Starting phenix.real_space_refine on Fri Jan 19 01:18:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze8_14685/01_2024/7ze8_14685_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze8_14685/01_2024/7ze8_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze8_14685/01_2024/7ze8_14685.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze8_14685/01_2024/7ze8_14685.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze8_14685/01_2024/7ze8_14685_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ze8_14685/01_2024/7ze8_14685_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21-5211/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: 5.70, per 1000 atoms: 0.57 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 - 3.50 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=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.11 Conformation dependent library (CDL) restraints added in 1.1 seconds 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 65.9% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.29 Creating SS restraints... Processing helix chain 'A' and resid 6 through 8 No H-bonds generated for 'chain 'A' and resid 6 through 8' Processing helix chain 'A' and resid 12 through 37 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 39 through 46 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 11 through 42 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 6 through 8 No H-bonds generated for 'chain 'C' and resid 6 through 8' Processing helix chain 'C' and resid 12 through 37 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 39 through 46 Processing helix chain 'D' and resid 11 through 42 removed outlier: 3.942A pdb=" N HIS D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 8 removed outlier: 4.382A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 37 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 39 through 46 removed outlier: 3.507A pdb=" N TRP E 45 " --> pdb=" O PHE E 41 " (cutoff:3.500A) Processing helix chain 'F' and resid 11 through 42 removed outlier: 3.821A pdb=" N HIS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 6 through 8 No H-bonds generated for 'chain 'G' and resid 6 through 8' Processing helix chain 'G' and resid 12 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 39 through 46 removed outlier: 3.660A pdb=" N TRP G 45 " --> pdb=" O PHE G 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 11 through 41 removed outlier: 3.905A pdb=" N HIS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 6 through 8 No H-bonds generated for 'chain 'I' and resid 6 through 8' Processing helix chain 'I' and resid 12 through 36 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 39 through 46 removed outlier: 3.547A pdb=" N TRP I 45 " --> pdb=" O PHE I 41 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 41 removed outlier: 3.757A pdb=" N HIS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 6 through 8 No H-bonds generated for 'chain 'K' and resid 6 through 8' Processing helix chain 'K' and resid 12 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 46 Processing helix chain 'L' and resid 11 through 41 removed outlier: 3.995A pdb=" N HIS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 8 removed outlier: 4.310A pdb=" N TRP M 7 " --> pdb=" O GLY M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 36 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 39 through 46 Processing helix chain 'N' and resid 11 through 41 removed outlier: 3.929A pdb=" N HIS N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 6 through 8 No H-bonds generated for 'chain 'O' and resid 6 through 8' Processing helix chain 'O' and resid 12 through 36 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 39 through 46 removed outlier: 3.558A pdb=" N TRP O 45 " --> pdb=" O PHE O 41 " (cutoff:3.500A) Processing helix chain 'P' and resid 11 through 42 removed outlier: 3.536A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 6 through 8 No H-bonds generated for 'chain 'Q' and resid 6 through 8' Processing helix chain 'Q' and resid 12 through 36 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 39 through 46 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 11 through 42 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) 436 hydrogen bonds defined for protein. 1296 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: 2.68 Time building geometry restraints manager: 4.47 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: 84.81 - 99.87: 132 99.87 - 114.93: 6928 114.93 - 129.99: 7323 129.99 - 145.06: 362 145.06 - 160.12: 92 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: 712 2.74 - 3.28: 9128 3.28 - 3.82: 16662 3.82 - 4.36: 20856 4.36 - 4.90: 35796 Nonbonded interactions: 83154 Sorted by model distance: nonbonded pdb=" OD2 ASP H 23 " pdb=" OH TYR S 21 " model vdw 2.203 2.440 nonbonded pdb=" OD2 ASP F 23 " pdb=" OH TYR S 5 " model vdw 2.280 2.440 nonbonded pdb=" OD2 ASP N 23 " pdb=" OH TYR S 69 " model vdw 2.289 2.440 nonbonded pdb=" ON2 CXM M 1 " pdb=" NE2 HIS N 18 " model vdw 2.323 2.520 nonbonded pdb=" ON2 CXM C 1 " pdb=" NE2 HIS D 18 " model vdw 2.340 2.520 ... (remaining 83149 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 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: 1.340 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: 5.460 Check model and map are aligned: 0.150 Set scattering table: 0.100 Process input model: 28.650 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.080 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.440 ------------------------------------------------------------------------------- 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= 0.270 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 fitting. rotamer outliers: 0 poor density : 58 time to evaluate : 0.898 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: 0.1822 time to fit residues: 16.4722 Evaluate side-chains 39 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.844 ------------------------------------------------------------------------------- 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: 4.9990 chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 8.9990 chunk 41 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 47 optimal weight: 1.9990 chunk 73 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 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: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7638 moved from start: 0.1468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10558 Z= 0.240 Angle : 0.772 8.806 14837 Z= 0.293 Chirality : 0.038 0.125 1480 Planarity : 0.005 0.034 1772 Dihedral : 14.401 102.368 1988 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 5.