Starting phenix.real_space_refine on Wed Sep 17 14:10:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ek8_48112/09_2025/9ek8_48112.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ek8_48112/09_2025/9ek8_48112.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/9ek8_48112/09_2025/9ek8_48112.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ek8_48112/09_2025/9ek8_48112.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ek8_48112/09_2025/9ek8_48112.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ek8_48112/09_2025/9ek8_48112.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= -0.040 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 6318 2.51 5 N 1134 2.21 5 O 1359 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8847 Number of models: 1 Model: "" Number of chains: 36 Chain: "A" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "C" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "E" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "G" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "I" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "K" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "M" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "O" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "Q" Number of atoms: 369 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 369 Classifications: {'peptide': 48} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 44} 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: 324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 324 Classifications: {'peptide': 41} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain: "A" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 2, 'LDA': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'IRM': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} 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: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'IRM': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 183 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 183 Unusual residues: {'BCL': 2, 'LDA': 1, 'LMT': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "J" 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: "K" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'IRM': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "M" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "N" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'IRM': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "O" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "P" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'IRM': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 148 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 148 Unusual residues: {'BCL': 2, 'LDA': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "R" Number of atoms: 142 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 142 Unusual residues: {'BCL': 1, 'IRM': 1, 'LMT': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 2.57, per 1000 atoms: 0.29 Number of scatterers: 8847 At special positions: 0 Unit cell: (90.252, 90.252, 69.324, 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 1359 8.00 N 1134 7.00 C 6318 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: 1.22 Conformation dependent library (CDL) restraints added in 268.5 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 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 85.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.22 Creating SS restraints... Processing helix chain 'A' and resid 5 through 9 Processing helix chain 'A' and resid 11 through 38 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 39 through 47 Processing helix chain 'B' and resid 4 through 37 removed outlier: 3.671A pdb=" N TYR B 14 " --> pdb=" O GLU B 10 " (cutoff:3.500A) Processing helix chain 'C' and resid 5 through 9 Processing helix chain 'C' and resid 11 through 38 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 39 through 47 Processing helix chain 'D' and resid 4 through 37 removed outlier: 3.700A pdb=" N TYR D 14 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing helix chain 'E' and resid 5 through 9 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 4 through 37 removed outlier: 3.718A pdb=" N TYR F 14 " --> pdb=" O GLU F 10 " (cutoff:3.500A) Processing helix chain 'G' and resid 5 through 9 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 4 through 37 removed outlier: 3.636A pdb=" N TYR H 14 " --> pdb=" O GLU H 10 " (cutoff:3.500A) Processing helix chain 'I' and resid 5 through 9 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 4 through 37 removed outlier: 3.711A pdb=" N TYR J 14 " --> pdb=" O GLU J 10 " (cutoff:3.500A) Processing helix chain 'K' and resid 5 through 9 Processing helix chain 'K' and resid 11 through 38 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'L' and resid 4 through 37 removed outlier: 3.704A pdb=" N TYR L 14 " --> pdb=" O