Starting phenix.real_space_refine on Wed Sep 25 09:46:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/09_2024/7zcu_14633.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/09_2024/7zcu_14633.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/09_2024/7zcu_14633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/09_2024/7zcu_14633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/09_2024/7zcu_14633.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/09_2024/7zcu_14633.cif" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Mg 33 5.21 5 S 9 5.16 5 C 7184 2.51 5 N 1383 2.21 5 O 1540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 10149 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 744 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PCIS': 6, 'TRANS': 87} Chain: "C" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "K" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} 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: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 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: "M" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 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: "O" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 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: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.68, per 1000 atoms: 0.66 Number of scatterers: 10149 At special positions: 0 Unit cell: (102.05, 95.55, 76.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 9 16.00 Mg 33 11.99 O 1540 8.00 N 1383 7.00 C 7184 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.59 Conformation dependent library (CDL) restraints added in 826.2 milliseconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1778 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 0 sheets defined 73.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.72 Creating SS restraints... Processing helix chain 'A' and resid 3 through 9 removed outlier: 3.838A pdb=" N TRP A 7 " --> pdb=" O ALA 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 10 through 43 removed outlier: 3.781A pdb=" N HIS B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 3 through 9 removed outlier: 3.783A pdb=" N TRP C 7 " --> pdb=" O ALA 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 10 through 43 removed outlier: 3.588A pdb=" N HIS D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 9 removed outlier: 4.039A pdb=" N TRP E 7 " --> pdb=" O ALA 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 10 through 43 removed outlier: 3.758A pdb=" N HIS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 3 through 9 removed outlier: 4.201A pdb=" N TRP G 7 " --> pdb=" O ALA G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 11 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 39 through 47 Processing helix chain 'H' and resid 10 through 43 removed outlier: 3.858A pdb=" N HIS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 3 through 9 removed outlier: 3.846A pdb=" N TRP I 7 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 11 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 39 through 47 Processing helix chain 'J' and resid 10 through 43 removed outlier: 3.877A pdb=" N HIS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 9 removed outlier: 4.055A pdb=" N TRP K 7 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 11 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 47 Processing helix chain 'L' and resid 10 through 43 removed outlier: 3.732A pdb=" N HIS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 3 through 9 removed outlier: 4.172A pdb=" N TRP M 7 " --> pdb=" O ALA 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 10 through 43 removed outlier: 3.712A pdb=" N HIS N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 3 through 9 removed outlier: 3.887A pdb=" N TRP O 7 " --> pdb=" O ALA 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 10 through 43 removed outlier: 3.615A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 3 through 9 removed outlier: 3.993A pdb=" N TRP Q 7 " --> pdb=" O ALA 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 10 through 43 removed outlier: 3.822A pdb=" N HIS R 20 " --> pdb=" O GLU R 16 " (cutoff:3.500A) 519 hydrogen bonds defined for protein. 