Starting phenix.real_space_refine on Wed Feb 4 04:47:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dwz_47275/02_2026/9dwz_47275.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dwz_47275/02_2026/9dwz_47275.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9dwz_47275/02_2026/9dwz_47275.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dwz_47275/02_2026/9dwz_47275.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9dwz_47275/02_2026/9dwz_47275.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dwz_47275/02_2026/9dwz_47275.map" } resolution = 2.35 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= -0.041 sd= 0.576 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 27 5.21 5 S 9 5.16 5 C 6282 2.51 5 N 1134 2.21 5 O 1314 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8766 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "C" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "E" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "G" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "I" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "K" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "M" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "O" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "Q" Number of atoms: 361 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 361 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 3, 'TRANS': 44} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'FME:plan-2': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 323 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 323 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 2, 'TRANS': 38} Chain: "A" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "D" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "F" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "H" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "L" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "N" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "P" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 189 Unusual residues: {'BCL': 2, 'IRM': 1, 'LDA': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "R" Number of atoms: 101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 101 Unusual residues: {'BCL': 1, 'LMT': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 1.78, per 1000 atoms: 0.20 Number of scatterers: 8766 At special positions: 0 Unit cell: (90.906, 90.252, 68.67, 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 27 11.99 O 1314 8.00 N 1134 7.00 C 6282 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=27, symmetry=0 Number of additional bonds: simple=27, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.91 Conformation dependent library (CDL) restraints added in 180.9 milliseconds 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1476 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 87.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 4.222A pdb=" N TRP A 7 " --> pdb=" O GLY A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 11 through 38 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'B' and resid 5 through 38 removed outlier: 3.942A pdb=" N TYR B 15 " --> pdb=" O GLU B 11 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 removed outlier: 4.222A pdb=" N TRP C 7 " --> pdb=" O GLY C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 11 through 38 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'D' and resid 5 through 38 removed outlier: 3.941A pdb=" N TYR D 15 " --> pdb=" O GLU D 11 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 removed outlier: 4.222A 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 39 through 47 Processing helix chain 'F' and resid 5 through 38 removed outlier: 3.942A pdb=" N TYR F 15 " --> pdb=" O GLU F 11 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 removed outlier: 4.222A pdb=" N TRP G 7 " --> pdb=" O GLY G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 38 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'H' and resid 5 through 38 removed outlier: 3.941A pdb=" N TYR H 15 " --> pdb=" O GLU H 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 removed outlier: 4.222A pdb=" N TRP I 7 " --> pdb=" O GLY I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 38 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 39 through 47 Processing helix chain 'J' and resid 5 through 38 removed outlier: 3.943A pdb=" N TYR J 15 " --> pdb=" O GLU J 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 9 removed outlier: 4.222A pdb=" N TRP K 7 " --> pdb=" O GLY K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 38 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'L' and resid 5 through 38 removed outlier: 3.942A pdb=" N TYR L 15 " --> pdb=" O GLU L 11 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 