Starting phenix.real_space_refine on Thu Mar 14 23:36:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/03_2024/7zcu_14633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/03_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_14633/03_2024/7zcu_14633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/03_2024/7zcu_14633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/03_2024/7zcu_14633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/03_2024/7zcu_14633_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/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: 5.65, per 1000 atoms: 0.56 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=33, symmetry=0 Number of additional bonds: simple=33, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.39 Conformation dependent library (CDL) restraints added in 1.4 seconds 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... running ksdssp... Secondary structure from input PDB file: 36 helices and 0 sheets defined 65.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.838A pdb=" N TRP A 7 " --> pdb=" O ALA A 4 " (cutoff:3.500A) Processing helix chain 'A' and resid 12 through 37 Proline residue: A 17 - end of helix Processing helix chain 'A' and resid 40 through 46 Processing helix chain 'B' and resid 11 through 42 removed outlier: 3.781A pdb=" N HIS B 20 " --> pdb=" O GLU B 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.783A pdb=" N TRP C 7 " --> pdb=" O ALA C 4 " (cutoff:3.500A) Processing helix chain 'C' and resid 12 through 37 Proline residue: C 17 - end of helix Processing helix chain 'C' and resid 40 through 46 Processing helix chain 'D' and resid 11 through 42 removed outlier: 3.588A pdb=" N HIS D 20 " --> pdb=" O GLU D 16 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 8 removed outlier: 4.039A pdb=" N TRP E 7 " --> pdb=" O ALA E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 37 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'F' and resid 11 through 42 removed outlier: 3.758A pdb=" N HIS F 20 " --> pdb=" O GLU F 16 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 4.201A pdb=" N TRP G 7 " --> pdb=" O ALA G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 36 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'H' and resid 11 through 42 removed outlier: 3.858A pdb=" N HIS H 20 " --> pdb=" O GLU H 16 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.846A pdb=" N TRP I 7 " --> pdb=" O ALA I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 36 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'J' and resid 11 through 42 removed outlier: 3.877A pdb=" N HIS J 20 " --> pdb=" O GLU J 16 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 8 removed outlier: 4.055A pdb=" N TRP K 7 " --> pdb=" O ALA K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 36 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 40 through 46 Processing helix chain 'L' and resid 11 through 42 removed outlier: 3.732A pdb=" N HIS L 20 " --> pdb=" O GLU L 16 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 8 removed outlier: 4.172A pdb=" N TRP M 7 " --> pdb=" O ALA M 4 " (cutoff:3.500A) Processing helix chain 'M' and resid 12 through 37 Proline residue: M 17 - end of helix Processing helix chain 'M' and resid 40 through 46 Processing helix chain 'N' and resid 11 through 42 removed outlier: 3.712A pdb=" N HIS N 20 " --> pdb=" O GLU N 16 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 8 removed outlier: 3.887A pdb=" N TRP O 7 " --> pdb=" O ALA O 4 " (cutoff:3.500A) Processing helix chain 'O' and resid 12 through 37 Proline residue: O 17 - end of helix Processing helix chain 'O' and resid 40 through 46 Processing helix chain 'P' and resid 11 through 42 removed outlier: 3.615A pdb=" N HIS P 20 " --> pdb=" O GLU P 16 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 8 removed outlier: 3.993A pdb=" N TRP Q 7 " --> pdb=" O ALA Q 4 " (cutoff:3.500A) Processing helix chain 'Q' and resid 12 through 37 Proline residue: Q 17 - end of helix Processing helix chain 'Q' and resid 40 through 46 Processing helix chain 'R' and resid 11 through 42 removed outlier: 3.822A pdb=" N HIS R 20 " --> pdb=" O GLU R 16 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1314 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: 2.33 Time building geometry restraints manager: 4.68 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: 84.78 - 99.93: 132 99.93 - 115.07: 7003 115.07 - 130.22: 7363 130.22 - 145.36: 308 145.36 - 160.51: 94 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: 1101 2.75 - 3.29: 9216 3.29 - 3.83: 18203 3.83 - 4.36: 22343 4.36 - 4.90: 36986 Nonbonded interactions: 87849 Sorted by model distance: nonbonded pdb=" OE1 GLU S 18 " pdb=" NH2 ARG Q 5 " model vdw 2.218 2.520 nonbonded pdb=" O THR O 38 " pdb=" O