GLU L 10 " (cutoff:3.500A) Processing helix chain 'M' and resid 5 through 9 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 4 through 37 removed outlier: 3.669A pdb=" N TYR N 14 " --> pdb=" O GLU N 10 " (cutoff:3.500A) Processing helix chain 'O' and resid 5 through 9 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 4 through 37 removed outlier: 3.673A pdb=" N TYR P 14 " --> pdb=" O GLU P 10 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 9 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 4 through 37 removed outlier: 3.719A pdb=" N TYR R 14 " --> pdb=" O GLU R 10 " (cutoff:3.500A) 513 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: 1.35 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.10 - 1.34: 2150 1.34 - 1.59: 6967 1.59 - 1.83: 18 1.83 - 2.08: 23 2.08 - 2.33: 85 Bond restraints: 9243 Sorted by residual: bond pdb=" C27 IRM B 102 " pdb=" C28 IRM B 102 " ideal model delta sigma weight residual 1.537 1.340 0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" C27 IRM D 103 " pdb=" C28 IRM D 103 " ideal model delta sigma weight residual 1.537 1.340 0.197 2.00e-02 2.50e+03 9.73e+01 bond pdb=" C27 IRM J 102 " pdb=" C28 IRM J 102 " ideal model delta sigma weight residual 1.537 1.340 0.197 2.00e-02 2.50e+03 9.69e+01 bond pdb=" C27 IRM L 103 " pdb=" C28 IRM L 103 " ideal model delta sigma weight residual 1.537 1.340 0.197 2.00e-02 2.50e+03 9.68e+01 bond pdb=" C27 IRM H 103 " pdb=" C28 IRM H 103 " ideal model delta sigma weight residual 1.537 1.341 0.196 2.00e-02 2.50e+03 9.65e+01 ... (remaining 9238 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.67: 11857 3.67 - 7.35: 994 7.35 - 11.02: 46 11.02 - 14.70: 34 14.70 - 18.37: 20 Bond angle restraints: 12951 Sorted by residual: angle pdb=" NB BCL O 301 " pdb="MG BCL O 301 " pdb=" ND BCL O 301 " ideal model delta sigma weight residual 157.70 176.07 -18.37 2.51e+00 1.58e-01 5.34e+01 angle pdb=" NB BCL K 301 " pdb="MG BCL K 301 " pdb=" ND BCL K 301 " ideal model delta sigma weight residual 157.70 176.04 -18.34 2.51e+00 1.58e-01 5.32e+01 angle pdb=" NB BCL I 301 " pdb="MG BCL I 301 " pdb=" ND BCL I 301 " ideal model delta sigma weight residual 157.70 175.64 -17.94 2.51e+00 1.58e-01 5.10e+01 angle pdb=" NB BCL Q 301 " pdb="MG BCL Q 301 " pdb=" ND BCL Q 301 " ideal model delta sigma weight residual 157.70 175.44 -17.74 2.51e+00 1.58e-01 4.99e+01 angle pdb=" NB BCL M 301 " pdb="MG BCL M 301 " pdb=" ND BCL M 301 " ideal model delta sigma weight residual 157.70 175.12 -17.42 2.51e+00 1.58e-01 4.80e+01 ... (remaining 12946 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.09: 4895 32.09 - 64.18: 111 64.18 - 96.27: 11 96.27 - 128.36: 12 128.36 - 160.45: 11 Dihedral angle restraints: 5040 sinusoidal: 2763 harmonic: 2277 Sorted by residual: dihedral pdb=" CBD BCL A 302 " pdb=" CGD BCL A 302 " pdb=" O2D BCL A 302 " pdb=" CED BCL A 302 " ideal model delta sinusoidal sigma weight residual -180.00 -28.71 -151.29 1 5.00e+00 4.00e-02 7.21e+02 dihedral pdb=" CBD BCL Q 302 " pdb=" CGD BCL Q 302 " pdb=" O2D BCL Q 302 " pdb=" CED BCL Q 302 " ideal model delta sinusoidal sigma weight residual -180.00 -30.33 -149.67 1 5.00e+00 4.00e-02 7.15e+02 dihedral pdb=" CBD BCL G 302 " pdb=" CGD BCL G 302 " pdb=" O2D BCL G 302 " pdb=" CED BCL G 302 " ideal model delta sinusoidal sigma weight residual -180.00 -32.72 -147.28 1 5.00e+00 4.00e-02 7.07e+02 ... (remaining 5037 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 922 0.073 - 0.145: 255 0.145 - 0.217: 135 0.217 - 0.290: 36 0.290 - 0.362: 11 Chirality restraints: 1359 Sorted by residual: chirality pdb=" C2A BCL I 302 " pdb=" C1A BCL I 302 " pdb=" C3A BCL I 302 " pdb=" CAA BCL I 302 " both_signs ideal model delta sigma weight residual False 2.70 3.06 -0.36 2.00e-01 2.50e+01 3.28e+00 chirality pdb=" C1B LMT L 101 " pdb=" C2B LMT L 101 " pdb=" O1B LMT L 101 " pdb=" O5B LMT L 101 " both_signs ideal model delta sigma weight residual False -2.20 -2.56 0.36 2.00e-01 2.50e+01 3.26e+00 chirality pdb=" C1B LMT H 101 " pdb=" C2B LMT H 101 " pdb=" O1B LMT H 101 " pdb=" O5B LMT H 101 " both_signs ideal model delta sigma weight residual False -2.20 -2.55 0.35 2.00e-01 2.50e+01 3.12e+00 ... (remaining 1356 not shown) Planarity restraints: 1503 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CBD BCL J 101 " -0.020 8.00e-03 1.56e+04 4.01e-02 1.01e+02 pdb=" CGD BCL J 101 " 0.069 8.00e-03 1.56e+04 pdb=" O1D BCL J 101 " -0.028 8.00e-03 1.56e+04 pdb=" O2D BCL J 101 " -0.022 8.00e-03 1.56e+04 delta sigma weight rms_deltas residual plane pdb=" CBD BCL D 102 " 0.020 8.00e-03 1.56e+04 3.99e-02 9.95e+01 pdb=" CGD BCL D 102 " -0.069 8.00e-03 1.56e+04 pdb=" O1D BCL D 102 " 0.027 8.00e-03 1.56e+04 pdb=" O2D BCL D 102 " 0.022 8.00e-03 1.56e+04 delta sigma weight rms_deltas residual plane pdb=" CBD BCL L 102 " -0.019 8.00e-03 1.56e+04 3.95e-02 9.75e+01 pdb=" CGD BCL L 102 " 0.068 8.00e-03 1.56e+04 pdb=" O1D BCL L 102 " -0.027 8.00e-03 1.56e+04 pdb=" O2D BCL L 102 " -0.022 8.00e-03 1.56e+04 ... (remaining 1500 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 198 2.73 - 3.27: 7453 3.27 - 3.81: 15107 3.81 - 4.36: 20359 4.36 - 4.90: 32928 Nonbonded interactions: 76045 Sorted by model distance: nonbonded pdb=" O HIS B 41 " pdb=" OXT GLY Q 48 " model vdw 2.182 3.040 nonbonded pdb=" OXT GLY G 48 " pdb=" O HIS J 41 " model vdw 2.193 3.040 nonbonded pdb=" OXT GLY O 48 " pdb=" O HIS R 41 " model vdw 2.361 3.040 nonbonded pdb=" O LYS Q 5 " pdb=" OG1 THR Q 8 " model vdw 2.440 3.040 nonbonded pdb=" ON1 CXM O 1 " pdb=" NE2 HIS P 12 " model vdw 2.453 3.120 ... (remaining 76040 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 302) selection = (chain 'C' and resid 1 through 302) selection = (chain 'E' and resid 1 through 302) selection = (chain 'G' and resid 1 through 302) selection = (chain 'I' and resid 1 through 302) selection = (chain 'K' and resid 1 through 302) selection = (chain 'M' and resid 1 through 302) selection = (chain 'O' and resid 1 through 302) selection = (chain 'Q' and resid 1 through 302) } ncs_group { reference = (chain 'B' and resid 1 through 41) selection = (chain 'D' and resid 1 through 41) selection = (chain 'F' and resid 1 through 41) selection = (chain 'H' and resid 1 through 41) selection = (chain 'J' and resid 1 through 41) selection = (chain 'L' and resid 1 through 41) selection = (chain 'N' and resid 1 through 41) selection = (chain 'P' and resid 1 through 41) selection = (chain 'R' and resid 1 through 41) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.190 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.690 Find NCS groups from input model: 0.230 Set up NCS constraints: 0.020 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:7.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 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 : 0.032 0.838 9270 Z= 1.595 Angle : 2.219 18.369 12951 Z= 1.169 Chirality : 0.091 0.362 1359 Planarity : 0.019 0.139 1503 Dihedral : 17.069 160.445 3564 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 0.79 % Allowed : 4.92 % 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 aren not related in a simple way. whole: 1.81 (0.27), residues: 756 helix: 1.60 (0.18), residues: 594 sheet: None (None), residues: 0 loop : -0.14 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 20 TYR 0.049 0.005 TYR R 14 PHE 0.038 0.009 PHE H 34 TRP 0.082 0.019 TRP M 40 HIS 0.012 0.003 HIS N 30 Details of bonding type rmsd covalent geometry : bond 0.02363 ( 9243) covalent geometry : angle 2.21851 (12951) hydrogen bonds : bond 0.13642 ( 513) hydrogen bonds : angle 4.56055 ( 1485) Misc. bond : bond 0.40036 ( 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 96 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.264 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 91 average time/residue: 0.6551 time to fit residues: 63.2403 Evaluate side-chains 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 60 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 14 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 49 optimal weight: 0.5980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN F 7 GLN J 7 GLN K 11 ASN O 11 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2419 r_free = 0.2419 target = 0.042866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2286 r_free = 0.2286 target = 0.038497 restraints weight = 19010.275| |-----------------------------------------------------------------------------| r_work (start): 0.2286 rms_B_bonded: 0.70 r_work: 0.2181 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2082 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9258 moved from start: 0.3248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.430 9270 Z= 0.169 Angle : 0.793 10.429 12951 Z= 0.304 Chirality : 0.039 0.123 1359 Planarity : 0.005 0.043 1503 Dihedral : 16.233 176.139 2342 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 2.38 % Allowed : 5.40 % Favored : 92.22 % 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 aren not related in a simple way. whole: 3.02 (0.28), residues: 756 helix: 2.50 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.13 (0.51), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG L 20 TYR 0.007 0.001 TYR I 44 PHE 0.010 0.001 PHE I 41 TRP 0.014 0.002 TRP F 39 HIS 0.003 0.001 HIS Q 31 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 9243) covalent geometry : angle 0.79269 (12951) hydrogen bonds : bond 0.05069 ( 513) hydrogen bonds : angle 3.52239 ( 1485) Misc. bond : bond 0.18509 ( 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 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 59 time to evaluate : 0.310 Fit side-chains REVERT: A 14 ILE cc_start: 0.8985 (OUTLIER) cc_final: 0.8760 (mp) REVERT: H 13 LYS cc_start: 0.9380 (OUTLIER) cc_final: 0.9146 (mptm) outliers start: 15 outliers final: 11 residues processed: 62 average time/residue: 0.8172 time to fit residues: 53.3074 Evaluate