1476 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.42 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.36: 2715 1.36 - 1.57: 7747 1.57 - 1.77: 9 1.77 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10612 Sorted by residual: bond pdb=" SD CXM G 1 " pdb=" CE CXM G 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.31e+00 bond pdb=" SD CXM O 1 " pdb=" CE CXM O 1 " ideal model delta sigma weight residual 1.808 1.762 0.046 2.00e-02 2.50e+03 5.23e+00 bond pdb=" SD CXM I 1 " pdb=" CE CXM I 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.13e+00 bond pdb=" SD CXM C 1 " pdb=" CE CXM C 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.07e+00 bond pdb=" SD CXM K 1 " pdb=" CE CXM K 1 " ideal model delta sigma weight residual 1.808 1.763 0.045 2.00e-02 2.50e+03 5.07e+00 ... (remaining 10607 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.33: 14765 4.33 - 8.66: 130 8.66 - 12.99: 1 12.99 - 17.32: 2 17.32 - 21.65: 2 Bond angle restraints: 14900 Sorted by residual: angle pdb=" C1 BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CGA BCL S 102 " ideal model delta sigma weight residual 116.11 137.77 -21.65 4.27e+00 5.48e-02 2.57e+01 angle pdb=" C1 BCL I 102 " pdb=" C2 BCL I 102 " pdb=" C3 BCL I 102 " ideal model delta sigma weight residual 123.38 143.61 -20.23 4.41e+00 5.14e-02 2.11e+01 angle pdb=" C1 BCL J 101 " pdb=" C2 BCL J 101 " pdb=" C3 BCL J 101 " ideal model delta sigma weight residual 123.38 137.21 -13.84 4.41e+00 5.14e-02 9.85e+00 angle pdb=" C5 IRM G 101 " pdb=" C6 IRM G 101 " pdb=" C7 IRM G 101 " ideal model delta sigma weight residual 126.95 119.33 7.62 3.00e+00 1.11e-01 6.46e+00 angle pdb=" N ALA O 4 " pdb=" CA ALA O 4 " pdb=" C ALA O 4 " ideal model delta sigma weight residual 110.80 116.02 -5.22 2.13e+00 2.20e-01 6.00e+00 ... (remaining 14895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.67: 5245 30.67 - 61.34: 103 61.34 - 92.01: 7 92.01 - 122.68: 12 122.68 - 153.35: 1 Dihedral angle restraints: 5368 sinusoidal: 2615 harmonic: 2753 Sorted by residual: dihedral pdb=" CBD BCL G 102 " pdb=" CGD BCL G 102 " pdb=" O2D BCL G 102 " pdb=" CED BCL G 102 " ideal model delta sinusoidal sigma weight residual -180.00 -26.65 -153.35 1 5.00e+00 4.00e-02 7.27e+02 dihedral pdb=" C1 BCL S 102 " pdb=" CGA BCL S 102 " pdb=" O2A BCL S 102 " pdb=" CBA BCL S 102 " ideal model delta sinusoidal sigma weight residual 180.00 152.12 27.88 1 6.00e+00 2.78e-02 3.10e+01 dihedral pdb=" CA SER S 55 " pdb=" C SER S 55 " pdb=" N PHE S 56 " pdb=" CA PHE S 56 " ideal model delta harmonic sigma weight residual 180.00 153.91 26.09 0 5.00e+00 4.00e-02 2.72e+01 ... (remaining 5365 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1006 0.035 - 0.070: 366 0.070 - 0.105: 100 0.105 - 0.140: 42 0.140 - 0.176: 2 Chirality restraints: 1516 Sorted by residual: chirality pdb=" C13 BCL M 101 " pdb=" C12 BCL M 101 " pdb=" C14 BCL M 101 " pdb=" C15 BCL M 101 " both_signs ideal model delta sigma weight residual False 2.74 2.57 0.18 2.00e-01 2.50e+01 7.71e-01 chirality pdb=" C8 BCL S 103 " pdb=" C10 BCL S 103 " pdb=" C7 BCL S 103 " pdb=" C9 BCL S 103 " both_signs ideal model delta sigma weight residual False 2.70 2.54 0.16 2.00e-01 2.50e+01 6.64e-01 chirality pdb=" CA TRP O 7 " pdb=" N TRP O 7 " pdb=" C TRP O 7 " pdb=" CB TRP O 7 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.42e-01 ... (remaining 1513 not shown) Planarity restraints: 1781 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL I 102 " -0.065 1.50e-02 4.44e+03 5.55e-02 6.85e+01 pdb=" C2 BCL I 102 " 0.095 1.50e-02 4.44e+03 pdb=" C3 BCL I 102 " 0.016 1.50e-02 4.44e+03 pdb=" C4 BCL I 102 " -0.000 1.50e-02 4.44e+03 pdb=" C5 BCL I 102 " -0.045 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL S 102 " 0.116 3.00e-02 1.11e+03 1.03e-01 5.87e+01 pdb=" CBA BCL S 102 " 0.072 3.00e-02 1.11e+03 pdb=" CGA BCL S 102 " -0.002 3.00e-02 