Starting phenix.real_space_refine on Fri Mar 15 17:16:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhx_11220/03_2024/6zhx_11220.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhx_11220/03_2024/6zhx_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhx_11220/03_2024/6zhx_11220.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhx_11220/03_2024/6zhx_11220.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhx_11220/03_2024/6zhx_11220.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zhx_11220/03_2024/6zhx_11220.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 6.29, per 1000 atoms: 0.51 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 - 3.50 Amino acid : False - 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: 6.11 Conformation dependent library (CDL) restraints added in 1.1 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: 5.99 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: 5.17 Time building geometry restraints manager: 6.51 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: 98.30 - 105.17: 1194 105.17 - 112.04: 6686 112.04 - 118.91: 3919 118.91 - 125.78: 6032 125.78 - 132.65: 914 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 2.440 nonbonded pdb=" O LEU G 23 " pdb=" O HOH G 201 " model vdw 2.257 2.440 nonbonded pdb=" O ALA A 135 " pdb=" O HOH A 201 " model vdw 2.273 2.440 nonbonded pdb=" OE2 GLU B 53 " pdb=" O HOH B1001 " model vdw 2.277 2.440 nonbonded pdb=" O HOH B1015 " pdb=" O HOH I 102 " model vdw 2.284 2.440 ... (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 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: 1.450 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: 6.200 Check model and map are aligned: 0.170 Set scattering table: 0.110 Process input model: 39.810 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.090 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:15.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.010 ------------------------------------------------------------------------------- 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= 0.275 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 *********************** 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 fitting. rotamer outliers: 3 poor density : 178 time to evaluate : 0.840 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: 1.9774 time to fit residues: 372.0569 Evaluate side-chains 149 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.060 ------------------------------------------------------------------------------- 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: 7.9990 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- 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 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 104 GLN D 46 HIS F 27 GLN H 44 GLN H 46 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 12968 Z= 0.469 Angle : 0.687 8.703 18745 Z= 0.412 Chirality : 0.043 0.144 2134 Planarity : 0.005 0.041 1366 Dihedral : 31.931 165.103 4054 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.52 % Favored : 99.48 % Rotamer: Outliers : 2.31 % Allowed : 10.46 % Favored : 87.23 % 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: 2.26 (0.28), residues: 764 helix: 2.01 (0.21), residues: 558 sheet: None (None), residues: 0 loop : 0.16 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.014 0.002 PHE A 67 TYR 0.019 0.002 TYR C 57 ARG 0.004 0.001 ARG G 88 *********************** 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 164 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 149 time to evaluate : 1.013 Fit side-chains REVERT: C 64 GLU cc_start: 0.8150 (OUTLIER) cc_final: 0.7536 (tp30) REVERT: G 13 LYS cc_start: 0.8794 (OUTLIER) cc_final: 0.8418 (tmtm) REVERT: G 64 GLU cc_start: 0.8269 (OUTLIER) cc_final: 0.7289 (tp30) REVERT: G 92 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.7603 (mt-10) outliers start: 15 outliers final: 4 residues processed: 152 average time/residue: 2.0534 time to fit residues: 328.3444 Evaluate side-chains 150 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 142 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 GLN Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain D residue 68 GLU 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 77 optimal weight: 6.9990 chunk 63 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 5.9990 chunk 100 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN C 104 GLN E 108 ASN F 27 GLN H 46 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8645 moved from start: 0.2161 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= 0.228 Angle : 0.617 8.716 18745 Z= 0.378 Chirality : 0.037 0.124 2134 Planarity : 0.005 0.049 1366 Dihedral : 31.766 166.534 4048 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 2.62 % Allowed : 12.00 % Favored : 85.38 % 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: 2.59 (0.29), residues: 764 helix: 2.30 (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 0.003 0.001 HIS D 46 PHE 0.010 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.006 0.000 ARG D 30 *********************** 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 162 