Starting phenix.real_space_refine on Thu Sep 18 02:14:54 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/5kgf_8246/09_2025/5kgf_8246.cif Found real_map, /net/cci-nas-00/data/ceres_data/5kgf_8246/09_2025/5kgf_8246.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.54 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2025/5kgf_8246.cif" } default_model = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2025/5kgf_8246.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2025/5kgf_8246.map" default_real_map = "/net/cci-nas-00/data/ceres_data/5kgf_8246/09_2025/5kgf_8246.map" } resolution = 4.54 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 16 5.16 5 C 7741 2.51 5 N 2597 2.21 5 O 3140 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13782 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 832 Classifications: {'peptide': 101} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Chain: "B" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "C" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "D" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 788 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 97} Chain: "E" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 825 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "F" Number of atoms: 675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 675 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'M2L:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "G" Number of atoms: 874 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 874 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "H" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 766 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Chain: "O" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "M" Number of atoms: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 166 Classifications: {'peptide': 21} Modifications used: {'COO': 1} Link IDs: {'TRANS': 20} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N LEU B 22 " occ=0.00 ... (6 atoms not shown) pdb=" CD2 LEU B 22 " occ=0.00 residue: pdb=" N ARG B 23 " occ=0.00 ... (9 atoms not shown) pdb=" NH2 ARG B 23 " occ=0.00 residue: pdb=" N LYS C 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS C 9 " occ=0.00 residue: pdb=" N ALA C 14 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA C 14 " occ=0.00 residue: pdb=" N GLU C 121 " occ=0.00 ... (7 atoms not shown) pdb=" OE2 GLU C 121 " occ=0.00 residue: pdb=" N LYS G 9 " occ=0.00 ... (7 atoms not shown) pdb=" NZ LYS G 9 " occ=0.00 residue: pdb=" N ALA G 12 " occ=0.00 ... (3 atoms not shown) pdb=" CB ALA G 12 " occ=0.00 Time building chain proxies: 3.16, per 1000 atoms: 0.23 Number of scatterers: 13782 At special positions: 0 Unit cell: (120.35, 124.7, 116, 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 16 16.00 P 288 15.00 O 3140 8.00 N 2597 7.00 C 7741 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Atom "ATOM 8125 O4' DA I 17 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.27 Conformation dependent library (CDL) restraints added in 445.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1838 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 7 sheets defined 62.5% alpha, 4.1% beta 118 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 2.30 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.656A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.710A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLU A 105 " --> pdb=" O VAL A 101 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N ASP A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.977A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.970A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 removed outlier: 3.690A pdb=" N ARG B 35 " --> pdb=" O LYS B 31 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.504A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN B 64 " --> pdb=" O VAL B 60 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA B 69 " --> pdb=" O VAL B 65 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.546A pdb=" N ARG B 92 " --> pdb=" O TYR B 88 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 removed outlier: 3.741A pdb=" N ARG C 35 " --> pdb=" O HIS C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.551A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL C 54 " --> pdb=" O TYR C 50 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU C 55 " --> pdb=" O LEU C 51 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ALA C 60 " --> pdb=" O GLU C 56 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.597A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 98 removed outlier: 4.216A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.517A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 82 removed outlier: 3.797A pdb=" N ASN D 64 " --> pdb=" O ASN D 60 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE D 66 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS D 79 " --> pdb=" O SER D 75 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.553A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 removed outlier: 3.559A pdb=" N ALA D 104 " --> pdb=" O PRO D 100 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N LYS D 105 " --> pdb=" O GLY D 101 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.912A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.712A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLU E 105 " --> pdb=" O VAL E 101 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ALA E 111 " --> pdb=" O THR E 107 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.976A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.971A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.689A pdb=" N ARG F 35 " --> pdb=" O LYS F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.505A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N ASN F 64 " --> pdb=" O VAL F 60 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA F 69 " --> pdb=" O VAL F 65 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.546A pdb=" N ARG F 92 " --> pdb=" O TYR F 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 removed outlier: 3.742A pdb=" N ARG G 35 " --> pdb=" O HIS G 31 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.550A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL G 54 " --> pdb=" O TYR G 50 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N LEU G 55 " --> pdb=" O LEU G 51 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ALA G 60 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.599A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 98 removed outlier: 4.218A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.518A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 82 removed outlier: 3.796A pdb=" N ASN H 64 " --> pdb=" O ASN H 60 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE H 66 " --> pdb=" O PHE H 62 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N HIS H 79 " --> pdb=" O SER H 75 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.556A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 120 removed outlier: 3.560A pdb=" N ALA H 104 " --> pdb=" O PRO H 100 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LYS H 105 " --> pdb=" O GLY H 101 " (cutoff:3.500A) Processing helix chain 'L' and resid 1623 through 1630 removed outlier: 3.535A pdb=" N ARG L1627 " --> pdb=" O VAL L1623 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 35 Processing helix chain 'O' and resid 37 through 39 No H-bonds generated for 'chain 'O' and resid 37 through 39' Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'K' and resid 1623 through 1630 removed outlier: 3.536A pdb=" N ARG K1627 " --> pdb=" O VAL K1623 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.562A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.061A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA4, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.525A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.771A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 15 through 16 removed outlier: 3.551A pdb=" N PHE O 45 " --> pdb=" O LYS O 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'M' and resid 15 through 16 removed outlier: 3.548A pdb=" N PHE M 45 " --> pdb=" O LYS M 48 " (cutoff:3.500A) 412 hydrogen bonds defined for protein. 1200 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 285 hydrogen bonds 566 hydrogen bond angles 0 basepair planarities 118 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 2.59 Time building geometry restraints manager: 1.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2701 1.33 - 1.45: 4263 1.45 - 1.57: 7028 1.57 - 1.68: 577 1.68 - 1.80: 26 Bond restraints: 14595 Sorted by residual: bond pdb=" SG M2L F 20 " pdb=" CD M2L F 20 " ideal model delta sigma weight residual 1.822 1.524 0.298 2.00e-02 2.50e+03 2.22e+02 bond pdb=" SG M2L B 20 " pdb=" CD M2L B 20 " ideal model delta sigma weight residual 1.822 1.525 0.297 2.00e-02 2.50e+03 2.20e+02 bond pdb=" CB M2L B 20 " pdb=" SG M2L B 20 " ideal model delta sigma weight residual 1.815 1.523 0.292 2.00e-02 2.50e+03 2.13e+02 bond pdb=" CB M2L F 20 " pdb=" SG M2L F 20 " ideal model delta sigma weight residual 1.815 1.525 0.290 2.00e-02 2.50e+03 2.10e+02 bond pdb=" O5' DA I -72 " pdb=" C5' DA I -72 " ideal model delta sigma weight residual 1.423 1.649 -0.226 3.00e-02 1.11e+03 5.70e+01 ... (remaining 14590 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.97: 20710 4.97 - 9.95: 194 9.95 - 14.92: 9 14.92 - 19.89: 3 19.89 - 24.86: 2 Bond angle restraints: 20918 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 81.26 22.74 1.50e+00 4.44e-01 2.30e+02 angle pdb=" N ARG G 11 " pdb=" CA ARG G 11 " pdb=" C ARG G 11 " ideal model delta sigma weight residual 111.33 121.82 -10.49 1.21e+00 