Starting phenix.real_space_refine on Fri Feb 14 10:07:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7ze8_14685/02_2025/7ze8_14685.cif Found real_map, /net/cci-nas-00/data/ceres_data/7ze8_14685/02_2025/7ze8_14685.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7ze8_14685/02_2025/7ze8_14685.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7ze8_14685/02_2025/7ze8_14685.map" model { file = "/net/cci-nas-00/data/ceres_data/7ze8_14685/02_2025/7ze8_14685.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7ze8_14685/02_2025/7ze8_14685.cif" } resolution = 3.6 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= 0.012 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 33 5.21 5 S 9 5.16 5 C 7166 2.51 5 N 1374 2.21 5 O 1486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 10068 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "C" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "E" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "G" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "I" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "K" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "M" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "O" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "Q" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 371 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 43} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 744 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PCIS': 6, 'TRANS': 87} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" 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: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" 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: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" 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: "P" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" 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: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Time building chain proxies: 6.62, per 1000 atoms: 0.66 Number of scatterers: 10068 At special positions: 0 Unit cell: (95.55, 104, 76.05, 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 9 16.00 Mg 33 11.99 O 1486 8.00 N 1374 7.00 C 7166 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.29 Conformation dependent library (CDL) restraints added in 850.4 milliseconds 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 73.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.79 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 38 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 38 through 47 removed outlier: 3.637A pdb=" N SER A 42 " --> pdb=" O THR A 38 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N TRP A 45 " --> pdb=" O PHE A 41 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ASN A 46 " --> pdb=" O SER A 42 " (cutoff:3.500A) Processing helix chain 'B' and resid 10 through 43 removed outlier: 4.089A pdb=" N HIS B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL B 34 " --> pdb=" O ALA B 30 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 11 through 38 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 38 through 47 removed outlier: 3.855A pdb=" N SER C 42 " --> pdb=" O THR C 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 10 through 43 removed outlier: 3.942A pdb=" N HIS D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 1 through 9 removed outlier: 4.112A pdb=" N GLY E 4 " --> pdb=" O CXM E 1 " (cutoff:3.500A) removed outlier: 4.421A pdb=" N ARG E 5 " --> pdb=" O ASN E 2 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 11 through 38 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 38 through 47 removed outlier: 3.795A pdb=" N SER E 42 " --> pdb=" O THR E 38 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N TRP E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 10 through 43 removed outlier: 3.821A pdb=" N HIS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 Processing helix chain 'G' and resid 11 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 38 through 47 removed outlier: 3.775A pdb=" N SER G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N TRP G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 10 through 42 removed outlier: 3.905A pdb=" N HIS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 Processing helix chain 'I' and resid 11 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 38 through 47 removed outlier: 3.836A pdb=" N SER I 42 " --> pdb=" O THR I 38 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N TRP I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 10 through 42 removed outlier: 3.757A pdb=" N HIS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 38 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 38 through 47 removed outlier: 3.903A pdb=" N SER K 42 " --> pdb=" O THR K 38 " (cutoff:3.500A) Processing helix chain 'L' and resid 10 through 42 removed outlier: 3.995A pdb=" N HIS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 