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.979 Fit side-chains REVERT: A 133 GLU cc_start: 0.8205 (OUTLIER) cc_final: 0.7480 (mt-10) REVERT: C 64 GLU cc_start: 0.8118 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: C 74 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8542 (mtmm) REVERT: D 68 GLU cc_start: 0.7665 (OUTLIER) cc_final: 0.7425 (tt0) REVERT: G 13 LYS cc_start: 0.8786 (OUTLIER) cc_final: 0.8382 (tmtm) REVERT: G 92 GLU cc_start: 0.8259 (OUTLIER) cc_final: 0.7541 (mt-10) REVERT: H 68 GLU cc_start: 0.7728 (OUTLIER) cc_final: 0.7442 (mp0) outliers start: 17 outliers final: 7 residues processed: 148 average time/residue: 2.0259 time to fit residues: 315.1500 Evaluate side-chains 157 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 143 time to evaluate : 0.949 ------------------------------------------------------------------------------- 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 52 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 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 92 GLU Chi-restraints excluded: chain H residue 68 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 10 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 62 optimal weight: 0.8980 chunk 93 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 5.9990 chunk 82 optimal weight: 5.9990 chunk 55 optimal weight: 5.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- 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 F 93 GLN H 46 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 12968 Z= 0.361 Angle : 0.616 9.676 18745 Z= 0.370 Chirality : 0.038 0.138 2134 Planarity : 0.005 0.035 1366 Dihedral : 31.178 169.402 4048 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 3.08 % Allowed : 12.46 % Favored : 84.46 % 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: 2.59 (0.29), residues: 764 helix: 2.37 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.10 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS D 46 PHE 0.013 0.002 PHE A 67 TYR 0.014 0.002 TYR C 57 ARG 0.008 0.000 ARG D 30 *********************** 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 163 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 143 time to evaluate : 1.002 Fit side-chains REVERT: A 133 GLU cc_start: 0.8236 (OUTLIER) cc_final: 0.7488 (mt-10) REVERT: C 64 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7612 (tp30) REVERT: C 74 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8516 (mtmm) REVERT: D 68 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7435 (tt0) REVERT: D 102 GLU cc_start: 0.8113 (mm-30) cc_final: 0.7871 (mm-30) REVERT: G 13 LYS cc_start: 0.8816 (OUTLIER) cc_final: 0.8320 (tttm) REVERT: G 64 GLU cc_start: 0.8219 (OUTLIER) cc_final: 0.7268 (tp30) REVERT: G 92 GLU cc_start: 0.8297 (OUTLIER) cc_final: 0.7592 (mt-10) outliers start: 20 outliers final: 5 residues processed: 147 average time/residue: 2.1170 time to fit residues: 327.0419 Evaluate side-chains 151 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 G residue 92 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 3.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 68 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 G 73 ASN H 46 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12968 Z= 0.208 Angle : 0.585 9.746 18745 Z= 0.355 Chirality : 0.034 0.121 2134 Planarity : 0.004 0.047 1366 Dihedral : 31.177 169.746 4048 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.77 % Allowed : 13.23 % Favored : 84.00 % 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: 2.70 (0.29), residues: 764 helix: 2.46 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.07 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.010 0.001 PHE A 67 TYR 0.011 0.001 TYR C 57 ARG 0.014 0.000 ARG D 30 *********************** 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 fitting. rotamer outliers: 18 poor density : 143 time to evaluate : 0.871 Fit side-chains REVERT: A 133 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7447 (mt-10) REVERT: C 64 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7619 (tp30) REVERT: C 74 LYS cc_start: 0.9039 (OUTLIER) cc_final: 0.8532 (mtmm) REVERT: D 68 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7410 (tt0) REVERT: G 13 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8336 (tttm) REVERT: G 64 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.7233 (tp30) REVERT: G 92 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7556 (mt-10) outliers start: 18 outliers final: 6 residues processed: 145 average time/residue: 2.0222 time to fit residues: 307.9185 Evaluate side-chains 155 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 LYS Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 52 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 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 G residue 92 GLU Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 95 optimal weight: 5.9990 chunk 11 optimal weight: 0.0030 chunk 56 optimal weight: 3.