Starting phenix.real_space_refine (version: dev) on Sun Feb 19 12:55:23 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633_ligands.cif 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 { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zcu_14633/02_2023/7zcu_14633_updated.pdb" } resolution = 2.7 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= 0.004 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 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: 10149 Number of models: 1 Model: "" Number of chains: 47 Chain: "A" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "B" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "S" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 744 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PCIS': 6, 'TRANS': 87} Chain: "C" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "E" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "F" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "H" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "I" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "J" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "K" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "L" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "M" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "N" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "O" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "P" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "Q" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 395 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 2, 'TRANS': 47} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'CXM:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "R" Number of atoms: 366 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 366 Classifications: {'peptide': 46} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 44} Chain: "A" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 396 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 396 Unusual residues: {'BCL': 6} Classifications: {'undetermined': 6} Link IDs: {None: 5} Chain: "C" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 66 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 66 Unusual residues: {'BCL': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 173 Unusual residues: {'BCL': 2, 'IRM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "N" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "P" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "Q" Number of atoms: 132 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 132 Unusual residues: {'BCL': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 107 Unusual residues: {'BCL': 1, 'IRM': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Time building chain proxies: 6.00, per 1000 atoms: 0.59 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: 4.80 Conformation dependent library (CDL) restraints added in 1.2 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: 0.37 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: 2.45 Time building geometry restraints manager: 5.15 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=" C14 IRM L 101 " pdb=" C15 IRM L 101 " ideal model delta sigma weight residual 1.553 1.416 0.137 2.00e-02 2.50e+03 4.73e+01 bond pdb=" C20 IRM I 101 " pdb=" C21 IRM I 101 " ideal model delta sigma weight residual 1.552 1.416 0.136 2.00e-02 2.50e+03 4.60e+01 bond pdb=" C24 IRM L 101 " pdb=" C25 IRM L 101 " ideal model delta sigma weight residual 1.549 1.414 0.135 2.00e-02 2.50e+03 4.53e+01 bond pdb=" C24 IRM P 102 " pdb=" C25 IRM P 102 " ideal model delta sigma weight residual 1.549 1.415 0.134 2.00e-02 2.50e+03 4.49e+01 bond pdb=" C20 IRM L 101 " pdb=" C21 IRM L 101 " ideal model delta sigma weight residual 1.552 1.418 0.134 2.00e-02 2.50e+03 4.48e+01 ... (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=" C11 IRM A 103 " pdb=" C12 IRM A 103 " pdb=" C13 IRM A 103 " ideal model delta sigma weight residual 85.87 128.33 -42.46 3.00e+00 1.11e-01 2.00e+02 angle pdb=" C7 IRM A 103 " pdb=" C8 IRM A 103 " pdb=" C9 IRM A 103 " ideal model delta sigma weight residual 85.86 128.09 -42.23 3.00e+00 1.11e-01 1.98e+02 angle pdb=" C11 IRM L 101 " pdb=" C12 IRM L 101 " pdb=" C13 IRM L 101 " ideal model delta sigma weight residual 85.87 128.02 -42.15 3.00e+00 1.11e-01 1.97e+02 angle pdb=" C11 IRM P 102 " pdb=" C12 IRM P 102 " pdb=" C13 IRM P 102 " ideal model delta sigma weight residual 85.87 127.96 -42.09 3.00e+00 1.11e-01 1.97e+02 angle pdb=" C7 IRM P 102 " pdb=" C8 IRM P 102 " pdb=" C9 IRM P 102 " ideal model delta sigma weight residual 85.86 127.91 -42.05 3.00e+00 1.11e-01 1.97e+02 ... (remaining 14895 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.67: 5090 30.67 - 61.34: 161 61.34 - 92.01: 25 92.01 - 122.68: 19 122.68 - 153.35: 1 Dihedral angle restraints: 5296 sinusoidal: 2543 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 5293 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 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. 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: 2.030 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: 4.920 Check model and map are aligned: 0.150 Process input model: 29.090 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:11.540 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8066 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 0.137 10612 Z= 0.580 Angle : 2.779 42.459 14900 Z= 0.948 Chirality : 0.042 0.176 1516 Planarity : 0.010 0.103 1781 Dihedral : 17.078 153.350 3518 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 % 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 *********************** 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 : 1.022 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 1.3688 time to fit residues: 203.0175 Evaluate side-chains 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 92 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2533 ------------------------------------------------------------------------------- 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: 0.7980 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.0370 chunk 46 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 70 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 81 optimal weight: 