Starting phenix.real_space_refine on Thu Nov 14 00:23:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwj_60529/11_2024/8zwj_60529.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwj_60529/11_2024/8zwj_60529.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwj_60529/11_2024/8zwj_60529.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwj_60529/11_2024/8zwj_60529.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwj_60529/11_2024/8zwj_60529.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8zwj_60529/11_2024/8zwj_60529.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 P 6 5.49 5 C 1704 2.51 5 N 486 2.21 5 O 564 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 2760 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 63, 438 Classifications: {'peptide': 63} Link IDs: {'TRANS': 62} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 66 Classifications: {'RNA': 3} Modifications used: {'rna3p_pur': 3} Link IDs: {'rna3p': 2} Restraints were copied for chains: Q, C, B, E, D, G Time building chain proxies: 2.07, per 1000 atoms: 0.75 Number of scatterers: 2760 At special positions: 0 Unit cell: (83.83, 103.75, 31.54, 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) P 6 15.00 O 564 8.00 N 486 7.00 C 1704 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 349.6 milliseconds 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 648 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 46.0% beta 0 base pairs and 2 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 46 through 58 removed outlier: 7.446A pdb=" N GLY G 47 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N HIS C 50 " --> pdb=" O GLY G 47 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL G 49 " --> pdb=" O HIS C 50 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL C 52 " --> pdb=" O VAL G 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY G 51 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR C 54 " --> pdb=" O GLY G 51 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA G 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA C 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL G 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS C 58 " --> pdb=" O VAL G 55 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU G 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 8.680A pdb=" N GLU G 46 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL D 49 " --> pdb=" O GLU G 46 " (cutoff:3.500A) removed outlier: 9.095A pdb=" N VAL G 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLY D 51 " --> pdb=" O VAL G 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS G 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 9.000A pdb=" N ALA D 53 " --> pdb=" O HIS G 50 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL G 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL D 55 " --> pdb=" O VAL G 52 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR G 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU D 57 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA G 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 62 through 66 removed outlier: 6.577A pdb=" N GLN G 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N ASN C 65 " --> pdb=" O GLN G 62 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR G 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 69 through 82 removed outlier: 6.917A pdb=" N VAL C 74 " --> pdb=" O GLY G 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR G 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N ALA C 76 " --> pdb=" O THR G 75 " (cutoff:3.500A) removed outlier: 6.317A pdb=" N VAL G 70 " --> pdb=" O VAL D 71 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY D 73 " --> pdb=" O VAL G 70 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR G 72 " --> pdb=" O GLY D 73 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR D 75 " --> pdb=" O THR G 72 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N VAL G 74 " --> pdb=" O THR D 75 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N VAL D 77 " --> pdb=" O VAL G 74 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA G 76 " --> pdb=" O VAL D 77 " (cutoff:3.500A) removed outlier: 8.479A pdb=" N GLN D 79 " --> pdb=" O ALA G 76 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA G 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR D 81 " --> pdb=" O ALA G 78 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N LYS G 80 " --> pdb=" O THR D 81 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 46 through 58 removed outlier: 7.446A pdb=" N GLY E 47 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 10.167A pdb=" N HIS A 50 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 8.906A pdb=" N VAL E 49 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N VAL A 52 " --> pdb=" O VAL E 49 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLY E 51 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N THR A 54 " --> pdb=" O GLY E 51 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ALA E 53 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.289A pdb=" N ALA A 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.715A pdb=" N VAL E 55 " --> pdb=" O ALA A 56 " (cutoff:3.500A) removed outlier: 8.000A pdb=" N LYS A 58 " --> pdb=" O VAL E 55 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N GLU