1.11e+03 pdb=" O1A BCL S 102 " -0.000 3.00e-02 1.11e+03 pdb=" O2A BCL S 102 " -0.185 3.00e-02 1.11e+03 delta sigma weight rms_deltas residual plane pdb=" C16 IRM K 101 " -0.078 2.00e-02 2.50e+03 6.55e-02 5.36e+01 pdb=" C17 IRM K 101 " 0.094 2.00e-02 2.50e+03 pdb=" C18 IRM K 101 " 0.047 2.00e-02 2.50e+03 pdb=" C19 IRM K 101 " -0.066 2.00e-02 2.50e+03 pdb=" C36 IRM K 101 " 0.003 2.00e-02 2.50e+03 ... (remaining 1778 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 1090 2.75 - 3.29: 9151 3.29 - 3.83: 18085 3.83 - 4.36: 22249 4.36 - 4.90: 36986 Nonbonded interactions: 87561 Sorted by model distance: nonbonded pdb=" OE1 GLU S 18 " pdb=" NH2 ARG Q 5 " model vdw 2.218 3.120 nonbonded pdb=" O THR O 38 " pdb=" O HOH O 201 " model vdw 2.224 3.040 nonbonded pdb=" O THR I 38 " pdb=" O HOH I 201 " model vdw 2.239 3.040 nonbonded pdb=" O THR A 38 " pdb=" O HOH A 201 " model vdw 2.252 3.040 nonbonded pdb=" O THR C 38 " pdb=" O HOH C 201 " model vdw 2.260 3.040 ... (remaining 87556 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 50 or resid 102)) selection = (chain 'C' and (resid 1 through 50 or resid 102)) selection = (chain 'E' and (resid 1 through 50 or resid 102)) selection = (chain 'G' and (resid 1 through 50 or resid 102)) selection = (chain 'I' and (resid 1 through 50 or resid 102)) selection = (chain 'K' and (resid 1 through 50 or resid 102)) selection = (chain 'M' and (resid 1 through 50 or resid 102)) selection = (chain 'O' and (resid 1 through 50 or resid 102)) selection = (chain 'Q' and (resid 1 through 50 or resid 102)) } ncs_group { reference = (chain 'B' and resid 2 through 47) selection = (chain 'D' and resid 2 through 47) selection = (chain 'F' and resid 2 through 47) selection = (chain 'H' and resid 2 through 47) selection = (chain 'J' and resid 2 through 47) selection = (chain 'L' and resid 2 through 47) selection = (chain 'N' and resid 2 through 47) selection = (chain 'P' and resid 2 through 47) selection = (chain 'R' and resid 2 through 47) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.430 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: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 24.070 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:12.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7843 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10612 Z= 0.268 Angle : 0.946 21.650 14900 Z= 0.374 Chirality : 0.042 0.176 1516 Planarity : 0.010 0.103 1781 Dihedral : 14.366 153.350 3590 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % Rotamer: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.25), residues: 911 helix: 1.69 (0.19), residues: 612 sheet: None (None), residues: 0 loop : -0.45 (0.34), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP M 7 HIS 0.008 0.002 HIS I 37 PHE 0.015 0.002 PHE A 32 TYR 0.023 0.004 TYR S 85 ARG 0.020 0.003 ARG R 26 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 0.936 Fit side-chains REVERT: A 43 LYS cc_start: 0.7859 (tttt) cc_final: 0.7585 (ttpt) REVERT: B 19 LYS cc_start: 0.8207 (mttt) cc_final: 0.8002 (mttm) REVERT: D 16 GLU cc_start: 0.7407 (tp30) cc_final: 0.7081 (tp30) REVERT: G 43 LYS cc_start: 0.8164 (tttt) cc_final: 0.7838 (tmtt) REVERT: I 11 LYS cc_start: 0.8010 (mttt) cc_final: 0.7739 (mtmt) REVERT: J 15 GLU cc_start: 0.7958 (mt-10) cc_final: 0.7608 (mt-10) REVERT: L 23 ASP cc_start: 0.7278 (t70) cc_final: 0.7076 (t70) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 1.3935 time to fit residues: 207.2518 Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.0170 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 46 optimal weight: 2.9990 chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 42 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 81 optimal weight: 6.9990 overall best weight: 2.2024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 HIS E 37 HIS L 47 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10612 Z= 0.262 Angle : 0.903 15.429 14900 Z= 0.319 Chirality : 0.043 0.124 1516 Planarity : 0.005 0.033 1781 Dihedral : 14.345 109.034 2006 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.52 % Allowed : 8.37 % Favored : 90.