Starting phenix.real_space_refine on Thu Nov 14 09:20:30 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/11_2024/8sel_40421_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/11_2024/8sel_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/11_2024/8sel_40421.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/11_2024/8sel_40421.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/11_2024/8sel_40421_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sel_40421/11_2024/8sel_40421_neut.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.010 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/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: D, F, H, J, L, N, P, R, T, C, E, G, I, K, M, O, Q, S Time building chain proxies: 2.12, per 1000 atoms: 0.39 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: 1.38 Conformation dependent library (CDL) restraints added in 685.1 milliseconds 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: 0.85 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: 1.41 Time building geometry restraints manager: 1.57 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: 0.00 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: 1.370 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: 0.010 Extract box with map and model: 0.170 Check model and map are aligned: 0.040 Set scattering table: 0.040 Process input model: 15.130 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.760 ------------------------------------------------------------------------------- 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= 1.721 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.003 0.001 HIS J 13 PHE 0.017 0.006 PHE R 19 TYR 0.029 0.010 TYR R 10 ARG 0.001 0.000 ARG T 5 *********************** 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 : 0.611 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: 0.8001 (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: 0.8064 (tp) REVERT: N 16 LYS cc_start: 0.7781 (tttt) cc_final: 0.7459 (mmtm) REVERT: Q 26 SER cc_start: 0.8867 (t) cc_final: 0.8562 (m) REVERT: S 26 SER cc_start: 0.8852 (t) cc_final: 0.8416 (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: 0.1503 time to fit residues: 44.1031 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 : 0.735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 33 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7154 moved from start: 0.4495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 5600 Z= 0.310 Angle : 0.900 7.845 7520 Z= 0.491 Chirality : 0.063 0.221 810 Planarity : 0.003 0.017 990 Dihedral : 12.932 86.739 760 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 14.40 Ramachandran Plot: Outliers : 1.45 % Allowed : 10.14 % Favored : 88.41 % Rotamer: Outliers : 4.46 % Allowed : 14.29 % Favored : 81.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.70 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS R 14 PHE 0.017 0.003 PHE O 19 TYR 0.011 0.002 TYR J 10 ARG 0.001 0.000 ARG L 5 *********************** 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 215 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 190 time to evaluate : 0.660 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: 0.8146 (OUTLIER) cc_final: 0.6356 (p90) REVERT: D 10 TYR cc_start: 0.8174 (OUTLIER) cc_final: 0.6412 (p90) REVERT: E 34 LEU cc_start: 0.8410 (tp) cc_final: 0.8189 (tp) REVERT: F 10 TYR cc_start: 0.8090 (OUTLIER) cc_final: 0.6600 (p90) REVERT: H 10 TYR cc_start: 0.8116 (OUTLIER) cc_final: 0.6542 (p90) REVERT: H 16 LYS cc_start: 0.7610 (mmtm) cc_final: 0.7314 (mmtm) REVERT: J 10 TYR cc_start: 0.8351 (OUTLIER) cc_final: 0.7015 (p90) REVERT: L 10 TYR cc_start: 0.8411 (OUTLIER) cc_final: 0.7024 (p90) REVERT: R 5 ARG cc_start: 0.8015 (mtp180) cc_final: 0.7112 (tpp-160) REVERT: R 7 ASP cc_start: 0.8032 (t0) cc_final: 0.7742 (t0) REVERT: S 26 SER cc_start: 0.8616 (t) cc_final: 0.8266 (m) REVERT: T 5 ARG cc_start: 0.7991 (mtp180) cc_final: 0.7124 (tpp-160) REVERT: T 7 ASP cc_start: 0.7957 (t0) cc_final: 0.7671 (t0) REVERT: T 27 ASN cc_start: 0.7205 (t0) cc_final: 0.5273 (p0) outliers start: 25 outliers final: 6 residues processed: 192 average time/residue: 0.1794 time to fit residues: 44.1334 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 : 0.639 ------------------------------------------------------------------------------- 