9 removed outlier: 4.223A pdb=" N TRP M 7 " --> pdb=" O GLY M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 11 through 38 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 39 through 47 Processing helix chain 'N' and resid 5 through 38 removed outlier: 3.942A pdb=" N TYR N 15 " --> pdb=" O GLU N 11 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 9 removed outlier: 4.222A pdb=" N TRP O 7 " --> pdb=" O GLY O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 11 through 38 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 39 through 47 Processing helix chain 'P' and resid 5 through 38 removed outlier: 3.942A pdb=" N TYR P 15 " --> pdb=" O GLU P 11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 9 removed outlier: 4.223A pdb=" N TRP Q 7 " --> pdb=" O GLY Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 11 through 38 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 39 through 47 Processing helix chain 'R' and resid 5 through 38 removed outlier: 3.941A pdb=" N TYR R 15 " --> pdb=" O GLU R 11 " (cutoff:3.500A) 522 hydrogen bonds defined for protein. 1485 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.00 Time building geometry restraints manager: 1.05 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.99 - 1.26: 1078 1.26 - 1.53: 6176 1.53 - 1.81: 1773 1.81 - 2.08: 72 2.08 - 2.35: 54 Bond restraints: 9153 Sorted by residual: bond pdb=" C27 IRM E 102 " pdb=" C28 IRM E 102 " ideal model delta sigma weight residual 1.537 1.347 0.190 2.00e-02 2.50e+03 9.02e+01 bond pdb=" C27 IRM O 102 " pdb=" C28 IRM O 102 " ideal model delta sigma weight residual 1.537 1.348 0.189 2.00e-02 2.50e+03 8.98e+01 bond pdb=" C27 IRM I 102 " pdb=" C28 IRM I 102 " ideal model delta sigma weight residual 1.537 1.348 0.189 2.00e-02 2.50e+03 8.95e+01 bond pdb=" C27 IRM C 104 " pdb=" C28 IRM C 104 " ideal model delta sigma weight residual 1.537 1.348 0.189 2.00e-02 2.50e+03 8.93e+01 bond pdb=" C27 IRM A 104 " pdb=" C28 IRM A 104 " ideal model delta sigma weight residual 1.537 1.348 0.189 2.00e-02 2.50e+03 8.92e+01 ... (remaining 9148 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.79: 12385 6.79 - 13.57: 310 13.57 - 20.36: 83 20.36 - 27.14: 11 27.14 - 33.93: 9 Bond angle restraints: 12798 Sorted by residual: angle pdb=" C7 BCL G 101 " pdb=" C8 BCL G 101 " pdb=" C9 BCL G 101 " ideal model delta sigma weight residual 110.55 77.08 33.47 3.28e+00 9.28e-02 1.04e+02 angle pdb=" C2 BCL G 101 " pdb=" C3 BCL G 101 " pdb=" C4 BCL G 101 " ideal model delta sigma weight residual 124.96 99.70 25.26 2.80e+00 1.28e-01 8.15e+01 angle pdb=" C3D BCL G 101 " pdb=" CAD BCL G 101 " pdb=" OBD BCL G 101 " ideal model delta sigma weight residual 130.61 114.56 16.05 2.00e+00 2.50e-01 6.44e+01 angle pdb=" CBA BCL K 103 " pdb=" CGA BCL K 103 " pdb=" O1A BCL K 103 " ideal model delta sigma weight residual 125.50 100.09 25.41 3.25e+00 9.47e-02 6.12e+01 angle pdb=" CBA BCL A 101 " pdb=" CGA BCL A 101 " pdb=" O1A BCL A 101 " ideal model delta sigma weight residual 125.50 100.94 24.56 3.25e+00 9.47e-02 5.72e+01 ... (remaining 12793 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.91: 4881 35.91 - 71.82: 116 71.82 - 107.73: 17 107.73 - 143.64: 8 143.64 - 179.55: 9 Dihedral angle restraints: 5031 sinusoidal: 2763 harmonic: 2268 Sorted by residual: dihedral pdb=" C1 BCL A 101 " pdb=" CGA BCL A 101 " pdb=" O2A BCL A 101 " pdb=" CBA BCL A 101 " ideal model delta sinusoidal sigma weight residual -180.00 -39.72 -140.28 1 6.00e+00 2.78e-02 4.72e+02 dihedral pdb=" C1 BCL O 103 " pdb=" CGA BCL O 103 " pdb=" O2A BCL O 103 " pdb=" CBA BCL O 103 " ideal model delta sinusoidal sigma weight residual -180.00 -50.78 -129.22 1 6.00e+00 2.78e-02 4.35e+02 dihedral pdb=" C1 BCL K 103 " pdb=" CGA BCL K 103 " pdb=" O2A BCL K 103 " pdb=" CBA BCL K 103 " ideal model delta sinusoidal sigma weight residual -180.00 -60.74 -119.26 1 6.00e+00 2.78e-02 3.97e+02 ... (remaining 5028 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.092: 863 0.092 - 0.183: 284 0.183 - 0.275: 161 0.275 - 0.366: 29 0.366 - 0.458: 13 Chirality restraints: 1350 Sorted by residual: chirality pdb=" CBD BCL O 103 " pdb=" CAD BCL O 103 " pdb=" CGD BCL O 103 " pdb=" CHA BCL O 103 " both_signs ideal model delta sigma weight residual False 2.62 2.16 0.46 2.00e-01 2.50e+01 5.24e+00 chirality pdb=" CBD BCL K 103 " pdb=" CAD BCL K 103 " pdb=" CGD BCL K 103 " pdb=" CHA BCL K 103 " both_signs ideal model delta sigma weight residual False 2.62 2.20 0.43 2.00e-01 2.50e+01 4.52e+00 chirality pdb=" CBD BCL I 103 " pdb=" CAD BCL I 103 " pdb=" CGD BCL I 103 " pdb=" CHA BCL I 103 " both_signs ideal model delta sigma weight residual False 2.62 2.23 0.39 2.00e-01 2.50e+01 3.85e+00 ... (remaining 1347 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL C 101 " -0.321 3.00e-02 1.11e+03 2.65e-01 3.89e+02 pdb=" CBA