Starting phenix.real_space_refine (version: dev) on Sun Feb 19 14:49:34 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zdi_14650/02_2023/7zdi_14650_updated.pdb" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- 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= 0.013 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 10284 Number of models: 1 Model: "" Number of chains: 38 Chain: "A" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} 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: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "E" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "G" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "I" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "K" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "M" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "O" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "Q" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 383 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 394 Classifications: {'peptide': 49} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "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: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} 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: 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: "G" 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: "H" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 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: "N" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 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: "P" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 5.98, per 1000 atoms: 0.58 Number of scatterers: 10284 At special positions: 0 Unit cell: (96.2, 102.7, 80.6, 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 1567 8.00 N 1401 7.00 C 7274 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: 4.24 Conformation dependent library (CDL) restraints added in 1.1 seconds 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 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 64.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.41 Creating SS restraints... Processing helix chain 'A' and resid 4 through 8 removed outlier: 3.944A pdb=" N TRP A 7 " --> pdb=" O GLY 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 15 through 46 removed outlier: 3.951A pdb=" N HIS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N VAL B 25 " --> pdb=" O LEU B 21 " (cutoff:3.500A) Processing helix chain 'C' and resid 4 through 8 removed outlier: 3.950A pdb=" N TRP C 7 " --> pdb=" O GLY 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 15 through 46 removed outlier: 3.945A pdb=" N HIS D 24 " --> pdb=" O GLU D 20 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL D 25 " --> pdb=" O LEU D 21 " (cutoff:3.500A) Processing helix chain 'E' and resid 4 through 8 removed outlier: 3.965A pdb=" N TRP E 7 " --> pdb=" O GLY E 4 " (cutoff:3.500A) Processing helix chain 'E' and resid 12 through 37 Proline residue: E 17 - end of helix Processing helix chain 'E' and resid 40 through 46 Processing helix chain 'F' and resid 15 through 46 removed outlier: 4.006A pdb=" N HIS F 24 " --> pdb=" O GLU F 20 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL F 25 " --> pdb=" O LEU F 21 " (cutoff:3.500A) Processing helix chain 'G' and resid 4 through 8 removed outlier: 3.979A pdb=" N TRP G 7 " --> pdb=" O GLY G 4 " (cutoff:3.500A) Processing helix chain 'G' and resid 12 through 37 Proline residue: G 17 - end of helix Processing helix chain 'G' and resid 40 through 46 Processing helix chain 'H' and resid 15 through 46 removed outlier: 3.935A pdb=" N HIS H 24 " --> pdb=" O GLU H 20 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 removed outlier: 3.997A pdb=" N TRP I 7 " --> pdb=" O GLY I 4 " (cutoff:3.500A) Processing helix chain 'I' and resid 12 through 37 Proline residue: I 17 - end of helix Processing helix chain 'I' and resid 40 through 46 Processing helix chain 'J' and resid 15 through 46 removed outlier: 3.965A pdb=" N HIS J 24 " --> pdb=" O GLU J 20 " (cutoff:3.500A) Processing helix chain 'K' and resid 4 through 8 removed outlier: 3.928A pdb=" N TRP K 7 " --> pdb=" O GLY K 4 " (cutoff:3.500A) Processing helix chain 'K' and resid 12 through 37 Proline residue: K 17 - end of helix Processing helix chain 'K' and resid 39 through 46 Processing helix chain 'L' and resid 15 through 46 removed outlier: 3.938A pdb=" N HIS L 24 " --> pdb=" O GLU L 20 " (cutoff:3.500A) Processing helix chain 'M' and resid 4 through 8 removed outlier: 3.927A pdb=" N TRP M 7 " --> pdb=" O GLY 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 15 through 46 removed outlier: 3.894A pdb=" N HIS N 24 " --> pdb=" O GLU N 20 " (cutoff:3.500A) Processing helix chain 'O' and resid 4 through 8 removed outlier: 3.907A pdb=" N TRP O 7 " --> pdb=" O GLY 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 15 through 46 removed outlier: 3.884A pdb=" N HIS P 24 " --> pdb=" O GLU P 20 " (cutoff:3.500A) Processing helix chain 'Q' and resid 4 through 8 removed outlier: 3.884A pdb=" N TRP Q 7 " --> pdb=" O GLY 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 15 through 46 removed outlier: 3.904A pdb=" N HIS R 24 " --> pdb=" O GLU R 20 " (cutoff:3.500A) 448 hydrogen bonds defined for protein. 