Starting phenix.real_space_refine on Tue Jul 29 23:26:29 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zhx_11220/07_2025/6zhx_11220.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zhx_11220/07_2025/6zhx_11220.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zhx_11220/07_2025/6zhx_11220.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zhx_11220/07_2025/6zhx_11220.map" model { file = "/net/cci-nas-00/data/ceres_data/6zhx_11220/07_2025/6zhx_11220.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zhx_11220/07_2025/6zhx_11220.cif" } resolution = 2.5 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= 0.004 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: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 10 5.16 5 C 6740 2.51 5 N 2299 2.21 5 O 2976 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 12313 Number of models: 1 Model: "" Number of chains: 22 Chain: "A" Number of atoms: 806 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 806 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "D" Number of atoms: 767 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 767 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 807 Classifications: {'peptide': 98} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 94} Chain: "F" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 850 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "L" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 29 Classifications: {'peptide': 4} Link IDs: {'TRANS': 3} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 19, 19 Classifications: {'water': 19} Link IDs: {None: 18} Chain: "B" Number of atoms: 25 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 25 Classifications: {'water': 25} Link IDs: {None: 24} Chain: "C" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "D" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "E" Number of atoms: 21 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 21 Classifications: {'water': 21} Link IDs: {None: 20} Chain: "F" Number of atoms: 20 Number of conformers: 1 Conformer: "" Number of residues, atoms: 20, 20 Classifications: {'water': 20} Link IDs: {None: 19} Chain: "G" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "H" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "I" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 4 Classifications: {'water': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 5 Classifications: {'water': 5} Link IDs: {None: 4} Time building chain proxies: 8.03, per 1000 atoms: 0.65 Number of scatterers: 12313 At special positions: 0 Unit cell: (117.066, 103.986, 115.758, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 288 15.00 O 2976 8.00 N 2299 7.00 C 6740 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: 2.97 Conformation dependent library (CDL) restraints added in 1.2 seconds 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1468 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.3% alpha, 2.6% beta 145 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.950A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.344A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 122 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.957A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.375A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.714A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.894A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.641A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.652A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.845A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 426 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 145 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 7.52 Time building geometry restraints manager: 3.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2483 1.33 - 1.45: 4038 1.45 - 1.57: 5850 1.57 - 1.69: 577 1.69 - 1.80: 20 Bond restraints: 12968 Sorted by residual: bond pdb=" C3' DT J 54 " pdb=" C2' DT J 54 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.00e-02 2.50e+03 3.10e+00 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.525 1.560 -0.035 2.00e-02 2.50e+03 3.04e+00 bond pdb=" C3' DC I 6 " pdb=" C2' DC I 6 " ideal model delta sigma weight residual 1.525 1.559 -0.034 2.00e-02 2.50e+03 2.87e+00 bond pdb=" C3' DT J 69 " pdb=" C2' DT J 69 " ideal model delta sigma weight residual 1.525 1.558 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C3' DG I 54 " pdb=" C2' DG I 54 " ideal model delta sigma weight residual 1.525 1.557 -0.032 2.00e-02 2.50e+03 2.52e+00 ... (remaining 12963 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.46: 16687 1.46 - 2.91: 1758 2.91 - 4.37: 261 4.37 - 5.82: 34 5.82 - 7.28: 5 Bond angle restraints: 18745 Sorted by residual: angle pdb=" C3' DG I 25 " pdb=" O3' DG I 25 " pdb=" P DG I 26 " ideal model delta sigma weight residual 120.20 126.48 -6.28 1.50e+00 4.44e-01 1.75e+01 angle pdb=" C2' DT I 31 " pdb=" C1' DT I 31 " pdb=" N1 DT I 31 " ideal model delta sigma weight residual 113.50 119.56 -6.06 1.50e+00 4.44e-01 1.63e+01 angle pdb=" C2' DT I 30 " pdb=" C1' DT I 30 " pdb=" N1 DT I 30 " ideal model delta sigma weight residual 113.50 119.54 -6.04 1.50e+00 4.44e-01 1.62e+01 angle pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sigma weight residual 120.20 126.19 -5.99 1.50e+00 4.44e-01 1.59e+01 angle pdb=" C2' DC I 4 " pdb=" C1' DC I 4 " pdb=" N1 DC I 4 " ideal model delta sigma weight residual 113.50 119.02 -5.52 1.50e+00 4.44e-01 1.35e+01 ... (remaining 18740 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.43: 5872 35.43 - 70.85: 1186 70.85 - 106.28: 17 106.28 - 141.71: 0 141.71 - 177.14: 3 Dihedral angle restraints: 7078 sinusoidal: 4806 harmonic: 2272 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual 180.00 156.29 23.71 0 5.00e+00 4.00e-02 2.25e+01 dihedral pdb=" CA ARG A 40 " pdb=" C ARG A 40 " pdb=" N TYR A 41 " pdb=" CA TYR A 41 " ideal model delta harmonic sigma weight residual 180.00 157.58 22.42 0 5.00e+00 4.00e-02 2.01e+01 dihedral pdb=" CA THR D 85 " pdb=" C THR D 85 " pdb=" N ILE D 86 " pdb=" CA ILE D 86 " ideal model delta harmonic sigma weight residual 180.00 159.50 20.50 0 5.00e+00 4.00e-02 1.68e+01 ... (remaining 7075 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.072: 1734 0.072 - 0.144: 342 0.144 - 0.215: 32 0.215 - 0.287: 21 0.287 - 0.359: 5 Chirality restraints: 2134 Sorted by residual: chirality pdb=" C1' DT I 31 " pdb=" O4' DT I 31 " pdb=" C2' DT I 31 " pdb=" N1 DT I 31 " both_signs ideal model delta sigma weight residual False 2.47 2.11 0.36 2.00e-01 2.50e+01 3.22e+00 chirality pdb=" C1' DT I 30 " pdb=" O4' DT I 30 " pdb=" C2' DT I 30 " pdb=" N1 DT I 30 " both_signs ideal model delta sigma weight residual False 2.47 2.12 0.35 2.00e-01 2.50e+01 3.06e+00 chirality pdb=" C4' DT J 69 " pdb=" C5' DT J 69 " pdb=" O4' DT J 69 " pdb=" C3' DT J 69 " both_signs ideal model delta sigma weight residual False -2.53 -2.21 -0.31 2.00e-01 2.50e+01 2.43e+00 ... (remaining 2131 not shown) Planarity restraints: 1366 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I 6 " -0.058 2.00e-02 2.50e+03 3.17e-02 2.26e+01 pdb=" N1 DC I 6 " 0.068 2.00e-02 2.50e+03 pdb=" C2 DC I 6 " -0.012 2.00e-02 2.50e+03 pdb=" O2 DC I 6 " 0.016 2.00e-02 2.50e+03 pdb=" N3 DC I 6 " -0.002 2.00e-02 2.50e+03 pdb=" C4 DC I 6 " -0.006 2.00e-02 2.50e+03 pdb=" N4 DC I 6 " -0.020 2.00e-02 2.50e+03 pdb=" C5 DC I 6 " 0.010 2.00e-02 2.50e+03 pdb=" C6 DC I 6 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC I 4 " -0.050 2.00e-02 2.50e+03 2.79e-02 1.76e+01 pdb=" N1 DC I 4 " 0.064 2.00e-02 2.50e+03 pdb=" C2 DC I 4 " -0.011 2.00e-02 2.50e+03 pdb=" O2 DC I 4 " 0.010 2.00e-02 2.50e+03 pdb=" N3 DC I 4 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DC I 4 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC I 4 " -0.014 2.00e-02 2.50e+03 pdb=" C5 DC I 4 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DC I 4 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 60 " 0.037 2.00e-02 2.50e+03 2.72e-02 1.66e+01 pdb=" N1 DC J 60 " -0.067 2.00e-02 2.50e+03 pdb=" C2 DC J 60 " 0.025 2.00e-02 2.50e+03 pdb=" O2 DC J 60 " -0.008 2.00e-02 2.50e+03 pdb=" N3 DC J 60 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DC J 60 " 0.004 2.00e-02 2.50e+03 pdb=" N4 DC J 60 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 60 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 60 " 0.003 2.00e-02 2.50e+03 ... (remaining 1363 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1046 2.74 - 3.28: 10966 3.28 - 3.82: 24662 3.82 - 4.36: 30772 4.36 - 4.90: 42868 Nonbonded interactions: 110314 Sorted by model distance: nonbonded pdb=" OXT GLY F 102 " pdb=" O HOH F1001 " model vdw 2.203 3.040 nonbonded pdb=" O LEU G 23 " pdb=" O HOH G 201 " model vdw 2.257 3.040 nonbonded pdb=" O ALA A 135 " pdb=" O HOH A 201 " model vdw 2.273 3.040 nonbonded pdb=" OE2 GLU B 53 " pdb=" O HOH B1001 " model vdw 2.277 3.040 nonbonded pdb=" O HOH B1015 " pdb=" O HOH I 102 " model vdw 2.284 3.040 ... (remaining 110309 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 'E' and (resid 38 through 134 or (resid 135 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 26 through 121 or (resid 122 and (name N or name CA or nam \ e C or name O or name CB or name CG or name CD or name CE or name NZ )))) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 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: 0.560 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 41.150 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 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:19.080 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 