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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 H 46 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12968 Z= 0.193 Angle : 0.578 9.803 18745 Z= 0.351 Chirality : 0.034 0.123 2134 Planarity : 0.004 0.046 1366 Dihedral : 31.137 170.165 4048 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.31 % Allowed : 13.85 % 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: 2.80 (0.29), residues: 764 helix: 2.54 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.07 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 46 PHE 0.011 0.002 PHE A 67 TYR 0.012 0.001 TYR F 51 ARG 0.007 0.000 ARG D 30 *********************** 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 158 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 143 time to evaluate : 1.011 Fit side-chains REVERT: A 133 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7411 (mt-10) REVERT: C 64 GLU cc_start: 0.8060 (OUTLIER) cc_final: 0.7616 (tp30) REVERT: C 74 LYS cc_start: 0.9037 (OUTLIER) cc_final: 0.8530 (mtmm) REVERT: D 68 GLU cc_start: 0.7632 (OUTLIER) cc_final: 0.7408 (tt0) REVERT: G 13 LYS cc_start: 0.8814 (OUTLIER) cc_final: 0.8344 (tttm) REVERT: G 64 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7238 (tp30) REVERT: G 92 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7568 (mt-10) outliers start: 15 outliers final: 6 residues processed: 145 average time/residue: 2.0442 time to fit residues: 311.2772 Evaluate side-chains 153 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 52 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 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 G residue 92 GLU Chi-restraints excluded: chain H residue 31 LYS 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 72 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 98 optimal weight: 6.9990 chunk 61 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 104 GLN F 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 12968 Z= 0.339 Angle : 0.597 10.210 18745 Z= 0.361 Chirality : 0.037 0.135 2134 Planarity : 0.004 0.035 1366 Dihedral : 31.113 170.449 4048 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % 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: 2.67 (0.29), residues: 764 helix: 2.46 (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 0.005 0.001 HIS D 46 PHE 0.011 0.002 PHE A 67 TYR 0.013 0.001 TYR C 57 ARG 0.007 0.000 ARG D 30 *********************** 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 159 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 144 time to evaluate : 0.952 Fit side-chains REVERT: A 133 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7483 (mt-10) REVERT: C 64 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7601 (tp30) REVERT: C 74 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8541 (mtmm) REVERT: D 54 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.7882 (mptp) REVERT: G 13 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8347 (tttm) REVERT: G 64 GLU cc_start: 0.8203 (OUTLIER) cc_final: 0.7247 (tp30) REVERT: G 92 GLU cc_start: 0.8294 (OUTLIER) cc_final: 0.7579 (mt-10) REVERT: H 68 GLU cc_start: 0.7841 (OUTLIER) cc_final: 0.7495 (mp0) outliers start: 15 outliers final: 6 residues processed: 146 average time/residue: 2.0909 time to fit residues: 320.6237 Evaluate side-chains 155 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 52 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 54 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 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 19 optimal weight: 2.9990 chunk 62 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 55 optimal weight: 1.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2558 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= 0.242 Angle : 0.589 10.324 18745 Z= 0.355 Chirality : 0.034 0.130 2134 Planarity : 0.004 0.035 1366 Dihedral : 31.127 170.426 4048 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.62 % Allowed : 13.38 % Favored : 84.00 % 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: 2.74 (0.29), residues: 764 helix: 2.52 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.16 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS D 46 PHE 0.012 0.002 PHE A 67 TYR 0.012 0.001 TYR C 57 ARG 0.009 0.000 ARG D 30 *********************** 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 158 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 141 time to evaluate : 0.910 Fit side-chains REVERT: A 133 GLU cc_start: 0.8225 (OUTLIER) cc_final: 0.7470 (mt-10) REVERT: C 64 GLU cc_start: 0.8081 (OUTLIER) cc_final: 0.7593 (tp30) REVERT: C 74 LYS cc_start: 0.9038 (OUTLIER) cc_final: 0.8556 (mtmm) REVERT: D 54 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.7876 (mptp) REVERT: G 13 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8355 (tttm) REVERT: G 64 GLU cc_start: 0.8195 (OUTLIER) cc_final: 0.7246 (tp30) REVERT: G 92 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7561 (mt-10) outliers start: 17 outliers final: 6 residues processed: 144 average time/residue: 2.1380 time to fit residues: 322.8617 Evaluate side-chains 153 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 140 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 52 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 54 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 64 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain H residue 31 LYS Chi-restraints excluded: chain H residue 120 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 6.9990 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 0.7980 chunk 67 optimal weight: 2.