1317 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: 2.53 Time building geometry restraints manager: 4.56 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.37: 2950 1.37 - 1.57: 7692 1.57 - 1.77: 9 1.77 - 1.98: 9 1.98 - 2.18: 132 Bond restraints: 10792 Sorted by residual: bond pdb=" C20 IRM O 103 " pdb=" C21 IRM O 103 " ideal model delta sigma weight residual 1.552 1.419 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C20 IRM B1801 " pdb=" C21 IRM B1801 " ideal model delta sigma weight residual 1.552 1.419 0.133 2.00e-02 2.50e+03 4.44e+01 bond pdb=" C24 IRM K 103 " pdb=" C25 IRM K 103 " ideal model delta sigma weight residual 1.549 1.418 0.131 2.00e-02 2.50e+03 4.32e+01 bond pdb=" C24 IRM M 103 " pdb=" C25 IRM M 103 " ideal model delta sigma weight residual 1.549 1.418 0.131 2.00e-02 2.50e+03 4.29e+01 bond pdb=" C14 IRM I 103 " pdb=" C15 IRM I 103 " ideal model delta sigma weight residual 1.553 1.422 0.131 2.00e-02 2.50e+03 4.27e+01 ... (remaining 10787 not shown) Histogram of bond angle deviations from ideal: 84.94 - 99.98: 132 99.98 - 115.03: 7014 115.03 - 130.07: 7644 130.07 - 145.11: 317 145.11 - 160.15: 99 Bond angle restraints: 15206 Sorted by residual: angle pdb=" C7 IRM H 102 " pdb=" C8 IRM H 102 " pdb=" C9 IRM H 102 " ideal model delta sigma weight residual 85.86 127.57 -41.71 3.00e+00 1.11e-01 1.93e+02 angle pdb=" C11 IRM A 103 " pdb=" C12 IRM A 103 " pdb=" C13 IRM A 103 " ideal model delta sigma weight residual 85.87 127.57 -41.70 3.00e+00 1.11e-01 1.93e+02 angle pdb=" C11 IRM J1801 " pdb=" C12 IRM J1801 " pdb=" C13 IRM J1801 " ideal model delta sigma weight residual 85.87 127.50 -41.63 3.00e+00 1.11e-01 1.93e+02 angle pdb=" C7 IRM I 103 " pdb=" C8 IRM I 103 " pdb=" C9 IRM I 103 " ideal model delta sigma weight residual 85.86 127.49 -41.63 3.00e+00 1.11e-01 1.93e+02 angle pdb=" C7 IRM O 103 " pdb=" C8 IRM O 103 " pdb=" C9 IRM O 103 " ideal model delta sigma weight residual 85.86 127.46 -41.60 3.00e+00 1.11e-01 1.92e+02 ... (remaining 15201 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.18: 5035 24.18 - 48.37: 240 48.37 - 72.55: 52 72.55 - 96.73: 20 96.73 - 120.92: 12 Dihedral angle restraints: 5359 sinusoidal: 2579 harmonic: 2780 Sorted by residual: dihedral pdb=" C3 BCL M 102 " pdb=" C5 BCL M 102 " pdb=" C6 BCL M 102 " pdb=" C7 BCL M 102 " ideal model delta sinusoidal sigma weight residual 60.00 116.83 -56.83 3 9.00e+00 1.23e-02 2.62e+01 dihedral pdb=" C3 BCL K 102 " pdb=" C5 BCL K 102 " pdb=" C6 BCL K 102 " pdb=" C7 BCL K 102 " ideal model delta sinusoidal sigma weight residual 60.00 116.57 -56.57 3 9.00e+00 1.23e-02 2.61e+01 dihedral pdb=" C3 BCL Q 102 " pdb=" C5 BCL Q 102 " pdb=" C6 BCL Q 102 " pdb=" C7 BCL Q 102 " ideal model delta sinusoidal sigma weight residual 60.00 114.36 -54.36 3 9.00e+00 1.23e-02 2.58e+01 ... (remaining 5356 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 942 0.029 - 0.058: 333 0.058 - 0.086: 108 0.086 - 0.115: 96 0.115 - 0.144: 28 Chirality restraints: 1507 Sorted by residual: chirality pdb=" CA PRO J 10 " pdb=" N PRO J 10 " pdb=" C PRO J 10 " pdb=" CB PRO J 10 " both_signs ideal model delta sigma weight residual False 2.72 2.57 0.14 2.00e-01 2.50e+01 5.17e-01 chirality pdb=" CA PRO N 10 " pdb=" N PRO N 10 " pdb=" C PRO N 10 " pdb=" CB PRO N 10 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.76e-01 chirality pdb=" CA PRO L 10 " pdb=" N PRO L 10 " pdb=" C PRO L 10 " pdb=" CB PRO L 10 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.13 2.00e-01 2.50e+01 4.54e-01 ... (remaining 1504 not shown) Planarity restraints: 1853 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1 BCL A 101 " -0.056 1.50e-02 4.44e+03 4.85e-02 5.23e+01 pdb=" C2 BCL A 101 " 0.086 1.50e-02 4.44e+03 pdb=" C3 BCL A 101 " 0.006 1.50e-02 4.44e+03 pdb=" C4 BCL A 101 " -0.000 1.50e-02 4.44e+03 pdb=" C5 BCL A 101 " -0.036 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL E 101 " 0.055 1.50e-02 4.44e+03 4.82e-02 5.16e+01 pdb=" C2 BCL E 101 " -0.084 1.50e-02 4.44e+03 