Starting phenix.real_space_refine on Wed Feb 14 02:20:25 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6zxa_11516/02_2024/6zxa_11516_updated.pdb" } resolution = 2.38 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= 0.002 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 Mg 21 5.21 5 S 35 5.16 5 C 6034 2.51 5 N 1127 2.21 5 O 1225 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 19": "OE1" <-> "OE2" Residue "A ASP 20": "OD1" <-> "OD2" Residue "A ASP 62": "OD1" <-> "OD2" Residue "B GLU 18": "OE1" <-> "OE2" Residue "B PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 9": "OD1" <-> "OD2" Residue "C GLU 19": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "D GLU 18": "OE1" <-> "OE2" Residue "D PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 9": "OD1" <-> "OD2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E ASP 20": "OD1" <-> "OD2" Residue "E ASP 62": "OD1" <-> "OD2" Residue "F GLU 18": "OE1" <-> "OE2" Residue "F PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 9": "OD1" <-> "OD2" Residue "G GLU 19": "OE1" <-> "OE2" Residue "G ASP 20": "OD1" <-> "OD2" Residue "G ASP 62": "OD1" <-> "OD2" Residue "H GLU 18": "OE1" <-> "OE2" Residue "H PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I ASP 9": "OD1" <-> "OD2" Residue "I GLU 19": "OE1" <-> "OE2" Residue "I ASP 20": "OD1" <-> "OD2" Residue "I ASP 62": "OD1" <-> "OD2" Residue "J GLU 18": "OE1" <-> "OE2" Residue "J PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ASP 9": "OD1" <-> "OD2" Residue "K GLU 19": "OE1" <-> "OE2" Residue "K ASP 20": "OD1" <-> "OD2" Residue "K ASP 62": "OD1" <-> "OD2" Residue "L GLU 18": "OE1" <-> "OE2" Residue "L PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M ASP 9": "OD1" <-> "OD2" Residue "M GLU 19": "OE1" <-> "OE2" Residue "M ASP 20": "OD1" <-> "OD2" Residue "M ASP 62": "OD1" <-> "OD2" Residue "N GLU 18": "OE1" <-> "OE2" Residue "N PHE 19": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 48": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8442 Number of models: 1 Model: "" Number of chains: 28 Chain: "A" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "B" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "C" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "D" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "E" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "F" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "G" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "H" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "I" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "J" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "K" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "L" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "M" Number of atoms: 556 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 556 Classifications: {'peptide': 69} Link IDs: {'PTRANS': 6, 'TRANS': 62} Chain: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 366 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "A" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QS2': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QSE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'QS2': 1, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 109 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 109 Unusual residues: {'BCL': 1, 'QS2': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 152 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 152 Unusual residues: {'BCL': 1, 'QS2': 1, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 175 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 175 Unusual residues: {'BCL': 2, 'QSE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 4.91, per 1000 atoms: 0.58 Number of scatterers: 8442 At special positions: 0 Unit cell: (87.21, 87.21, 68.476, 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 35 16.00 Mg 21 11.99 O 1225 8.00 N 1127 7.00 C 6034 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=21, symmetry=0 Number of additional bonds: simple=21, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.5 seconds 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 0 sheets defined 52.