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 35 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 chunk 52 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 8.9990 chunk 63 optimal weight: 5.9990 chunk 68 optimal weight: 0.9980 chunk 56 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- 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** ** C 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 27 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7572 moved from start: 0.5892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.076 5600 Z= 0.674 Angle : 1.114 10.818 7520 Z= 0.618 Chirality : 0.074 0.252 810 Planarity : 0.005 0.020 990 Dihedral : 12.410 89.788 760 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 28.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.20 % Favored : 85.80 % Rotamer: Outliers : 8.04 % Allowed : 17.14 % Favored : 74.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.98 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS A 13 PHE 0.031 0.005 PHE Q 19 TYR 0.016 0.003 TYR E 10 ARG 0.001 0.000 ARG L 5 *********************** 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 242 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 197 time to evaluate : 0.609 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: 0.7344 (p90) cc_final: 0.6986 (p90) REVERT: B 10 TYR cc_start: 0.8514 (OUTLIER) cc_final: 0.7141 (p90) REVERT: C 11 GLU cc_start: 0.7833 (mp0) cc_final: 0.6923 (mp0) REVERT: D 10 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.7267 (p90) REVERT: E 34 LEU cc_start: 0.8431 (tp) cc_final: 0.8173 (tp) REVERT: F 10 TYR cc_start: 0.8457 (OUTLIER) cc_final: 0.6743 (p90) REVERT: G 13 HIS cc_start: 0.7272 (OUTLIER) cc_final: 0.6766 (p90) REVERT: H 10 TYR cc_start: 0.8451 (OUTLIER) cc_final: 0.6675 (p90) REVERT: I 19 PHE cc_start: 0.7272 (OUTLIER) cc_final: 0.6699 (p90) REVERT: J 10 TYR cc_start: 0.8699 (OUTLIER) cc_final: 0.7466 (p90) REVERT: K 19 PHE cc_start: 0.7263 (OUTLIER) cc_final: 0.6651 (p90) REVERT: L 10 TYR cc_start: 0.8709 (OUTLIER) cc_final: 0.7552 (p90) REVERT: M 13 HIS cc_start: 0.7411 (OUTLIER) cc_final: 0.6813 (p90) REVERT: M 34 LEU cc_start: 0.8453 (tp) cc_final: 0.8143 (tp) REVERT: N 10 TYR cc_start: 0.8248 (OUTLIER) cc_final: 0.7420 (p90) REVERT: P 10 TYR cc_start: 0.8324 (OUTLIER) cc_final: 0.7539 (p90) REVERT: Q 19 PHE cc_start: 0.7089 (OUTLIER) cc_final: 0.6543 (p90) REVERT: R 5 ARG cc_start: 0.8483 (mtp180) cc_final: 0.7134 (tpp-160) REVERT: R 27 ASN cc_start: 0.8180 (t0) cc_final: 0.6672 (p0) REVERT: S 19 PHE cc_start: 0.7101 (OUTLIER) cc_final: 0.6576 (p90) REVERT: S 26 SER cc_start: 0.8905 (t) cc_final: 0.8681 (m) REVERT: T 5 ARG cc_start: 0.8446 (mtp180) cc_final: 0.7119 (tpp-160) REVERT: T 27 ASN cc_start: 0.8281 (t0) cc_final: 0.6745 (p0) outliers start: 45 outliers final: 18 residues processed: 226 average time/residue: 0.1747 time to fit residues: 50.4457 Evaluate side-chains 216 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 184 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain B residue 10 TYR Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain C residue 17 LEU Chi-restraints excluded: chain D residue 10 TYR Chi-restraints excluded: chain D residue 12 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 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 J residue 10 TYR Chi-restraints excluded: chain J residue 12 VAL 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 P residue 36 VAL Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain S residue 19 PHE 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 47 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 5.9990 chunk 67 optimal weight: 0.8980 chunk 60 optimal weight: 0.8980 chunk 18 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 8.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- 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 ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** 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 27 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7400 moved from start: 0.6216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 5600 Z= 0.345 Angle : 0.870 11.221 7520 Z= 0.476 Chirality : 0.064 0.189 810 Planarity : 0.003 0.015 990 Dihedral : 12.100 89.655 760 Min Nonbonded Distance : 2.573 Molprobity Statistics. All-atom Clashscore : 23.