Processing helix chain 'M' and resid 11 through 37 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 38 through 47 removed outlier: 3.999A pdb=" N SER M 42 " --> pdb=" O THR M 38 " (cutoff:3.500A) Processing helix chain 'N' and resid 10 through 42 removed outlier: 3.929A pdb=" N HIS N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 Processing helix chain 'O' and resid 11 through 37 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 38 through 47 removed outlier: 3.837A pdb=" N SER O 42 " --> pdb=" O THR O 38 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N TRP O 45 " --> pdb=" O PHE O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 10 through 43 removed outlier: 3.536A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 Processing helix chain 'Q' and resid 11 through 37 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 38 through 47 removed outlier: 3.817A pdb=" N SER Q 42 " --> pdb=" O THR Q 38 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP Q 45 " --> pdb=" O PHE Q 41 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASN Q 46 " --> pdb=" O SER Q 42 " (cutoff:3.500A) Processing helix chain 'R' and resid 10 through 43 removed outlier: 3.879A pdb=" N HIS R 20 " --> pdb=" O GLU R 16 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N VAL R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1428 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: 2.40 Time building geometry restraints manager: 3.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 2887 1.37 - 1.57: 7521 1.57 - 1.78: 9 1.78 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10558 Sorted by residual: bond pdb=" SD CXM M 1 " pdb=" CE CXM M 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" SD CXM I 1 " pdb=" CE CXM I 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.22e+00 bond pdb=" SD CXM O 1 " pdb=" CE CXM O 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.19e+00 bond pdb=" SD CXM A 1 " pdb=" CE CXM A 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.09e+00 bond pdb=" SD CXM E 1 " pdb=" CE CXM E 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 10553 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.28: 14810 5.28 - 10.56: 22 10.56 - 15.84: 0 15.84 - 21.13: 2 21.13 - 26.41: 3 Bond angle restraints: 14837 Sorted by residual: angle pdb=" C1 BCL S 105 " pdb=" O2A BCL S 105 " pdb=" CGA BCL S 105 " ideal model delta sigma weight residual 116.11 142.52 -26.41 4.27e+00 5.48e-02 3.82e+01 angle pdb=" C1 BCL S 102 " pdb=" C2 BCL S 102 " pdb=" C3 BCL S 102 " ideal model delta sigma weight residual 123.38 147.16 -23.79 4.41e+00 5.14e-02 2.91e+01 angle pdb=" C1 BCL S 106 " pdb=" O2A BCL S 106 " pdb=" CGA BCL S 106 " ideal model delta sigma weight residual 116.11 137.48 -21.36 4.27e+00 5.48e-02 2.50e+01 angle pdb=" N GLY M 21 " pdb=" CA GLY M 21 " pdb=" C GLY M 21 " ideal model delta sigma weight residual 112.50 117.35 -4.85 1.16e+00 7.43e-01 1.75e+01 angle pdb=" C1 BCL I 101 " pdb=" C2 BCL I 101 " pdb=" C3 BCL I 101 " ideal model delta sigma weight residual 123.38 140.31 -16.93 4.41e+00 5.14e-02 1.48e+01 ... (remaining 14832 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.36: 4937 21.36 - 42.71: 314 42.71 - 64.07: 43 64.07 - 85.43: 4 85.43 - 106.78: 7 Dihedral angle restraints: 5305 sinusoidal: 2624 harmonic: 2681 Sorted by residual: dihedral pdb=" C1 BCL S 105 " pdb=" CGA BCL S 105 " pdb=" O2A BCL S 105 " pdb=" CBA BCL S 105 " ideal model delta sinusoidal sigma weight residual -180.00 -147.50 -32.50 1 6.00e+00 2.78e-02 4.18e+01 dihedral pdb=" CA LEU D 46 " pdb=" C LEU D 46 " pdb=" N HIS D 47 " pdb=" CA HIS D 47 " ideal model delta harmonic sigma weight residual 180.00 -151.80 -28.20 0 5.00e+00 4.00e-02 3.18e+01 dihedral pdb=" CA LEU N 46 " pdb=" C LEU N 46 " pdb=" N HIS N 47 " pdb=" CA HIS N 47 " ideal model delta harmonic sigma weight residual -180.00 -151.82 -28.18 0 5.00e+00 4.00e-02 3.18e+01 ... (remaining 5302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1071 0.041 - 0.082: 309 0.082 - 0.123: 92 0.123 - 0.164: 5 0.164 - 0.204: 3 Chirality restraints: 1480 Sorted by residual: chirality pdb=" CBD BCL A 101 " pdb=" CAD BCL A 101 " pdb=" CGD BCL A 101 " pdb=" CHA BCL A 101 " both_signs ideal model delta sigma weight residual False 2.62 2.42 0.20 2.00e-01 2.50e+01 1.05e+00 chirality pdb=" CBD BCL I 101 " pdb=" CAD BCL I 101 " pdb=" CGD BCL I 101 " pdb=" CHA BCL I 101 " both_signs ideal model delta sigma weight residual False 2.62 2.42 0.20 2.00e-01 2.50e+01 1.01e+00 chirality pdb=" CBD BCL G 101 " pdb=" CAD BCL G 101 " pdb=" CGD BCL G 101 " pdb=" CHA BCL G 101 " both_signs ideal model delta sigma weight residual False 2.62 2.45 0.17 2.00e-01 2.50e+01 7.46e-01 ... (remaining 1477 not shown) Planarity restraints: 1772 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C16 IRM P 101 " 0.085 2.00e-02 2.50e+03 7.14e-02 6.37e+01 pdb=" C17 IRM P 101 " -0.106 2.00e-02 2.50e+03 pdb=" C18 IRM P 101 " -0.045 2.00e-02 2.50e+03 pdb=" C19 IRM P 101 " 0.070 2.00e-02 2.50e+03 pdb=" C36 