HOH O 201 " model vdw 2.224 2.440 nonbonded pdb=" O THR I 38 " pdb=" O HOH I 201 " model vdw 2.239 2.440 nonbonded pdb=" O THR A 38 " pdb=" O HOH A 201 " model vdw 2.252 2.440 nonbonded pdb=" O THR C 38 " pdb=" O HOH C 201 " model vdw 2.260 2.440 ... (remaining 87844 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 1 through 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: 1.270 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: 4.520 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 29.430 Find NCS groups from input model: 0.670 Set up NCS constraints: 0.090 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: 0.010 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.720 ------------------------------------------------------------------------------- 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= 0.264 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 : 0.998 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: 1.3060 time to fit residues: 193.8692 Evaluate side-chains 94 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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: 0.6980 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 chunk 23 optimal weight: 0.0370 chunk 46 optimal weight: 5.9990 chunk 36 optimal weight: 10.0000 chunk 70 optimal weight: 1.9990 chunk 27 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 overall best weight: 1.5464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 HIS L 47 HIS ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.1506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 10612 Z= 0.201 Angle : 0.838 12.707 14900 Z= 0.289 Chirality : 0.040 0.119 1516 Planarity : 0.005 0.029 1781 Dihedral : 14.020 106.466 2006 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.52 % Allowed : 8.49 % Favored : 89.99 % 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: 3.28 (0.26), residues: 911 helix: 3.23 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.18 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 45 HIS 0.009 0.002 HIS C 37 PHE 0.007 0.001 PHE A 32 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 105 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 93 time to evaluate : 0.958 Fit side-chains REVERT: A 43 LYS cc_start: 0.7901 (tttt) cc_final: 0.7630 (ttpt) REVERT: B 16 GLU cc_start: 0.7471 (tp30) cc_final: 0.7075 (mm-30) REVERT: B 19 LYS cc_start: 0.8266 (mttt) cc_final: 0.7989 (mttm) REVERT: D 16 GLU cc_start: 0.7328 (tp30) cc_final: 0.6883 (tp30) REVERT: G 43 LYS cc_start: 0.8221 (tttt) cc_final: 0.7894 (tmtt) REVERT: I 11 LYS cc_start: 0.7991 (mttt) cc_final: 0.7669 (mttt) REVERT: L 23 ASP cc_start: 0.7203 (t70) cc_final: 0.7001 (t70) REVERT: L 37 PHE cc_start: 0.7773 (t80) cc_final: 0.7468 (t80) outliers start: 12 outliers final: 3 residues processed: 96 average time/residue: 1.4001 time to fit residues: 143.4938 Evaluate side-chains 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 86 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain C residue 42 SER 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: 7.9990 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 81 optimal weight: 4.9990 chunk 88 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 80 optimal weight: 0.6980 overall best weight: 3.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 47 HIS S 33 GLN S 65 GLN D 47 HIS K 3 GLN ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 20 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 10612 Z= 0.340 Angle : 0.957 18.866 14900 Z= 0.326 Chirality : 0.045 0.134 1516 Planarity : 0.005 0.031 1781 Dihedral : 14.659 113.568 2006 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer: Outliers : 1.52 % Allowed : 8.62 % Favored : 89.86 % 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: 2.83 (0.26), residues: 911 helix: 2.73 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.33 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP M 7 HIS 0.008 0.002 HIS M 37 PHE 0.011 0.002 PHE S 56 TYR 0.008 0.002 TYR P 40 ARG 0.002 0.000 ARG I 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 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 1.004 Fit side-chains REVERT: A 43 LYS cc_start: 0.7932 (tttt) cc_final: 0.7621 (ttpt) REVERT: B 16 GLU cc_start: 0.7579 (tp30) cc_final: 0.7166 (mm-30) REVERT: B 19 LYS cc_start: 0.8350 (mttt) cc_final: 0.8001 (mttm) REVERT: E 5 ARG cc_start: 0.7948 (OUTLIER) cc_final: 0.7604 (mtt-85) REVERT: G 43 LYS cc_start: 0.8399 (tttt) cc_final: 0.8054 (tmtt) REVERT: I 11 LYS cc_start: 0.7981 (mttt) cc_final: 0.7677 (mttt) REVERT: L 37 PHE cc_start: 0.7849 (t80) cc_final: 0.7604 (t80) REVERT: P 12 GLU cc_start: 0.7344 (mm-30) cc_final: 0.6988 (tp30) outliers start: 12 outliers final: 5 residues processed: 89 average time/residue: 1.4886 time