pdb=" C3 BCL E 101 " -0.008 1.50e-02 4.44e+03 pdb=" C4 BCL E 101 " 0.000 1.50e-02 4.44e+03 pdb=" C5 BCL E 101 " 0.037 1.50e-02 4.44e+03 delta sigma weight rms_deltas residual plane pdb=" C1 BCL C 102 " 0.053 1.50e-02 4.44e+03 4.60e-02 4.69e+01 pdb=" C2 BCL C 102 " -0.078 1.50e-02 4.44e+03 pdb=" C3 BCL C 102 " -0.014 1.50e-02 4.44e+03 pdb=" C4 BCL C 102 " 0.000 1.50e-02 4.44e+03 pdb=" C5 BCL C 102 " 0.038 1.50e-02 4.44e+03 ... (remaining 1850 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 2968 2.88 - 3.39: 9484 3.39 - 3.89: 18326 3.89 - 4.40: 21774 4.40 - 4.90: 35403 Nonbonded interactions: 87955 Sorted by model distance: nonbonded pdb=" OH TYR S 5 " pdb=" OD2 ASP J 27 " model vdw 2.378 2.440 nonbonded pdb=" ON2 CXM M 1 " pdb=" NE2 HIS N 22 " model vdw 2.385 2.520 nonbonded pdb=" OE1 GLU B 19 " pdb=" ND2 ASN S 96 " model vdw 2.415 2.520 nonbonded pdb=" N LEU S 15 " pdb=" O CXM I 1 " model vdw 2.449 2.520 nonbonded pdb=" OH TYR S 37 " pdb=" OD2 ASP N 27 " model vdw 2.467 2.440 ... (remaining 87950 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 49 or resid 101 through 102)) selection = chain 'C' selection = chain 'E' selection = chain 'G' selection = (chain 'I' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'K' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'M' and (resid 1 through 49 or resid 101 through 102)) selection = (chain 'O' and (resid 1 through 49 or resid 101 through 102)) selection = chain 'Q' } ncs_group { reference = (chain 'B' and resid 3 through 51) selection = (chain 'D' and resid 3 through 51) selection = (chain 'F' and resid 3 through 51) selection = (chain 'H' and resid 3 through 51) selection = (chain 'J' and resid 3 through 51) selection = (chain 'L' and resid 3 through 51) selection = (chain 'N' and resid 3 through 51) selection = (chain 'P' and resid 3 through 51) selection = (chain 'R' and resid 3 through 51) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators 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 7274 2.51 5 N 1401 2.21 5 O 1567 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.000 Extract box with map and model: 6.370 Check model and map are aligned: 0.150 Process input model: 27.830 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.100 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:11.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8355 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 : 0.013 0.133 10792 Z= 0.645 Angle : 2.742 41.708 15206 Z= 0.932 Chirality : 0.042 0.144 1507 Planarity : 0.009 0.087 1853 Dihedral : 16.490 120.917 3581 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.10 (0.24), residues: 929 helix: 1.39 (0.18), residues: 603 sheet: None (None), residues: 0 loop : -0.45 (0.31), residues: 326 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 83 time to evaluate : 0.825 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 1.4262 time to fit residues: 126.5120 Evaluate side-chains 57 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 57 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 68 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 73 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 10792 Z= 0.191 Angle : 1.448 22.556 15206 Z= 0.488 Chirality : 0.040 0.117 1507 Planarity : 0.004 0.031 1853 Dihedral : 17.148 113.942 1961 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.25), residues: 929 helix: 3.11 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.45 (0.33), residues: 326 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.966 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 57 average time/residue: 1.4458 time to fit residues: 88.6335 Evaluate side-chains 49 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 48 time to evaluate : 0.937 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.2205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 40 optimal weight: 9.9990 chunk 22 optimal weight: 0.9990 chunk 61 optimal weight: 0.9980 chunk 50 optimal weight: 0.8980 chunk 20 optimal weight: 0.9990 chunk 73 optimal weight: 0.7980 chunk 79 optimal weight: 7.9990 chunk 65 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 chunk 59 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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: 0.8332 moved from start: 0.1728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 10792 Z= 0.178 Angle : 1.394 22.577 15206 Z= 0.469 Chirality : 0.039 0.129 1507 Planarity : 0.004 0.031 1853 Dihedral : 16.892 109.227 1961 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.60 (0.25), residues: 929 helix: 3.27 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 0.79 