IRM P 101 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 IRM C 103 " 0.083 2.00e-02 2.50e+03 7.04e-02 6.19e+01 pdb=" C17 IRM C 103 " -0.100 2.00e-02 2.50e+03 pdb=" C18 IRM C 103 " -0.052 2.00e-02 2.50e+03 pdb=" C19 IRM C 103 " 0.071 2.00e-02 2.50e+03 pdb=" C36 IRM C 103 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL S 105 " -0.107 3.00e-02 1.11e+03 1.01e-01 5.71e+01 pdb=" CBA BCL S 105 " -0.053 3.00e-02 1.11e+03 pdb=" CGA BCL S 105 " -0.032 3.00e-02 1.11e+03 pdb=" O1A BCL S 105 " 0.002 3.00e-02 1.11e+03 pdb=" O2A BCL S 105 " 0.190 3.00e-02 1.11e+03 ... (remaining 1769 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 710 2.74 - 3.28: 9071 3.28 - 3.82: 16567 3.82 - 4.36: 20774 4.36 - 4.90: 35796 Nonbonded interactions: 82918 Sorted by model distance: nonbonded pdb=" OD2 ASP H 23 " pdb=" OH TYR S 21 " model vdw 2.203 3.040 nonbonded pdb=" OD2 ASP F 23 " pdb=" OH TYR S 5 " model vdw 2.280 3.040 nonbonded pdb=" OD2 ASP N 23 " pdb=" OH TYR S 69 " model vdw 2.289 3.040 nonbonded pdb=" ON2 CXM M 1 " pdb=" NE2 HIS N 18 " model vdw 2.323 3.120 nonbonded pdb=" ON2 CXM C 1 " pdb=" NE2 HIS D 18 " model vdw 2.340 3.120 ... (remaining 82913 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'C' and (resid 1 through 48 or resid 101 through 102)) selection = chain 'E' selection = (chain 'G' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'I' and (resid 1 through 48 or resid 101 through 102)) selection = (chain 'K' and (resid 1 through 48 or resid 101 through 102)) selection = chain 'M' selection = chain 'O' selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 2 through 47) selection = (chain 'D' and resid 2 through 47) selection = (chain 'F' and resid 2 through 47) selection = (chain 'H' and resid 2 through 47) selection = (chain 'J' and resid 2 through 47) selection = (chain 'L' and resid 2 through 47) selection = (chain 'N' and resid 2 through 47) selection = (chain 'P' and resid 2 through 47) selection = (chain 'R' and resid 2 through 47) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.100 Process input model: 24.740 Find NCS groups from input model: 0.510 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7607 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 0.046 10558 Z= 0.275 Angle : 0.942 26.408 14837 Z= 0.393 Chirality : 0.041 0.204 1480 Planarity : 0.011 0.101 1772 Dihedral : 14.048 106.781 3581 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 2.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 0.49 (0.25), residues: 893 helix: 0.72 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.27 (0.34), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP O 40 HIS 0.003 0.001 HIS N 18 PHE 0.019 0.001 PHE K 32 TYR 0.032 0.003 TYR S 53 ARG 0.019 0.005 ARG B 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.864 Fit side-chains REVERT: D 16 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6784 (tp30) REVERT: G 5 ARG cc_start: 0.7433 (mtt180) cc_final: 0.6977 (mtt180) REVERT: K 46 ASN cc_start: 0.7332 (t0) cc_final: 0.6996 (m-40) REVERT: O 2 ASN cc_start: 0.8977 (m110) cc_final: 0.8450 (m110) outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 0.1864 time to fit residues: 16.8189 Evaluate side-chains 39 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.1980 chunk 61 optimal weight: 3.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 5.9990 chunk 63 optimal weight: 0.8980 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN C 37 ASN J 20 HIS K 3 GLN L 20 HIS ** M 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 20 HIS Q 46 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.109523 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.093440 restraints weight = 11146.527| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.094856 restraints weight = 9052.060| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.096099 restraints weight = 7774.025| |-----------------------------------------------------------------------------| r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.1571 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10558 Z= 0.188 Angle : 0.723 8.135 14837 Z= 0.283 Chirality : 0.038 0.123 1480 Planarity : 0.005 0.035 1772 Dihedral : 14.173 102.143 1988 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.13 % Allowed : 3.42 % Favored : 96.