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.26), residues: 911 helix: 3.17 (0.18), residues: 585 sheet: None (None), residues: 0 loop : -0.13 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP M 7 HIS 0.010 0.002 HIS M 37 PHE 0.009 0.001 PHE S 56 TYR 0.009 0.001 TYR P 40 ARG 0.002 0.000 ARG P 26 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 90 time to evaluate : 0.958 Fit side-chains REVERT: A 43 LYS cc_start: 0.7866 (tttt) cc_final: 0.7547 (ttpt) REVERT: B 16 GLU cc_start: 0.7525 (tp30) cc_final: 0.7144 (mm-30) REVERT: B 19 LYS cc_start: 0.8278 (mttt) cc_final: 0.7927 (mttm) REVERT: E 5 ARG cc_start: 0.8046 (OUTLIER) cc_final: 0.7630 (mtt-85) REVERT: E 11 LYS cc_start: 0.8537 (OUTLIER) cc_final: 0.8284 (mttt) REVERT: G 43 LYS cc_start: 0.8160 (tttt) cc_final: 0.7811 (tmtt) REVERT: I 11 LYS cc_start: 0.8027 (mttt) cc_final: 0.7739 (mppt) REVERT: L 23 ASP cc_start: 0.7321 (t70) cc_final: 0.7120 (t70) outliers start: 12 outliers final: 3 residues processed: 93 average time/residue: 1.5064 time to fit residues: 149.0675 Evaluate side-chains 88 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 83 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain M residue 42 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 68 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 80 optimal weight: 0.6980 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 33 GLN S 65 GLN K 3 GLN P 20 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7923 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 10612 Z= 0.279 Angle : 0.898 15.985 14900 Z= 0.310 Chirality : 0.043 0.119 1516 Planarity : 0.005 0.033 1781 Dihedral : 14.364 110.333 2006 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.90 % Allowed : 8.75 % Favored : 89.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.11 (0.26), residues: 911 helix: 3.09 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.13 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP M 7 HIS 0.008 0.002 HIS C 37 PHE 0.009 0.001 PHE S 56 TYR 0.008 0.001 TYR R 42 ARG 0.002 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.956 Fit side-chains REVERT: A 43 LYS cc_start: 0.7857 (tttt) cc_final: 0.7521 (ttpt) REVERT: B 19 LYS cc_start: 0.8298 (mttt) cc_final: 0.8041 (mttm) REVERT: D 16 GLU cc_start: 0.7470 (tp30) cc_final: 0.6981 (tp30) REVERT: E 5 ARG cc_start: 0.8078 (OUTLIER) cc_final: 0.7672 (mtt-85) REVERT: E 11 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.8257 (mttt) REVERT: F 15 GLU cc_start: 0.7997 (OUTLIER) cc_final: 0.7754 (mt-10) REVERT: G 43 LYS cc_start: 0.8100 (tttt) cc_final: 0.7757 (tmtt) REVERT: I 11 LYS cc_start: 0.8063 (mttt) cc_final: 0.7820 (mttt) outliers start: 15 outliers final: 6 residues processed: 87 average time/residue: 1.6285 time to fit residues: 150.2377 Evaluate side-chains 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.963 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain F residue 15 GLU Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 7.9990 chunk 54 optimal weight: 7.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 10.0000 chunk 23 optimal weight: 0.0010 chunk 72 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.9392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 10612 Z= 0.230 Angle : 0.840 13.273 14900 Z= 0.287 Chirality : 0.040 0.110 1516 Planarity : 0.005 0.033 1781 Dihedral : 14.070 106.289 2006 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.90 % Allowed : 9.13 % Favored : 88.