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 56 time to evaluate : 0.960 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 57 average time/residue: 1.3428 time to fit residues: 82.6535 Evaluate side-chains 50 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 1.1783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 55 optimal weight: 0.6980 chunk 38 optimal weight: 6.9990 chunk 8 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 49 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 78 optimal weight: 0.9980 chunk 70 optimal weight: 4.9990 chunk 21 optimal weight: 0.0040 chunk 65 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 46 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.1954 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10792 Z= 0.157 Angle : 1.357 22.224 15206 Z= 0.455 Chirality : 0.038 0.141 1507 Planarity : 0.004 0.030 1853 Dihedral : 16.954 137.182 1961 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.82 (0.25), residues: 929 helix: 3.38 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 1.02 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 1.010 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.2472 time to fit residues: 71.8427 Evaluate side-chains 48 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 1.015 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 1 optimal weight: 0.0000 chunk 58 optimal weight: 0.3980 chunk 32 optimal weight: 10.0000 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 0 optimal weight: 7.9990 chunk 39 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 26 optimal weight: 0.0870 chunk 15 optimal weight: 0.7980 overall best weight: 0.4562 ------------------------------------------------------------------------------- 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: 0.8254 moved from start: 0.2211 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 10792 Z= 0.134 Angle : 1.312 22.723 15206 Z= 0.439 Chirality : 0.038 0.149 1507 Planarity : 0.003 0.029 1853 Dihedral : 16.819 139.918 1961 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 4.12 (0.25), residues: 929 helix: 3.55 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 1.26 (0.34), residues: 335 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 51 time to evaluate : 0.993 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 53 average time/residue: 1.3705 time to fit residues: 78.2527 Evaluate side-chains 46 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.828 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.0328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 45 optimal weight: 0.9980 chunk 19 optimal weight: 4.9990 chunk 78 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 36 optimal weight: 8.9990 chunk 6 optimal weight: 5.9990 chunk 25 optimal weight: 10.0000 chunk 41 optimal weight: 0.8980 chunk 75 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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: 0.8406 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.053 10792 Z= 0.378 Angle : 1.511 22.518 15206 Z= 0.510 Chirality : 0.047 0.168 1507 Planarity : 0.004 0.036 1853 Dihedral : 16.783 125.381 1961 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.92 (0.24), residues: 929 helix: 2.52 (0.17), residues: 603 sheet: None (None), residues: 0 loop : 0.92 (0.33), residues: 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 53 time to evaluate : 1.032 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 1.3371 time to fit residues: 79.9014 Evaluate side-chains 54 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 57 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8339 moved from start: 0.2105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 10792 Z= 0.172 Angle : 1.372 22.414 15206 Z= 0.460 Chirality : 0.039 0.152 1507 Planarity : 0.004 0.033 1853 Dihedral : 16.775 128.510 1961 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.49 (0.25), residues: 929 helix: 3.06 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 1.01 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.973 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 52 average time/residue: 1.1744 time to fit residues: 66.8605 Evaluate side-chains 51 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.920 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 15 optimal weight: 10.0000 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.7980 chunk 38 optimal weight: 0.8980 chunk 7 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 chunk 71 optimal weight: 7.9990 chunk 74 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 43 optimal weight: 4.9990 