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.26), residues: 893 helix: 3.28 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.46 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 45 HIS 0.004 0.001 HIS B 36 PHE 0.009 0.001 PHE K 32 TYR 0.007 0.001 TYR Q 44 ARG 0.002 0.000 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.877 Fit side-chains REVERT: G 5 ARG cc_start: 0.7647 (mtt180) cc_final: 0.7274 (mtt180) outliers start: 1 outliers final: 1 residues processed: 34 average time/residue: 0.2356 time to fit residues: 12.0676 Evaluate side-chains 29 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 69 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 46 optimal weight: 4.9990 chunk 61 optimal weight: 7.9990 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 44 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 42 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 37 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.108284 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.092886 restraints weight = 11343.742| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.094254 restraints weight = 9295.930| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.095416 restraints weight = 8002.317| |-----------------------------------------------------------------------------| r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 10558 Z= 0.221 Angle : 0.737 9.555 14837 Z= 0.277 Chirality : 0.038 0.124 1480 Planarity : 0.005 0.038 1772 Dihedral : 14.251 99.977 1988 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.38 % Allowed : 5.32 % Favored : 94.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.05 (0.26), residues: 893 helix: 3.22 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.32 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 40 HIS 0.005 0.001 HIS R 36 PHE 0.011 0.001 PHE K 32 TYR 0.006 0.001 TYR S 69 ARG 0.003 0.000 ARG Q 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.962 Fit side-chains REVERT: G 5 ARG cc_start: 0.7690 (mtt180) cc_final: 0.7263 (mtt180) outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.1967 time to fit residues: 12.3526 Evaluate side-chains 37 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain F residue 7 THR Chi-restraints excluded: chain O residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 3 optimal weight: 5.9990 chunk 49 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 0 optimal weight: 7.9990 chunk 50 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 52 optimal weight: 4.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3121 r_free = 0.3121 target = 0.110963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.2939 r_free = 0.2939 target = 0.095824 restraints weight = 11045.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.097100 restraints weight = 9030.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.098337 restraints weight = 7830.413| |-----------------------------------------------------------------------------| r_work (final): 0.2945 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8059 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10558 Z= 0.169 Angle : 0.665 9.007 14837 Z= 0.251 Chirality : 0.036 0.116 1480 Planarity : 0.005 0.039 1772 Dihedral : 14.123 98.692 1988 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.38 % Allowed : 7.48 % Favored : 92.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.26), residues: 893 helix: 3.35 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.34 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 40 HIS 0.004 0.001 HIS H 20 PHE 0.006 0.001 PHE E 41 TYR 0.010 0.001 TYR S 21 ARG 0.002 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 43 time to evaluate : 1.015 Fit side-chains REVERT: G 5 ARG cc_start: 0.7681 (mtt180) cc_final: 0.7266 (mtt180) outliers start: 3 outliers final: 1 residues processed: 44 average time/residue: 0.1992 time to fit residues: 13.9362 Evaluate side-chains 37 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 12 optimal weight: 7.9990 chunk 72 optimal weight: 20.0000 chunk 62 optimal weight: 6.9990 chunk 43 optimal weight: 4.9990 chunk 65 optimal weight: 0.9980 chunk 55 optimal weight: 3.9990 chunk 52 optimal weight: 7.9990 chunk 49 optimal weight: 0.0470 chunk 38 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 56 optimal weight: 6.9990 overall best weight: 2.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 2 ASN Q 46 ASN S 8 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.103490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.2832 r_free = 0.2832 target = 0.088053 restraints weight = 11514.704| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.089376 restraints weight = 9556.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.089901 restraints weight = 8333.563| |-----------------------------------------------------------------------------| r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.2429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 10558 Z= 0.374 Angle : 0.878 13.340 14837 Z= 0.322 Chirality : 0.043 0.130 1480 Planarity : 0.005 0.039 1772 Dihedral : 15.042 98.265 1988 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 0.38 % Allowed : 9.25 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.19 (0.26), residues: 893 helix: 2.69 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.77 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 40 HIS 0.007 0.002 HIS R 36 PHE 0.013 0.002 PHE K 32 TYR 0.013 0.002 TYR F 40 ARG 0.002 0.000 ARG A 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.930 Fit side-chains REVERT: G 5 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7200 (mtt180) outliers start: 3 outliers final: 3 residues processed: 44 average time/residue: 0.1957 time to fit residues: 13.7102 Evaluate side-chains 42 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain O residue 42 SER Chi-restraints excluded: chain Q residue 46 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 38 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 52 optimal weight: 6.9990 chunk 75 optimal weight: 7.9990 chunk 76 optimal weight: 0.0010 chunk 40 optimal weight: 6.9990 chunk 37 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 79 optimal weight: 10.0000 chunk 32 optimal weight: 3.9990 overall best weight: 0.