E 57 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLU E 46 " --> pdb=" O GLY B 47 " (cutoff:3.500A) removed outlier: 8.385A pdb=" N VAL B 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N VAL E 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 10.367A pdb=" N GLY B 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N HIS E 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 9.001A pdb=" N ALA B 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N VAL E 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 8.049A pdb=" N VAL B 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N THR E 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 8.135A pdb=" N GLU B 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ALA E 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 62 through 66 removed outlier: 6.577A pdb=" N GLN E 62 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 8.253A pdb=" N ASN A 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N THR E 64 " --> pdb=" O ASN A 65 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.917A pdb=" N VAL A 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N THR E 75 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N ALA A 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N VAL E 70 " --> pdb=" O VAL B 71 " (cutoff:3.500A) removed outlier: 8.230A pdb=" N GLY B 73 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 8.716A pdb=" N THR E 72 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N THR B 75 " --> pdb=" O THR E 72 " (cutoff:3.500A) removed outlier: 8.985A pdb=" N VAL E 74 " --> pdb=" O THR B 75 " (cutoff:3.500A) removed outlier: 9.274A pdb=" N VAL B 77 " --> pdb=" O VAL E 74 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ALA E 76 " --> pdb=" O VAL B 77 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLN B 79 " --> pdb=" O ALA E 76 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ALA E 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) removed outlier: 8.451A pdb=" N THR B 81 " --> pdb=" O ALA E 78 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N LYS E 80 " --> pdb=" O THR B 81 " (cutoff:3.500A) 28 hydrogen bonds defined for protein. 84 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 2 stacking parallelities Total time for adding SS restraints: 0.51 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.30: 462 1.30 - 1.38: 503 1.38 - 1.46: 317 1.46 - 1.53: 1397 1.53 - 1.61: 109 Bond restraints: 2788 Sorted by residual: bond pdb=" C THR B 92 " pdb=" N GLY B 93 " ideal model delta sigma weight residual 1.329 1.309 0.020 1.62e-02 3.81e+03 1.53e+00 bond pdb=" C THR D 92 " pdb=" N GLY D 93 " ideal model delta sigma weight residual 1.329 1.309 0.020 1.62e-02 3.81e+03 1.47e+00 bond pdb=" C THR G 92 " pdb=" N GLY G 93 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.62e-02 3.81e+03 1.45e+00 bond pdb=" C THR E 92 " pdb=" N GLY E 93 " ideal model delta sigma weight residual 1.329 1.309 0.019 1.62e-02 3.81e+03 1.40e+00 bond pdb=" C THR A 92 " pdb=" N GLY A 93 " ideal model delta sigma weight residual 1.329 1.310 0.019 1.62e-02 3.81e+03 1.39e+00 ... (remaining 2783 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.82: 3184 0.82 - 1.65: 435 1.65 - 2.47: 113 2.47 - 3.29: 27 3.29 - 4.12: 37 Bond angle restraints: 3796 Sorted by residual: angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.94 117.82 4.12 1.76e+00 3.23e-01 5.47e+00 angle pdb=" C VAL D 49 " pdb=" N HIS D 50 " pdb=" CA HIS D 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.46e+00 angle pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.46e+00 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.46e+00 angle pdb=" C VAL E 49 " pdb=" N HIS E 50 " pdb=" CA HIS E 50 " ideal model delta sigma weight residual 121.94 117.83 4.11 1.76e+00 3.23e-01 5.44e+00 ... (remaining 3791 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.39: 1514 24.39 - 48.77: 94 48.77 - 73.15: 0 73.15 - 97.53: 0 97.53 - 121.91: 6 Dihedral angle restraints: 1614 sinusoidal: 588 harmonic: 1026 Sorted by residual: dihedral pdb=" CA VAL G 40 " pdb=" C VAL G 40 " pdb=" N GLY G 41 " pdb=" CA GLY G 41 " ideal model delta harmonic sigma weight residual 180.00 162.06 17.94 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL E 40 " pdb=" C VAL E 40 " pdb=" N GLY E 41 " pdb=" CA GLY E 41 " ideal model delta harmonic sigma weight residual 180.00 162.07 17.93 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA VAL A 40 " pdb=" C VAL A 40 " pdb=" N GLY A 41 " pdb=" CA GLY A 41 " ideal model delta harmonic sigma weight residual 180.00 162.09 17.91 0 5.00e+00 4.00e-02 1.28e+01 ... (remaining 1611 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 186 0.028 - 0.055: 190 0.055 - 0.083: 48 0.083 - 0.110: 44 0.110 - 0.138: 30 Chirality restraints: 498 Sorted by residual: chirality pdb=" CA VAL A 49 " pdb=" N VAL A 49 " pdb=" C VAL A 49 " pdb=" CB VAL A 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.73e-01 chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA VAL B 49 " pdb=" N VAL B 49 " pdb=" C VAL B 49 " pdb=" CB VAL B 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 495 not shown) Planarity restraints: 450 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS G 50 " 0.010 2.00e-02 2.50e+03 8.45e-03 1.07e+00 pdb=" CG HIS G 50 " -0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS G 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS G 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS G 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS G 50 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS E 50 " -0.009 2.00e-02 2.50e+03 8.36e-03 1.05e+00 pdb=" CG HIS E 50 " 0.018 2.00e-02 2.50e+03 pdb=" ND1 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS E 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS E 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS E 50 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 50 " 0.009 2.00e-02 2.50e+03 8.24e-03 1.02e+00 pdb=" CG HIS D 50 " -0.017 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " 0.004 2.00e-02 2.50e+03 ... (remaining 447 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 298 2.75 - 3.29: 2572 3.29 - 3.83: 4155 3.83 - 4.36: 4725 4.36 - 4.90: 9688 Nonbonded interactions: 21438 Sorted by model distance: nonbonded pdb=" OE2 GLU B 46 " pdb=" NZ LYS B 80 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU A 46 " pdb=" NZ LYS A 80 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU E 46 " pdb=" NZ LYS E 80 " model vdw 2.218 3.120 nonbonded pdb=" OE2 GLU D 46 " pdb=" NZ LYS D 80 " model vdw 2.219 3.120 nonbonded pdb=" OE2 GLU G 46 " pdb=" NZ LYS G 80 " model vdw 2.219 3.120 ... (remaining 21433 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'G' } ncs_group { reference = chain 'F' selection = chain 'Q' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.050 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 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 : 0.006 0.030 2788 Z= 0.435 Angle : 0.737 4.117 3796 Z= 0.412 Chirality : 0.054 0.138 498 Planarity : 0.002 0.009 450 Dihedral : 15.838 121.909 966 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 0.00 % Allowed : 17.78 % Favored : 82.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.10 (0.30), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.12 (0.23), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS G 50 PHE 0.013 0.004 PHE A 94 TYR 0.010 0.003 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.290 Fit side-chains REVERT: G 60 LYS cc_start: 0.8316 (ttpt) cc_final: 0.7928 (ttmm) REVERT: G 96 LYS cc_start: 0.6397 (mttt) cc_final: 0.6197 (mttm) REVERT: C 62 GLN cc_start: 0.7188 (mt0) cc_final: 0.6770 (tt0) REVERT: C 83 GLU cc_start: 0.7574 (tm-30) cc_final: 0.7321 (tm-30) REVERT: E 62 GLN cc_start: 0.7018 (mt0) cc_final: 0.6599 (tt0) REVERT: E 83 GLU cc_start: 0.7560 (tm-30) cc_final: 0.7314 (tm-30) REVERT: A 60 LYS cc_start: 0.8371 (ttpt) cc_final: 0.8102 (ttmm) REVERT: A 62 GLN cc_start: 0.7293 (mt0) cc_final: 0.6866 (tt0) REVERT: A 83 GLU cc_start: 0.7635 (tm-30) cc_final: 0.7423 (tm-30) REVERT: B 60 LYS cc_start: 0.8311 (ttpt) cc_final: 0.8063 (ttmm) outliers start: 0 outliers final: 0 residues processed: 30 average time/residue: 0.2779 time to fit residues: 9.5054 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 29 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 0.0050 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 18 optimal weight: 9.9990 chunk 14 optimal weight: 4.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 6.9990 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN C 62 GLN D 62 GLN E 62 GLN A 62 GLN B 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 2788 Z= 0.150 Angle : 0.483 3.184 3796 Z= 0.265 Chirality : 0.051 0.137 498 Planarity : 0.002 0.010 450 Dihedral : 14.653 107.639 444 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 3.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.74 % Allowed : 16.30 % Favored : 82.96 % 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: -3.54 (0.34), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.69 (0.26), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS E 50 PHE 0.004 0.001 PHE C 94 TYR 0.002 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.292 Fit side-chains REVERT: G 60 LYS cc_start: 0.8124 (ttpt) cc_final: 0.7852 (ttmm) REVERT: C 62 GLN cc_start: 0.7200 (mt0) cc_final: 0.6932 (tt0) REVERT: E 62 GLN cc_start: 0.6984 (mt0) cc_final: 0.6699 (tt0) REVERT: E 83 GLU cc_start: 0.7490 (tm-30) cc_final: 0.7234 (tm-30) REVERT: A 62 GLN cc_start: 0.7274 (mt0) cc_final: 0.6816 (tt0) REVERT: B 60 LYS cc_start: 0.8166 (ttpt) cc_final: 0.7906 (ttmm) outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.2309 time to fit residues: 7.5117 Evaluate side-chains 30 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 28 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 26 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN D 62 GLN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8158 moved from start: 0.1515 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2788 Z= 0.281 Angle : 0.536 3.827 3796 Z= 0.298 Chirality : 0.051 0.138 498 Planarity : 0.002 0.011 450 Dihedral : 14.181 103.859 444 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.11 % Favored : 89.89 % Rotamer: Outliers : 4.07 % Allowed : 14.07 % Favored : 81.85 % 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: -3.18 (0.36), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.41 (0.28), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS G 50 PHE 0.010 0.003 PHE A 94 TYR 0.008 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 17 time to evaluate : 0.298 Fit