to fit residues: 141.0373 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.945 ------------------------------------------------------------------------------- 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 M residue 42 SER Chi-restraints excluded: chain O residue 42 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 61 optimal weight: 0.9990 chunk 42 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 39 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 86 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 23 optimal weight: 0.4980 chunk 72 optimal weight: 0.9980 chunk 49 optimal weight: 0.8980 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.2019 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= 0.172 Angle : 0.782 11.973 14900 Z= 0.261 Chirality : 0.037 0.108 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.855 104.291 2006 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.14 % Allowed : 9.38 % Favored : 89.48 % 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: 3.32 (0.26), residues: 911 helix: 3.14 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.46 (0.37), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP M 7 HIS 0.006 0.001 HIS C 37 PHE 0.005 0.001 PHE B 28 TYR 0.007 0.001 TYR S 37 ARG 0.001 0.000 ARG I 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 91 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.963 Fit side-chains REVERT: A 43 LYS cc_start: 0.7939 (tttt) cc_final: 0.7652 (ttpt) REVERT: B 16 GLU cc_start: 0.7501 (tp30) cc_final: 0.7094 (mm-30) REVERT: B 19 LYS cc_start: 0.8278 (mttt) cc_final: 0.7983 (mttm) REVERT: G 43 LYS cc_start: 0.8301 (tttt) cc_final: 0.7961 (tmtt) REVERT: H 13 GLU cc_start: 0.7836 (mt-10) cc_final: 0.7509 (mt-10) REVERT: I 11 LYS cc_start: 0.7991 (mttt) cc_final: 0.7736 (mttt) REVERT: L 37 PHE cc_start: 0.7819 (t80) cc_final: 0.7529 (t80) REVERT: P 12 GLU cc_start: 0.7278 (mm-30) cc_final: 0.6951 (tp30) outliers start: 9 outliers final: 4 residues processed: 86 average time/residue: 1.4390 time to fit residues: 132.1251 Evaluate side-chains 82 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain O residue 42 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 74 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 0 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 78 optimal weight: 0.5980 chunk 21 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7884 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 10612 Z= 0.162 Angle : 0.766 12.145 14900 Z= 0.251 Chirality : 0.037 0.108 1516 Planarity : 0.004 0.026 1781 Dihedral : 13.410 100.286 2006 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.52 % Allowed : 10.27 % Favored : 88.21 % 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: 3.51 (0.26), residues: 911 helix: 3.31 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.48 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 40 HIS 0.006 0.001 HIS C 37 PHE 0.006 0.001 PHE H 28 TYR 0.006 0.001 TYR S 37 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 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.937 Fit side-chains REVERT: A 43 LYS cc_start: 0.7909 (tttt) cc_final: 0.7638 (ttpt) REVERT: B 16 GLU cc_start: 0.7492 (tp30) cc_final: 0.7087 (mm-30) REVERT: B 19 LYS cc_start: 0.8279 (mttt) cc_final: 0.7994 (mttm) REVERT: G 43 LYS cc_start: 0.8313 (tttt) cc_final: 0.7970 (tmtt) REVERT: I 11 LYS cc_start: 0.8009 (mttt) cc_final: 0.7793 (mppt) REVERT: L 37 PHE cc_start: 0.7825 (t80) cc_final: 0.7539 (t80) outliers start: 12 outliers final: 4 residues processed: 83 average time/residue: 1.3894 time to fit residues: 123.2119 Evaluate side-chains 79 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain B residue 41 VAL Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 9.9990 chunk 21 optimal weight: 9.9990 chunk 87 optimal weight: 0.9980 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 83 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 49 optimal weight: 4.9990 overall best weight: 2.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 20 HIS ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7921 moved from start: 0.2159 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 10612 Z= 0.259 Angle : 0.870 16.265 14900 Z= 0.287 Chirality : 0.041 0.114 1516 Planarity : 0.004 0.028 1781 Dihedral : 13.844 106.924 2006 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 1.01 % Allowed : 11.41 % 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: 3.18 (0.26), residues: 911 helix: 3.02 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.41 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP M 7 HIS 0.006 0.001 HIS C 37 PHE 0.008 0.001 PHE J 28 TYR 0.006 0.001 TYR F 40 ARG 0.001 0.000 ARG I 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 87 