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 7.86 % Allowed : 21.25 % Favored : 70.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.96 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 13 PHE 0.025 0.003 PHE S 19 TYR 0.011 0.002 TYR L 10 ARG 0.001 0.000 ARG H 5 *********************** 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 242 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 198 time to evaluate : 0.600 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7273 (p90) cc_final: 0.6934 (p-80) REVERT: A 19 PHE cc_start: 0.6744 (OUTLIER) cc_final: 0.6461 (p90) REVERT: B 10 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.6507 (p90) REVERT: C 11 GLU cc_start: 0.7653 (mp0) cc_final: 0.6789 (mp0) REVERT: C 13 HIS cc_start: 0.7308 (p90) cc_final: 0.6964 (p-80) REVERT: C 19 PHE cc_start: 0.6722 (OUTLIER) cc_final: 0.6413 (p90) REVERT: D 10 TYR cc_start: 0.8310 (OUTLIER) cc_final: 0.6684 (p90) REVERT: E 13 HIS cc_start: 0.7199 (OUTLIER) cc_final: 0.6590 (p90) REVERT: F 10 TYR cc_start: 0.8060 (OUTLIER) cc_final: 0.6411 (p90) REVERT: F 36 VAL cc_start: 0.8479 (p) cc_final: 0.8256 (m) REVERT: G 13 HIS cc_start: 0.7103 (OUTLIER) cc_final: 0.6647 (p90) REVERT: H 10 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6318 (p90) REVERT: H 36 VAL cc_start: 0.8609 (p) cc_final: 0.8254 (m) REVERT: I 13 HIS cc_start: 0.7176 (OUTLIER) cc_final: 0.6669 (p90) REVERT: J 10 TYR cc_start: 0.8390 (OUTLIER) cc_final: 0.7166 (p90) REVERT: L 10 TYR cc_start: 0.8331 (OUTLIER) cc_final: 0.7087 (p90) REVERT: M 13 HIS cc_start: 0.7011 (OUTLIER) cc_final: 0.6613 (p90) REVERT: N 10 TYR cc_start: 0.7893 (OUTLIER) cc_final: 0.7149 (p90) REVERT: O 34 LEU cc_start: 0.8299 (tp) cc_final: 0.8080 (tp) REVERT: P 10 TYR cc_start: 0.7946 (OUTLIER) cc_final: 0.7226 (p90) REVERT: P 22 GLU cc_start: 0.8352 (tp30) cc_final: 0.8135 (tp30) REVERT: P 34 LEU cc_start: 0.9245 (tt) cc_final: 0.8989 (tt) REVERT: T 35 MET cc_start: 0.6848 (OUTLIER) cc_final: 0.6497 (ttm) outliers start: 44 outliers final: 19 residues processed: 227 average time/residue: 0.1560 time to fit residues: 46.3208 Evaluate side-chains 219 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE 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 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 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 13 HIS Chi-restraints excluded: chain I residue 17 LEU 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 36 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 R residue 10 TYR Chi-restraints excluded: chain T residue 10 TYR Chi-restraints excluded: chain T residue 35 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 13 optimal weight: 0.0870 chunk 39 optimal weight: 0.9990 overall best weight: 1.4166 ------------------------------------------------------------------------------- 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** ** C 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7453 moved from start: 0.6525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 5600 Z= 0.393 Angle : 0.895 8.436 7520 Z= 0.495 Chirality : 0.065 0.201 810 Planarity : 0.004 0.016 990 Dihedral : 12.036 89.446 760 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 23.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.52 % Favored : 83.48 % Rotamer: Outliers : 9.64 % Allowed : 22.50 % Favored : 67.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.11 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.36 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 13 PHE 0.034 0.004 PHE I 19 TYR 0.010 0.002 TYR J 10 ARG 0.002 0.001 ARG B 5 *********************** 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 237 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 183 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7388 (p90) cc_final: 0.6926 (p-80) REVERT: A 19 PHE cc_start: 0.6876 (OUTLIER) cc_final: 0.6570 (p90) REVERT: B 10 TYR cc_start: 0.8360 (OUTLIER) cc_final: 0.6623 (p90) REVERT: C 11 GLU cc_start: 0.7685 (mp0) cc_final: 0.6808 (mp0) REVERT: C 19 PHE cc_start: 0.6972 (OUTLIER) cc_final: 0.6496 (p90) REVERT: D 10 TYR cc_start: 0.8363 (OUTLIER) cc_final: 0.6592 (p90) REVERT: E 13 HIS cc_start: 0.7088 (OUTLIER) cc_final: 0.6428 (p90) REVERT: F 10 TYR cc_start: 0.8218 (OUTLIER) cc_final: 0.6551 (p90) REVERT: G 13 HIS cc_start: 