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.64 Creating SS restraints... Processing helix chain 'A' and resid 17 through 20 No H-bonds generated for 'chain 'A' and resid 17 through 20' Processing helix chain 'A' and resid 24 through 26 No H-bonds generated for 'chain 'A' and resid 24 through 26' Processing helix chain 'A' and resid 35 through 54 Processing helix chain 'B' and resid 13 through 44 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 24 through 26 No H-bonds generated for 'chain 'C' and resid 24 through 26' Processing helix chain 'C' and resid 35 through 54 Processing helix chain 'D' and resid 13 through 44 Processing helix chain 'E' and resid 17 through 20 No H-bonds generated for 'chain 'E' and resid 17 through 20' Processing helix chain 'E' and resid 24 through 26 No H-bonds generated for 'chain 'E' and resid 24 through 26' Processing helix chain 'E' and resid 35 through 54 Processing helix chain 'F' and resid 13 through 44 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 24 through 26 No H-bonds generated for 'chain 'G' and resid 24 through 26' Processing helix chain 'G' and resid 35 through 54 Processing helix chain 'H' and resid 13 through 44 Processing helix chain 'I' and resid 17 through 20 No H-bonds generated for 'chain 'I' and resid 17 through 20' Processing helix chain 'I' and resid 24 through 26 No H-bonds generated for 'chain 'I' and resid 24 through 26' Processing helix chain 'I' and resid 35 through 54 Processing helix chain 'J' and resid 13 through 44 Processing helix chain 'K' and resid 17 through 20 No H-bonds generated for 'chain 'K' and resid 17 through 20' Processing helix chain 'K' and resid 24 through 26 No H-bonds generated for 'chain 'K' and resid 24 through 26' Processing helix chain 'K' and resid 35 through 54 Processing helix chain 'L' and resid 13 through 44 Processing helix chain 'M' and resid 17 through 20 No H-bonds generated for 'chain 'M' and resid 17 through 20' Processing helix chain 'M' and resid 24 through 26 No H-bonds generated for 'chain 'M' and resid 24 through 26' Processing helix chain 'M' and resid 35 through 54 Processing helix chain 'N' and resid 13 through 44 308 hydrogen bonds defined for protein. 924 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.92 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.35: 2163 1.35 - 1.55: 6552 1.55 - 1.76: 7 1.76 - 1.96: 70 1.96 - 2.17: 84 Bond restraints: 8876 Sorted by residual: bond pdb=" C10 QSE H 101 " pdb=" C9 QSE H 101 " ideal model delta sigma weight residual 1.565 1.409 0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" C10 QSE C 101 " pdb=" C9 QSE C 101 " ideal model delta sigma weight residual 1.565 1.409 0.156 2.00e-02 2.50e+03 6.05e+01 bond pdb=" C10 QSE M 101 " pdb=" C9 QSE M 101 " ideal model delta sigma weight residual 1.565 1.410 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C10 QSE F 101 " pdb=" C9 QSE F 101 " ideal model delta sigma weight residual 1.565 1.410 0.155 2.00e-02 2.50e+03 6.04e+01 bond pdb=" C10 QSE J 101 " pdb=" C9 QSE J 101 " ideal model delta sigma weight residual 1.565 1.410 0.155 2.00e-02 2.50e+03 6.04e+01 ... (remaining 8871 not shown) Histogram of bond angle deviations from ideal: 84.94 - 100.55: 91 100.55 - 116.16: 5726 116.16 - 131.77: 6398 131.77 - 147.38: 161 147.38 - 163.00: 42 Bond angle restraints: 12418 Sorted by residual: angle pdb=" C26 QS2 I 102 " pdb=" C5 QS2 I 102 " pdb=" C4 QS2 I 102 " ideal model delta sigma weight residual 74.50 119.35 -44.85 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C26 QS2 M 103 " pdb=" C5 QS2 M 103 " pdb=" C4 QS2 M 103 " ideal model delta sigma weight residual 74.50 119.33 -44.83 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C26 QS2 E 103 " pdb=" C5 QS2 E 103 " pdb=" C4 QS2 E 103 " ideal model delta sigma weight residual 74.50 119.32 -44.82 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C26 QS2 G 102 " pdb=" C5 QS2 G 102 " pdb=" C4 QS2 G 102 " ideal model delta sigma weight residual 74.50 119.32 -44.82 3.00e+00 1.11e-01 2.23e+02 angle pdb=" C26 QS2 K 102 " pdb=" C5 QS2 K 102 " pdb=" C4 QS2 K 102 " ideal model delta sigma weight residual 74.50 119.30 -44.80 3.00e+00 1.11e-01 2.23e+02 ... (remaining 12413 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.34: 4165 33.34 - 66.69: 189 66.69 - 100.03: 21 100.03 - 133.37: 0 133.37 - 166.71: 14 Dihedral angle restraints: 4389 sinusoidal: 2079 harmonic: 2310 Sorted by residual: dihedral