side-chains REVERT: D 60 LYS cc_start: 0.8434 (ttmm) cc_final: 0.8185 (tttm) REVERT: A 62 GLN cc_start: 0.7361 (mt0) cc_final: 0.6877 (tt0) REVERT: B 60 LYS cc_start: 0.8257 (ttpt) cc_final: 0.7978 (ttmm) outliers start: 11 outliers final: 8 residues processed: 27 average time/residue: 0.2861 time to fit residues: 9.0586 Evaluate side-chains 24 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 16 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 9.9990 chunk 15 optimal weight: 6.9990 chunk 21 optimal weight: 10.0000 chunk 32 optimal weight: 0.0570 chunk 34 optimal weight: 0.0040 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 overall best weight: 0.9914 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN D 62 GLN B 62 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 2788 Z= 0.139 Angle : 0.434 3.538 3796 Z= 0.242 Chirality : 0.050 0.132 498 Planarity : 0.002 0.006 450 Dihedral : 13.569 101.124 444 Min Nonbonded Distance : 2.601 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 2.22 % Allowed : 19.26 % Favored : 78.52 % 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: -3.00 (0.38), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.28 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.005 0.001 PHE A 94 TYR 0.003 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.303 Fit side-chains REVERT: D 60 LYS cc_start: 0.8348 (ttmm) cc_final: 0.8123 (tttm) REVERT: A 62 GLN cc_start: 0.7396 (mt0) cc_final: 0.6921 (tt0) REVERT: B 60 LYS cc_start: 0.8200 (ttpt) cc_final: 0.7963 (ttmm) outliers start: 6 outliers final: 6 residues processed: 21 average time/residue: 0.1903 time to fit residues: 4.9308 Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 31 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 11 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2788 Z= 0.214 Angle : 0.482 3.345 3796 Z= 0.268 Chirality : 0.050 0.137 498 Planarity : 0.002 0.009 450 Dihedral : 12.885 96.722 444 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 5.19 % Allowed : 18.15 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.76 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS G 50 PHE 0.010 0.003 PHE A 94 TYR 0.008 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 18 time to evaluate : 0.316 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.7362 (mt0) cc_final: 0.6891 (tt0) REVERT: B 60 LYS cc_start: 0.8302 (ttpt) cc_final: 0.7995 (ttmm) outliers start: 14 outliers final: 11 residues processed: 27 average time/residue: 0.1932 time to fit residues: 6.4333 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 18 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 37 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 6.9990 chunk 28 optimal weight: 0.6980 chunk 16 optimal weight: 0.0870 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.7564 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.2309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2788 Z= 0.217 Angle : 0.481 4.006 3796 Z= 0.267 Chirality : 0.050 0.138 498 Planarity : 0.002 0.007 450 Dihedral : 12.264 93.596 444 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.74 % Favored : 91.26 % Rotamer: Outliers : 4.44 % Allowed : 19.26 % Favored : 76.30 % 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: -2.62 (0.39), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.99 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS E 50 PHE 0.007 0.002 PHE A 94 TYR 0.007 0.002 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: G 37 VAL cc_start: 0.4505 (OUTLIER) cc_final: 0.4282 (p) REVERT: E 37 VAL cc_start: 0.4965 (OUTLIER) cc_final: 0.4749 (p) REVERT: A 62 GLN cc_start: 0.7405 (mt0) cc_final: 0.6926 (tt0) REVERT: B 60 LYS cc_start: 0.8255 (ttpt) cc_final: 0.8008 (ttmm) outliers start: 12 outliers final: 10 residues processed: 26 average time/residue: 0.1905 time to fit residues: 5.9646 Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 19 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 0.4980 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 6 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.2608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2788 Z= 0.166 Angle : 0.433 4.092 3796 Z= 0.243 Chirality : 0.049 0.135 498 Planarity : 0.001 0.007 450 Dihedral : 11.644 90.290 444 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 2.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.56 % Favored : 90.44 % Rotamer: Outliers : 4.81 % Allowed : 19.63 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.51 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.90 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.005 0.001 PHE D 94 TYR 0.005 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 21 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 83 GLU cc_start: 0.7622 (tm-30) cc_final: 0.7376 (tm-30) REVERT: E 83 GLU cc_start: 0.7515 (OUTLIER) cc_final: 0.6986 (tm-30) REVERT: A 62 GLN cc_start: 0.7395 (mt0) cc_final: 0.6856 (tt0) REVERT: A 83 GLU cc_start: 0.7697 (tm-30) cc_final: 0.7470 (tm-30) outliers start: 13 outliers final: 10 residues processed: 29 average time/residue: 0.1743 time to fit residues: 6.2035 Evaluate side-chains 33 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 22 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 37 VAL Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2788 Z= 0.177 Angle : 0.458 5.377 3796 Z= 0.254 Chirality : 0.050 0.137 498 Planarity : 0.001 0.008 450 Dihedral : 11.212 87.354 444 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 4.07 % Allowed : 20.37 % Favored : 75.