints weight = 1241.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.5101 r_free = 0.5101 target = 0.182214 restraints weight = 917.413| |-----------------------------------------------------------------------------| r_work (final): 0.5110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6955 moved from start: 0.7040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 5600 Z= 0.191 Angle : 0.844 8.363 7520 Z= 0.454 Chirality : 0.062 0.211 810 Planarity : 0.003 0.014 990 Dihedral : 11.698 89.314 760 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.94 % Favored : 84.06 % Rotamer: Outliers : 9.82 % Allowed : 24.64 % Favored : 65.54 % 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 aren not related in a simple way. whole: -3.20 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.43 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG P 5 TYR 0.011 0.001 TYR J 10 PHE 0.031 0.003 PHE A 19 HIS 0.004 0.001 HIS F 13 Details of bonding type rmsd covalent geometry : bond 0.00456 ( 5600) covalent geometry : angle 0.84384 ( 7520) hydrogen bonds : bond 0.03095 ( 176) hydrogen bonds : angle 5.20539 ( 528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 170 time to evaluate : 0.212 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 10 TYR cc_start: 0.8578 (OUTLIER) cc_final: 0.6458 (p90) REVERT: C 11 GLU cc_start: 0.7487 (mp0) cc_final: 0.6493 (mp0) REVERT: C 19 PHE cc_start: 0.6668 (OUTLIER) cc_final: 0.6316 (p90) REVERT: D 10 TYR cc_start: 0.8512 (OUTLIER) cc_final: 0.6478 (p90) REVERT: D 16 LYS cc_start: 0.7630 (mmtm) cc_final: 0.7386 (mmtm) REVERT: E 13 HIS cc_start: 0.6809 (OUTLIER) cc_final: 0.5739 (p90) REVERT: F 10 TYR cc_start: 0.8241 (OUTLIER) cc_final: 0.5792 (p90) REVERT: F 22 GLU cc_start: 0.8054 (tp30) cc_final: 0.7558 (tp30) REVERT: G 13 HIS cc_start: 0.6923 (OUTLIER) cc_final: 0.5896 (p90) REVERT: H 7 ASP cc_start: 0.7871 (t0) cc_final: 0.7606 (m-30) REVERT: H 10 TYR cc_start: 0.8076 (OUTLIER) cc_final: 0.6141 (p90) REVERT: H 22 GLU cc_start: 0.8038 (tp30) cc_final: 0.7555 (tp30) REVERT: I 13 HIS cc_start: 0.7095 (OUTLIER) cc_final: 0.6232 (p90) REVERT: I 19 PHE cc_start: 0.6613 (OUTLIER) cc_final: 0.5912 (p90) REVERT: J 10 TYR cc_start: 0.8337 (OUTLIER) cc_final: 0.6723 (p90) REVERT: K 13 HIS cc_start: 0.7024 (OUTLIER) cc_final: 0.6353 (p90) REVERT: K 19 PHE cc_start: 0.6572 (OUTLIER) cc_final: 0.5827 (p90) REVERT: K 35 MET cc_start: 0.7466 (mmm) cc_final: 0.7015 (mmm) REVERT: L 10 TYR cc_start: 0.8304 (OUTLIER) cc_final: 0.7120 (p90) REVERT: M 13 HIS cc_start: 0.6885 (OUTLIER) cc_final: 0.6236 (p90) REVERT: M 34 LEU cc_start: 0.8195 (tp) cc_final: 0.7869 (tp) REVERT: N 16 LYS cc_start: 0.7113 (tttt) cc_final: 0.6395 (mmtm) REVERT: N 35 MET cc_start: 0.7590 (ttm) cc_final: 0.7107 (ttm) REVERT: P 22 GLU cc_start: 0.8089 (tp30) cc_final: 0.7673 (tp30) REVERT: Q 26 SER cc_start: 0.8469 (t) cc_final: 0.8173 (m) REVERT: Q 35 MET cc_start: 0.7537 (mmm) cc_final: 0.6882 (mmt) REVERT: S 26 SER cc_start: 0.8947 (t) cc_final: 0.8513 (m) REVERT: S 35 MET cc_start: 0.7432 (mmm) cc_final: 0.6996 (mmm) outliers start: 55 outliers final: 31 residues processed: 192 average time/residue: 0.0659 time to fit residues: 17.1678 Evaluate side-chains 215 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 170 time to evaluate : 0.207 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain F residue 39 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 24 VAL Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 46 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 31 optimal weight: 4.9990 chunk 37 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 1 optimal weight: 0.6980 chunk 38 optimal weight: 8.9990 chunk 69 optimal weight: 0.5980 chunk 59 optimal weight: 8.9990 chunk 20 optimal weight: 0.5980 chunk 52 optimal weight: 1.