side-chains 66 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 ILE Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain G residue 14 ILE Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain H residue 13 LYS Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 48 optimal weight: 0.0870 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 0.0050 chunk 1 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 64 optimal weight: 0.0670 chunk 53 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 43 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.2910 ------------------------------------------------------------------------------- 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 = 0.2467 r_free = 0.2467 target = 0.044651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2332 r_free = 0.2332 target = 0.040157 restraints weight = 19154.970| |-----------------------------------------------------------------------------| r_work (start): 0.2328 rms_B_bonded: 0.74 r_work: 0.2227 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.2131 rms_B_bonded: 2.63 restraints_weight: 0.2500 r_work (final): 0.2131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9211 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.241 9270 Z= 0.111 Angle : 0.662 12.084 12951 Z= 0.243 Chirality : 0.034 0.109 1359 Planarity : 0.004 0.038 1503 Dihedral : 12.597 178.824 2342 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.90 % Allowed : 6.03 % Favored : 92.06 % 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 aren not related in a simple way. whole: 3.92 (0.28), residues: 756 helix: 3.17 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.26 (0.55), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG J 20 TYR 0.003 0.001 TYR Q 44 PHE 0.006 0.001 PHE M 41 TRP 0.012 0.002 TRP M 40 HIS 0.003 0.001 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00238 ( 9243) covalent geometry : angle 0.66206 (12951) hydrogen bonds : bond 0.04040 ( 513) hydrogen bonds : angle 3.25948 ( 1485) Misc. bond : bond 0.12000 ( 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 74 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 62 time to evaluate : 0.286 Fit side-chains outliers start: 12 outliers final: 10 residues processed: 62 average time/residue: 0.8160 time to fit residues: 53.2424 Evaluate side-chains 56 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 30 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 32 optimal weight: 0.0030 chunk 59 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.0570 chunk 58 optimal weight: 0.7980 overall best weight: 0.5712 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 11 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2369 r_free = 0.2369 target = 0.041421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2230 r_free = 0.2230 target = 0.036979 restraints weight = 19241.003| |-----------------------------------------------------------------------------| r_work (start): 0.2228 rms_B_bonded: 0.71 r_work: 0.2122 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2023 rms_B_bonded: 2.53 restraints_weight: 0.2500 r_work (final): 0.2023 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9283 moved from start: 0.4061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.292 9270 Z= 0.135 Angle : 0.707 12.465 12951 Z= 0.262 Chirality : 0.036 0.113 1359 Planarity : 0.004 0.034 1503 Dihedral : 12.507 177.420 2342 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.06 % Allowed : 6.19 % 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 aren not related in a simple way. whole: 3.83 (0.28), residues: 756 helix: 3.09 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.31 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 20 TYR 0.004 0.001 TYR Q 44 PHE 0.006 0.001 PHE M 41 TRP 0.010 0.001 TRP N 39 HIS 0.003 0.001 HIS Q 37 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9243) covalent geometry : angle 0.70660 (12951) hydrogen bonds : bond 0.04901 ( 513) hydrogen bonds : angle 3.36473 ( 1485) Misc. bond : bond 0.14599 ( 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 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 54 time to evaluate : 0.286 Fit side-chains outliers start: 13 outliers final: 12 residues processed: 55 average time/residue: 0.8021 time to fit residues: 46.4424 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 45 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain O residue 14 ILE Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 8 optimal weight: 0.0970 chunk 38 optimal weight: 3.9990 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 0.4980 chunk 61 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5778 ------------------------------------------------------------------------------- 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 = 0.2374 r_free = 0.2374 target = 0.041427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2237 r_free = 