BCL C 101 " -0.051 3.00e-02 1.11e+03 pdb=" CGA BCL C 101 " 0.071 3.00e-02 1.11e+03 pdb=" O1A BCL C 101 " -0.162 3.00e-02 1.11e+03 pdb=" O2A BCL C 101 " 0.462 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL K 103 " 0.255 3.00e-02 1.11e+03 2.28e-01 2.88e+02 pdb=" CBA BCL K 103 " -0.018 3.00e-02 1.11e+03 pdb=" CGA BCL K 103 " -0.076 3.00e-02 1.11e+03 pdb=" O1A BCL K 103 " 0.215 3.00e-02 1.11e+03 pdb=" O2A BCL K 103 " -0.376 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C3D BCL O 103 " -0.022 5.00e-03 4.00e+04 4.16e-02 2.77e+02 pdb=" CAD BCL O 103 " 0.072 5.00e-03 4.00e+04 pdb=" CBD BCL O 103 " -0.021 5.00e-03 4.00e+04 pdb=" OBD BCL O 103 " -0.029 5.00e-03 4.00e+04 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 135 2.71 - 3.26: 7384 3.26 - 3.81: 14111 3.81 - 4.35: 20126 4.35 - 4.90: 33074 Nonbonded interactions: 74830 Sorted by model distance: nonbonded pdb=" CAA BCL A 101 " pdb=" O1A BCL A 101 " model vdw 2.168 2.752 nonbonded pdb=" CAA BCL I 103 " pdb=" O1A BCL I 103 " model vdw 2.226 2.752 nonbonded pdb=" CAA BCL E 103 " pdb=" O1A BCL E 103 " model vdw 2.232 2.752 nonbonded pdb=" CAA BCL C 101 " pdb=" O1A BCL C 101 " model vdw 2.263 2.752 nonbonded pdb=" CAA BCL O 103 " pdb=" O1A BCL O 103 " model vdw 2.272 2.752 ... (remaining 74825 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) selection = (chain 'C' and resid 1 through 48) selection = (chain 'E' and resid 1 through 48) selection = (chain 'G' and resid 1 through 48) selection = (chain 'I' and resid 1 through 48) selection = (chain 'K' and resid 1 through 48) selection = (chain 'M' and resid 1 through 48) selection = (chain 'O' and resid 1 through 48) selection = (chain 'Q' and resid 1 through 48) } ncs_group { reference = chain 'B' selection = chain 'D' selection = chain 'F' selection = chain 'H' selection = chain 'J' selection = chain 'L' selection = chain 'N' selection = chain 'P' selection = chain 'R' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.380 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: 0.140 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 8.010 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.010 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:6.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9312 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 : 0.041 0.750 9180 Z= 1.575 Angle : 3.052 33.929 12798 Z= 1.421 Chirality : 0.120 0.458 1350 Planarity : 0.024 0.265 1494 Dihedral : 18.586 179.554 3555 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 1.43 % Favored : 98.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.28), residues: 756 helix: 2.12 (0.19), residues: 594 sheet: None (None), residues: 0 loop : -0.72 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG R 21 TYR 0.023 0.009 TYR R 15 PHE 0.030 0.005 PHE G 41 TRP 0.036 0.014 TRP G 40 HIS 0.012 0.003 HIS P 31 Details of bonding type rmsd covalent geometry : bond 0.03365 ( 9153) covalent geometry : angle 3.05206 (12798) hydrogen bonds : bond 0.13655 ( 522) hydrogen bonds : angle 4.90736 ( 1485) Misc. bond : bond 0.44465 ( 27) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 74 time to evaluate : 0.175 Fit side-chains REVERT: J 37 LEU cc_start: 0.9233 (mt) cc_final: 0.8993 (mp) REVERT: L 37 LEU cc_start: 0.9244 (mt) cc_final: 0.9007 (mp) outliers start: 0 outliers final: 2 residues processed: 74 average time/residue: 0.6197 time to fit residues: 48.6497 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 53 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 16 LEU Chi-restraints excluded: chain I residue 16 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 2.9990 chunk 53 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.7980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.2261 r_free = 0.2261 target = 0.036524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2140 r_free = 0.2140 target = 0.032843 restraints weight = 20096.097| |-----------------------------------------------------------------------------| r_work (start): 0.2140 rms_B_bonded: 0.58 r_work: 0.2048 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.1953 rms_B_bonded: 2.40 restraints_weight: 0.2500 r_work (final): 0.1953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9333 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.018 0.584 9180 Z= 0.178 Angle : 0.854 12.957 12798 Z= 0.309 Chirality : 0.040 0.121 1350 Planarity : 0.006 0.033 1494 Dihedral : 18.911 179.990 2308 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 7.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.63 % Allowed : 5.08 % Favored : 94.