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.38 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.81 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS G 50 PHE 0.007 0.002 PHE B 94 TYR 0.006 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 20 time to evaluate : 0.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.7255 (mt0) cc_final: 0.7036 (tt0) REVERT: C 83 GLU cc_start: 0.7629 (tm-30) cc_final: 0.7361 (tm-30) REVERT: E 83 GLU cc_start: 0.7518 (OUTLIER) cc_final: 0.7010 (tm-30) REVERT: A 62 GLN cc_start: 0.7384 (mt0) cc_final: 0.6865 (tt0) REVERT: A 83 GLU cc_start: 0.7681 (tm-30) cc_final: 0.7458 (tm-30) outliers start: 11 outliers final: 9 residues processed: 26 average time/residue: 0.1820 time to fit residues: 5.7764 Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 19 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain C residue 54 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 9.9990 chunk 30 optimal weight: 0.0030 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 16 optimal weight: 0.0000 chunk 23 optimal weight: 0.9990 chunk 35 optimal weight: 6.9990 chunk 33 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 overall best weight: 0.4794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8036 moved from start: 0.3281 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.001 0.012 2788 Z= 0.087 Angle : 0.370 3.533 3796 Z= 0.209 Chirality : 0.050 0.131 498 Planarity : 0.001 0.005 450 Dihedral : 10.646 85.263 444 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 1.85 % Allowed : 22.96 % Favored : 75.19 % 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: -2.28 (0.43), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS G 50 PHE 0.004 0.001 PHE B 94 TYR 0.002 0.000 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 24 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 62 GLN cc_start: 0.7189 (mt0) cc_final: 0.6966 (tt0) REVERT: C 83 GLU cc_start: 0.7616 (tm-30) cc_final: 0.7367 (tm-30) REVERT: D 62 GLN cc_start: 0.7158 (OUTLIER) cc_final: 0.6928 (mt0) REVERT: E 83 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: A 83 GLU cc_start: 0.7705 (tm-30) cc_final: 0.7466 (tm-30) outliers start: 5 outliers final: 3 residues processed: 27 average time/residue: 0.1914 time to fit residues: 6.2398 Evaluate side-chains 27 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 22 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 83 GLU Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8202 moved from start: 0.2760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 2788 Z= 0.481 Angle : 0.669 4.718 3796 Z= 0.370 Chirality : 0.053 0.140 498 Planarity : 0.003 0.010 450 Dihedral : 10.611 81.023 444 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 5.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 2.59 % Allowed : 22.96 % Favored : 74.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.39 (0.40), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.005 HIS G 50 PHE 0.016 0.004 PHE B 94 TYR 0.016 0.003 TYR G 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 732 Ramachandran restraints generated. 366 Oldfield, 0 Emsley, 366 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.260 Fit side-chains REVERT: C 83 GLU cc_start: 0.7581 (tm-30) cc_final: 0.7287 (tm-30) REVERT: E 83 GLU cc_start: 0.7674 (tm-30) cc_final: 0.7175 (tm-30) REVERT: A 62 GLN cc_start: 0.7344 (mt0) cc_final: 0.6866 (tt0) REVERT: A 83 GLU cc_start: 0.7700 (tm-30) cc_final: 0.7448 (tm-30) REVERT: B 60 LYS cc_start: 0.8384 (ttpt) cc_final: 0.8090 (ttmm) outliers start: 7 outliers final: 7 residues processed: 32 average time/residue: 0.1968 time to fit residues: 7.4548 Evaluate side-chains 35 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 28 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain D residue 59 THR Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain E residue 59 THR Chi-restraints excluded: chain B residue 59 THR Chi-restraints excluded: chain B residue 62 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 6.9990 chunk 25 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.193138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.143306 restraints weight = 2714.316| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 2.28 r_work: 0.3864 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3748 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.3068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2788 Z= 0.168 Angle : 0.462 4.224 3796 Z= 0.260 Chirality : 0.050 0.139 498 Planarity : 0.002 0.009 450 Dihedral : 9.819 79.346 444 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 3.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 2.59 % Allowed : 24.07 % Favored : 73.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -2.28 (0.41), residues: 366 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.31), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS E 50 PHE 0.008 0.001 PHE B 94 TYR 0.005 0.001 TYR D 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1161.96 seconds wall clock time: 21 minutes 28.24 seconds (1288.24 seconds total)