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 14 HIS ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 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 = 0.5312 r_free = 0.5312 target = 0.248783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.5261 r_free = 0.5261 target = 0.195859 restraints weight = 7337.367| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5335 r_free = 0.5335 target = 0.201724 restraints weight = 3289.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.5368 r_free = 0.5368 target = 0.205198 restraints weight = 1806.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.5395 r_free = 0.5395 target = 0.207745 restraints weight = 1179.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5411 r_free = 0.5411 target = 0.209248 restraints weight = 830.846| |-----------------------------------------------------------------------------| r_work (final): 0.5266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 moved from start: 0.7257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5600 Z= 0.162 Angle : 0.812 8.320 7520 Z= 0.435 Chirality : 0.061 0.176 810 Planarity : 0.003 0.015 990 Dihedral : 11.577 89.493 760 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 22.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 9.11 % Allowed : 25.54 % Favored : 65.36 % 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 aren not related in a simple way. whole: -3.16 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.40 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 5 TYR 0.011 0.001 TYR J 10 PHE 0.036 0.003 PHE A 19 HIS 0.003 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00396 ( 5600) covalent geometry : angle 0.81209 ( 7520) hydrogen bonds : bond 0.03514 ( 176) hydrogen bonds : angle 5.33258 ( 528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 172 time to evaluate : 0.231 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: A 11 GLU cc_start: 0.7552 (mp0) cc_final: 0.7313 (mp0) REVERT: B 10 TYR cc_start: 0.8426 (OUTLIER) cc_final: 0.6302 (p90) REVERT: B 16 LYS cc_start: 0.7607 (mmtm) cc_final: 0.7334 (mmtm) REVERT: C 11 GLU cc_start: 0.7371 (mp0) cc_final: 0.6402 (mp0) REVERT: C 19 PHE cc_start: 0.6271 (OUTLIER) cc_final: 0.5973 (p90) REVERT: D 10 TYR cc_start: 0.8347 (OUTLIER) cc_final: 0.6242 (p90) REVERT: D 16 LYS cc_start: 0.7664 (mmtm) cc_final: 0.7382 (mmtm) REVERT: D 34 LEU cc_start: 0.8731 (tt) cc_final: 0.8459 (tt) REVERT: E 13 HIS cc_start: 0.6461 (OUTLIER) cc_final: 0.5411 (p90) REVERT: F 10 TYR cc_start: 0.7860 (OUTLIER) cc_final: 0.5283 (p90) REVERT: G 13 HIS cc_start: 0.6583 (OUTLIER) cc_final: 0.5815 (p90) REVERT: H 7 ASP cc_start: 0.7586 (t0) cc_final: 0.7320 (m-30) REVERT: H 10 TYR cc_start: 0.7675 (OUTLIER) cc_final: 0.5968 (p90) REVERT: H 22 GLU cc_start: 0.7772 (tp30) cc_final: 0.7244 (tp30) REVERT: H 34 LEU cc_start: 0.9463 (tt) cc_final: 0.9022 (tp) REVERT: I 13 HIS cc_start: 0.6661 (OUTLIER) cc_final: 0.5782 (p90) REVERT: I 19 PHE cc_start: 0.6007 (OUTLIER) cc_final: 0.5379 (p90) REVERT: I 35 MET cc_start: 0.7369 (mmm) cc_final: 0.6881 (mmm) REVERT: J 10 TYR cc_start: 0.8066 (OUTLIER) cc_final: 0.6545 (p90) REVERT: K 19 PHE cc_start: 0.5846 (OUTLIER) cc_final: 0.5182 (p90) REVERT: K 35 MET cc_start: 0.7221 (mmm) cc_final: 0.6681 (mmm) REVERT: L 10 TYR cc_start: 0.7905 (OUTLIER) cc_final: 0.6876 (p90) REVERT: M 13 HIS cc_start: 0.6649 (OUTLIER) cc_final: 0.6079 (p90) REVERT: M 34 LEU cc_start: 0.8006 (tp) cc_final: 0.7608 (tp) REVERT: N 16 LYS cc_start: 0.6909 (tttt) cc_final: 0.6171 (mmtm) REVERT: N 20 PHE cc_start: 0.7701 (t80) cc_final: 0.7430 (t80) REVERT: N 22 GLU cc_start: 0.7504 (tp30) cc_final: 0.7120 (tp30) REVERT: N 35 MET cc_start: 0.7477 (ttm) cc_final: 0.6920 (ttm) REVERT: P 22 GLU cc_start: 0.7566 (tp30) cc_final: 0.7117 (tp30) REVERT: Q 35 MET cc_start: 0.7406 (mmm) cc_final: 0.6863 (mmm) REVERT: S 26 SER cc_start: 0.8870 (t) cc_final: 0.8538 (m) REVERT: S 35 MET cc_start: 0.7197 (mmm) cc_final: 0.6661 (mmm) outliers start: 51 outliers final: 32 residues processed: 193 average time/residue: 0.0617 time to fit residues: 16.4232 Evaluate side-chains 212 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 167 time to evaluate : 0.