1.9990 overall best weight: 0.9462 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 HIS K 3 GLN ** 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: 0.8058 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10612 Z= 0.166 Angle : 1.492 23.430 14900 Z= 0.502 Chirality : 0.038 0.114 1516 Planarity : 0.004 0.028 1781 Dihedral : 17.551 104.480 1934 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 1.52 % 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: 3.45 (0.26), residues: 911 helix: 3.39 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.16 (0.35), residues: 326 *********************** 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 106 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 94 time to evaluate : 1.008 Fit side-chains outliers start: 12 outliers final: 1 residues processed: 97 average time/residue: 1.4537 time to fit residues: 150.8784 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 85 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1053 time to fit residues: 1.3500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 45 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 68 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 81 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 72 optimal weight: 8.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 80 optimal weight: 0.7980 overall best weight: 3.7588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 HIS ** K 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 47 HIS ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.064 10612 Z= 0.376 Angle : 1.612 23.561 14900 Z= 0.543 Chirality : 0.047 0.142 1516 Planarity : 0.005 0.031 1781 Dihedral : 19.210 126.310 1934 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 1.27 % 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: 2.79 (0.26), residues: 911 helix: 2.70 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.30 (0.37), residues: 326 *********************** 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 93 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 1.086 Fit side-chains outliers start: 10 outliers final: 4 residues processed: 88 average time/residue: 1.6071 time to fit residues: 150.2568 Evaluate side-chains 81 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.1982 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 5.9990 chunk 9 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 86 optimal weight: 0.4980 chunk 77 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 72 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 overall best weight: 0.7782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: S 65 GLN ** 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: 0.8073 moved from start: 0.2231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 10612 Z= 0.146 Angle : 1.413 22.566 14900 Z= 0.470 Chirality : 0.036 0.111 1516 Planarity : 0.003 0.025 1781 Dihedral : 18.882 123.822 1934 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.88 % Favored : 99.12 % Rotamer Outliers : 1.14 % 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: 3.39 (0.26), residues: 911 helix: 3.22 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.41 (0.36), residues: 326 *********************** 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 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.009 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 85 average time/residue: 1.4388 time to fit residues: 130.7841 Evaluate side-chains 80 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 76 time to evaluate : 0.906 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 1.0630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 74 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 21 optimal weight: 9.9990 chunk 29 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 20 HIS ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.072 10612 Z= 0.425 Angle : 1.644 23.199 14900 Z= 0.550 Chirality : 0.049 0.172 1516 Planarity : 0.005 0.033 1781 Dihedral : 19.291 132.226 1934 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 2.28 % 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: 2.62 (0.26), residues: 911 helix: 2.53 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.30 (0.37), residues: 326 *********************** 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 97 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 1.069 Fit side-chains outliers start: 18 outliers final: 8 residues processed: 90 average time/residue: 1.4611 time to fit residues: 140.3220 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 78 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 1.5783 time to fit residues: 2.7228 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 51 optimal weight: 1.9990 chunk 21 optimal weight: 4.9990 chunk 87 optimal weight: 0.7980 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 0.3980 chunk 7 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 9 optimal weight: 10.0000 chunk 49 optimal weight: 0.9980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8090 moved from start: 0.2415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10612 Z= 0.164 Angle : 1.425 22.705 14900 Z= 0.474 Chirality : 0.037 0.108 1516 Planarity : 0.003 0.027 1781 Dihedral : 18.815 125.307 1934 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.44 % Favored : 99.56 % Rotamer Outliers : 1.90 % 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: 3.22 (0.26), residues: 911 helix: 3.10 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.33 (0.36), residues: 326 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 1.043 Fit side-chains outliers start: 15 outliers final: 7 residues processed: 86 average time/residue: 1.4596 time to fit residues: 134.3435 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 1.197 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.0870 time to fit residues: 1.2354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 63 optimal weight: 9.9990 chunk 49 optimal weight: 0.8980 chunk 73 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 86 optimal weight: 8.9990 chunk 54 optimal weight: 0.8980 chunk 52 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 53 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8084 moved from start: 0.2491 