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: 0.8347 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 10792 Z= 0.192 Angle : 1.379 22.532 15206 Z= 0.463 Chirality : 0.040 0.148 1507 Planarity : 0.004 0.032 1853 Dihedral : 16.689 129.305 1961 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.52 (0.25), residues: 929 helix: 3.08 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 1.03 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 52 time to evaluate : 0.852 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 55 average time/residue: 1.1694 time to fit residues: 70.3156 Evaluate side-chains 54 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 1.066 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 31 optimal weight: 0.9990 chunk 57 optimal weight: 0.6980 chunk 22 optimal weight: 4.9990 chunk 65 optimal weight: 0.0170 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 47 optimal weight: 0.7980 chunk 76 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 overall best weight: 0.9022 ------------------------------------------------------------------------------- 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: 0.8327 moved from start: 0.2221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 10792 Z= 0.169 Angle : 1.353 22.504 15206 Z= 0.454 Chirality : 0.039 0.151 1507 Planarity : 0.004 0.032 1853 Dihedral : 16.602 130.647 1961 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.68 (0.25), residues: 929 helix: 3.20 (0.18), residues: 594 sheet: None (None), residues: 0 loop : 1.11 (0.33), residues: 335 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.962 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 54 average time/residue: 1.1399 time to fit residues: 67.5481 Evaluate side-chains 54 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 52 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.1702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 80 optimal weight: 9.9990 chunk 74 optimal weight: 0.9990 chunk 64 optimal weight: 6.9990 chunk 6 optimal weight: 7.9990 chunk 49 optimal weight: 0.0970 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 68 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 9 optimal weight: 6.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.8377 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 : 0.004 0.033 10792 Z= 0.253 Angle : 1.428 22.430 15206 Z= 0.480 Chirality : 0.042 0.156 1507 Planarity : 0.004 0.034 1853 Dihedral : 16.499 128.773 1961 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.22 (0.24), residues: 929 helix: 2.78 (0.17), residues: 603 sheet: None (None), residues: 0 loop : 0.98 (0.33), residues: 326 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1858 Ramachandran restraints generated. 929 Oldfield, 0 Emsley, 929 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.940 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 55 average time/residue: 1.2175 time to fit residues: 73.1390 Evaluate side-chains 55 residues out of total 807 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 1.075 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 1.2521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 81 random chunks: chunk 17 optimal weight: 8.9990 chunk 64 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 66 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 56 optimal weight: 5.9990 chunk 3 optimal weight: 8.9990 chunk 46 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 43 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- 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 = 0.3059 r_free = 0.3059 target = 0.106213 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.2710 r_free = 0.2710 target = 0.081763 restraints weight = 11429.779| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 1.42 r_work: 0.2511 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.2377 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.2377 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.2163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 10792 Z= 0.284 Angle : 1.458 23.099 15206 Z= 0.490 Chirality : 0.043 0.161 1507 Planarity : 0.004 0.036 1853 Dihedral : 16.657 124.639 1961 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.97 % Favored : 99.03 % Rotamer Outliers : 0.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 3.01 (0.24), residues: 929 helix: 2.62 (0.17), residues: 603 sheet: None (None), residues: 0 loop : 0.91 (0.33), residues: 326 =============================================================================== Job complete usr+sys time: 2342.67 seconds wall clock time: 43 minutes 26.09 seconds (2606.09 seconds total)