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.38 % Allowed : 3.04 % Favored : 96.58 % 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: 2.59 (0.27), residues: 893 helix: 2.93 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.44 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 40 HIS 0.004 0.001 HIS J 20 PHE 0.015 0.002 PHE K 32 TYR 0.008 0.001 TYR O 44 ARG 0.002 0.000 ARG Q 5 *********************** 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 36 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.843 Fit side-chains REVERT: G 5 ARG cc_start: 0.7588 (mtt180) cc_final: 0.7092 (mtt180) REVERT: I 3 GLN cc_start: 0.8197 (mm-40) cc_final: 0.7983 (mm-40) outliers start: 3 outliers final: 3 residues processed: 36 average time/residue: 0.1705 time to fit residues: 10.3280 Evaluate side-chains 33 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 30 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain Q residue 38 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 7.9990 chunk 22 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 73 optimal weight: 0.7980 chunk 79 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 59 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10558 Z= 0.147 Angle : 0.658 8.570 14837 Z= 0.245 Chirality : 0.035 0.113 1480 Planarity : 0.005 0.035 1772 Dihedral : 14.007 99.975 1988 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 0.13 % Allowed : 5.32 % Favored : 94.55 % 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: 3.24 (0.26), residues: 893 helix: 3.34 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.20 (0.33), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 45 HIS 0.002 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 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 36 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.919 Fit side-chains REVERT: G 5 ARG cc_start: 0.7545 (mtt180) cc_final: 0.7001 (mtt180) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2123 time to fit residues: 11.8440 Evaluate side-chains 32 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 8 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 3.9990 chunk 65 optimal weight: 0.6980 chunk 44 optimal weight: 0.0970 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7618 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10558 Z= 0.184 Angle : 0.678 9.507 14837 Z= 0.250 Chirality : 0.036 0.120 1480 Planarity : 0.004 0.035 1772 Dihedral : 13.989 98.685 1988 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.13 % Allowed : 6.84 % Favored : 93.03 % 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: 3.28 (0.19), residues: 576 sheet: None (None), residues: 0 loop : -0.32 (0.32), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 5 HIS 0.004 0.001 HIS H 20 PHE 0.009 0.001 PHE K 32 TYR 0.011 0.001 TYR S 21 ARG 0.002 0.000 ARG Q 5 *********************** 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 36 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.908 Fit side-chains REVERT: G 5 ARG cc_start: 0.7557 (mtt180) cc_final: 0.7030 (mtt180) outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.2078 time to fit residues: 11.6806 Evaluate side-chains 33 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 32 time to evaluate : 0.863 ------------------------------------------------------------------------------- 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 1 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 19 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 moved from start: 0.2288 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= 0.223 Angle : 0.711 12.617 14837 Z= 0.260 Chirality : 0.037 0.120 1480 Planarity : 0.004 0.038 1772 Dihedral : 14.253 98.709 1988 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.51 % Allowed : 7.73 % Favored : 91.76 % 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: 2.80 (0.26), residues: 893 helix: 3.24 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.66 (0.31), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 40 HIS 0.004 0.001 HIS R 18 PHE 0.010 0.001 PHE K 32 TYR 0.012 0.001 TYR G 44 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 40 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.988 Fit side-chains REVERT: G 5 ARG cc_start: 0.7619 (mtt180) cc_final: 0.7063 (mtt180) outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 0.2010 time to fit residues: 12.2661 Evaluate side-chains 38 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain D residue 47 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 5.9990 chunk 78 optimal weight: 3.9990 chunk 65 optimal weight: 0.3980 chunk 36 optimal weight: 0.4980 chunk 6 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 9.9990 chunk 8 optimal weight: 7.9990 chunk 44 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.2448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10558 Z= 0.188 Angle : 0.676 13.032 14837 Z= 0.247 Chirality : 0.036 0.116 1480 Planarity : 0.004 0.036 1772 Dihedral : 14.113 99.591 1988 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.76 % Allowed : 8.24 % Favored : 91.00 % 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: 2.92 (0.26), residues: 893 helix: 3.28 (0.19), residues: 567 sheet: None (None), residues: 0 loop : -0.63 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP M 40 HIS 0.004 0.001 HIS R 18 PHE 0.007 0.001 PHE E 41 TYR 0.011 0.001 TYR G 44 ARG 0.002 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 40 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.896 Fit side-chains REVERT: G 5 ARG cc_start: 0.7585 (mtt180) cc_final: 0.7239 (mtt180) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1974 time to fit residues: 11.6997 Evaluate side-chains 38 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain J residue 47 HIS Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain N residue 47 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 65 optimal weight: 0.3980 chunk 43 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 10558 Z= 0.161 Angle : 0.647 13.085 14837 Z= 0.236 Chirality : 0.035 0.113 1480 Planarity : 0.004 0.036 1772 Dihedral : 13.916 98.495 