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 7 ASP Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 69 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 30 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 23 optimal weight: 0.1980 chunk 11 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 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 = 0.5285 r_free = 0.5285 target = 0.197833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.5090 r_free = 0.5090 target = 0.179113 restraints weight = 7193.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.5137 r_free = 0.5137 target = 0.183455 restraints weight = 3316.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.5168 r_free = 0.5168 target = 0.186352 restraints weight = 1899.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5185 r_free = 0.5185 target = 0.188233 restraints weight = 1267.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.5200 r_free = 0.5200 target = 0.189666 restraints weight = 952.484| |-----------------------------------------------------------------------------| r_work (final): 0.5227 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 moved from start: 0.7319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 5600 Z= 0.201 Angle : 0.864 8.317 7520 Z= 0.466 Chirality : 0.064 0.236 810 Planarity : 0.003 0.018 990 Dihedral : 11.527 89.663 760 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.80 % Favored : 84.20 % Rotamer: Outliers : 8.21 % Allowed : 27.68 % Favored : 64.11 % 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 aren not related in a simple way. whole: -3.22 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.45 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG P 5 TYR 0.010 0.001 TYR J 10 PHE 0.042 0.003 PHE A 19 HIS 0.004 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00491 ( 5600) covalent geometry : angle 0.86448 ( 7520) hydrogen bonds : bond 0.03177 ( 176) hydrogen bonds : angle 5.25953 ( 528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1380 Ramachandran restraints generated. 690 Oldfield, 0 Emsley, 690 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 168 time to evaluate : 0.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 11 GLU cc_start: 0.7544 (mp0) cc_final: 0.7334 (mp0) REVERT: B 10 TYR cc_start: 0.8576 (OUTLIER) cc_final: 0.6602 (p90) REVERT: C 11 GLU cc_start: 0.7568 (mp0) cc_final: 0.6652 (mp0) REVERT: C 19 PHE cc_start: 0.6700 (OUTLIER) cc_final: 0.6430 (p90) REVERT: D 10 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.6483 (p90) REVERT: D 16 LYS cc_start: 0.7784 (mmtm) cc_final: 0.7480 (mmtm) REVERT: E 13 HIS cc_start: 0.6854 (OUTLIER) cc_final: 0.5760 (p90) REVERT: F 10 TYR cc_start: 0.8227 (OUTLIER) cc_final: 0.6092 (p90) REVERT: F 22 GLU cc_start: 0.8163 (tp30) cc_final: 0.7732 (tp30) REVERT: F 34 LEU cc_start: 0.9535 (tt) cc_final: 0.9241 (tp) REVERT: G 13 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.5864 (p90) REVERT: H 7 ASP cc_start: 0.7861 (t0) cc_final: 0.7624 (m-30) REVERT: H 10 TYR cc_start: 0.8006 (OUTLIER) cc_final: 0.6370 (p90) REVERT: H 22 GLU cc_start: 0.8147 (tp30) cc_final: 0.7679 (tp30) REVERT: I 13 HIS cc_start: 0.7126 (OUTLIER) cc_final: 0.6294 (p90) REVERT: I 19 PHE cc_start: 0.6711 (OUTLIER) cc_final: 0.6011 (p90) REVERT: I 35 MET cc_start: 0.7622 (mmm) cc_final: 0.7395 (mmm) REVERT: J 10 TYR cc_start: 0.8357 (OUTLIER) cc_final: 0.7269 (p90) REVERT: K 13 HIS cc_start: 0.7073 (OUTLIER) cc_final: 0.6422 (p90) REVERT: K 19 PHE cc_start: 0.6623 (OUTLIER) cc_final: 0.5929 (p90) REVERT: K 34 LEU cc_start: 0.8221 (tp) cc_final: 0.7829 (tp) REVERT: K 35 MET cc_start: 0.7490 (mmm) cc_final: 0.7017 (mmm) REVERT: L 10 TYR cc_start: 0.8297 (OUTLIER) cc_final: 0.7508 (p90) REVERT: M 13 HIS cc_start: 0.6971 (OUTLIER) cc_final: 0.6336 (p90) REVERT: M 34 LEU cc_start: 0.8162 (tp) cc_final: 0.7945 (tp) REVERT: N 16 LYS cc_start: 0.7269 (tttt) cc_final: 0.6679 (mmtm) REVERT: P 22 GLU cc_start: 0.7968 (tp30) cc_final: 0.7557 (tp30) REVERT: Q 35 MET cc_start: 0.7527 (mmm) cc_final: 0.6919 (mmt) REVERT: S 26 SER cc_start: 0.8586 (t) cc_final: 0.8229 (m) REVERT: S 35 MET cc_start: 0.7435 (mmm) cc_final: 0.7001 (mmt) outliers start: 46 outliers final: 32 residues processed: 186 average time/residue: 0.0659 time to fit residues: 16.7243 Evaluate side-chains 209 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 163 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 ASN Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 35 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 19 PHE Chi-restraints excluded: chain C residue 27 ASN Chi-restraints excluded: chain C residue 31 ILE Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 13 HIS Chi-restraints excluded: chain E residue 19 PHE Chi-restraints excluded: chain F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 13 HIS Chi-restraints excluded: chain G residue 19 PHE Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain H residue 1 ASP Chi-restraints excluded: chain H residue 10 TYR Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain I residue 13 HIS Chi-restraints excluded: chain I residue 17 LEU Chi-restraints excluded: chain I residue 19 PHE Chi-restraints excluded: chain I residue 36 VAL Chi-restraints excluded: chain J residue 7 ASP Chi-restraints excluded: chain J residue 10 TYR Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain K residue 36 VAL Chi-restraints excluded: chain L residue 7 ASP Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain M residue 13 HIS Chi-restraints excluded: chain M residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain P residue 10 TYR Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain Q residue 32 ILE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 19 PHE Chi-restraints excluded: chain S residue 32 ILE Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 14 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.6980 chunk 64 optimal weight: 0.5980 chunk 38 optimal weight: 6.9990 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 31 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 41 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 ASN ** B 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 27 ASN ** D 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 15 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 = 0.5322 r_free = 0.5322 target = 0.246444 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.196447 restraints weight = 7434.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.5334 r_free = 0.5334 target = 0.201977 restraints weight = 3306.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5377 r_free = 0.5377 target = 0.205484 restraints weight = 1823.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.5400 r_free = 0.5400 target = 0.207797 restraints weight = 1176.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.5416 r_free = 0.5416 target = 0.209358 restraints weight = 844.493| |-----------------------------------------------------------------------------| r_work (final): 0.5270 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6964 moved from start: 0.7490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5600 Z= 0.174 Angle : 0.850 8.438 7520 Z= 0.451 Chirality : 0.062 0.260 810 Planarity : 0.003 0.017 990 Dihedral : 11.443 89.683 760 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 23.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.67 % Favored : 83.33 % Rotamer: Outliers : 8.57 % Allowed : 27.32 % Favored : 64.11 % 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 aren not related in a simple way. whole: -3.23 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.46 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG P 5 TYR 0.010 0.001 TYR J 10 PHE 0.039 0.003 PHE A 19 HIS 0.004 0.001 HIS H 13 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 5600) covalent geometry : angle 0.84993 ( 7520) hydrogen bonds : bond 0.03276 ( 176) hydrogen bonds : angle 5.25552 ( 528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1088.29 seconds wall clock time: 19 minutes 31.91 seconds (1171.91 seconds total)