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 : 0.005 0.077 12968 Z= 0.245 Angle : 0.924 7.276 18745 Z= 0.599 Chirality : 0.062 0.359 2134 Planarity : 0.013 0.140 1366 Dihedral : 26.790 177.136 5610 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 0.46 % Allowed : 0.77 % Favored : 98.77 % 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: 0.63 (0.26), residues: 764 helix: 0.55 (0.19), residues: 550 sheet: None (None), residues: 0 loop : 0.44 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 106 PHE 0.013 0.002 PHE F 100 TYR 0.024 0.005 TYR C 57 ARG 0.027 0.004 ARG G 88 Details of bonding type rmsd hydrogen bonds : bond 0.13232 ( 796) hydrogen bonds : angle 4.52145 ( 1988) covalent geometry : bond 0.00527 (12968) covalent geometry : angle 0.92434 (18745) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 178 time to evaluate : 0.948 Fit side-chains REVERT: D 105 LYS cc_start: 0.8464 (mtmt) cc_final: 0.8084 (mttt) outliers start: 3 outliers final: 2 residues processed: 179 average time/residue: 2.3906 time to fit residues: 450.5915 Evaluate side-chains 149 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 147 time to evaluate : 1.797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 24 ASP Chi-restraints excluded: chain L residue 9 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN B 75 HIS C 104 GLN D 46 HIS F 27 GLN H 44 GLN H 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.094036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.065885 restraints weight = 18929.295| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 1.39 r_work: 0.2669 rms_B_bonded: 2.67 restraints_weight: 0.5000 r_work: 0.2523 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9017 moved from start: 0.2040 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.047 12968 Z= 0.375 Angle : 0.696 8.576 18745 Z= 0.416 Chirality : 0.043 0.151 2134 Planarity : 0.005 0.036 1366 Dihedral : 31.834 164.728 4054 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.62 % Allowed : 10.46 % Favored : 86.92 % 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: 2.20 (0.28), residues: 764 helix: 1.95 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.20 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.013 0.002 PHE A 67 TYR 0.019 0.002 TYR C 57 ARG 0.003 0.001 ARG E 42 Details of bonding type rmsd hydrogen bonds : bond 0.06279 ( 796) hydrogen bonds : angle 3.24574 ( 1988) covalent geometry : bond 0.00862 (12968) covalent geometry : angle 0.69588 (18745) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 149 time to evaluate : 0.958 Fit side-chains REVERT: A 59 GLU cc_start: 0.8542 (OUTLIER) cc_final: 0.8268 (pm20) REVERT: A 133 GLU cc_start: 0.8218 (OUTLIER) cc_final: 0.7803 (mt-10) REVERT: C 64 GLU cc_start: 0.8972 (OUTLIER) cc_final: 0.8374 (tp30) REVERT: C 74 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8610 (mtmm) REVERT: D 105 LYS cc_start: 0.8891 (mtmt) cc_final: 0.8622 (mttp) REVERT: E 59 GLU cc_start: 0.8978 (pm20) cc_final: 0.8754 (pm20) REVERT: G 13 LYS cc_start: 0.8954 (OUTLIER) cc_final: 0.8324 (tttm) REVERT: G 64 GLU cc_start: 0.9024 (OUTLIER) cc_final: 0.8099 (tp30) REVERT: L 9 ARG cc_start: 0.7345 (OUTLIER) cc_final: 0.6921 (mmp80) outliers start: 17 outliers final: 5 residues processed: 152 average time/residue: 2.1670 time to fit residues: 346.1390 Evaluate side-chains 154 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 142 time to evaluate : 0.857 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 9 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 43 optimal weight: 1.9990 chunk 99 optimal weight: 5.9990 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 65 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 59 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN F 27 GLN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.095460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.067435 restraints weight = 18937.890| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 1.32 r_work: 0.2707 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2561 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8987 moved from start: 0.2117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 12968 Z= 0.198 Angle : 0.630 8.752 18745 Z= 0.384 Chirality : 0.037 0.123 2134 Planarity : 0.004 0.042 1366 Dihedral : 31.783 165.704 4052 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 3.