pdb=" CA MET M 6 " pdb=" C MET M 6 " pdb=" N MET M 7 " pdb=" CA MET M 7 " ideal model delta harmonic sigma weight residual 180.00 144.13 35.87 0 5.00e+00 4.00e-02 5.15e+01 dihedral pdb=" CA MET C 6 " pdb=" C MET C 6 " pdb=" N MET C 7 " pdb=" CA MET C 7 " ideal model delta harmonic sigma weight residual 180.00 144.14 35.86 0 5.00e+00 4.00e-02 5.14e+01 dihedral pdb=" CA MET K 6 " pdb=" C MET K 6 " pdb=" N MET K 7 " pdb=" CA MET K 7 " ideal model delta harmonic sigma weight residual 180.00 144.16 35.84 0 5.00e+00 4.00e-02 5.14e+01 ... (remaining 4386 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 1006 0.082 - 0.164: 107 0.164 - 0.245: 14 0.245 - 0.327: 7 0.327 - 0.408: 7 Chirality restraints: 1141 Sorted by residual: chirality pdb=" CA HIS K 17 " pdb=" N HIS K 17 " pdb=" C HIS K 17 " pdb=" CB HIS K 17 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.17e+00 chirality pdb=" CA HIS A 17 " pdb=" N HIS A 17 " pdb=" C HIS A 17 " pdb=" CB HIS A 17 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.15e+00 chirality pdb=" CA HIS I 17 " pdb=" N HIS I 17 " pdb=" C HIS I 17 " pdb=" CB HIS I 17 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.13e+00 ... (remaining 1138 not shown) Planarity restraints: 1533 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C22 QS2 B 103 " -0.079 2.00e-02 2.50e+03 8.41e-02 7.08e+01 pdb=" C30 QS2 B 103 " 0.063 2.00e-02 2.50e+03 pdb=" C33 QS2 B 103 " 0.103 2.00e-02 2.50e+03 pdb=" C35 QS2 B 103 " -0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 QS2 E 103 " 0.079 2.00e-02 2.50e+03 8.40e-02 7.06e+01 pdb=" C30 QS2 E 103 " -0.062 2.00e-02 2.50e+03 pdb=" C33 QS2 E 103 " -0.103 2.00e-02 2.50e+03 pdb=" C35 QS2 E 103 " 0.087 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C22 QS2 G 102 " 0.079 2.00e-02 2.50e+03 8.39e-02 7.04e+01 pdb=" C30 QS2 G 102 " -0.063 2.00e-02 2.50e+03 pdb=" C33 QS2 G 102 " -0.103 2.00e-02 2.50e+03 pdb=" C35 QS2 G 102 " 0.087 2.00e-02 2.50e+03 ... (remaining 1530 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.84: 2566 2.84 - 3.35: 7951 3.35 - 3.87: 16315 3.87 - 4.38: 18907 4.38 - 4.90: 28880 Nonbonded interactions: 74619 Sorted by model distance: nonbonded pdb=" O LYS K 23 " pdb=" OG1 THR K 26 " model vdw 2.324 2.440 nonbonded pdb=" O LYS C 23 " pdb=" OG1 THR C 26 " model vdw 2.324 2.440 nonbonded pdb=" O LYS M 23 " pdb=" OG1 THR M 26 " model vdw 2.324 2.440 nonbonded pdb=" O LYS A 23 " pdb=" OG1 THR A 26 " model vdw 2.325 2.440 nonbonded pdb=" O LYS I 23 " pdb=" OG1 THR I 26 " model vdw 2.325 2.440 ... (remaining 74614 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' and resid 2 through 70) selection = (chain 'C' and resid 2 through 70) selection = (chain 'E' and resid 2 through 70) selection = (chain 'G' and resid 2 through 70) selection = (chain 'I' and resid 2 through 70) selection = (chain 'K' and resid 2 through 70) selection = (chain 'M' and resid 2 through 70) } ncs_group { reference = (chain 'B' and (resid 5 through 48 or resid 102)) selection = (chain 'D' and (resid 5 through 48 or resid 102)) selection = (chain 'F' and (resid 5 through 48 or resid 102)) selection = (chain 'H' and (resid 5 through 48 or resid 102)) selection = (chain 'J' and (resid 5 through 48 or resid 102)) selection = (chain 'L' and (resid 5 through 48 or resid 102)) selection = (chain 'N' and (resid 5 through 48 or resid 102)) } 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: 6.240 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: 26.630 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 27.410 Find NCS groups from input model: 0.520 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 74.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8934 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 : 0.019 0.156 8876 Z= 0.964 Angle : 3.606 44.848 12418 Z= 1.245 Chirality : 0.067 0.408 1141 Planarity : 0.012 0.084 1533 Dihedral : 21.621 166.713 2877 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.84 % Favored : 87.16 % Rotamer: Outliers : 5.21 % Allowed : 11.46 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.92 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.27), residues: 763 helix: 1.68 (0.20), residues: 343 sheet: None (None), residues: 0 loop : -2.92 (0.28), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP M 33 HIS 0.022 0.004 HIS G 