0.6976 (OUTLIER) cc_final: 0.6322 (p90) REVERT: H 10 TYR cc_start: 0.8138 (OUTLIER) cc_final: 0.6504 (p90) REVERT: I 13 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6707 (p90) REVERT: J 10 TYR cc_start: 0.8435 (OUTLIER) cc_final: 0.7242 (p90) REVERT: K 13 HIS cc_start: 0.7306 (OUTLIER) cc_final: 0.6854 (p90) REVERT: K 19 PHE cc_start: 0.6878 (OUTLIER) cc_final: 0.6306 (p90) REVERT: L 10 TYR cc_start: 0.8425 (OUTLIER) cc_final: 0.7156 (p90) REVERT: M 13 HIS cc_start: 0.7028 (OUTLIER) cc_final: 0.6532 (p90) REVERT: N 10 TYR cc_start: 0.7943 (OUTLIER) cc_final: 0.7221 (p90) REVERT: P 10 TYR cc_start: 0.8008 (OUTLIER) cc_final: 0.7266 (p90) REVERT: R 35 MET cc_start: 0.6059 (OUTLIER) cc_final: 0.5773 (ttm) REVERT: S 15 GLN cc_start: 0.7593 (OUTLIER) cc_final: 0.7108 (tm130) REVERT: T 14 HIS cc_start: 0.6935 (OUTLIER) cc_final: 0.6606 (t-90) REVERT: T 35 MET cc_start: 0.6033 (OUTLIER) cc_final: 0.5742 (ttm) outliers start: 54 outliers final: 28 residues processed: 213 average time/residue: 0.1426 time to fit residues: 40.6677 Evaluate side-chains 224 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 176 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE 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 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 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 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 J residue 12 VAL Chi-restraints excluded: chain J residue 32 ILE Chi-restraints excluded: chain K residue 13 HIS 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 M residue 24 VAL Chi-restraints excluded: chain N residue 10 TYR Chi-restraints excluded: chain O residue 19 PHE Chi-restraints excluded: chain O residue 24 VAL 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 31 ILE Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 15 GLN 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 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 16 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 0.0370 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 4.9990 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 7.9990 chunk 38 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 overall best weight: 0.6858 ------------------------------------------------------------------------------- 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 ** 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** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7303 moved from start: 0.6892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5600 Z= 0.277 Angle : 0.808 7.741 7520 Z= 0.441 Chirality : 0.061 0.166 810 Planarity : 0.003 0.016 990 Dihedral : 11.693 87.685 760 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Rotamer: Outliers : 8.39 % Allowed : 25.36 % Favored : 66.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.17 (0.26), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.20), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS P 13 PHE 0.031 0.003 PHE I 19 TYR 0.011 0.001 TYR J 10 ARG 0.002 0.000 ARG N 5 *********************** 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 229 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 182 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7287 (p90) cc_final: 0.6807 (p-80) REVERT: B 10 TYR cc_start: 0.8194 (OUTLIER) cc_final: 0.6498 (p90) REVERT: C 11 GLU cc_start: 0.7506 (mp0) cc_final: 0.6670 (mp0) REVERT: C 13 HIS cc_start: 0.7265 (p90) cc_final: 0.6921 (p-80) REVERT: C 19 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.6466 (p90) REVERT: D 10 TYR cc_start: 0.8189 (OUTLIER) cc_final: 0.6588 (p90) REVERT: E 13 HIS cc_start: 0.6970 (OUTLIER) cc_final: 0.6377 (p90) REVERT: F 10 TYR cc_start: 0.7864 (OUTLIER) cc_final: 0.6614 (p90) REVERT: F 36 VAL cc_start: 0.8430 (p) cc_final: 0.8206 (m) REVERT: H 10 TYR cc_start: 0.7841 (OUTLIER) cc_final: 0.6522 (p90) REVERT: H 36 VAL cc_start: 0.8688 (p) cc_final: 0.8155 (p) REVERT: I 13 HIS cc_start: 0.7122 (OUTLIER) cc_final: 0.6683 (p90) REVERT: I 19 PHE cc_start: 0.6443 (OUTLIER) cc_final: 0.6012 (p90) REVERT: J 10 TYR cc_start: 0.8192 (OUTLIER) cc_final: 0.7137 (p90) REVERT: K 13 HIS cc_start: 0.6964 (OUTLIER) cc_final: 0.6467 (p90) REVERT: K 19 PHE cc_start: 0.6466 (OUTLIER) cc_final: 0.5969 (p90) REVERT: P 34 LEU cc_start: 0.9331 (tt) cc_final: 0.9055 (tp) REVERT: R 