6.83e-01 7.51e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 83.14 24.86 3.00e+00 1.11e-01 6.87e+01 angle pdb=" C ASN K1621 " pdb=" CA ASN K1621 " pdb=" CB ASN K1621 " ideal model delta sigma weight residual 110.42 125.96 -15.54 1.99e+00 2.53e-01 6.10e+01 angle pdb=" C ASN L1621 " pdb=" CA ASN L1621 " pdb=" CB ASN L1621 " ideal model delta sigma weight residual 110.42 125.91 -15.49 1.99e+00 2.53e-01 6.06e+01 ... (remaining 20913 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.73: 6394 31.73 - 63.46: 1621 63.46 - 95.19: 83 95.19 - 126.92: 14 126.92 - 158.65: 3 Dihedral angle restraints: 8115 sinusoidal: 5271 harmonic: 2844 Sorted by residual: dihedral pdb=" CA ARG H 28 " pdb=" C ARG H 28 " pdb=" N SER H 29 " pdb=" CA SER H 29 " ideal model delta harmonic sigma weight residual -180.00 -115.57 -64.43 0 5.00e+00 4.00e-02 1.66e+02 dihedral pdb=" CA GLY D 23 " pdb=" C GLY D 23 " pdb=" N LYS D 24 " pdb=" CA LYS D 24 " ideal model delta harmonic sigma weight residual 180.00 117.45 62.55 0 5.00e+00 4.00e-02 1.57e+02 dihedral pdb=" CA ASP L1620 " pdb=" C ASP L1620 " pdb=" N ASN L1621 " pdb=" CA ASN L1621 " ideal model delta harmonic sigma weight residual 180.00 118.72 61.28 0 5.00e+00 4.00e-02 1.50e+02 ... (remaining 8112 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.327: 2377 0.327 - 0.655: 2 0.655 - 0.982: 0 0.982 - 1.310: 0 1.310 - 1.637: 1 Chirality restraints: 2380 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.71 1.64 2.00e-01 2.50e+01 6.70e+01 chirality pdb=" CA ASN L1621 " pdb=" N ASN L1621 " pdb=" C ASN L1621 " pdb=" CB ASN L1621 " both_signs ideal model delta sigma weight residual False 2.51 1.94 0.57 2.00e-01 2.50e+01 8.03e+00 chirality pdb=" CA ASN K1621 " pdb=" N ASN K1621 " pdb=" C ASN K1621 " pdb=" CB ASN K1621 " both_signs ideal model delta sigma weight residual False 2.51 1.95 0.57 2.00e-01 2.50e+01 7.99e+00 ... (remaining 2377 not shown) Planarity restraints: 1650 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 26 " 0.045 2.00e-02 2.50e+03 9.76e-02 9.52e+01 pdb=" C ARG D 26 " -0.168 2.00e-02 2.50e+03 pdb=" O ARG D 26 " 0.068 2.00e-02 2.50e+03 pdb=" N LYS D 27 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG H 26 " -0.027 2.00e-02 2.50e+03 5.26e-02 2.76e+01 pdb=" C ARG H 26 " 0.091 2.00e-02 2.50e+03 pdb=" O ARG H 26 " -0.034 2.00e-02 2.50e+03 pdb=" N LYS H 27 " -0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 23 " -0.024 2.00e-02 2.50e+03 4.86e-02 2.36e+01 pdb=" C GLY D 23 " 0.084 2.00e-02 2.50e+03 pdb=" O GLY D 23 " -0.032 2.00e-02 2.50e+03 pdb=" N LYS D 24 " -0.028 2.00e-02 2.50e+03 ... (remaining 1647 not shown) Histogram of nonbonded interaction distances: 1.24 - 1.97: 9 1.97 - 2.71: 915 2.71 - 3.44: 20298 3.44 - 4.17: 39352 4.17 - 4.90: 58510 Nonbonded interactions: 119084 Sorted by model distance: nonbonded pdb=" O ARG H 26 " pdb=" O3' DC J 30 " model vdw 1.243 3.040 nonbonded pdb=" CG1 VAL A 46 " pdb=" OP2 DT J 9 " model vdw 1.353 3.460 nonbonded pdb=" NH2 ARG E 63 " pdb=" C4' DA I 17 " model vdw 1.534 3.550 nonbonded pdb=" NH2 ARG E 63 " pdb=" O4' DA I 17 " model vdw 1.554 3.120 nonbonded pdb=" CD1 ILE L1617 " pdb=" CD2 HIS M 68 " model vdw 1.561 3.680 ... (remaining 119079 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 36 through 135) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 122) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = chain 'M' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.140 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.300 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 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 : 0.009 0.298 14595 Z= 0.447 Angle : 1.372 24.863 20918 Z= 0.819 Chirality : 0.069 1.637 2380 Planarity : 0.006 0.098 1650 Dihedral : 27.921 158.653 6277 Min Nonbonded Distance : 1.243 Molprobity Statistics. All-atom Clashscore : 27.14 Ramachandran Plot: Outliers : 0.42 % Allowed : 6.47 % Favored : 93.11 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.22 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 1.17 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -4.86 (0.19), residues: 958 helix: -3.93 (0.13), residues: 498 sheet: -2.89 (0.53), residues: 38 loop : -2.12 (0.24), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG D 96 TYR 0.031 0.004 TYR H 37 PHE 0.014 0.002 PHE C 25 HIS 0.015 0.003 HIS O 68 Details of bonding type rmsd covalent geometry : bond 0.00931 (14595) covalent geometry : angle 1.37168 (20918) hydrogen bonds : bond 0.28533 ( 697) hydrogen bonds : angle 11.50447 ( 1766) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 425 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 424 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8571 (m-80) cc_final: 0.7278 (m-10) REVERT: A 55 GLN cc_start: 0.8695 (mt0) cc_final: 0.8454 (mt0) REVERT: A 60 LEU cc_start: 0.9132 (mt) cc_final: 0.7934 (mp) REVERT: A 112 ILE cc_start: 0.9268 (mt) cc_final: 0.8808 (mm) REVERT: B 58 LEU cc_start: 0.9354 (tp) cc_final: 0.9128 (tp) REVERT: B 64 ASN cc_start: 0.9159 (m-40) cc_final: 0.8902 (p0) REVERT: C 39 TYR cc_start: 0.8169 (m-80) cc_final: 0.7889 (m-80) REVERT: C 56 GLU cc_start: 0.8622 (tt0) cc_final: 0.8357 (tt0) REVERT: C 61 GLU cc_start: 0.8488 (tp30) cc_final: 0.8199 (tp30) REVERT: C 92 GLU cc_start: 0.7870 (mt-10) cc_final: 0.6332 (tt0) REVERT: D 38 VAL cc_start: 0.9409 (t) cc_final: 0.9115 (t) REVERT: D 58 ILE cc_start: 0.8845 (mm) cc_final: 0.8645 (mt) REVERT: D 103 LEU cc_start: 0.9075 (tt) cc_final: 0.8485 (tp) REVERT: D 106 HIS cc_start: 0.8648 (m-70) cc_final: 0.7351 (m-70) REVERT: E 56 LYS cc_start: 0.9254 (tttt) cc_final: 0.8966 (tptm) REVERT: E 60 LEU cc_start: 0.9203 (mt) cc_final: 0.8502 (mp) REVERT: E 90 MET cc_start: 0.8530 (mmm) cc_final: 0.8210 (mmp) REVERT: E 94 GLU cc_start: 0.7782 (tp30) cc_final: 0.7566 (tp30) REVERT: E 112 ILE cc_start: 0.9266 (mt) cc_final: 0.8847 (mm) REVERT: E 119 ILE cc_start: 0.9248 (pt) cc_final: 0.8942 (pt) REVERT: E 125 GLN cc_start: 0.9201 (mt0) cc_final: 0.8957 (mm-40) REVERT: E 130 ILE cc_start: 0.9205 (mt) cc_final: 0.8915 (mt) REVERT: F 29 ILE cc_start: 0.9472 (mm) cc_final: 0.9222 (mm) REVERT: F 43 VAL cc_start: 0.9713 (t) cc_final: 0.9169 (p) REVERT: F 44 LYS cc_start: 0.9471 (tttt) cc_final: 0.9196 (ttpt) REVERT: F 84 MET cc_start: 0.8306 (mmm) cc_final: 0.8032 (tpp) REVERT: F 88 TYR cc_start: 0.9316 (m-10) cc_final: 0.8681 (m-80) REVERT: G 64 GLU cc_start: 0.8440 (tp30) cc_final: 0.8113 (tp30) REVERT: G 72 ASP cc_start: 0.9134 (m-30) cc_final: 0.8378 (m-30) REVERT: G 74 LYS cc_start: 0.8981 (mttp) cc_final: 0.8469 (tppt) REVERT: G 92 GLU cc_start: 0.8344 (mt-10) cc_final: 0.7883 (tt0) REVERT: G 107 VAL cc_start: 0.9032 (m) cc_final: 0.8829 (t) REVERT: O 3 ILE cc_start: 0.7138 (pt) cc_final: 0.6912 (pt) REVERT: O 17 VAL cc_start: 0.6987 (m) cc_final: 0.5772 (m) REVERT: M 17 VAL cc_start: 0.8074 (m) cc_final: 0.7750 (p) REVERT: M 23 ILE cc_start: 0.7350 (mm) cc_final: 0.6849 (mm) REVERT: M 67 LEU cc_start: 0.8359 (mt) cc_final: 0.8060 (mp) REVERT: M 70 VAL cc_start: 0.4845 (t) cc_final: 0.4542 (t) outliers start: 1 outliers final: 1 residues processed: 424 average time/residue: 0.1470 time to fit residues: 83.8469 Evaluate side-chains 278 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 277 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 108 optimal weight: 3.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 9.9990 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 51 optimal weight: 10.0000 chunk 117 optimal weight: 0.0370 overall best weight: 2.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN C 31 HIS ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 81 ASN E 68 GLN E 76 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 2 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.069235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.053058 restraints weight = 64973.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.054541 restraints weight = 37798.192| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 20)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.055443 restraints weight = 26826.279| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.056046 restraints weight = 21936.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.056448 restraints weight = 19297.660| |-----------------------------------------------------------------------------| r_work (final): 0.3004 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.3927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 14595 Z= 0.228 Angle : 0.843 10.232 20918 Z= 0.472 Chirality : 0.045 0.235 2380 Planarity : 0.008 0.149 1650 Dihedral : 32.199 159.229 4276 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 14.95 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.97 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.74 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.26 (0.24), residues: 958 helix: -0.26 (0.19), residues: 578 sheet: -2.44 (0.50), residues: 50 loop : -1.40 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 83 TYR 0.024 0.003 TYR G 39 PHE 0.013 0.002 PHE G 25 HIS 0.004 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00505 (14595) covalent geometry : angle 0.84257 (20918) hydrogen bonds : bond 0.06412 ( 697) hydrogen bonds : angle 4.92241 ( 1766) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 401 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9507 (p) cc_final: 0.8766 (m) REVERT: A 73 GLU cc_start: 0.8699 (tt0) cc_final: 0.8341 (tt0) REVERT: A 93 GLN cc_start: 0.8239 (tm-30) cc_final: 0.7812 (tm-30) REVERT: A 94 GLU cc_start: 0.8917 (tp30) cc_final: 0.8628 (tp30) REVERT: A 97 GLU cc_start: 0.8850 (mt-10) cc_final: 0.8626 (mt-10) REVERT: A 110 CYS cc_start: 0.9433 (m) cc_final: 0.8812 (t) REVERT: B 52 GLU cc_start: 0.8343 (tm-30) cc_final: 