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.63 (0.29), residues: 756 helix: 3.06 (0.19), residues: 594 sheet: None (None), residues: 0 loop : -0.24 (0.49), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG D 21 TYR 0.002 0.001 TYR H 15 PHE 0.010 0.002 PHE E 44 TRP 0.013 0.002 TRP M 40 HIS 0.006 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00428 ( 9153) covalent geometry : angle 0.85390 (12798) hydrogen bonds : bond 0.05396 ( 522) hydrogen bonds : angle 3.68692 ( 1485) Misc. bond : bond 0.31429 ( 27) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 65 time to evaluate : 0.281 Fit side-chains REVERT: H 37 LEU cc_start: 0.9312 (mt) cc_final: 0.9005 (mp) REVERT: J 37 LEU cc_start: 0.9252 (mt) cc_final: 0.8913 (mp) REVERT: L 37 LEU cc_start: 0.9247 (mt) cc_final: 0.8935 (mp) outliers start: 4 outliers final: 4 residues processed: 69 average time/residue: 0.4402 time to fit residues: 32.6569 Evaluate side-chains 53 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 49 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain H residue 24 LEU Chi-restraints excluded: chain H residue 38 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 62 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 16 optimal weight: 0.0060 chunk 2 optimal weight: 0.6980 chunk 8 optimal weight: 0.0870 chunk 22 optimal weight: 1.9990 overall best weight: 0.7176 ------------------------------------------------------------------------------- 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 = 0.2273 r_free = 0.2273 target = 0.036924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.2153 r_free = 0.2153 target = 0.033266 restraints weight = 19812.272| |-----------------------------------------------------------------------------| r_work (start): 0.2151 rms_B_bonded: 0.57 r_work: 0.2064 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.1971 rms_B_bonded: 2.36 restraints_weight: 0.2500 r_work (final): 0.1971 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.015 0.477 9180 Z= 0.157 Angle : 0.720 6.510 12798 Z= 0.281 Chirality : 0.038 0.115 1350 Planarity : 0.005 0.035 1494 Dihedral : 18.217 179.838 2304 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.43 % Allowed : 6.19 % Favored : 92.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.84 (0.29), residues: 756 helix: 3.19 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.10 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 21 TYR 0.002 0.001 TYR N 15 PHE 0.010 0.002 PHE E 44 TRP 0.012 0.002 TRP C 40 HIS 0.005 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 9153) covalent geometry : angle 0.71979 (12798) hydrogen bonds : bond 0.04957 ( 522) hydrogen bonds : angle 3.53743 ( 1485) Misc. bond : bond 0.26398 ( 27) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.182 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.3793 time to fit residues: 27.5794 Evaluate side-chains 54 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.274 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 38 THR Chi-restraints excluded: chain F residue 38 THR Chi-restraints excluded: chain H residue 38 THR Chi-restraints excluded: chain P residue 38 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 0.0980 chunk 1 optimal weight: 0.7980 chunk 32 optimal weight: 0.0030 chunk 57 optimal weight: 0.4980 chunk 42 optimal weight: 0.8980 chunk 48 optimal weight: 0.0980 chunk 53 optimal weight: 0.8980 chunk 41 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 overall best weight: 0.2590 ------------------------------------------------------------------------------- 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 = 0.2384 r_free = 0.2384 target = 0.040635 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.036900 restraints weight = 20101.212| |-----------------------------------------------------------------------------| r_work (start): 0.2266 rms_B_bonded: 0.60 r_work: 0.2181 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2091 rms_B_bonded: 2.47 restraints_weight: 0.2500 r_work (final): 0.2091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.250 9180 Z= 0.114 Angle : 0.618 5.362 12798 Z= 0.241 Chirality : 0.034 0.108 1350 Planarity : 0.005 0.035 1494 Dihedral : 17.820 179.841 2304 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer: Outliers : 0.48 % Allowed : 8.25 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.26 (0.28), residues: 756 helix: 3.55 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.23 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 21 TYR 0.001 0.000 TYR R 15 PHE 0.007 0.001 PHE G 44 TRP 0.010 0.001 TRP C 40 HIS 0.003 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 9153) covalent geometry : angle 0.61830 (12798) hydrogen bonds : bond 0.03840 ( 522) hydrogen bonds : angle 3.29282 ( 1485) Misc. bond : bond 0.14057 ( 27) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.202 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 67 average time/residue: 0.4528 time to fit residues: 32.6920 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 