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 79 time to evaluate : 0.974 Fit side-chains REVERT: A 43 LYS cc_start: 0.7930 (tttt) cc_final: 0.7622 (ttpt) REVERT: B 16 GLU cc_start: 0.7534 (tp30) cc_final: 0.7128 (mm-30) REVERT: B 19 LYS cc_start: 0.8316 (mttt) cc_final: 0.8004 (mttm) REVERT: E 5 ARG cc_start: 0.7893 (OUTLIER) cc_final: 0.7570 (mtt-85) REVERT: G 43 LYS cc_start: 0.8337 (tttt) cc_final: 0.8021 (tmtt) REVERT: L 37 PHE cc_start: 0.7845 (t80) cc_final: 0.7577 (t80) REVERT: L 46 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8535 (mp) REVERT: P 12 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6954 (tp30) outliers start: 8 outliers final: 4 residues processed: 85 average time/residue: 1.4764 time to fit residues: 133.7301 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.999 ------------------------------------------------------------------------------- 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 L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain O residue 42 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 52 optimal weight: 7.9990 chunk 40 optimal weight: 4.9990 chunk 53 optimal weight: 0.7980 chunk 34 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 10612 Z= 0.208 Angle : 0.810 12.668 14900 Z= 0.267 Chirality : 0.038 0.107 1516 Planarity : 0.004 0.027 1781 Dihedral : 13.513 103.358 2006 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.01 % Allowed : 11.91 % Favored : 87.07 % 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: 3.27 (0.26), residues: 911 helix: 3.11 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.40 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 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 I 5 *********************** 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 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.929 Fit side-chains REVERT: A 43 LYS cc_start: 0.7916 (tttt) cc_final: 0.7629 (ttpt) REVERT: B 16 GLU cc_start: 0.7522 (tp30) cc_final: 0.7133 (mm-30) REVERT: B 19 LYS cc_start: 0.8305 (mttt) cc_final: 0.7997 (mttm) REVERT: E 5 ARG cc_start: 0.7882 (OUTLIER) cc_final: 0.7556 (mtt-85) REVERT: F 15 GLU cc_start: 0.7974 (mt-10) cc_final: 0.7673 (mt-10) REVERT: G 43 LYS cc_start: 0.8330 (tttt) cc_final: 0.8016 (tmtt) REVERT: L 37 PHE cc_start: 0.7838 (t80) cc_final: 0.7570 (t80) REVERT: L 46 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8526 (mp) REVERT: P 12 GLU cc_start: 0.7298 (mm-30) cc_final: 0.6934 (tp30) outliers start: 8 outliers final: 5 residues processed: 84 average time/residue: 1.4803 time to fit residues: 132.3732 Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.959 ------------------------------------------------------------------------------- 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 L residue 46 LEU Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Chi-restraints excluded: chain O residue 42 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.9990 chunk 17 optimal weight: 7.9990 chunk 16 optimal weight: 0.6980 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 42 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 83 optimal weight: 0.8980 chunk 75 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7864 moved from start: 0.2330 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= 0.137 Angle : 0.730 12.252 14900 Z= 0.238 Chirality : 0.036 0.109 1516 Planarity : 0.004 0.026 1781 Dihedral : 12.997 97.198 2006 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.63 % Allowed : 12.29 % Favored : 87.07 % 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: 3.58 (0.26), residues: 911 helix: 3.40 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.42 (0.36), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP M 7 HIS 0.004 0.001 HIS C 37 PHE 0.005 0.001 PHE H 28 TYR 0.006 0.001 TYR S 37 ARG 0.001 0.000 ARG N 26 *********************** 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 90 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.944 Fit side-chains REVERT: A 43 LYS cc_start: 0.7924 (tttt) cc_final: 0.7637 (ttpt) REVERT: B 16 GLU cc_start: 0.7464 (tp30) cc_final: 0.7080 (mm-30) REVERT: B 19 LYS cc_start: 0.8293 (mttt) cc_final: 0.7993 (mttm) REVERT: F 15 GLU cc_start: 0.7920 (mt-10) cc_final: 0.7654 (mt-10) REVERT: G 43 LYS cc_start: 0.8290 (tttt) cc_final: 0.7808 (mptm) REVERT: H 13 GLU cc_start: 0.7803 (mt-10) cc_final: 0.7445 (mt-10) REVERT: L 37 PHE cc_start: 0.7819 (t80) cc_final: 0.7535 (t80) REVERT: P 12 GLU cc_start: 0.7293 (mm-30) cc_final: 0.6929 (tp30) outliers start: 5 outliers final: 3 residues processed: 88 average time/residue: 1.4075 time to fit residues: 132.6501 Evaluate side-chains 85 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.996 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 8.