0.7814 (tm-30) REVERT: B 59 LYS cc_start: 0.9345 (ttpt) cc_final: 0.8872 (tptp) REVERT: B 63 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8385 (tm-30) REVERT: B 64 ASN cc_start: 0.9291 (m-40) cc_final: 0.9007 (m-40) REVERT: C 56 GLU cc_start: 0.8809 (tt0) cc_final: 0.7915 (tt0) REVERT: C 57 TYR cc_start: 0.8920 (t80) cc_final: 0.8671 (t80) REVERT: C 65 LEU cc_start: 0.9477 (mt) cc_final: 0.9084 (mt) REVERT: C 94 ASN cc_start: 0.9204 (t0) cc_final: 0.8652 (t0) REVERT: C 95 LYS cc_start: 0.9078 (tppp) cc_final: 0.8661 (tppp) REVERT: D 58 ILE cc_start: 0.9527 (mm) cc_final: 0.9220 (mt) REVERT: D 65 ASP cc_start: 0.9227 (t0) cc_final: 0.8985 (t0) REVERT: D 66 ILE cc_start: 0.9341 (mt) cc_final: 0.9078 (mt) REVERT: D 83 ARG cc_start: 0.8342 (mmt-90) cc_final: 0.7927 (tpp80) REVERT: D 103 LEU cc_start: 0.9544 (tt) cc_final: 0.9241 (mt) REVERT: D 112 THR cc_start: 0.9692 (m) cc_final: 0.9490 (p) REVERT: D 115 VAL cc_start: 0.9137 (t) cc_final: 0.8916 (t) REVERT: E 54 TYR cc_start: 0.8409 (m-10) cc_final: 0.7624 (m-10) REVERT: E 56 LYS cc_start: 0.9428 (tttt) cc_final: 0.9189 (tptm) REVERT: E 57 SER cc_start: 0.9482 (p) cc_final: 0.8783 (m) REVERT: E 61 LEU cc_start: 0.9447 (mm) cc_final: 0.8995 (mm) REVERT: E 70 LEU cc_start: 0.9644 (tp) cc_final: 0.9204 (tp) REVERT: E 80 THR cc_start: 0.8485 (p) cc_final: 0.8198 (p) REVERT: E 90 MET cc_start: 0.9251 (mmm) cc_final: 0.8917 (mmp) REVERT: E 97 GLU cc_start: 0.9296 (mt-10) cc_final: 0.8906 (mt-10) REVERT: E 105 GLU cc_start: 0.8940 (mm-30) cc_final: 0.8672 (mm-30) REVERT: E 110 CYS cc_start: 0.9470 (m) cc_final: 0.8881 (t) REVERT: E 123 ASP cc_start: 0.8531 (m-30) cc_final: 0.8256 (t0) REVERT: F 25 ASN cc_start: 0.8756 (m-40) cc_final: 0.8420 (t0) REVERT: F 43 VAL cc_start: 0.9579 (t) cc_final: 0.9082 (p) REVERT: F 44 LYS cc_start: 0.9512 (tttt) cc_final: 0.8894 (mtmt) REVERT: F 59 LYS cc_start: 0.9376 (tttp) cc_final: 0.9065 (ttmm) REVERT: F 60 VAL cc_start: 0.9401 (t) cc_final: 0.9086 (t) REVERT: F 85 ASP cc_start: 0.8655 (m-30) cc_final: 0.8444 (m-30) REVERT: F 88 TYR cc_start: 0.9253 (m-10) cc_final: 0.8942 (m-80) REVERT: F 91 LYS cc_start: 0.9520 (ttmt) cc_final: 0.9318 (tttm) REVERT: G 39 TYR cc_start: 0.9344 (m-10) cc_final: 0.9054 (m-80) REVERT: G 56 GLU cc_start: 0.9084 (tt0) cc_final: 0.8142 (tt0) REVERT: G 61 GLU cc_start: 0.8917 (tp30) cc_final: 0.8698 (tp30) REVERT: G 64 GLU cc_start: 0.8863 (tp30) cc_final: 0.8200 (tp30) REVERT: G 72 ASP cc_start: 0.9341 (m-30) cc_final: 0.9070 (m-30) REVERT: G 83 LEU cc_start: 0.9801 (mt) cc_final: 0.9565 (mm) REVERT: G 92 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8134 (mt-10) REVERT: G 95 LYS cc_start: 0.9113 (tppp) cc_final: 0.8747 (tppt) REVERT: H 49 THR cc_start: 0.8522 (m) cc_final: 0.8033 (p) REVERT: H 92 GLN cc_start: 0.9393 (tt0) cc_final: 0.9003 (tt0) REVERT: H 99 LEU cc_start: 0.9376 (tp) cc_final: 0.9069 (tt) REVERT: H 108 VAL cc_start: 0.9426 (t) cc_final: 0.9132 (t) REVERT: H 110 GLU cc_start: 0.9525 (mm-30) cc_final: 0.9141 (mm-30) REVERT: O 17 VAL cc_start: 0.7536 (m) cc_final: 0.7064 (m) REVERT: O 23 ILE cc_start: 0.9118 (mp) cc_final: 0.8838 (mp) REVERT: O 41 GLN cc_start: 0.7783 (mt0) cc_final: 0.7217 (mt0) REVERT: O 43 LEU cc_start: 0.8824 (mm) cc_final: 0.8333 (mm) REVERT: O 44 ILE cc_start: 0.7099 (mt) cc_final: 0.6119 (mm) REVERT: O 51 GLU cc_start: 0.6417 (pm20) cc_final: 0.6200 (pm20) REVERT: O 68 HIS cc_start: 0.8272 (m170) cc_final: 0.7295 (m170) REVERT: M 6 LYS cc_start: 0.8376 (ttmm) cc_final: 0.8027 (ptmm) REVERT: M 13 ILE cc_start: 0.9098 (tt) cc_final: 0.8869 (tt) REVERT: M 23 ILE cc_start: 0.8742 (mm) cc_final: 0.8141 (mm) REVERT: M 44 ILE cc_start: 0.8530 (mt) cc_final: 0.8208 (mp) REVERT: M 66 THR cc_start: 0.6856 (m) cc_final: 0.6472 (m) REVERT: M 68 HIS cc_start: 0.8565 (m90) cc_final: 0.7643 (m170) outliers start: 0 outliers final: 0 residues processed: 401 average time/residue: 0.1261 time to fit residues: 71.1016 Evaluate side-chains 302 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 302 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 68 optimal weight: 0.6980 chunk 91 optimal weight: 20.0000 chunk 54 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 35 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 92 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 4 optimal weight: 0.4980 chunk 2 optimal weight: 5.9990 chunk 119 optimal weight: 0.0050 overall best weight: 2.2398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN ** O 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.069562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.051719 restraints weight = 64769.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.053280 restraints weight = 38128.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2960 r_free = 0.2960 target = 0.054299 restraints weight = 27071.