0.2237 target = 0.037011 restraints weight = 19072.629| |-----------------------------------------------------------------------------| r_work (start): 0.2234 rms_B_bonded: 0.71 r_work: 0.2128 rms_B_bonded: 1.49 restraints_weight: 0.5000 r_work: 0.2028 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2028 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9279 moved from start: 0.4237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.304 9270 Z= 0.131 Angle : 0.696 11.429 12951 Z= 0.257 Chirality : 0.036 0.112 1359 Planarity : 0.004 0.032 1503 Dihedral : 12.235 178.323 2342 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.90 % Allowed : 6.19 % 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 aren not related in a simple way. whole: 3.91 (0.28), residues: 756 helix: 3.16 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.30 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 20 TYR 0.004 0.001 TYR Q 44 PHE 0.006 0.001 PHE M 41 TRP 0.010 0.001 TRP I 40 HIS 0.003 0.001 HIS G 37 Details of bonding type rmsd covalent geometry : bond 0.00299 ( 9243) covalent geometry : angle 0.69606 (12951) hydrogen bonds : bond 0.04760 ( 513) hydrogen bonds : angle 3.30917 ( 1485) Misc. bond : bond 0.14846 ( 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 64 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.271 Fit side-chains outliers start: 12 outliers final: 12 residues processed: 52 average time/residue: 0.7898 time to fit residues: 43.3182 Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 46 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.1980 chunk 1 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 48 optimal weight: 0.0000 chunk 70 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 41 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- 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 = 0.2358 r_free = 0.2358 target = 0.041029 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2221 r_free = 0.2221 target = 0.036665 restraints weight = 18967.136| |-----------------------------------------------------------------------------| r_work (start): 0.2218 rms_B_bonded: 0.71 r_work: 0.2112 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.2013 rms_B_bonded: 2.48 restraints_weight: 0.2500 r_work (final): 0.2013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9287 moved from start: 0.4284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.315 9270 Z= 0.135 Angle : 0.704 10.892 12951 Z= 0.261 Chirality : 0.036 0.110 1359 Planarity : 0.004 0.032 1503 Dihedral : 12.199 178.347 2342 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.75 % Allowed : 6.51 % 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 aren not related in a simple way. whole: 3.89 (0.27), residues: 756 helix: 3.13 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.33 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 20 TYR 0.005 0.001 TYR Q 44 PHE 0.005 0.001 PHE M 41 TRP 0.010 0.001 TRP I 40 HIS 0.003 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00310 ( 9243) covalent geometry : angle 0.70418 (12951) hydrogen bonds : bond 0.04908 ( 513) hydrogen bonds : angle 3.31844 ( 1485) Misc. bond : bond 0.15118 ( 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 61 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 50 time to evaluate : 0.292 Fit side-chains outliers start: 11 outliers final: 11 residues processed: 50 average time/residue: 0.7974 time to fit residues: 42.0725 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 0 optimal weight: 0.0170 chunk 26 optimal weight: 0.8980 chunk 43 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 65 optimal weight: 0.5980 chunk 23 optimal weight: 0.0040 chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.5030 ------------------------------------------------------------------------------- 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 = 0.041758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2249 r_free = 0.2249 target = 0.037381 restraints weight = 19082.543| |-----------------------------------------------------------------------------| r_work (start): 0.2246 rms_B_bonded: 0.71 r_work: 0.2141 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2042 rms_B_bonded: 2.51 restraints_weight: 0.2500 r_work (final): 0.2042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9272 moved from start: 0.4339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.288 9270 Z= 0.126 Angle : 0.684 9.680 12951 Z= 0.252 Chirality : 0.035 0.110 1359 Planarity : 0.004 0.031 1503 Dihedral : 11.979 178.473 2342 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 2.22 % Allowed : 6.19 % 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 aren not related in a simple way. whole: 4.00 (0.27), residues: 756 helix: 3.23 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.28 (0.54), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 20 TYR 0.004 0.001 TYR Q 44 PHE 0.004 0.001 PHE