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.31 % Allowed : 11.54 % Favored : 86.15 % 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: 2.49 (0.29), residues: 764 helix: 2.22 (0.22), residues: 558 sheet: None (None), residues: 0 loop : 0.13 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.010 0.002 PHE A 67 TYR 0.013 0.001 TYR C 57 ARG 0.010 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05240 ( 796) hydrogen bonds : angle 3.09946 ( 1988) covalent geometry : bond 0.00439 (12968) covalent geometry : angle 0.63029 (18745) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 3.000 Fit side-chains REVERT: A 59 GLU cc_start: 0.8482 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: A 133 GLU cc_start: 0.8160 (OUTLIER) cc_final: 0.7701 (mt-10) REVERT: C 64 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8414 (tp30) REVERT: C 74 LYS cc_start: 0.9197 (OUTLIER) cc_final: 0.8618 (mtmm) REVERT: D 102 GLU cc_start: 0.8828 (mm-30) cc_final: 0.8538 (mm-30) REVERT: D 105 LYS cc_start: 0.8850 (mtmt) cc_final: 0.8562 (mttp) REVERT: G 13 LYS cc_start: 0.8955 (OUTLIER) cc_final: 0.8339 (tttm) REVERT: G 92 GLU cc_start: 0.8742 (OUTLIER) cc_final: 0.7965 (mt-10) REVERT: H 30 ARG cc_start: 0.8222 (ttm170) cc_final: 0.7940 (ttm170) REVERT: H 68 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8217 (mp0) outliers start: 15 outliers final: 4 residues processed: 147 average time/residue: 3.5401 time to fit residues: 547.7276 Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 142 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 67 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 93 optimal weight: 6.9990 chunk 17 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 39 optimal weight: 0.0870 chunk 41 optimal weight: 5.9990 chunk 68 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 65 optimal weight: 4.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN F 27 GLN F 93 GLN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.095997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.068110 restraints weight = 18774.717| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.29 r_work: 0.2690 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2545 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12968 Z= 0.208 Angle : 0.617 9.006 18745 Z= 0.373 Chirality : 0.036 0.125 2134 Planarity : 0.004 0.051 1366 Dihedral : 31.520 166.855 4048 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.46 % Allowed : 12.31 % Favored : 85.23 % 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: 2.71 (0.29), residues: 764 helix: 2.41 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.11 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.013 0.002 PHE A 67 TYR 0.013 0.001 TYR F 51 ARG 0.012 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04718 ( 796) hydrogen bonds : angle 2.99774 ( 1988) covalent geometry : bond 0.00468 (12968) covalent geometry : angle 0.61741 (18745) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 142 time to evaluate : 0.940 Fit side-chains REVERT: A 59 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8196 (pm20) REVERT: A 133 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7710 (mt-10) REVERT: C 64 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8432 (tp30) REVERT: C 74 LYS cc_start: 0.9194 (OUTLIER) cc_final: 0.8613 (mtmm) REVERT: D 102 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8574 (mm-30) REVERT: D 105 LYS cc_start: 0.8829 (mtmt) cc_final: 0.8547 (mttp) REVERT: G 13 LYS cc_start: 0.8950 (OUTLIER) cc_final: 0.8321 (tttm) REVERT: G 15 LYS cc_start: 0.8422 (mtpp) cc_final: 0.8220 (mtmm) REVERT: G 64 GLU cc_start: 0.8962 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: G 92 GLU cc_start: 0.8746 (OUTLIER) cc_final: 0.7972 (mt-10) REVERT: L 9 ARG cc_start: 0.7272 (OUTLIER) cc_final: 0.7002 (mmt-90) outliers start: 16 outliers final: 6 residues processed: 146 average time/residue: 2.1309 time to fit residues: 326.4763 Evaluate side-chains 155 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 141 time to evaluate : 0.860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 9 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 5.9990 chunk 5 optimal weight: 0.9980 chunk 0 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 78 optimal weight: 7.9990 chunk 94 optimal weight: 6.9990 chunk 73 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 14 optimal weight: 0.3980 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 81 ASN F 27 GLN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.097463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069677 restraints weight = 18895.524| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 1.29 r_work: 0.2754 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2610 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8956 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12968 Z= 0.186 Angle : 0.569 8.971 18745 Z= 0.346 Chirality : 0.034 0.131 2134 Planarity : 0.004 0.039 1366 Dihedral : 30.853 171.499 4048 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.62 % Allowed : 13.23 % Favored : 84.15 % 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: 2.94 (0.29), residues: 764 helix: 