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.054961 restraints weight = 21890.329| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.055252 restraints weight = 19211.017| |-----------------------------------------------------------------------------| r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 14595 Z= 0.192 Angle : 0.732 9.227 20918 Z= 0.414 Chirality : 0.040 0.199 2380 Planarity : 0.006 0.115 1650 Dihedral : 31.299 161.089 4276 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.07 % Favored : 95.62 % Rotamer: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 958 helix: 0.89 (0.21), residues: 578 sheet: -2.71 (0.53), residues: 48 loop : -1.06 (0.33), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG O 42 TYR 0.020 0.002 TYR G 39 PHE 0.012 0.002 PHE B 61 HIS 0.006 0.002 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00427 (14595) covalent geometry : angle 0.73151 (20918) hydrogen bonds : bond 0.05042 ( 697) hydrogen bonds : angle 4.24934 ( 1766) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 376 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8406 (tp30) cc_final: 0.8009 (mm-30) REVERT: A 54 TYR cc_start: 0.8265 (m-10) cc_final: 0.7654 (m-10) REVERT: A 93 GLN cc_start: 0.8342 (tm-30) cc_final: 0.7826 (tm-30) REVERT: A 96 SER cc_start: 0.9632 (t) cc_final: 0.9258 (p) REVERT: A 130 ILE cc_start: 0.9398 (mp) cc_final: 0.9105 (tp) REVERT: B 44 LYS cc_start: 0.9463 (mtpp) cc_final: 0.9241 (mttt) REVERT: B 59 LYS cc_start: 0.9247 (ttpp) cc_final: 0.8934 (tptp) REVERT: C 39 TYR cc_start: 0.8643 (m-80) cc_final: 0.8334 (m-10) REVERT: C 56 GLU cc_start: 0.8670 (tt0) cc_final: 0.7822 (tt0) REVERT: C 64 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8709 (tp30) REVERT: C 79 ILE cc_start: 0.9643 (tt) cc_final: 0.9286 (mm) REVERT: C 82 HIS cc_start: 0.9249 (m90) cc_final: 0.8816 (m-70) REVERT: C 92 GLU cc_start: 0.8319 (mt-10) cc_final: 0.7448 (mt-10) REVERT: C 94 ASN cc_start: 0.9094 (t0) cc_final: 0.8378 (t0) REVERT: D 58 ILE cc_start: 0.9598 (mm) cc_final: 0.9305 (mt) REVERT: D 66 ILE cc_start: 0.9473 (mt) cc_final: 0.9263 (mt) REVERT: D 99 LEU cc_start: 0.9457 (mt) cc_final: 0.8706 (tt) REVERT: E 50 GLU cc_start: 0.8379 (tp30) cc_final: 0.7499 (tp30) REVERT: E 60 LEU cc_start: 0.8875 (mm) cc_final: 0.8533 (pt) REVERT: E 76 GLN cc_start: 0.9280 (tt0) cc_final: 0.8698 (pt0) REVERT: E 80 THR cc_start: 0.8543 (p) cc_final: 0.8098 (p) REVERT: E 96 SER cc_start: 0.9613 (t) cc_final: 0.9376 (p) REVERT: E 107 THR cc_start: 0.9208 (p) cc_final: 0.8349 (t) REVERT: E 110 CYS cc_start: 0.9498 (m) cc_final: 0.8730 (m) REVERT: E 123 ASP cc_start: 0.8517 (m-30) cc_final: 0.8188 (t0) REVERT: F 26 ILE cc_start: 0.9616 (tt) cc_final: 0.9224 (tt) REVERT: F 44 LYS cc_start: 0.9492 (tttt) cc_final: 0.8935 (mtmt) REVERT: F 52 GLU cc_start: 0.8739 (tp30) cc_final: 0.8482 (tm-30) REVERT: F 85 ASP cc_start: 0.8915 (m-30) cc_final: 0.8669 (m-30) REVERT: F 88 TYR cc_start: 0.9351 (m-10) cc_final: 0.8771 (m-80) REVERT: F 98 TYR cc_start: 0.8817 (m-80) cc_final: 0.8473 (m-80) REVERT: G 50 TYR cc_start: 0.9241 (t80) cc_final: 0.8509 (t80) REVERT: G 56 GLU cc_start: 0.9041 (tt0) cc_final: 0.8116 (tt0) REVERT: G 64 GLU cc_start: 0.8851 (tp30) cc_final: 0.8184 (tp30) REVERT: G 72 ASP cc_start: 0.9387 (m-30) cc_final: 0.9020 (m-30) REVERT: G 74 LYS cc_start: 0.9540 (mtmm) cc_final: 0.8661 (tppt) REVERT: G 78 ILE cc_start: 0.8930 (pt) cc_final: 0.8727 (pt) REVERT: G 92 GLU cc_start: 0.8557 (mt-10) cc_final: 0.8127 (mt-10) REVERT: G 116 LEU cc_start: 0.9145 (mt) cc_final: 0.8831 (mm) REVERT: H 49 THR cc_start: 0.8671 (m) cc_final: 0.8428 (p) REVERT: H 68 GLU cc_start: 0.8330 (tt0) cc_final: 0.8060 (tt0) REVERT: H 92 GLN cc_start: 0.9359 (tt0) cc_final: 0.9115 (tt0) REVERT: H 98 LEU cc_start: 0.9455 (tp) cc_final: 0.9179 (tt) REVERT: H 102 GLU cc_start: 0.8129 (tp30) cc_final: 0.7469 (tp30) REVERT: H 110 GLU cc_start: 0.9454 (mm-30) cc_final: 0.9064 (mm-30) REVERT: O 17 VAL cc_start: 0.8068 (m) cc_final: 0.7325 (m) REVERT: O 43 LEU cc_start: 0.8899 (mm) cc_final: 0.8659 (mm) REVERT: O 51 GLU cc_start: 0.6124 (pm20) cc_final: 0.5787 (pm20) REVERT: O 58 ASP cc_start: 0.8525 (t70) cc_final: 0.8299 (t70) REVERT: O 68 HIS cc_start: 0.7657 (m170) cc_final: 0.7268 (m170) REVERT: M 23 ILE cc_start: 0.8369 (mm) cc_final: 0.8096 (mm) REVERT: M 43 LEU cc_start: 0.8148 (mm) cc_final: 0.7351 (mm) REVERT: M 44 ILE cc_start: 0.8186 (mt) cc_final: 0.7601 (mm) REVERT: M 48 LYS cc_start: 0.8712 (mmpt) cc_final: 0.8327 (mmmt) REVERT: M 68 HIS cc_start: 0.8336 (m90) cc_final: 0.8095 (m-70) outliers start: 0 outliers final: 0 residues processed: 376 average time/residue: 0.1246 time to fit residues: 66.4397 Evaluate side-chains 293 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 293 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 21 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 106 optimal weight: 2.9990 chunk 111 optimal weight: 30.0000 chunk 3 optimal weight: 7.9990 chunk 2 optimal weight: 4.9990 chunk 62 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 104 optimal weight: 20.0000 chunk 63 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN H 106 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.065020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2778 r_free = 0.2778 target = 0.047466 restraints weight = 65381.