17 PHE 0.030 0.005 PHE D 19 TYR 0.006 0.001 TYR K 58 ARG 0.001 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 120 time to evaluate : 0.845 Fit side-chains REVERT: C 17 HIS cc_start: 0.6664 (OUTLIER) cc_final: 0.6267 (t70) REVERT: M 17 HIS cc_start: 0.6767 (OUTLIER) cc_final: 0.6374 (t70) outliers start: 35 outliers final: 17 residues processed: 155 average time/residue: 1.0699 time to fit residues: 177.7274 Evaluate side-chains 127 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 108 time to evaluate : 0.850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 64 VAL Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain E residue 17 HIS Chi-restraints excluded: chain E residue 64 VAL Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 64 VAL Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain I residue 17 HIS Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain K residue 17 HIS Chi-restraints excluded: chain K residue 64 VAL Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 64 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 0.5980 chunk 53 optimal weight: 0.5980 chunk 29 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 63 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 16 ASN C 16 ASN E 16 ASN G 16 ASN I 16 ASN K 16 ASN M 16 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8837 moved from start: 0.1354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 8876 Z= 0.259 Angle : 1.953 25.446 12418 Z= 0.685 Chirality : 0.050 0.251 1141 Planarity : 0.006 0.057 1533 Dihedral : 24.498 172.110 1502 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.88 % Favored : 89.12 % Rotamer: Outliers : 4.32 % Allowed : 13.84 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.10 % 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: 0.19 (0.29), residues: 763 helix: 3.23 (0.20), residues: 357 sheet: None (None), residues: 0 loop : -3.08 (0.27), residues: 406 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 33 HIS 0.012 0.002 HIS E 17 PHE 0.025 0.004 PHE J 19 TYR 0.005 0.001 TYR H 44 ARG 0.000 0.000 ARG E 65 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 112 time to evaluate : 0.802 Fit side-chains outliers start: 29 outliers final: 9 residues processed: 132 average time/residue: 1.1045 time to fit residues: 156.3469 Evaluate side-chains 111 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 102 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 11 SER Chi-restraints excluded: chain G residue 11 SER Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 11 SER Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 52 optimal weight: 0.0040 chunk 43 optimal weight: 0.2980 chunk 17 optimal weight: 1.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 62 optimal weight: 0.0870 overall best weight: 0.4774 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 45 GLN ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 8876 Z= 0.226 Angle : 1.868 24.950 12418 Z= 0.652 Chirality : 0.047 0.222 1141 Planarity : 0.006 0.044 1533 Dihedral : 23.726 169.179 1483 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.50 % Favored : 86.50 % Rotamer: Outliers : 4.91 % Allowed : 14.14 % Favored : 80.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: 0.58 (0.30), residues: 763 helix: 2.85 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.73 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.004 0.001 HIS M 17 PHE 0.023 0.003 PHE J 19 TYR 0.006 0.001 TYR N 44 ARG 0.000 0.000 ARG K 65 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 95 time to evaluate : 0.912 Fit side-chains outliers start: 33 outliers final: 10 residues processed: 114 average time/residue: 1.2678 time to fit residues: 153.5731 Evaluate side-chains 104 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 94 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 17 HIS Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain I residue 7 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 42 optimal weight: 0.0980 chunk 63 optimal weight: 1.9990 chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 0.0970 chunk 18 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8864 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 8876 Z= 0.276 Angle : 1.922 25.265 12418 Z= 0.672 Chirality : 0.051 0.267 1141 Planarity : 0.007 0.055 1533 Dihedral : 23.950 174.339 1478 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 11.