35 MET cc_start: 0.6717 (OUTLIER) cc_final: 0.6436 (ttm) REVERT: S 15 GLN cc_start: 0.7486 (OUTLIER) cc_final: 0.7071 (tm130) REVERT: S 17 LEU cc_start: 0.7481 (tp) cc_final: 0.7249 (tt) outliers start: 47 outliers final: 24 residues processed: 202 average time/residue: 0.1446 time to fit residues: 38.8164 Evaluate side-chains 212 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 175 time to evaluate : 0.612 ------------------------------------------------------------------------------- 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 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 19 PHE 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 J residue 32 ILE Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain N residue 10 TYR 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 15 GLN 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 8.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 42 optimal weight: 8.9990 chunk 41 optimal weight: 0.5980 chunk 31 optimal weight: 9.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 20 optimal weight: 0.6980 chunk 13 optimal weight: 5.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- 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 ** 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 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.7043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 5600 Z= 0.349 Angle : 0.861 8.132 7520 Z= 0.468 Chirality : 0.064 0.182 810 Planarity : 0.003 0.015 990 Dihedral : 11.762 88.414 760 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 23.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.09 % Favored : 83.91 % Rotamer: Outliers : 9.29 % Allowed : 26.96 % Favored : 63.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 13 PHE 0.032 0.004 PHE K 19 TYR 0.010 0.001 TYR J 10 ARG 0.002 0.000 ARG P 5 *********************** 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 226 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 174 time to evaluate : 0.587 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7383 (p90) cc_final: 0.6839 (p-80) REVERT: A 19 PHE cc_start: 0.6854 (OUTLIER) cc_final: 0.6532 (p90) REVERT: B 10 TYR cc_start: 0.8358 (OUTLIER) cc_final: 0.6750 (p90) REVERT: C 11 GLU cc_start: 0.7520 (mp0) cc_final: 0.6729 (mp0) REVERT: C 19 PHE cc_start: 0.6845 (OUTLIER) cc_final: 0.6495 (p90) REVERT: D 10 TYR cc_start: 0.8353 (OUTLIER) cc_final: 0.6592 (p90) REVERT: D 35 MET cc_start: 0.7465 (tpp) cc_final: 0.6961 (tpt) REVERT: E 13 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6397 (p90) REVERT: F 10 TYR cc_start: 0.7967 (OUTLIER) cc_final: 0.6814 (p90) REVERT: F 36 VAL cc_start: 0.8612 (p) cc_final: 0.8341 (m) REVERT: G 13 HIS cc_start: 0.6983 (OUTLIER) cc_final: 0.6275 (p90) REVERT: G 15 GLN cc_start: 0.7944 (tm-30) cc_final: 0.7534 (tm-30) REVERT: H 10 TYR cc_start: 0.7920 (OUTLIER) cc_final: 0.6740 (p90) REVERT: H 36 VAL cc_start: 0.8769 (p) cc_final: 0.8436 (m) REVERT: I 13 HIS cc_start: 0.7253 (OUTLIER) cc_final: 0.6699 (p90) REVERT: I 19 PHE cc_start: 0.6555 (OUTLIER) cc_final: 0.6008 (p90) REVERT: J 10 TYR cc_start: 0.8338 (OUTLIER) cc_final: 0.7245 (p90) REVERT: K 13 HIS cc_start: 0.7233 (OUTLIER) cc_final: 0.6742 (p90) REVERT: K 19 PHE cc_start: 0.6564 (OUTLIER) cc_final: 0.6023 (p90) REVERT: L 10 TYR cc_start: 0.8359 (OUTLIER) cc_final: 0.7470 (p90) REVERT: M 13 HIS cc_start: 0.6676 (OUTLIER) cc_final: 0.6262 (p90) REVERT: N 27 ASN cc_start: 0.8496 (t0) cc_final: 0.8114 (t0) REVERT: P 34 LEU cc_start: 0.9298 (tt) cc_final: 0.9047 (tp) REVERT: R 35 MET cc_start: 0.6715 (OUTLIER) cc_final: 0.6305 (ttm) REVERT: S 15 GLN cc_start: 0.7519 (OUTLIER) cc_final: 0.7079 (tm130) REVERT: S 17 LEU cc_start: 0.7380 (tp) cc_final: 0.7178 (tt) REVERT: T 35 MET cc_start: 0.6657 (OUTLIER) cc_final: 0.6176 (ttm) outliers start: 52 outliers final: 29 residues processed: 199 average time/residue: 0.1470 time to fit residues: 39.2989 Evaluate side-chains 217 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 170 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE Chi-restraints excluded: chain A residue 27 ASN 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 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 10 TYR Chi-restraints excluded: chain J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE 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 