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 46 ASN ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.2332 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= 0.169 Angle : 0.766 12.610 14900 Z= 0.250 Chirality : 0.037 0.108 1516 Planarity : 0.004 0.026 1781 Dihedral : 13.009 99.231 2006 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.76 % Allowed : 12.42 % Favored : 86.82 % 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: 3.50 (0.26), residues: 911 helix: 3.34 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.40 (0.36), 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 0.006 0.001 TYR P 40 ARG 0.004 0.000 ARG I 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 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 80 time to evaluate : 0.894 Fit side-chains REVERT: A 43 LYS cc_start: 0.7939 (tttt) cc_final: 0.7653 (ttpt) REVERT: B 16 GLU cc_start: 0.7479 (tp30) cc_final: 0.7146 (mm-30) REVERT: B 19 LYS cc_start: 0.8302 (mttt) cc_final: 0.8006 (mttm) REVERT: D 27 ILE cc_start: 0.8414 (OUTLIER) cc_final: 0.8191 (mp) REVERT: F 15 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7697 (mt-10) REVERT: G 43 LYS cc_start: 0.8304 (tttt) cc_final: 0.7965 (tmtt) REVERT: H 13 GLU cc_start: 0.7802 (mt-10) cc_final: 0.7449 (mt-10) REVERT: L 37 PHE cc_start: 0.7830 (t80) cc_final: 0.7553 (t80) REVERT: P 12 GLU cc_start: 0.7322 (mm-30) cc_final: 0.6990 (tp30) outliers start: 6 outliers final: 3 residues processed: 83 average time/residue: 1.4408 time to fit residues: 127.6751 Evaluate side-chains 82 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 SER Chi-restraints excluded: chain D residue 27 ILE Chi-restraints excluded: chain M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP 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: 5.9990 chunk 89 optimal weight: 0.9980 chunk 82 optimal weight: 0.6980 chunk 71 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 55 optimal weight: 0.9990 chunk 43 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 0.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10612 Z= 0.178 Angle : 0.776 12.717 14900 Z= 0.254 Chirality : 0.037 0.108 1516 Planarity : 0.004 0.026 1781 Dihedral : 13.061 100.639 2006 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 1.14 % Allowed : 12.17 % Favored : 86.69 % 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: 3.29 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.41 (0.36), 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 0.003 0.000 ARG I 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 88 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 79 time to evaluate : 0.979 Fit side-chains REVERT: A 43 LYS cc_start: 0.7933 (tttt) cc_final: 0.7651 (ttpt) REVERT: B 16 GLU cc_start: 0.7482 (tp30) cc_final: 0.7151 (mm-30) REVERT: B 19 LYS cc_start: 0.8316 (mttt) cc_final: 0.8015 (mttm) REVERT: E 5 ARG cc_start: 0.7857 (OUTLIER) cc_final: 0.7578 (mtt-85) REVERT: F 15 GLU cc_start: 0.7985 (mt-10) cc_final: 0.7702 (mt-10) REVERT: G 43 LYS cc_start: 0.8327 (tttt) cc_final: 0.7998 (tmtt) REVERT: H 13 GLU cc_start: 0.7822 (mt-10) cc_final: 0.7501 (mt-10) REVERT: L 37 PHE cc_start: 0.7837 (t80) cc_final: 0.7565 (t80) REVERT: P 12 GLU cc_start: 0.7319 (mm-30) cc_final: 0.6965 (tp30) outliers start: 9 outliers final: 5 residues processed: 85 average time/residue: 1.4319 time to fit residues: 129.9135 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.933 ------------------------------------------------------------------------------- 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 M residue 42 SER Chi-restraints excluded: chain N residue 23 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 9 optimal weight: 6.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.126609 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.097499 restraints weight = 10801.565| |-----------------------------------------------------------------------------| r_work (start): 0.3007 rms_B_bonded: 1.44 r_work: 0.2822 rms_B_bonded: 2.44 restraints_weight: 0.5000 r_work: 0.2679 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8386 moved from start: 0.2360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10612 Z= 0.177 Angle : 0.774 12.676 14900 Z= 0.253 Chirality : 0.037 0.109 1516 Planarity : 0.004 0.026 1781 Dihedral : 13.055 100.549 2006 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer: Outliers : 0.89 % Allowed : 12.29 % Favored : 86.82 % 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: 3.44 (0.26), residues: 911 helix: 3.28 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.39 (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 0.001 0.000 ARG G 5 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3040.71 seconds wall clock time: 54 minutes 46.87 seconds (3286.87 seconds total)