D 31 TRP 0.010 0.001 TRP I 40 HIS 0.002 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00282 ( 9243) covalent geometry : angle 0.68356 (12951) hydrogen bonds : bond 0.04613 ( 513) hydrogen bonds : angle 3.27165 ( 1485) Misc. bond : bond 0.14141 ( 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 68 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 54 time to evaluate : 0.258 Fit side-chains REVERT: I 5 LYS cc_start: 0.9537 (OUTLIER) cc_final: 0.8290 (mptt) REVERT: J 9 GLU cc_start: 0.9341 (mm-30) cc_final: 0.8832 (mm-30) outliers start: 14 outliers final: 12 residues processed: 56 average time/residue: 0.7706 time to fit residues: 45.5730 Evaluate side-chains 58 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain M residue 14 ILE Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 50 optimal weight: 0.1980 chunk 23 optimal weight: 0.0170 chunk 43 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 67 optimal weight: 4.9990 chunk 48 optimal weight: 0.0970 chunk 69 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.0570 overall best weight: 0.1934 ------------------------------------------------------------------------------- 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 = 0.2488 r_free = 0.2488 target = 0.045286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2356 r_free = 0.2356 target = 0.040856 restraints weight = 19261.193| |-----------------------------------------------------------------------------| r_work (start): 0.2354 rms_B_bonded: 0.74 r_work: 0.2254 rms_B_bonded: 1.53 restraints_weight: 0.5000 r_work: 0.2158 rms_B_bonded: 2.62 restraints_weight: 0.2500 r_work (final): 0.2158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9198 moved from start: 0.4468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.207 9270 Z= 0.102 Angle : 0.630 9.171 12951 Z= 0.229 Chirality : 0.033 0.110 1359 Planarity : 0.004 0.032 1503 Dihedral : 11.574 179.166 2342 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Rotamer: Outliers : 1.75 % Allowed : 6.83 % 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 aren not related in a simple way. whole: 4.35 (0.27), residues: 756 helix: 3.54 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.09 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 20 TYR 0.004 0.001 TYR Q 44 PHE 0.003 0.000 PHE N 31 TRP 0.010 0.001 TRP K 40 HIS 0.002 0.000 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00214 ( 9243) covalent geometry : angle 0.63020 (12951) hydrogen bonds : bond 0.03713 ( 513) hydrogen bonds : angle 3.16035 ( 1485) Misc. bond : bond 0.10492 ( 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 67 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.288 Fit side-chains REVERT: I 5 LYS cc_start: 0.9523 (OUTLIER) cc_final: 0.8272 (mptt) REVERT: J 9 GLU cc_start: 0.9240 (mm-30) cc_final: 0.8829 (mm-30) outliers start: 11 outliers final: 10 residues processed: 57 average time/residue: 0.7699 time to fit residues: 46.2571 Evaluate side-chains 57 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.279 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain L residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 68 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 69 optimal weight: 0.7980 chunk 67 optimal weight: 3.9990 chunk 0 optimal weight: 0.0370 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 60 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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 = 0.2366 r_free = 0.2366 target = 0.041325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2229 r_free = 0.2229 target = 0.036934 restraints weight = 19089.313| |-----------------------------------------------------------------------------| r_work (start): 0.2227 rms_B_bonded: 0.72 r_work: 0.2121 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2022 rms_B_bonded: 2.52 restraints_weight: 0.2500 r_work (final): 0.2022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9281 moved from start: 0.4343 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.279 9270 Z= 0.134 Angle : 0.695 9.019 12951 Z= 0.258 Chirality : 0.036 0.111 1359 Planarity : 0.004 0.031 1503 Dihedral : 11.861 178.665 2342 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.13 % Favored : 99.87 % Rotamer: Outliers : 2.22 % Allowed : 6.35 % 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 aren not related in a simple way. whole: 4.02 (0.27), residues: 756 helix: 3.26 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.22 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG F 20 TYR 0.005 0.001 TYR Q 44 PHE 0.005 0.001 PHE H 31 TRP 0.010 0.001 TRP I 40 HIS 0.003 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 9243) covalent geometry : angle 0.69550 (12951) hydrogen bonds : bond 0.04845 ( 513) hydrogen bonds : angle 3.30379 ( 1485) Misc. bond : bond 0.13433 ( 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 60 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 