48 optimal weight: 0.0980 chunk 8 optimal weight: 0.0980 chunk 64 optimal weight: 0.0030 chunk 71 optimal weight: 0.0980 chunk 56 optimal weight: 0.0060 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 60 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 overall best weight: 0.0606 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN E 3 GLN M 3 GLN Q 3 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2549 r_free = 0.2549 target = 0.046654 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2439 r_free = 0.2439 target = 0.042894 restraints weight = 20039.420| |-----------------------------------------------------------------------------| r_work (start): 0.2437 rms_B_bonded: 0.62 r_work: 0.2360 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2275 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.2275 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9152 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9180 Z= 0.097 Angle : 0.565 6.115 12798 Z= 0.222 Chirality : 0.033 0.107 1350 Planarity : 0.005 0.036 1494 Dihedral : 17.507 179.804 2304 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Rotamer: Outliers : 0.63 % Allowed : 8.25 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.51 (0.28), residues: 756 helix: 3.83 (0.18), residues: 576 sheet: None (None), residues: 0 loop : -0.09 (0.46), residues: 180 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 21 TYR 0.002 0.000 TYR B 15 PHE 0.007 0.001 PHE Q 44 TRP 0.010 0.001 TRP C 40 HIS 0.002 0.000 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 9153) covalent geometry : angle 0.56474 (12798) hydrogen bonds : bond 0.03080 ( 522) hydrogen bonds : angle 3.09616 ( 1485) Misc. bond : bond 0.03413 ( 27) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.259 Fit side-chains REVERT: D 37 LEU cc_start: 0.9061 (mt) cc_final: 0.8817 (mp) outliers start: 4 outliers final: 1 residues processed: 91 average time/residue: 0.4192 time to fit residues: 41.3468 Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 57 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 1 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 47 optimal weight: 0.0270 chunk 30 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 4.9990 chunk 37 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 26 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 overall best weight: 0.9440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2259 r_free = 0.2259 target = 0.036459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2135 r_free = 0.2135 target = 0.032701 restraints weight = 20098.047| |-----------------------------------------------------------------------------| r_work (start): 0.2134 rms_B_bonded: 0.57 r_work: 0.2046 rms_B_bonded: 1.40 restraints_weight: 0.5000 r_work: 0.1953 rms_B_bonded: 2.39 restraints_weight: 0.2500 r_work (final): 0.1953 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9338 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.016 0.528 9180 Z= 0.175 Angle : 0.726 6.551 12798 Z= 0.289 Chirality : 0.040 0.120 1350 Planarity : 0.005 0.038 1494 Dihedral : 17.540 179.604 2304 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.43 % Allowed : 7.94 % Favored : 90.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.96 (0.28), residues: 756 helix: 3.27 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.05 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG B 21 TYR 0.003 0.001 TYR P 15 PHE 0.011 0.002 PHE E 44 TRP 0.009 0.002 TRP M 40 HIS 0.005 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00427 ( 9153) covalent geometry : angle 0.72625 (12798) hydrogen bonds : bond 0.05282 ( 522) hydrogen bonds : angle 3.55108 ( 1485) Misc. bond : bond 0.29094 ( 27) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.281 Fit side-chains REVERT: D 14 LYS cc_start: 0.9555 (OUTLIER) cc_final: 0.9019 (mtmm) outliers start: 9 outliers final: 4 residues processed: 64 average time/residue: 0.4350 time to fit residues: 30.5037 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain Q residue 16 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 56 optimal weight: 0.0060 chunk 10 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 44 optimal weight: 0.0030 chunk 64 optimal weight: 0.0670 chunk 62 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 40 optimal weight: 0.0060 overall best weight: 0.1760 ------------------------------------------------------------------------------- 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 = 0.2430 r_free = 0.2430 target = 0.042328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2315 r_free = 0.2315 target = 0.038527 restraints weight = 19935.036| |-----------------------------------------------------------------------------| r_work (start): 0.2313 rms_B_bonded: 0.61 r_work: 0.2231 