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 37 ASN Q 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109910 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.094513 restraints weight = 11116.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.095864 restraints weight = 9091.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.097056 restraints weight = 7837.180| |-----------------------------------------------------------------------------| r_work (final): 0.2924 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 10558 Z= 0.166 Angle : 0.675 13.398 14837 Z= 0.252 Chirality : 0.036 0.115 1480 Planarity : 0.005 0.041 1772 Dihedral : 14.518 100.105 1988 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 0.51 % Allowed : 9.38 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.79 (0.26), residues: 893 helix: 3.27 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.75 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP Q 45 HIS 0.003 0.001 HIS H 20 PHE 0.006 0.001 PHE O 41 TYR 0.009 0.001 TYR F 40 ARG 0.001 0.000 ARG Q 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.850 Fit side-chains REVERT: G 5 ARG cc_start: 0.7703 (mtt180) cc_final: 0.7294 (mtt180) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.1938 time to fit residues: 12.8942 Evaluate side-chains 36 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 34 time to evaluate : 0.952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain J residue 47 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 75 optimal weight: 7.9990 chunk 54 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 72 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 69 optimal weight: 5.9990 chunk 47 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 5 optimal weight: 6.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN E 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.094442 restraints weight = 11313.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.2936 r_free = 0.2936 target = 0.095728 restraints weight = 9240.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.096919 restraints weight = 8000.611| |-----------------------------------------------------------------------------| r_work (final): 0.2922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8091 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 10558 Z= 0.179 Angle : 0.689 13.585 14837 Z= 0.254 Chirality : 0.037 0.117 1480 Planarity : 0.005 0.040 1772 Dihedral : 14.304 100.647 1988 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.25 % Allowed : 10.14 % Favored : 89.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % 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: 2.90 (0.26), residues: 893 helix: 3.37 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.72 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 45 HIS 0.003 0.001 HIS R 18 PHE 0.007 0.001 PHE O 41 TYR 0.009 0.001 TYR S 21 ARG 0.001 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.884 Fit side-chains REVERT: G 5 ARG cc_start: 0.7717 (mtt180) cc_final: 0.7292 (mtt180) outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.1953 time to fit residues: 12.2441 Evaluate side-chains 40 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 6 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 5.9990 chunk 73 optimal weight: 0.0060 chunk 28 optimal weight: 0.0030 chunk 34 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 44 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 overall best weight: 0.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN S 8 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.114372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.099326 restraints weight = 11034.376| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.100945 restraints weight = 8851.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.101880 restraints weight = 7582.181| |-----------------------------------------------------------------------------| r_work (final): 0.2990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10558 Z= 0.124 Angle : 0.625 13.528 14837 Z= 0.233 Chirality : 0.035 0.112 1480 Planarity : 0.004 0.041 1772 Dihedral : 14.081 100.419 1988 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.02 % Favored : 97.98 % Rotamer: Outliers : 0.38 % Allowed : 10.14 % Favored : 89.