46 time to evaluate : 0.293 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 47 average time/residue: 0.7927 time to fit residues: 39.3661 Evaluate side-chains 55 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 43 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain E residue 14 ILE Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 53 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 3 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 19 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 44 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 24 optimal weight: 0.4980 chunk 4 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- 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 = 0.2367 r_free = 0.2367 target = 0.041167 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2231 r_free = 0.2231 target = 0.036812 restraints weight = 19014.670| |-----------------------------------------------------------------------------| r_work (start): 0.2226 rms_B_bonded: 0.71 r_work: 0.2120 rms_B_bonded: 1.48 restraints_weight: 0.5000 r_work: 0.2022 rms_B_bonded: 2.50 restraints_weight: 0.2500 r_work (final): 0.2022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9281 moved from start: 0.4346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.301 9270 Z= 0.134 Angle : 0.697 8.809 12951 Z= 0.259 Chirality : 0.036 0.110 1359 Planarity : 0.004 0.031 1503 Dihedral : 11.886 178.754 2342 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % Rotamer: Outliers : 2.06 % Allowed : 6.51 % 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 aren not related in a simple way. whole: 3.92 (0.27), residues: 756 helix: 3.18 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.20 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG H 20 TYR 0.005 0.001 TYR Q 44 PHE 0.005 0.001 PHE D 31 TRP 0.010 0.001 TRP I 40 HIS 0.003 0.001 HIS C 37 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 9243) covalent geometry : angle 0.69694 (12951) hydrogen bonds : bond 0.04803 ( 513) hydrogen bonds : angle 3.29667 ( 1485) Misc. bond : bond 0.14667 ( 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: 13 poor density : 44 time to evaluate : 0.340 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 11 residues processed: 46 average time/residue: 0.7734 time to fit residues: 37.6939 Evaluate side-chains 53 residues out of total 630 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 42 time to evaluate : 0.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 2 THR Chi-restraints excluded: chain C residue 14 ILE Chi-restraints excluded: chain D residue 2 THR Chi-restraints excluded: chain F residue 2 THR Chi-restraints excluded: chain H residue 2 THR Chi-restraints excluded: chain I residue 5 LYS Chi-restraints excluded: chain I residue 14 ILE Chi-restraints excluded: chain J residue 2 THR Chi-restraints excluded: chain N residue 2 THR Chi-restraints excluded: chain P residue 2 THR Chi-restraints excluded: chain R residue 2 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 40 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.1980 chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 32 optimal weight: 0.0170 chunk 50 optimal weight: 0.1980 chunk 66 optimal weight: 0.7980 chunk 67 optimal weight: 1.9990 overall best weight: 0.3618 ------------------------------------------------------------------------------- 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 = 0.2416 r_free = 0.2416 target = 0.042751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2281 r_free = 0.2281 target = 0.038355 restraints weight = 19064.186| |-----------------------------------------------------------------------------| r_work (start): 0.2280 rms_B_bonded: 0.72 r_work: 0.2177 rms_B_bonded: 1.50 restraints_weight: 0.5000 r_work: 0.2080 rms_B_bonded: 2.55 restraints_weight: 0.2500 r_work (final): 0.2080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9252 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.259 9270 Z= 0.115 Angle : 0.660 8.852 12951 Z= 0.243 Chirality : 0.034 0.110 1359 Planarity : 0.004 0.031 1503 Dihedral : 11.653 178.970 2342 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Rotamer: Outliers : 1.59 % Allowed : 7.14 % 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 aren not related in a simple way. whole: 4.14 (0.27), residues: 756 helix: 3.38 (0.17), residues: 594 sheet: None (None), residues: 0 loop : 0.13 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG D 20 TYR 0.004 0.001 TYR Q 44 PHE 0.004 0.001 PHE D 31 TRP 0.010 0.001 TRP I 40 HIS 0.002 0.001 HIS H 12 Details of bonding type rmsd covalent geometry : bond 0.00250 ( 9243) covalent geometry : angle 0.65980 (12951) hydrogen bonds : bond 0.04268 ( 513) hydrogen bonds : angle 3.22907 ( 1485) Misc. bond : bond 0.12813 ( 27) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2643.29 seconds wall clock time: 46 minutes 9.19 seconds (2769.19 seconds total)