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 12968 Z= 0.384 Angle : 0.613 10.663 18745 Z= 0.368 Chirality : 0.038 0.138 2134 Planarity : 0.004 0.035 1366 Dihedral : 31.065 170.563 4048 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.15 % Allowed : 13.85 % Favored : 84.00 % 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: 2.58 (0.29), residues: 764 helix: 2.40 (0.21), residues: 558 sheet: None (None), residues: 0 loop : -0.26 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 46 PHE 0.013 0.002 PHE A 67 TYR 0.013 0.002 TYR C 57 ARG 0.008 0.000 ARG D 30 *********************** 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 154 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 140 time to evaluate : 0.926 Fit side-chains REVERT: A 133 GLU cc_start: 0.8292 (OUTLIER) cc_final: 0.7592 (mt-10) REVERT: C 64 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.7591 (tp30) REVERT: C 74 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8550 (mtmm) REVERT: F 77 LYS cc_start: 0.9056 (OUTLIER) cc_final: 0.8797 (mttp) REVERT: G 13 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8329 (tttm) REVERT: G 64 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7252 (tp30) REVERT: G 92 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7612 (mt-10) outliers start: 14 outliers final: 6 residues processed: 140 average time/residue: 2.1037 time to fit residues: 309.1342 Evaluate side-chains 152 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 139 time to evaluate : 0.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 52 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 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 77 LYS 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 31 LYS 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 101 optimal weight: 10.0000 chunk 93 optimal weight: 6.9990 chunk 80 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 3.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.2631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 12968 Z= 0.253 Angle : 0.604 10.497 18745 Z= 0.362 Chirality : 0.035 0.126 2134 Planarity : 0.005 0.085 1366 Dihedral : 31.079 170.434 4048 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.00 % Allowed : 14.15 % 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: 2.66 (0.29), residues: 764 helix: 2.47 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.24 (0.35), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.012 0.002 TYR C 57 ARG 0.016 0.000 ARG D 30 ********************** 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 155 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 142 time to evaluate : 0.959 Fit side-chains REVERT: A 133 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7547 (mt-10) REVERT: C 64 GLU cc_start: 0.8097 (OUTLIER) cc_final: 0.7577 (tp30) REVERT: C 74 LYS cc_start: 0.9041 (OUTLIER) cc_final: 0.8548 (mtmm) REVERT: G 13 LYS cc_start: 0.8822 (OUTLIER) cc_final: 0.8330 (tttm) REVERT: G 64 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7232 (tp30) REVERT: G 92 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.7586 (mt-10) outliers start: 13 outliers final: 6 residues processed: 143 average time/residue: 2.0688 time to fit residues: 310.6412 Evaluate side-chains 151 residues out of total 650 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 139 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain B residue 52 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 68 GLU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain F residue 49 LEU 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 120 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 chunk 33 optimal weight: 4.9990 chunk 83 optimal weight: 6.9990 chunk 10 optimal weight: 3.9990 chunk 14 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 4 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3409 r_free = 0.3409 target = 0.095748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.067316 restraints weight = 18470.967| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 1.31 r_work: 0.2690 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2544 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8989 moved from start: 0.2651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 12968 Z= 0.201 Angle : 0.589 10.470 18745 Z= 0.356 Chirality : 0.034 0.122 2134 Planarity : 0.004 0.059 1366 Dihedral : 31.054 170.638 4048 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % Rotamer: Outliers : 2.15 % Allowed : 14.00 % 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: 2.67 (0.29), residues: 764 helix: 2.47 (0.22), residues: 558 sheet: None (None), residues: 0 loop : -0.19 (0.36), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 75 PHE 0.013 0.002 PHE A 67 TYR 0.011 0.001 TYR F 51 ARG 0.019 0.001 ARG D 30 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5198.91 seconds wall clock time: 92 minutes 42.46 seconds (5562.46 seconds total)