1988 Min Nonbonded Distance : 2.040 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.63 % Allowed : 9.00 % 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: 3.14 (0.26), residues: 893 helix: 3.47 (0.18), residues: 567 sheet: None (None), residues: 0 loop : -0.57 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 45 HIS 0.003 0.001 HIS R 18 PHE 0.006 0.001 PHE O 41 TYR 0.011 0.001 TYR G 44 ARG 0.001 0.000 ARG Q 5 *********************** 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 42 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.917 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 40 average time/residue: 0.1896 time to fit residues: 12.2034 Evaluate side-chains 38 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 36 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain K residue 32 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 61 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 72 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN G 37 ASN Q 2 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7685 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 10558 Z= 0.267 Angle : 0.761 13.625 14837 Z= 0.275 Chirality : 0.038 0.122 1480 Planarity : 0.004 0.037 1772 Dihedral : 14.315 98.332 1988 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.76 % Allowed : 8.87 % 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: 2.56 (0.26), residues: 893 helix: 3.05 (0.19), residues: 558 sheet: None (None), residues: 0 loop : -0.75 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP M 40 HIS 0.005 0.001 HIS R 18 PHE 0.010 0.001 PHE K 32 TYR 0.010 0.001 TYR G 44 ARG 0.001 0.000 ARG A 5 *********************** 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 40 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.970 Fit side-chains REVERT: G 5 ARG cc_start: 0.7593 (mtt180) cc_final: 0.6906 (mtt180) outliers start: 6 outliers final: 4 residues processed: 37 average time/residue: 0.1976 time to fit residues: 11.8386 Evaluate side-chains 38 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain K residue 32 PHE Chi-restraints excluded: chain S residue 25 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 65 optimal weight: 0.0870 chunk 68 optimal weight: 0.0170 chunk 72 optimal weight: 0.0570 chunk 47 optimal weight: 2.9990 chunk 76 optimal weight: 5.9990 chunk 46 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 53 optimal weight: 0.9990 overall best weight: 0.3714 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 2 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 moved from start: 0.2759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 10558 Z= 0.123 Angle : 0.618 13.525 14837 Z= 0.226 Chirality : 0.035 0.112 1480 Planarity : 0.004 0.035 1772 Dihedral : 14.001 97.748 1988 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.51 % Allowed : 9.13 % 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: 3.24 (0.27), residues: 893 helix: 3.58 (0.18), residues: 567 sheet: None (None), residues: 0 loop : -0.59 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 45 HIS 0.003 0.001 HIS R 18 PHE 0.005 0.001 PHE B 28 TYR 0.014 0.001 TYR S 21 ARG 0.001 0.000 ARG L 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 40 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.893 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 38 average time/residue: 0.1940 time to fit residues: 11.8356 Evaluate side-chains 37 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain N residue 47 HIS Chi-restraints excluded: chain S residue 25 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 20.0000 chunk 74 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 51 optimal weight: 8.9990 chunk 68 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 9 optimal weight: 0.0020 overall best weight: 1.0990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7635 moved from start: 0.2729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 10558 Z= 0.186 Angle : 0.672 13.658 14837 Z= 0.244 Chirality : 0.036 0.117 1480 Planarity : 0.004 0.036 1772 Dihedral : 14.034 97.341 1988 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 0.51 % Allowed : 9.51 % Favored : 89.99 % 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: 3.09 (0.26), residues: 893 helix: 3.43 (0.18), residues: 567 sheet: None (None), residues: 0 loop : -0.58 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 45 HIS 0.004 0.001 HIS R 18 PHE 0.007 0.001 PHE K 32 TYR 0.011 0.001 TYR G 44 ARG 0.001 0.000 ARG Q 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 39 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.829 Fit side-chains REVERT: G 5 ARG cc_start: 0.7577 (mtt180) cc_final: 0.6951 (mtt180) outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.1921 time to fit residues: 11.6414 Evaluate side-chains 36 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain B residue 47 HIS Chi-restraints excluded: chain K residue 32 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 0.0060 chunk 64 optimal weight: 0.0570 chunk 26 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 8.9990 chunk 56 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 46 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 43 optimal weight: 0.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- 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 = 0.3149 r_free = 0.3149 target = 0.112985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.104907 restraints weight = 10946.087| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.095518 restraints weight = 22523.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.096516 restraints weight = 15620.879| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8078 moved from start: 0.2852 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= 0.134 Angle : 0.619 13.597 14837 Z= 0.226 Chirality : 0.035 0.111 1480 Planarity : 0.004 0.036 1772 Dihedral : 13.835 96.006 1988 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.51 % Allowed : 9.63 % Favored : 89.86 % 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: 3.37 (0.26), residues: 893 helix: 3.51 (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 0.011 0.001 TRP E 45 HIS 0.003 0.001 HIS N 18 PHE 0.005 0.001 PHE B 28 TYR 0.013 0.001 TYR S 21 ARG 0.001 0.000 ARG Q 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1448.50 seconds wall clock time: 27 minutes 39.73 seconds (1659.73 seconds total)