2.59 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.12 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.011 0.001 TYR F 51 ARG 0.010 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04218 ( 796) hydrogen bonds : angle 2.86984 ( 1988) covalent geometry : bond 0.00408 (12968) covalent geometry : angle 0.56900 (18745) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 144 time to evaluate : 0.948 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8880 (OUTLIER) cc_final: 0.8659 (pt0) REVERT: A 133 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7561 (mt-10) REVERT: C 64 GLU cc_start: 0.8890 (OUTLIER) cc_final: 0.8428 (tp30) REVERT: D 54 LYS cc_start: 0.8883 (OUTLIER) cc_final: 0.8308 (mptp) REVERT: G 64 GLU cc_start: 0.8914 (OUTLIER) cc_final: 0.7967 (tp30) REVERT: G 92 GLU cc_start: 0.8695 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: H 68 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8157 (mp0) outliers start: 17 outliers final: 4 residues processed: 146 average time/residue: 2.0477 time to fit residues: 314.3933 Evaluate side-chains 151 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 65 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 37 optimal weight: 8.9990 chunk 10 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 75 optimal weight: 10.0000 chunk 82 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 52 optimal weight: 2.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN E 68 GLN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.097321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.069067 restraints weight = 18871.395| |-----------------------------------------------------------------------------| r_work (start): 0.2919 rms_B_bonded: 1.31 r_work: 0.2725 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2580 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8964 moved from start: 0.2719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12968 Z= 0.193 Angle : 0.565 10.058 18745 Z= 0.342 Chirality : 0.034 0.133 2134 Planarity : 0.004 0.043 1366 Dihedral : 30.721 173.241 4048 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.77 % Allowed : 13.38 % Favored : 83.85 % 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: 2.98 (0.29), residues: 764 helix: 2.65 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.06 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.001 TYR B 51 ARG 0.008 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04267 ( 796) hydrogen bonds : angle 2.86300 ( 1988) covalent geometry : bond 0.00427 (12968) covalent geometry : angle 0.56496 (18745) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 141 time to evaluate : 0.921 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8870 (OUTLIER) cc_final: 0.8652 (pt0) REVERT: A 133 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7608 (mt-10) REVERT: C 64 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8466 (tp30) REVERT: D 54 LYS cc_start: 0.8902 (OUTLIER) cc_final: 0.8320 (mptp) REVERT: D 105 LYS cc_start: 0.8864 (mtpm) cc_final: 0.8459 (mttp) REVERT: G 64 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8027 (tp30) REVERT: G 92 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: H 68 GLU cc_start: 0.8543 (OUTLIER) cc_final: 0.8205 (mp0) outliers start: 18 outliers final: 6 residues processed: 144 average time/residue: 2.0846 time to fit residues: 315.1174 Evaluate side-chains 151 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 138 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 91 optimal weight: 7.9990 chunk 63 optimal weight: 0.5980 chunk 12 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 75 optimal weight: 10.0000 chunk 36 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 20 optimal weight: 0.8980 overall best weight: 1.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.097503 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.069221 restraints weight = 18695.407| |-----------------------------------------------------------------------------| r_work (start): 0.2925 rms_B_bonded: 1.30 r_work: 0.2731 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2587 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8968 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 12968 Z= 0.181 Angle : 0.564 10.011 18745 Z= 0.341 Chirality : 0.033 0.131 2134 Planarity : 0.004 0.062 1366 Dihedral : 30.713 173.286 4048 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.15 % Allowed : 13.69 % Favored : 84.15 % 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: 3.01 (0.29), residues: 764 helix: 2.68 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.04 (0.37), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.011 0.001 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.014 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04185 ( 796) hydrogen bonds : angle 2.85374 ( 1988) covalent geometry : bond 0.00400 (12968) covalent geometry : angle 0.56447 (18745) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 139 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8867 (OUTLIER) cc_final: 0.8653 (pt0) REVERT: A 133 GLU cc_start: 0.8113 (OUTLIER) cc_final: 0.7614 (mt-10) REVERT: C 64 GLU cc_start: 0.8910 (OUTLIER) cc_final: 0.8471 (tp30) REVERT: D 54 LYS cc_start: 0.8903 (OUTLIER) cc_final: 0.8324 (mptp) REVERT: D 105 LYS cc_start: 0.8857 (mtpm) cc_final: 0.8484 (mttp) REVERT: G 64 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8032 (tp30) REVERT: G 92 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.7885 (mt-10) REVERT: H 68 GLU cc_start: 0.8532 (OUTLIER) cc_final: 0.8210 (mp0) outliers start: 14 outliers final: 5 residues processed: 141 average time/residue: 2.3038 time to fit residues: 340.8174 Evaluate side-chains 151 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 139 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 54 LYS Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 13 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 90 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 52 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 92 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.095688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.067185 restraints weight = 18749.531| |-----------------------------------------------------------------------------| r_work (start): 0.2886 rms_B_bonded: 1.32 r_work: 0.2687 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8999 moved from start: 0.2680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 12968 Z= 0.267 Angle : 0.596 10.336 18745 Z= 0.357 Chirality : 0.037 0.140 2134 Planarity : 0.005 0.059 1366 Dihedral : 30.817 171.925 4048 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.00 % Allowed : 13.85 % Favored : 84.15 % 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: 2.78 (0.29), residues: 764 helix: 2.53 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.11 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 46 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.013 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.05056 ( 796) hydrogen bonds : angle 2.96634 ( 1988) covalent geometry : bond 0.00605 (12968) covalent geometry : angle 0.59555 (18745) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 143 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8905 (OUTLIER) cc_final: 0.8680 (pt0) REVERT: A 133 GLU cc_start: 0.8180 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: C 64 GLU cc_start: 0.8955 (OUTLIER) cc_final: 0.8473 (tp30) REVERT: D 105 LYS cc_start: 0.8888 (mtpm) cc_final: 0.8500 (mttp) REVERT: G 64 GLU cc_start: 0.8977 (OUTLIER) cc_final: 0.8065 (tp30) REVERT: G 92 GLU cc_start: 0.8719 (OUTLIER) cc_final: 0.7928 (mt-10) REVERT: H 68 GLU cc_start: 0.8558 (OUTLIER) cc_final: 0.8213 (mp0) outliers start: 13 outliers final: 6 residues processed: 146 average time/residue: 2.7733 time to fit residues: 424.8867 Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 1.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 9 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 0 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 chunk 22 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 3 optimal weight: 2.9990 chunk 21 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 10 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN H 46 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.096256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.067826 restraints weight = 18618.146| |-----------------------------------------------------------------------------| r_work (start): 0.2896 rms_B_bonded: 1.30 r_work: 0.2698 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2551 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8994 moved from start: 0.2689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 12968 Z= 0.192 Angle : 0.585 10.331 18745 Z= 0.352 Chirality : 0.034 0.133 2134 Planarity : 0.004 0.062 1366 Dihedral : 30.836 171.841 4048 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.00 % Allowed : 13.85 % Favored : 84.15 % 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: 2.83 (0.29), residues: 764 helix: 2.57 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.09 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 46 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.016 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04822 ( 796) hydrogen bonds : angle 2.95687 ( 1988) covalent geometry : bond 0.00421 (12968) covalent geometry : angle 0.58471 (18745) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.890 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8893 (OUTLIER) cc_final: 