rms_B_bonded: 1.46 restraints_weight: 0.5000 r_work: 0.2143 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2143 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9232 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.197 9180 Z= 0.108 Angle : 0.586 5.382 12798 Z= 0.232 Chirality : 0.033 0.109 1350 Planarity : 0.005 0.036 1494 Dihedral : 17.119 179.869 2304 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.63 % Allowed : 7.46 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.28 (0.28), residues: 756 helix: 3.59 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.35 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG R 21 TYR 0.002 0.000 TYR B 15 PHE 0.007 0.001 PHE G 44 TRP 0.008 0.001 TRP E 40 HIS 0.002 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00239 ( 9153) covalent geometry : angle 0.58583 (12798) hydrogen bonds : bond 0.03532 ( 522) hydrogen bonds : angle 3.19969 ( 1485) Misc. bond : bond 0.10465 ( 27) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 56 time to evaluate : 0.286 Fit side-chains REVERT: D 37 LEU cc_start: 0.9093 (mt) cc_final: 0.8832 (mp) outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.4381 time to fit residues: 28.5782 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 24 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 33 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 71 optimal weight: 0.3980 chunk 36 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 47 optimal weight: 0.4980 chunk 6 optimal weight: 4.9990 chunk 13 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2236 r_free = 0.2236 target = 0.035713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2111 r_free = 0.2111 target = 0.031986 restraints weight = 19909.986| |-----------------------------------------------------------------------------| r_work (start): 0.2111 rms_B_bonded: 0.57 r_work: 0.2022 rms_B_bonded: 1.39 restraints_weight: 0.5000 r_work: 0.1927 rms_B_bonded: 2.37 restraints_weight: 0.2500 r_work (final): 0.1927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9353 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.019 0.602 9180 Z= 0.193 Angle : 0.765 7.401 12798 Z= 0.302 Chirality : 0.041 0.126 1350 Planarity : 0.006 0.038 1494 Dihedral : 17.534 179.562 2304 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 8.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 1.43 % Allowed : 6.67 % Favored : 91.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.81 (0.28), residues: 756 helix: 3.14 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.01 (0.52), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 21 TYR 0.004 0.001 TYR P 15 PHE 0.012 0.002 PHE E 44 TRP 0.009 0.002 TRP O 40 HIS 0.006 0.002 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00474 ( 9153) covalent geometry : angle 0.76525 (12798) hydrogen bonds : bond 0.05612 ( 522) hydrogen bonds : angle 3.62024 ( 1485) Misc. bond : bond 0.33339 ( 27) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.299 Fit side-chains REVERT: H 14 LYS cc_start: 0.9561 (OUTLIER) cc_final: 0.8886 (mtmm) REVERT: N 24 LEU cc_start: 0.9502 (OUTLIER) cc_final: 0.9192 (tm) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.4426 time to fit residues: 29.2917 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 16 LEU Chi-restraints excluded: chain H residue 14 LYS Chi-restraints excluded: chain M residue 16 LEU Chi-restraints excluded: chain N residue 14 LYS Chi-restraints excluded: chain N residue 24 LEU Chi-restraints excluded: chain Q residue 16 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 71 optimal weight: 0.0270 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 chunk 40 optimal weight: 0.0060 chunk 61 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 60 optimal weight: 3.9990 chunk 24 optimal weight: 0.0670 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.2341 r_free = 0.2341 target = 0.039217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2222 r_free = 0.2222 target = 0.035449 restraints weight = 19893.089| |-----------------------------------------------------------------------------| r_work (start): 0.2220 rms_B_bonded: 0.58 r_work: 0.2136 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.2045 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.2045 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9290 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.347 9180 Z= 0.126 Angle : 0.632 5.611 12798 Z= 0.251 Chirality : 0.035 0.107 1350 Planarity : 0.005 0.036 1494 Dihedral : 17.092 179.787 2304 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.48 % Allowed : 8.10 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.05 (0.28), residues: 756 helix: 3.39 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.24 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG P 21 TYR 