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= 0.167 Angle : 1.410 22.620 14900 Z= 0.468 Chirality : 0.037 0.109 1516 Planarity : 0.003 0.026 1781 Dihedral : 18.576 127.493 1934 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 1.14 % 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: 3.38 (0.26), residues: 911 helix: 3.25 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.32 (0.36), residues: 326 *********************** 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 89 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 80 time to evaluate : 1.045 Fit side-chains outliers start: 9 outliers final: 7 residues processed: 88 average time/residue: 1.4840 time to fit residues: 139.4536 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.988 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2982 time to fit residues: 1.7163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 26 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 16 optimal weight: 0.2980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 7.9990 chunk 42 optimal weight: 0.5980 chunk 8 optimal weight: 7.9990 chunk 68 optimal weight: 4.9990 chunk 78 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8065 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 10612 Z= 0.149 Angle : 1.373 22.483 14900 Z= 0.457 Chirality : 0.036 0.109 1516 Planarity : 0.003 0.026 1781 Dihedral : 18.376 133.789 1934 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 1.27 % 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: 3.35 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.36 (0.36), residues: 326 *********************** 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 92 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.990 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 90 average time/residue: 1.4757 time to fit residues: 141.8806 Evaluate side-chains 86 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 79 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2602 time to fit residues: 1.5499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 80 optimal weight: 0.6980 chunk 83 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 63 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 73 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 53 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 52 optimal weight: 3.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.8062 moved from start: 0.2651 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= 0.146 Angle : 1.365 22.416 14900 Z= 0.455 Chirality : 0.036 0.109 1516 Planarity : 0.003 0.026 1781 Dihedral : 18.271 133.168 1934 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.55 % Favored : 99.45 % Rotamer Outliers : 1.27 % 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: 3.66 (0.26), residues: 911 helix: 3.32 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.59 (0.37), residues: 308 *********************** 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 88 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 78 time to evaluate : 1.060 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 86 average time/residue: 1.5285 time to fit residues: 140.2773 Evaluate side-chains 84 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 77 time to evaluate : 0.982 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2255 time to fit residues: 1.4599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 40 optimal weight: 3.9990 chunk 59 optimal weight: 0.3980 chunk 89 optimal weight: 0.9990 chunk 82 optimal weight: 0.8980 chunk 71 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 chunk 43 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 76 optimal weight: 6.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.6278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** 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: 0.8037 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 10612 Z= 0.129 Angle : 1.332 22.333 14900 Z= 0.445 Chirality : 0.035 0.108 1516 Planarity : 0.003 0.026 1781 Dihedral : 18.138 138.196 1934 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.66 % Favored : 99.34 % Rotamer Outliers : 1.01 % 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: 3.76 (0.26), residues: 911 helix: 3.40 (0.18), residues: 603 sheet: None (None), residues: 0 loop : 0.62 (0.37), residues: 308 ********************** 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: 8 poor density : 80 time to evaluate : 1.020 Fit side-chains outliers start: 8 outliers final: 7 residues processed: 87 average time/residue: 1.3677 time to fit residues: 127.7072 Evaluate side-chains 83 residues out of total 789 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 76 time to evaluate : 1.046 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.2327 time to fit residues: 1.4673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 90 random chunks: chunk 65 optimal weight: 8.9990 chunk 10 optimal weight: 8.9990 chunk 19 optimal weight: 1.9990 chunk 71 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 73 optimal weight: 3.9990 chunk 9 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 51 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 46 ASN ** M 2 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 20 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3384 r_free = 0.3384 target = 0.125458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.096625 restraints weight = 10821.629| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.41 r_work: 0.2806 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2665 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2665 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.054 10612 Z= 0.327 Angle : 1.523 22.747 14900 Z= 0.509 Chirality : 0.044 0.123 1516 Planarity : 0.004 0.028 1781 Dihedral : 18.537 128.238 1934 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer Outliers : 1.39 % 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: 3.01 (0.26), residues: 911 helix: 2.89 (0.18), residues: 585 sheet: None (None), residues: 0 loop : 0.36 (0.36), residues: 326 =============================================================================== Job complete usr+sys time: 3041.05 seconds wall clock time: 55 minutes 36.37 seconds (3336.37 seconds total)