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.048970 restraints weight = 39037.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.049964 restraints weight = 27804.195| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.050615 restraints weight = 22438.733| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.050990 restraints weight = 19618.278| |-----------------------------------------------------------------------------| r_work (final): 0.2872 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.5703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 14595 Z= 0.252 Angle : 0.737 12.430 20918 Z= 0.417 Chirality : 0.041 0.177 2380 Planarity : 0.006 0.114 1650 Dihedral : 30.790 160.457 4276 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 15.31 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.18 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.53 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.26), residues: 958 helix: 0.83 (0.21), residues: 569 sheet: -2.68 (0.58), residues: 48 loop : -0.99 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 63 TYR 0.021 0.002 TYR D 37 PHE 0.012 0.002 PHE M 45 HIS 0.005 0.002 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00558 (14595) covalent geometry : angle 0.73685 (20918) hydrogen bonds : bond 0.05664 ( 697) hydrogen bonds : angle 4.33564 ( 1766) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 336 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8526 (tp30) cc_final: 0.8080 (mm-30) REVERT: A 54 TYR cc_start: 0.8280 (m-10) cc_final: 0.7550 (m-10) REVERT: A 57 SER cc_start: 0.9388 (m) cc_final: 0.9051 (m) REVERT: A 80 THR cc_start: 0.8559 (p) cc_final: 0.8038 (p) REVERT: A 93 GLN cc_start: 0.8571 (tm-30) cc_final: 0.8277 (tm-30) REVERT: A 110 CYS cc_start: 0.9489 (m) cc_final: 0.9279 (t) REVERT: B 44 LYS cc_start: 0.9618 (mtpp) cc_final: 0.9140 (mtpt) REVERT: B 52 GLU cc_start: 0.8214 (tm-30) cc_final: 0.7983 (tm-30) REVERT: B 53 GLU cc_start: 0.8575 (tp30) cc_final: 0.8110 (tp30) REVERT: B 85 ASP cc_start: 0.8761 (m-30) cc_final: 0.8545 (m-30) REVERT: C 39 TYR cc_start: 0.8944 (m-80) cc_final: 0.8567 (m-80) REVERT: C 56 GLU cc_start: 0.8953 (tt0) cc_final: 0.8071 (tt0) REVERT: C 64 GLU cc_start: 0.9077 (tm-30) cc_final: 0.8808 (tm-30) REVERT: C 79 ILE cc_start: 0.9605 (tt) cc_final: 0.9404 (mm) REVERT: C 94 ASN cc_start: 0.9165 (t0) cc_final: 0.8526 (t0) REVERT: C 95 LYS cc_start: 0.9289 (tppt) cc_final: 0.8989 (tppt) REVERT: E 57 SER cc_start: 0.9344 (m) cc_final: 0.8919 (m) REVERT: E 62 ILE cc_start: 0.9672 (mp) cc_final: 0.9293 (mp) REVERT: E 76 GLN cc_start: 0.9220 (tt0) cc_final: 0.8554 (pt0) REVERT: E 80 THR cc_start: 0.8604 (p) cc_final: 0.8180 (p) REVERT: E 93 GLN cc_start: 0.9020 (tp40) cc_final: 0.8678 (tp40) REVERT: E 96 SER cc_start: 0.9517 (t) cc_final: 0.9285 (p) REVERT: E 97 GLU cc_start: 0.9043 (mt-10) cc_final: 0.7939 (mm-30) REVERT: E 105 GLU cc_start: 0.9076 (mm-30) cc_final: 0.8834 (tp30) REVERT: E 107 THR cc_start: 0.9241 (p) cc_final: 0.8676 (t) REVERT: E 110 CYS cc_start: 0.9521 (m) cc_final: 0.9050 (m) REVERT: E 125 GLN cc_start: 0.9642 (mt0) cc_final: 0.9124 (mm-40) REVERT: F 26 ILE cc_start: 0.9533 (tt) cc_final: 0.9230 (tt) REVERT: F 44 LYS cc_start: 0.9548 (tttt) cc_final: 0.8871 (mtmt) REVERT: F 72 TYR cc_start: 0.9440 (m-80) cc_final: 0.9068 (m-10) REVERT: F 84 MET cc_start: 0.8788 (tpp) cc_final: 0.8423 (tpt) REVERT: F 88 TYR cc_start: 0.9273 (m-10) cc_final: 0.8772 (m-80) REVERT: G 56 GLU cc_start: 0.9195 (tt0) cc_final: 0.8642 (mt-10) REVERT: G 64 GLU cc_start: 0.8901 (tp30) cc_final: 0.8307 (tp30) REVERT: G 72 ASP cc_start: 0.9516 (m-30) cc_final: 0.9178 (m-30) REVERT: G 92 GLU cc_start: 0.8661 (mt-10) cc_final: 0.7756 (mt-10) REVERT: G 116 LEU cc_start: 0.9038 (mt) cc_final: 0.8731 (mm) REVERT: H 49 THR cc_start: 0.8840 (m) cc_final: 0.8547 (p) REVERT: H 56 MET cc_start: 0.8487 (tpt) cc_final: 0.8097 (tpt) REVERT: H 92 GLN cc_start: 0.9507 (tt0) cc_final: 0.9256 (tt0) REVERT: H 110 GLU cc_start: 0.9473 (mm-30) cc_final: 0.9172 (mm-30) REVERT: L 1621 ASN cc_start: 0.6833 (p0) cc_final: 0.6421 (t0) REVERT: O 4 PHE cc_start: 0.8863 (m-10) cc_final: 0.8618 (m-10) REVERT: O 17 VAL cc_start: 0.8310 (m) cc_final: 0.7453 (m) REVERT: O 23 ILE cc_start: 0.9016 (mp) cc_final: 0.8791 (mp) REVERT: O 66 THR cc_start: 0.6762 (m) cc_final: 0.6547 (m) REVERT: O 67 LEU cc_start: 0.8606 (mm) cc_final: 0.8251 (tt) REVERT: O 68 HIS cc_start: 0.7488 (m170) cc_final: 0.6796 (m170) REVERT: M 68 HIS cc_start: 0.8052 (m90) cc_final: 0.7728 (m170) outliers start: 0 outliers final: 0 residues processed: 336 average time/residue: 0.1233 time to fit residues: 59.1039 Evaluate side-chains 267 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.0170 chunk 42 optimal weight: 8.9990 chunk 82 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 122 optimal weight: 0.4980 chunk 100 optimal weight: 10.0000 chunk 97 optimal weight: 10.0000 chunk 76 optimal weight: 1.