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.29 (0.26), residues: 911 helix: 3.21 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.24 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 7 HIS 0.007 0.001 HIS C 37 PHE 0.007 0.001 PHE J 28 TYR 0.007 0.001 TYR P 40 ARG 0.001 0.000 ARG G 5 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.991 Fit side-chains REVERT: A 43 LYS cc_start: 0.7878 (tttt) cc_final: 0.7522 (ttpt) REVERT: B 16 GLU cc_start: 0.7547 (tp30) cc_final: 0.7136 (mm-30) REVERT: B 19 LYS cc_start: 0.8298 (mttt) cc_final: 0.7933 (mttm) REVERT: E 5 ARG cc_start: 0.8074 (OUTLIER) cc_final: 0.7683 (mtt-85) REVERT: E 11 LYS cc_start: 0.8489 (OUTLIER) cc_final: 0.8227 (mttt) REVERT: G 43 LYS cc_start: 0.8138 (tttt) cc_final: 0.7797 (tmtt) outliers start: 15 outliers final: 8 residues processed: 88 average time/residue: 1.4800 time to fit residues: 138.8203 Evaluate side-chains 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain C residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain I residue 43 LYS Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 2.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 44 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 6.9990 chunk 17 optimal weight: 10.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2242 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 10612 Z= 0.217 Angle : 0.830 13.190 14900 Z= 0.280 Chirality : 0.040 0.112 1516 Planarity : 0.004 0.031 1781 Dihedral : 13.885 104.705 2006 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.90 % Allowed : 10.52 % Favored : 87.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.36 (0.26), residues: 911 helix: 3.26 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.26 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 40 HIS 0.006 0.001 HIS C 37 PHE 0.007 0.001 PHE J 28 TYR 0.008 0.001 TYR P 40 ARG 0.001 0.000 ARG I 5 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 80 time to evaluate : 0.952 Fit side-chains REVERT: A 43 LYS cc_start: 0.7868 (tttt) cc_final: 0.7518 (ttpt) REVERT: B 16 GLU cc_start: 0.7576 (tp30) cc_final: 0.7172 (mm-30) REVERT: B 19 LYS cc_start: 0.8270 (mttt) cc_final: 0.8009 (mttm) REVERT: E 5 ARG cc_start: 0.8053 (OUTLIER) cc_final: 0.7686 (mtt-85) REVERT: E 11 LYS cc_start: 0.8494 (OUTLIER) cc_final: 0.8242 (mttt) REVERT: G 43 LYS cc_start: 0.8140 (tttt) cc_final: 0.7794 (tmtt) REVERT: L 46 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8576 (mp) outliers start: 15 outliers final: 6 residues processed: 84 average time/residue: 1.5657 time to fit residues: 139.7544 Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 7.9990 chunk 21 optimal weight: 8.9990 chunk 87 optimal weight: 0.8980 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.6980 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 45 optimal weight: 2.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 6.9990 overall best weight: 1.2582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7887 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10612 Z= 0.177 Angle : 0.784 12.313 14900 Z= 0.263 Chirality : 0.038 0.111 1516 Planarity : 0.004 0.029 1781 Dihedral : 13.568 100.960 2006 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.52 % Allowed : 11.15 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.26), residues: 911 helix: 3.40 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.33 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE J 28 TYR 0.008 0.001 TYR P 40 ARG 0.002 0.000 ARG K 5 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 81 time to evaluate : 0.959 Fit side-chains REVERT: A 43 LYS cc_start: 0.7874 (tttt) cc_final: 0.7519 (ttpt) REVERT: B 16 GLU cc_start: 0.7558 (tp30) cc_final: 0.7161 (mm-30) REVERT: B 19 LYS cc_start: 0.8306 (mttt) cc_final: 0.8006 (mttm) REVERT: D 16 GLU cc_start: 0.7500 (tp30) cc_final: 0.7005 (tp30) REVERT: E 5 ARG cc_start: 0.8007 (OUTLIER) cc_final: 0.7643 (mtt-85) REVERT: E 11 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8223 (mttt) REVERT: G 43 LYS cc_start: 0.8091 (tttt) cc_final: 0.7609 (mptm) REVERT: L 46 LEU cc_start: 0.8870 (OUTLIER) cc_final: 0.8507 (mp) REVERT: M 43 LYS cc_start: 0.8343 (ttpt) cc_final: 0.7700 (mttt) outliers start: 12 outliers final: 5 residues processed: 84 average time/residue: 1.5568 time to fit residues: 139.0432 Evaluate side-chains 87 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 86 optimal weight: 1.9990 chunk 54 optimal weight: 8.9990 chunk 52 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 53 optimal weight: 0.6980 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.2410 