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.19 % Favored : 87.81 % Rotamer: Outliers : 4.17 % Allowed : 15.62 % Favored : 80.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: 0.68 (0.30), residues: 763 helix: 2.91 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.64 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 22 HIS 0.006 0.001 HIS A 17 PHE 0.027 0.004 PHE J 19 TYR 0.007 0.001 TYR B 44 ARG 0.000 0.000 ARG G 65 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 100 time to evaluate : 0.792 Fit side-chains outliers start: 28 outliers final: 11 residues processed: 114 average time/residue: 1.2031 time to fit residues: 145.8838 Evaluate side-chains 110 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 99 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 SER Chi-restraints excluded: chain C residue 7 MET Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 11 SER Chi-restraints excluded: chain M residue 34 MET Chi-restraints excluded: chain N residue 17 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 34 optimal weight: 0.5980 chunk 60 optimal weight: 5.9990 chunk 17 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8896 moved from start: 0.1456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.046 8876 Z= 0.339 Angle : 1.998 25.758 12418 Z= 0.703 Chirality : 0.057 0.332 1141 Planarity : 0.007 0.051 1533 Dihedral : 24.361 172.425 1478 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.24 % Favored : 86.76 % Rotamer: Outliers : 4.61 % Allowed : 15.77 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: 0.68 (0.30), residues: 763 helix: 2.85 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.57 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP I 33 HIS 0.006 0.001 HIS M 17 PHE 0.031 0.004 PHE J 19 TYR 0.008 0.001 TYR H 44 ARG 0.000 0.000 ARG M 65 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 103 time to evaluate : 0.775 Fit side-chains outliers start: 31 outliers final: 12 residues processed: 119 average time/residue: 1.2021 time to fit residues: 152.6286 Evaluate side-chains 116 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 104 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 11 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 3.9990 chunk 67 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 35 optimal weight: 1.9990 chunk 65 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 45 GLN ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 45 GLN ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.1711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 8876 Z= 0.253 Angle : 1.903 24.916 12418 Z= 0.663 Chirality : 0.049 0.240 1141 Planarity : 0.006 0.045 1533 Dihedral : 23.983 175.144 1477 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.71 % Favored : 87.29 % Rotamer: Outliers : 4.91 % Allowed : 16.07 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.96 % 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: 0.82 (0.30), residues: 763 helix: 2.96 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.49 (0.30), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 33 HIS 0.005 0.001 HIS M 17 PHE 0.025 0.004 PHE D 19 TYR 0.008 0.001 TYR H 44 ARG 0.000 0.000 ARG G 65 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 101 time to evaluate : 0.788 Fit side-chains REVERT: M 17 HIS cc_start: 0.5457 (OUTLIER) cc_final: 0.5184 (m-70) outliers start: 33 outliers final: 16 residues processed: 117 average time/residue: 1.2313 time to fit residues: 153.1490 Evaluate side-chains 116 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 14 THR Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 17 HIS Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 2.9990 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 67 optimal weight: 0.6980 chunk 42 optimal weight: 0.0970 chunk 41 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 chunk 20 optimal weight: 0.0170 chunk 13 optimal weight: 0.6980 overall best weight: 0.4416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 8876 Z= 0.224 Angle : 1.857 24.814 12418 Z= 0.647 Chirality : 0.046 0.208 1141 Planarity : 0.006 0.060 1533 Dihedral : 23.457 178.888 1477 Min Nonbonded Distance : 2.283 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.37 % Favored : 86.63 % Rotamer: Outliers : 4.61 % Allowed : 16.07 % Favored : 79.