7 ASP 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 15 GLN 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 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 13 optimal weight: 1.9990 chunk 42 optimal weight: 6.9990 chunk 45 optimal weight: 8.9990 chunk 33 optimal weight: 4.9990 chunk 6 optimal weight: 0.4980 chunk 53 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 ** 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 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** 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 14 HIS ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7319 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 5600 Z= 0.310 Angle : 0.850 8.182 7520 Z= 0.457 Chirality : 0.062 0.176 810 Planarity : 0.003 0.015 990 Dihedral : 11.742 87.673 760 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 22.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.36 % Favored : 84.64 % Rotamer: Outliers : 9.29 % Allowed : 28.21 % Favored : 62.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.36 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.56 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 13 PHE 0.031 0.004 PHE K 19 TYR 0.010 0.001 TYR J 10 ARG 0.001 0.000 ARG N 5 *********************** 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 219 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 167 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7374 (p90) cc_final: 0.6841 (p-80) REVERT: B 10 TYR cc_start: 0.8290 (OUTLIER) cc_final: 0.6700 (p90) REVERT: C 11 GLU cc_start: 0.7563 (mp0) cc_final: 0.6745 (mp0) REVERT: C 19 PHE cc_start: 0.6795 (OUTLIER) cc_final: 0.6477 (p90) REVERT: E 13 HIS cc_start: 0.7017 (OUTLIER) cc_final: 0.6361 (p90) REVERT: F 10 TYR cc_start: 0.7819 (OUTLIER) cc_final: 0.6926 (p90) REVERT: G 13 HIS cc_start: 0.6943 (OUTLIER) cc_final: 0.6284 (p90) REVERT: H 10 TYR cc_start: 0.7791 (OUTLIER) cc_final: 0.6733 (p90) REVERT: I 13 HIS cc_start: 0.7232 (OUTLIER) cc_final: 0.6676 (p90) REVERT: I 19 PHE cc_start: 0.6411 (OUTLIER) cc_final: 0.5892 (p90) REVERT: I 35 MET cc_start: 0.8197 (mmm) cc_final: 0.7740 (mmm) REVERT: J 10 TYR cc_start: 0.8327 (OUTLIER) cc_final: 0.7289 (p90) REVERT: K 13 HIS cc_start: 0.7029 (OUTLIER) cc_final: 0.6556 (p90) REVERT: K 19 PHE cc_start: 0.6447 (OUTLIER) cc_final: 0.5907 (p90) REVERT: K 35 MET cc_start: 0.8066 (mmm) cc_final: 0.7786 (mmm) REVERT: L 10 TYR cc_start: 0.8264 (OUTLIER) cc_final: 0.7415 (p90) REVERT: L 34 LEU cc_start: 0.9057 (tp) cc_final: 0.8596 (tp) REVERT: M 13 HIS cc_start: 0.6558 (OUTLIER) cc_final: 0.6180 (p90) REVERT: N 27 ASN cc_start: 0.8477 (t0) cc_final: 0.8065 (t0) REVERT: P 34 LEU cc_start: 0.9339 (tt) cc_final: 0.9138 (tp) REVERT: S 15 GLN cc_start: 0.7551 (OUTLIER) cc_final: 0.7156 (tm130) REVERT: S 17 LEU cc_start: 0.7420 (tp) cc_final: 0.7218 (tt) REVERT: T 35 MET cc_start: 0.6699 (OUTLIER) cc_final: 0.6351 (ttm) outliers start: 52 outliers final: 29 residues processed: 193 average time/residue: 0.1441 time to fit residues: 37.0423 Evaluate side-chains 206 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 162 time to evaluate : 0.567 ------------------------------------------------------------------------------- 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 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 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 J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 17 LEU Chi-restraints excluded: chain K residue 19 PHE 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 7 ASP 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 S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.5980 chunk 49 optimal weight: 5.9990 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 3.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 3.9990 overall best weight: 2.4586 ------------------------------------------------------------------------------- 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 ** 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** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.7525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.076 5600 Z= 0.647 Angle : 1.115 15.782 7520 Z= 0.604 Chirality : 0.072 0.224 810 Planarity : 0.004 0.018 990 Dihedral : 12.617 89.753 760 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 30.