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 10612 Z= 0.167 Angle : 0.772 12.439 14900 Z= 0.258 Chirality : 0.037 0.111 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.266 99.248 2006 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.39 % Allowed : 11.66 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.62 (0.26), residues: 911 helix: 3.48 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.34 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.007 0.001 TYR P 40 ARG 0.001 0.000 ARG N 26 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 85 time to evaluate : 1.034 Fit side-chains REVERT: A 43 LYS cc_start: 0.7832 (tttt) cc_final: 0.7480 (ttpt) REVERT: B 16 GLU cc_start: 0.7539 (tp30) cc_final: 0.7139 (mm-30) REVERT: B 19 LYS cc_start: 0.8303 (mttt) cc_final: 0.8008 (mttm) REVERT: D 16 GLU cc_start: 0.7473 (tp30) cc_final: 0.6980 (tp30) REVERT: E 5 ARG cc_start: 0.7973 (OUTLIER) cc_final: 0.7597 (mtt-85) REVERT: F 15 GLU cc_start: 0.7880 (mt-10) cc_final: 0.7666 (mt-10) REVERT: G 43 LYS cc_start: 0.8061 (tttt) cc_final: 0.7590 (mptm) REVERT: H 13 GLU cc_start: 0.7911 (mt-10) cc_final: 0.7582 (mt-10) REVERT: M 43 LYS cc_start: 0.8331 (ttpt) cc_final: 0.7688 (mttt) outliers start: 11 outliers final: 4 residues processed: 88 average time/residue: 1.5399 time to fit residues: 144.0091 Evaluate side-chains 87 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 16 optimal weight: 0.0010 chunk 55 optimal weight: 5.9990 chunk 59 optimal weight: 0.0570 chunk 42 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 75 optimal weight: 5.9990 overall best weight: 1.8110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 10612 Z= 0.220 Angle : 0.835 13.944 14900 Z= 0.279 Chirality : 0.039 0.113 1516 Planarity : 0.004 0.028 1781 Dihedral : 13.454 103.494 2006 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.27 % Allowed : 12.80 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.42 (0.26), residues: 911 helix: 3.30 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.31 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 7 HIS 0.005 0.001 HIS C 37 PHE 0.007 0.001 PHE J 28 TYR 0.009 0.001 TYR P 40 ARG 0.001 0.000 ARG K 5 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.059 Fit side-chains REVERT: A 43 LYS cc_start: 0.7866 (tttt) cc_final: 0.7516 (ttpt) REVERT: B 16 GLU cc_start: 0.7580 (tp30) cc_final: 0.7179 (mm-30) REVERT: B 19 LYS cc_start: 0.8342 (mttt) cc_final: 0.8038 (mttm) REVERT: E 5 ARG cc_start: 0.8025 (OUTLIER) cc_final: 0.7645 (mtt-85) REVERT: E 11 LYS cc_start: 0.8511 (OUTLIER) cc_final: 0.8258 (mttt) REVERT: F 15 GLU cc_start: 0.7982 (mt-10) cc_final: 0.7706 (mt-10) REVERT: G 43 LYS cc_start: 0.8107 (tttt) cc_final: 0.7773 (tmtt) REVERT: L 46 LEU cc_start: 0.8879 (OUTLIER) cc_final: 0.8518 (mp) outliers start: 10 outliers final: 5 residues processed: 87 average time/residue: 1.5470 time to fit residues: 143.2134 Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 81 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 0.7980 chunk 76 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 85 optimal weight: 0.9990 chunk 52 optimal weight: 3.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10612 Z= 0.180 Angle : 0.787 12.611 14900 Z= 0.263 Chirality : 0.038 0.112 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.268 100.862 2006 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.27 % Allowed : 13.31 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.54 (0.26), residues: 911 helix: 3.41 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.32 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.008 0.001 TYR P 40 ARG 0.002 0.000 ARG K 5 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.955 Fit side-chains REVERT: A 43 LYS cc_start: 0.7870 (tttt) cc_final: 0.7519 (ttpt) REVERT: B 16 GLU cc_start: 0.7535 (tp30) cc_final: 0.7137 (mm-30) REVERT: B 19 LYS cc_start: 0.8322 (mttt) cc_final: 0.8025 (mttm) REVERT: E 5 ARG cc_start: 0.7989 (OUTLIER) cc_final: 0.7610 (mtt-85) REVERT: E 11 LYS cc_start: 0.8493 (OUTLIER) cc_final: 