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.82 % 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: 0.91 (0.30), residues: 763 helix: 3.02 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.42 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 33 HIS 0.008 0.001 HIS E 17 PHE 0.022 0.003 PHE J 19 TYR 0.009 0.001 TYR H 44 ARG 0.000 0.000 ARG K 65 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 95 time to evaluate : 0.868 Fit side-chains revert: symmetry clash REVERT: C 10 GLU cc_start: 0.6671 (OUTLIER) cc_final: 0.6416 (tm-30) REVERT: E 10 GLU cc_start: 0.6562 (OUTLIER) cc_final: 0.6311 (tm-30) REVERT: M 10 GLU cc_start: 0.6598 (OUTLIER) cc_final: 0.6204 (tm-30) outliers start: 31 outliers final: 19 residues processed: 114 average time/residue: 1.3651 time to fit residues: 164.6032 Evaluate side-chains 114 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 92 time to evaluate : 0.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 10 GLU Chi-restraints excluded: chain G residue 14 THR Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain I residue 34 MET Chi-restraints excluded: chain J residue 39 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 10 GLU Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 0.3980 chunk 42 optimal weight: 0.0270 chunk 45 optimal weight: 1.9990 chunk 33 optimal weight: 0.0970 chunk 6 optimal weight: 3.9990 chunk 53 optimal weight: 0.7980 chunk 61 optimal weight: 0.0980 chunk 64 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 62 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 overall best weight: 0.1636 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** I 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 16 ASN ** K 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 45 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 17 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 8876 Z= 0.202 Angle : 1.784 24.396 12418 Z= 0.622 Chirality : 0.042 0.154 1141 Planarity : 0.006 0.063 1533 Dihedral : 22.192 169.800 1477 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 3.57 % Allowed : 18.01 % Favored : 78.42 % 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: 0.45 (0.30), residues: 763 helix: 2.64 (0.23), residues: 413 sheet: None (None), residues: 0 loop : -2.87 (0.27), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 47 HIS 0.005 0.001 HIS E 17 PHE 0.018 0.003 PHE F 19 TYR 0.009 0.001 TYR H 44 ARG 0.000 0.000 ARG K 65 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 0.813 Fit side-chains REVERT: A 7 MET cc_start: 0.7254 (tpp) cc_final: 0.6750 (tpt) REVERT: C 10 GLU cc_start: 0.6387 (OUTLIER) cc_final: 0.6143 (tm-30) REVERT: E 10 GLU cc_start: 0.6351 (OUTLIER) cc_final: 0.6116 (tm-30) REVERT: G 7 MET cc_start: 0.7621 (OUTLIER) cc_final: 0.7276 (tpt) REVERT: I 7 MET cc_start: 0.7122 (tpp) cc_final: 0.6859 (tpt) outliers start: 24 outliers final: 11 residues processed: 102 average time/residue: 1.4234 time to fit residues: 153.5811 Evaluate side-chains 93 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 79 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 7 MET Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 59 optimal weight: 0.7980 chunk 62 optimal weight: 0.0980 chunk 41 optimal weight: 0.9990 chunk 66 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 0.0000 chunk 46 optimal weight: 3.9990 overall best weight: 0.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8798 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 8876 Z= 0.230 Angle : 1.845 24.865 12418 Z= 0.646 Chirality : 0.046 0.208 1141 Planarity : 0.006 0.049 1533 Dihedral : 22.982 173.003 1477 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.40 % Favored : 88.60 % Rotamer: Outliers : 2.98 % Allowed : 18.75 % Favored : 78.