0.8659 (pt0) REVERT: A 133 GLU cc_start: 0.8175 (OUTLIER) cc_final: 0.7705 (mt-10) REVERT: C 64 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8453 (tp30) REVERT: D 105 LYS cc_start: 0.8877 (mtpm) cc_final: 0.8522 (mttt) REVERT: G 64 GLU cc_start: 0.8956 (OUTLIER) cc_final: 0.8042 (tp30) REVERT: G 92 GLU cc_start: 0.8697 (OUTLIER) cc_final: 0.7905 (mt-10) REVERT: H 68 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8218 (mp0) outliers start: 13 outliers final: 6 residues processed: 144 average time/residue: 2.1015 time to fit residues: 317.9553 Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.922 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 3.9990 chunk 86 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 87 optimal weight: 10.0000 chunk 76 optimal weight: 6.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 27 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.096285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.067889 restraints weight = 18583.986| |-----------------------------------------------------------------------------| r_work (start): 0.2897 rms_B_bonded: 1.30 r_work: 0.2700 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2554 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8993 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 12968 Z= 0.209 Angle : 0.582 10.427 18745 Z= 0.350 Chirality : 0.034 0.132 2134 Planarity : 0.004 0.062 1366 Dihedral : 30.826 172.014 4048 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 3.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.85 % Allowed : 14.00 % Favored : 84.15 % 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: 2.81 (0.29), residues: 764 helix: 2.56 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.10 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.015 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04724 ( 796) hydrogen bonds : angle 2.94664 ( 1988) covalent geometry : bond 0.00469 (12968) covalent geometry : angle 0.58197 (18745) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1528 Ramachandran restraints generated. 764 Oldfield, 0 Emsley, 764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.980 Fit side-chains revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8890 (OUTLIER) cc_final: 0.8661 (pt0) REVERT: A 133 GLU cc_start: 0.8171 (OUTLIER) cc_final: 0.7703 (mt-10) REVERT: C 64 GLU cc_start: 0.8943 (OUTLIER) cc_final: 0.8465 (tp30) REVERT: D 105 LYS cc_start: 0.8881 (mtpm) cc_final: 0.8518 (mttt) REVERT: G 64 GLU cc_start: 0.8965 (OUTLIER) cc_final: 0.8056 (tp30) REVERT: G 92 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.7912 (mt-10) REVERT: H 68 GLU cc_start: 0.8551 (OUTLIER) cc_final: 0.8217 (mp0) outliers start: 12 outliers final: 6 residues processed: 144 average time/residue: 2.1596 time to fit residues: 326.5877 Evaluate side-chains 153 residues out of total 650 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 141 time to evaluate : 0.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 53 SER Chi-restraints excluded: chain G residue 13 LYS Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Chi-restraints excluded: chain L residue 9 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 41 optimal weight: 4.9990 chunk 40 optimal weight: 0.9990 chunk 21 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 80 optimal weight: 6.9990 chunk 96 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 100 optimal weight: 7.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN F 27 GLN H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.096358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.067955 restraints weight = 18551.830| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.30 r_work: 0.2704 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2558 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8984 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12968 Z= 0.187 Angle : 0.579 10.457 18745 Z= 0.349 Chirality : 0.034 0.131 2134 Planarity : 0.004 0.061 1366 Dihedral : 30.824 172.040 4048 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 4.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.31 % Allowed : 13.38 % Favored : 84.31 % 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: 2.83 (0.29), residues: 764 helix: 2.57 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.09 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.012 0.001 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.015 0.000 ARG D 30 Details of bonding type rmsd hydrogen bonds : bond 0.04692 ( 796) hydrogen bonds : angle 2.94247 ( 1988) covalent geometry : bond 0.00415 (12968) covalent geometry : angle 0.57871 (18745) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12509.12 seconds wall clock time: 222 minutes 45.72 seconds (13365.72 seconds total)