0.8237 (mttt) REVERT: F 15 GLU cc_start: 0.7910 (mt-10) cc_final: 0.7681 (mt-10) REVERT: G 43 LYS cc_start: 0.8088 (tttt) cc_final: 0.7616 (mptm) REVERT: L 46 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8482 (mp) REVERT: M 43 LYS cc_start: 0.8301 (ttpt) cc_final: 0.7694 (mttt) outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 1.5448 time to fit residues: 139.4979 Evaluate side-chains 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 2.9990 chunk 59 optimal weight: 6.9990 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 0.9990 chunk 71 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 55 optimal weight: 5.9990 chunk 43 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 21 optimal weight: 8.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.2442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 10612 Z= 0.202 Angle : 0.813 12.797 14900 Z= 0.272 Chirality : 0.039 0.112 1516 Planarity : 0.004 0.028 1781 Dihedral : 13.328 101.836 2006 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer: Outliers : 1.27 % Allowed : 13.56 % Favored : 85.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.46 (0.26), residues: 911 helix: 3.33 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.31 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP M 7 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.008 0.001 TYR P 40 ARG 0.002 0.000 ARG K 5 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 1.025 Fit side-chains REVERT: A 43 LYS cc_start: 0.7864 (tttt) cc_final: 0.7519 (ttpt) REVERT: B 16 GLU cc_start: 0.7546 (tp30) cc_final: 0.7205 (mm-30) REVERT: B 19 LYS cc_start: 0.8335 (mttt) cc_final: 0.8031 (mttm) REVERT: E 5 ARG cc_start: 0.8016 (OUTLIER) cc_final: 0.7643 (mtt-85) REVERT: E 11 LYS cc_start: 0.8498 (OUTLIER) cc_final: 0.8247 (mttt) REVERT: F 15 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7726 (mt-10) REVERT: G 43 LYS cc_start: 0.8092 (tttt) cc_final: 0.7764 (tmtt) REVERT: L 46 LEU cc_start: 0.8842 (OUTLIER) cc_final: 0.8503 (mp) outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 1.5705 time to fit residues: 142.3090 Evaluate side-chains 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 82 time to evaluate : 0.930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain E residue 5 ARG Chi-restraints excluded: chain E residue 11 LYS Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain P residue 9 LEU Chi-restraints excluded: chain Q residue 43 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 71 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 73 optimal weight: 0.6980 chunk 9 optimal weight: 50.0000 chunk 13 optimal weight: 8.9990 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 51 optimal weight: 6.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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 = 0.3397 r_free = 0.3397 target = 0.126656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.097991 restraints weight = 10784.015| |-----------------------------------------------------------------------------| r_work (start): 0.3028 rms_B_bonded: 1.40 r_work: 0.2855 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2716 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.2716 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.2506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 10612 Z= 0.173 Angle : 0.780 12.604 14900 Z= 0.261 Chirality : 0.037 0.112 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.190 99.943 2006 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.14 % Allowed : 13.81 % Favored : 85.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 18.18 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.56 (0.26), residues: 911 helix: 3.43 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.32 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 40 HIS 0.005 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.007 0.001 TYR P 40 ARG 0.002 0.000 ARG K 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3160.31 seconds wall clock time: 56 minutes 30.26 seconds (3390.26 seconds total)