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.30), residues: 763 helix: 3.07 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 22 HIS 0.009 0.002 HIS M 17 PHE 0.023 0.003 PHE D 19 TYR 0.011 0.001 TYR H 44 ARG 0.000 0.000 ARG I 65 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 84 time to evaluate : 0.855 Fit side-chains REVERT: A 7 MET cc_start: 0.7261 (tpp) cc_final: 0.6777 (tpt) REVERT: C 10 GLU cc_start: 0.6454 (OUTLIER) cc_final: 0.6204 (tm-30) REVERT: E 7 MET cc_start: 0.7350 (tpp) cc_final: 0.6997 (tpt) REVERT: E 10 GLU cc_start: 0.6390 (OUTLIER) cc_final: 0.6184 (tm-30) REVERT: I 7 MET cc_start: 0.7358 (tpp) cc_final: 0.7027 (tpt) outliers start: 20 outliers final: 13 residues processed: 100 average time/residue: 1.2702 time to fit residues: 134.9171 Evaluate side-chains 99 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 14 THR Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.6980 chunk 64 optimal weight: 3.9990 chunk 55 optimal weight: 0.8980 chunk 5 optimal weight: 0.6980 chunk 42 optimal weight: 0.0050 chunk 34 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.5980 chunk 17 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8797 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 8876 Z= 0.234 Angle : 1.853 24.859 12418 Z= 0.651 Chirality : 0.046 0.201 1141 Planarity : 0.006 0.041 1533 Dihedral : 22.934 175.561 1477 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.01 % Favored : 88.99 % Rotamer: Outliers : 3.42 % Allowed : 18.15 % Favored : 78.42 % 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: 0.98 (0.29), residues: 763 helix: 2.96 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 HIS 0.007 0.001 HIS M 17 PHE 0.023 0.003 PHE D 19 TYR 0.012 0.001 TYR H 44 ARG 0.000 0.000 ARG E 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1526 Ramachandran restraints generated. 763 Oldfield, 0 Emsley, 763 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.865 Fit side-chains REVERT: A 7 MET cc_start: 0.7227 (tpp) cc_final: 0.6521 (tpt) REVERT: C 10 GLU cc_start: 0.6493 (OUTLIER) cc_final: 0.6264 (tm-30) REVERT: E 7 MET cc_start: 0.7362 (tpp) cc_final: 0.6995 (tpt) REVERT: E 10 GLU cc_start: 0.6385 (OUTLIER) cc_final: 0.6173 (tm-30) REVERT: I 7 MET cc_start: 0.7271 (tpp) cc_final: 0.6984 (tpt) outliers start: 23 outliers final: 18 residues processed: 101 average time/residue: 1.2616 time to fit residues: 135.5120 Evaluate side-chains 105 residues out of total 672 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 85 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 THR Chi-restraints excluded: chain A residue 34 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 10 GLU Chi-restraints excluded: chain C residue 14 THR Chi-restraints excluded: chain C residue 32 THR Chi-restraints excluded: chain C residue 34 MET Chi-restraints excluded: chain E residue 5 VAL Chi-restraints excluded: chain E residue 10 GLU Chi-restraints excluded: chain E residue 32 THR Chi-restraints excluded: chain E residue 34 MET Chi-restraints excluded: chain G residue 5 VAL Chi-restraints excluded: chain G residue 17 HIS Chi-restraints excluded: chain G residue 34 MET Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 34 MET Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 34 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 0.9990 chunk 55 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 3 optimal weight: 0.9990 chunk 40 optimal weight: 0.2980 chunk 63 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 45 GLN ** J 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 25 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.142987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117471 restraints weight = 8511.073| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 1.16 r_work: 0.3094 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.2964 rms_B_bonded: 3.07 restraints_weight: 0.2500 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8876 Z= 0.238 Angle : 1.862 24.929 12418 Z= 0.653 Chirality : 0.047 0.209 1141 Planarity : 0.006 0.041 1533 Dihedral : 23.104 178.745 1477 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.93 % Favored : 88.07 % Rotamer: Outliers : 3.87 % Allowed : 17.41 % Favored : 78.72 % 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: 0.95 (0.30), residues: 763 helix: 2.92 (0.22), residues: 399 sheet: None (None), residues: 0 loop : -2.23 (0.29), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 22 HIS 0.008 0.001 HIS M 17 PHE 0.024 0.003 PHE D 19 TYR 0.012 0.001 TYR H 44 ARG 0.000 0.000 ARG E 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3420.83 seconds wall clock time: 61 minutes 49.99 seconds (3709.99 seconds total)