0.001 0.000 TYR B 15 PHE 0.008 0.001 PHE G 44 TRP 0.008 0.001 TRP O 40 HIS 0.003 0.001 HIS K 37 Details of bonding type rmsd covalent geometry : bond 0.00281 ( 9153) covalent geometry : angle 0.63195 (12798) hydrogen bonds : bond 0.04192 ( 522) hydrogen bonds : angle 3.33728 ( 1485) Misc. bond : bond 0.18944 ( 27) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 54 time to evaluate : 0.262 Fit side-chains REVERT: D 14 LYS cc_start: 0.9525 (OUTLIER) cc_final: 0.8969 (mtmm) outliers start: 3 outliers final: 1 residues processed: 56 average time/residue: 0.4876 time to fit residues: 29.5127 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 54 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 14 LYS Chi-restraints excluded: chain N residue 14 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 41 optimal weight: 0.9990 chunk 40 optimal weight: 0.0010 chunk 46 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 4 optimal weight: 0.0270 chunk 49 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 57 optimal weight: 1.9990 chunk 64 optimal weight: 0.0000 overall best weight: 0.3848 ------------------------------------------------------------------------------- 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 = 0.2354 r_free = 0.2354 target = 0.039634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2233 r_free = 0.2233 target = 0.035846 restraints weight = 19817.279| |-----------------------------------------------------------------------------| r_work (start): 0.2232 rms_B_bonded: 0.59 r_work: 0.2147 rms_B_bonded: 1.43 restraints_weight: 0.5000 r_work: 0.2055 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.2055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9283 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.324 9180 Z= 0.125 Angle : 0.625 5.413 12798 Z= 0.248 Chirality : 0.035 0.107 1350 Planarity : 0.005 0.036 1494 Dihedral : 16.915 179.798 2304 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Rotamer: Outliers : 0.16 % Allowed : 8.25 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.12 (0.28), residues: 756 helix: 3.44 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.24 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG L 21 TYR 0.001 0.000 TYR B 15 PHE 0.008 0.001 PHE E 44 TRP 0.009 0.001 TRP M 40 HIS 0.003 0.001 HIS M 37 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 9153) covalent geometry : angle 0.62490 (12798) hydrogen bonds : bond 0.04187 ( 522) hydrogen bonds : angle 3.32898 ( 1485) Misc. bond : bond 0.18028 ( 27) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1512 Ramachandran restraints generated. 756 Oldfield, 0 Emsley, 756 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.287 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 56 average time/residue: 0.4730 time to fit residues: 28.5818 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 14 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 61 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 43 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 24 optimal weight: 0.0980 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 23 optimal weight: 0.0040 chunk 64 optimal weight: 0.0070 chunk 1 optimal weight: 5.9990 chunk 4 optimal weight: 0.9990 overall best weight: 0.3210 ------------------------------------------------------------------------------- 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 = 0.2386 r_free = 0.2386 target = 0.040751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2267 r_free = 0.2267 target = 0.036952 restraints weight = 19695.485| |-----------------------------------------------------------------------------| r_work (start): 0.2265 rms_B_bonded: 0.60 r_work: 0.2182 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.2091 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.2091 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9263 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.268 9180 Z= 0.117 Angle : 0.606 5.401 12798 Z= 0.241 Chirality : 0.034 0.107 1350 Planarity : 0.005 0.037 1494 Dihedral : 16.715 179.834 2304 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 0.32 % Allowed : 7.94 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 4.21 (0.28), residues: 756 helix: 3.51 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.28 (0.50), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG J 21 TYR 0.001 0.000 TYR B 15 PHE 0.007 0.001 PHE G 44 TRP 0.009 0.001 TRP E 40 HIS 0.003 0.001 HIS E 31 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 9153) covalent geometry : angle 0.60646 (12798) hydrogen bonds : bond 0.03924 ( 522) hydrogen bonds : angle 3.27292 ( 1485) Misc. bond : bond 0.14956 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2205.34 seconds wall clock time: 38 minutes 35.15 seconds (2315.15 seconds total)