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.27), residues: 893 helix: 3.58 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.32 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 45 HIS 0.003 0.001 HIS H 20 PHE 0.005 0.001 PHE E 41 TYR 0.017 0.001 TYR E 44 ARG 0.001 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.826 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.1902 time to fit residues: 14.7626 Evaluate side-chains 41 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.869 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 7.9990 chunk 64 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 63 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 8 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.111465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.096276 restraints weight = 11155.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.097726 restraints weight = 9071.974| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.098830 restraints weight = 7842.517| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 10558 Z= 0.168 Angle : 0.662 13.525 14837 Z= 0.245 Chirality : 0.036 0.117 1480 Planarity : 0.004 0.039 1772 Dihedral : 14.042 100.039 1988 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 0.25 % Allowed : 11.41 % Favored : 88.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.33 (0.26), residues: 893 helix: 3.48 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.33 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 40 HIS 0.003 0.001 HIS R 36 PHE 0.006 0.001 PHE O 41 TYR 0.011 0.001 TYR S 21 ARG 0.001 0.000 ARG F 26 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 41 time to evaluate : 0.908 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 41 average time/residue: 0.1921 time to fit residues: 12.6990 Evaluate side-chains 40 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 73 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 0.0970 chunk 42 optimal weight: 3.9990 chunk 41 optimal weight: 0.0060 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN F 2 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.109162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.094069 restraints weight = 11293.178| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2930 r_free = 0.2930 target = 0.095409 restraints weight = 9246.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.096171 restraints weight = 8026.542| |-----------------------------------------------------------------------------| r_work (final): 0.2907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.2903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 10558 Z= 0.198 Angle : 0.696 13.231 14837 Z= 0.256 Chirality : 0.037 0.118 1480 Planarity : 0.004 0.039 1772 Dihedral : 14.193 99.117 1988 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.38 % Allowed : 11.15 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.12 (0.26), residues: 893 helix: 3.57 (0.18), residues: 549 sheet: None (None), residues: 0 loop : -0.57 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 45 HIS 0.004 0.001 HIS R 18 PHE 0.007 0.001 PHE O 41 TYR 0.013 0.001 TYR S 21 ARG 0.001 0.000 ARG K 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1786 Ramachandran restraints generated. 893 Oldfield, 0 Emsley, 893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.873 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.1906 time to fit residues: 12.0680 Evaluate side-chains 40 residues out of total 789 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain P residue 38 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.9990 chunk 41 optimal weight: 0.1980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 63 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 4 optimal weight: 7.9990 chunk 54 optimal weight: 0.6980 chunk 74 optimal weight: 0.3980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN S 8 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.113673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.099087 restraints weight = 10981.294| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.100283 restraints weight = 8979.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.101276 restraints weight = 7769.021| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8026 moved from start: 0.3064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 10558 Z= 0.133 Angle : 0.625 12.599 14837 Z= 0.233 Chirality : 0.035 0.112 1480 Planarity : 0.004 0.040 1772 Dihedral : 13.983 97.984 1988 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 0.25 % Allowed : 11.79 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 14.29 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.26), residues: 893 helix: 3.61 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.30 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP E 45 HIS 0.003 0.001 HIS N 20 PHE 0.005 0.001 PHE B 28 TYR 0.013 0.001 TYR S 21 ARG 0.001 0.000 ARG F 26 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2345.19 seconds wall clock time: 43 minutes 13.53 seconds (2593.53 seconds total)