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.55 % Favored : 81.45 % Rotamer: Outliers : 8.39 % Allowed : 28.93 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.74 (0.24), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS N 6 PHE 0.041 0.005 PHE A 19 TYR 0.015 0.002 TYR O 10 ARG 0.003 0.001 ARG B 5 *********************** 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 203 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 156 time to evaluate : 0.609 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.6985 (OUTLIER) cc_final: 0.6538 (p90) REVERT: B 10 TYR cc_start: 0.8399 (OUTLIER) cc_final: 0.6855 (p90) REVERT: C 19 PHE cc_start: 0.7491 (OUTLIER) cc_final: 0.6754 (p90) REVERT: D 10 TYR cc_start: 0.8496 (OUTLIER) cc_final: 0.6924 (p90) REVERT: E 13 HIS cc_start: 0.7158 (OUTLIER) cc_final: 0.6442 (p90) REVERT: E 19 PHE cc_start: 0.7653 (OUTLIER) cc_final: 0.7249 (p90) REVERT: F 10 TYR cc_start: 0.8382 (OUTLIER) cc_final: 0.6665 (p90) REVERT: F 36 VAL cc_start: 0.8496 (p) cc_final: 0.8217 (m) REVERT: G 13 HIS cc_start: 0.7077 (OUTLIER) cc_final: 0.6245 (p90) REVERT: H 10 TYR cc_start: 0.8369 (OUTLIER) cc_final: 0.6718 (p90) REVERT: I 13 HIS cc_start: 0.7302 (OUTLIER) cc_final: 0.6741 (p90) REVERT: J 10 TYR cc_start: 0.8686 (OUTLIER) cc_final: 0.7725 (p90) REVERT: K 13 HIS cc_start: 0.7284 (OUTLIER) cc_final: 0.6734 (p90) REVERT: L 10 TYR cc_start: 0.8629 (OUTLIER) cc_final: 0.7871 (p90) REVERT: M 13 HIS cc_start: 0.7257 (OUTLIER) cc_final: 0.6695 (p90) REVERT: M 35 MET cc_start: 0.8415 (mpp) cc_final: 0.8026 (mmt) REVERT: N 10 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.7287 (p90) REVERT: O 13 HIS cc_start: 0.7294 (OUTLIER) cc_final: 0.6767 (p90) REVERT: P 10 TYR cc_start: 0.8308 (OUTLIER) cc_final: 0.7310 (p90) REVERT: P 34 LEU cc_start: 0.9477 (tt) cc_final: 0.9266 (tp) REVERT: Q 19 PHE cc_start: 0.7225 (OUTLIER) cc_final: 0.6620 (p90) REVERT: S 15 GLN cc_start: 0.7787 (OUTLIER) cc_final: 0.7110 (tm130) REVERT: S 19 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6693 (p90) REVERT: S 35 MET cc_start: 0.7956 (mmt) cc_final: 0.7749 (mmt) outliers start: 47 outliers final: 22 residues processed: 182 average time/residue: 0.1464 time to fit residues: 35.5284 Evaluate side-chains 194 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 152 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE 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 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 36 VAL 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 J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE 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 13 HIS 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 R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 3.9990 chunk 64 optimal weight: 0.7980 chunk 55 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 0.5980 chunk 59 optimal weight: 7.9990 chunk 17 optimal weight: 10.0000 chunk 51 optimal weight: 0.0980 chunk 8 optimal weight: 0.7980 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 ** 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** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7311 moved from start: 0.7810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5600 Z= 0.314 Angle : 0.919 10.736 7520 Z= 0.484 Chirality : 0.062 0.226 810 Planarity : 0.003 0.014 990 Dihedral : 12.197 88.287 760 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 25.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.22 % Favored : 84.78 % Rotamer: Outliers : 7.86 % Allowed : 29.46 % Favored : 62.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.67 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.79 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS T 13 PHE 0.033 0.004 PHE A 19 TYR 0.012 0.001 TYR J 10 ARG 0.002 0.000 ARG D 5 ********************** 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 202 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 158 time to evaluate : 0.627 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 13 HIS cc_start: 0.7293 (p90) cc_final: 0.6765 (p-80) REVERT: A 19 PHE cc_start: 0.6445 (OUTLIER) cc_final: 0.6033 (p90) REVERT: B 10 TYR cc_start: 0.8271 (OUTLIER) cc_final: 0.6643 (p90) REVERT: C 19 PHE cc_start: 0.7247 (OUTLIER) cc_final: 0.6768 (p90) REVERT: D 10 TYR cc_start: 0.8277 (OUTLIER) cc_final: 0.6631 (p90) REVERT: E 13 HIS cc_start: 0.6989 (OUTLIER) cc_final: 0.6307 (p90) REVERT: F 10 TYR cc_start: 0.7918 (OUTLIER) cc_final: 0.6606 (p90) REVERT: H 10 TYR cc_start: 0.7868 (OUTLIER) cc_final: 0.6499 (p90) REVERT: I 13 HIS cc_start: 0.6978 (OUTLIER) cc_final: 0.6549 (p90) REVERT: I 19 PHE cc_start: 0.6465 (OUTLIER) cc_final: 0.6011 (p90) REVERT: I 35 MET cc_start: 0.8308 (mmt) cc_final: 0.8013 (mmm) REVERT: J 10 TYR cc_start: 0.8301 (OUTLIER) cc_final: 0.7151 (p90) REVERT: K 13 HIS cc_start: 0.7054 (OUTLIER) cc_final: 0.6594 (p90) REVERT: K 19 PHE cc_start: 0.6431 (OUTLIER) cc_final: 0.5903 (p90) REVERT: L 10 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7269 (p90) REVERT: M 15 GLN cc_start: 0.8019 (tm-30) cc_final: 0.7733 (tm-30) REVERT: M 35 MET cc_start: 0.8167 (mpp) cc_final: 0.7623 (mmm) REVERT: N 27 ASN cc_start: 0.8632 (t0) cc_final: 0.8340 (t0) REVERT: Q 15 GLN cc_start: 0.7588 (OUTLIER) cc_final: 0.6932 (tm130) REVERT: R 35 MET cc_start: 0.6746 (OUTLIER) cc_final: 0.6361 (ttm) REVERT: S 15 GLN cc_start: 0.7595 (OUTLIER) cc_final: 0.7152 (tm130) REVERT: S 17 LEU cc_start: 0.7399 (tp) cc_final: 0.7198 (tt) outliers start: 44 outliers final: 24 residues processed: 178 average time/residue: 0.1449 time to fit residues: 34.5123 Evaluate side-chains 189 residues out of total 560 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 149 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 PHE 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 F residue 10 TYR Chi-restraints excluded: chain F residue 12 VAL Chi-restraints excluded: chain G residue 19 PHE 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 J residue 12 VAL Chi-restraints excluded: chain K residue 13 HIS Chi-restraints excluded: chain K residue 19 PHE Chi-restraints excluded: chain L residue 10 TYR Chi-restraints excluded: chain L residue 12 VAL 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 15 GLN Chi-restraints excluded: chain Q residue 19 PHE Chi-restraints excluded: chain R residue 10 TYR Chi-restraints excluded: chain R residue 35 MET Chi-restraints excluded: chain S residue 15 GLN Chi-restraints excluded: chain S residue 19 PHE 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9980 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 0.0470 chunk 7 optimal weight: 6.9990 chunk 10 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 3 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 63 optimal weight: 0.4980 chunk 37 optimal weight: 2.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- 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** C 27 ASN ** 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** ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 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** ** M 27 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 14 HIS ** 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** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5799 r_free = 0.5799 target = 0.359166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.6157 r_free = 0.6157 target = 0.281040 restraints weight = 8852.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.6204 r_free = 0.6204 target = 0.283640 restraints weight = 4561.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.6244 r_free = 0.6244 target = 0.285309 restraints weight = 2648.909| |-----------------------------------------------------------------------------| r_work (final): 0.5769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7096 moved from start: 0.7959 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5600 Z= 0.298 Angle : 0.908 9.198 7520 Z= 0.478 Chirality : 0.062 0.183 810 Planarity : 0.003 0.017 990 Dihedral : 11.967 89.225 760 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 25.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.23 % Favored : 83.77 % Rotamer: Outliers : 7.50 % Allowed : 31.25 % Favored : 61.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.60 (0.25), residues: 690 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.74 (0.19), residues: 690 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS R 13 PHE 0.032 0.003 PHE A 19 TYR 0.011 0.001 TYR J 10 ARG 0.001 0.000 ARG B 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1610.56 seconds wall clock time: 30 minutes 12.61 seconds (1812.61 seconds total)