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 overall best weight: 2.5024 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.066546 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.049052 restraints weight = 63877.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.050572 restraints weight = 38030.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.051561 restraints weight = 26994.571| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.052226 restraints weight = 21778.669| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.052651 restraints weight = 18987.065| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8351 moved from start: 0.6087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 14595 Z= 0.175 Angle : 0.666 9.698 20918 Z= 0.379 Chirality : 0.038 0.171 2380 Planarity : 0.005 0.070 1650 Dihedral : 30.549 160.997 4276 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.55 % Favored : 96.03 % Rotamer: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.32 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.22 (0.27), residues: 958 helix: 1.06 (0.21), residues: 580 sheet: -2.41 (0.62), residues: 50 loop : -1.01 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L1627 TYR 0.016 0.002 TYR D 37 PHE 0.013 0.002 PHE G 25 HIS 0.020 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00383 (14595) covalent geometry : angle 0.66554 (20918) hydrogen bonds : bond 0.04393 ( 697) hydrogen bonds : angle 3.86989 ( 1766) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 350 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 350 time to evaluate : 0.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8438 (tp30) cc_final: 0.7956 (mm-30) REVERT: A 54 TYR cc_start: 0.8223 (m-10) cc_final: 0.7478 (m-10) REVERT: A 56 LYS cc_start: 0.9571 (tptm) cc_final: 0.9313 (tttt) REVERT: A 57 SER cc_start: 0.9291 (m) cc_final: 0.8972 (m) REVERT: A 76 GLN cc_start: 0.9423 (tt0) cc_final: 0.8819 (pt0) REVERT: A 80 THR cc_start: 0.8523 (p) cc_final: 0.8172 (p) REVERT: A 93 GLN cc_start: 0.8665 (tm-30) cc_final: 0.8069 (tm-30) REVERT: B 22 LEU cc_start: -0.0794 (tp) cc_final: -0.1271 (mp) REVERT: B 30 THR cc_start: 0.9249 (p) cc_final: 0.8809 (t) REVERT: C 39 TYR cc_start: 0.8864 (m-80) cc_final: 0.8539 (m-80) REVERT: C 56 GLU cc_start: 0.8900 (tt0) cc_final: 0.7992 (tt0) REVERT: C 64 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8611 (tp30) REVERT: C 72 ASP cc_start: 0.9437 (m-30) cc_final: 0.9215 (m-30) REVERT: C 79 ILE cc_start: 0.9575 (tt) cc_final: 0.9372 (mm) REVERT: D 58 ILE cc_start: 0.9662 (mm) cc_final: 0.9431 (mt) REVERT: D 103 LEU cc_start: 0.9408 (mt) cc_final: 0.8929 (mt) REVERT: E 50 GLU cc_start: 0.8357 (tp30) cc_final: 0.7949 (tp30) REVERT: E 57 SER cc_start: 0.9343 (m) cc_final: 0.8946 (m) REVERT: E 62 ILE cc_start: 0.9594 (mp) cc_final: 0.9029 (mm) REVERT: E 76 GLN cc_start: 0.9151 (tt0) cc_final: 0.8440 (pt0) REVERT: E 80 THR cc_start: 0.8418 (p) cc_final: 0.7816 (p) REVERT: E 93 GLN cc_start: 0.8944 (tp40) cc_final: 0.8548 (tp40) REVERT: E 110 CYS cc_start: 0.9408 (m) cc_final: 0.9196 (m) REVERT: E 125 GLN cc_start: 0.9585 (mt0) cc_final: 0.8816 (mm110) REVERT: F 44 LYS cc_start: 0.9479 (tttt) cc_final: 0.8909 (mtmt) REVERT: F 52 GLU cc_start: 0.8483 (tp30) cc_final: 0.7945 (tm-30) REVERT: F 84 MET cc_start: 0.8680 (tpp) cc_final: 0.8350 (tpt) REVERT: F 88 TYR cc_start: 0.9275 (m-10) cc_final: 0.8823 (m-80) REVERT: F 98 TYR cc_start: 0.8620 (m-80) cc_final: 0.8246 (m-80) REVERT: G 39 TYR cc_start: 0.9458 (m-80) cc_final: 0.8476 (m-80) REVERT: G 56 GLU cc_start: 0.9184 (tt0) cc_final: 0.8571 (mt-10) REVERT: G 64 GLU cc_start: 0.8833 (tp30) cc_final: 0.8248 (tp30) REVERT: G 72 ASP cc_start: 0.9497 (m-30) cc_final: 0.9115 (m-30) REVERT: G 74 LYS cc_start: 0.9522 (mtmm) cc_final: 0.8528 (tppt) REVERT: G 116 LEU cc_start: 0.9019 (mt) cc_final: 0.8721 (mm) REVERT: H 49 THR cc_start: 0.8831 (m) cc_final: 0.8551 (p) REVERT: H 110 GLU cc_start: 0.9374 (mm-30) cc_final: 0.9117 (mm-30) REVERT: O 4 PHE cc_start: 0.8638 (m-10) cc_final: 0.8398 (m-10) REVERT: O 17 VAL cc_start: 0.8304 (m) cc_final: 0.7734 (m) REVERT: O 23 ILE cc_start: 0.9073 (mp) cc_final: 0.8868 (mp) REVERT: O 43 LEU cc_start: 0.8841 (mm) cc_final: 0.8529 (mm) REVERT: O 68 HIS cc_start: 0.7521 (m170) cc_final: 0.6402 (m170) REVERT: M 18 GLU cc_start: 0.7397 (mm-30) cc_final: 0.7057 (mm-30) REVERT: M 23 ILE cc_start: 0.8854 (mm) cc_final: 0.8612 (mm) REVERT: M 41 GLN cc_start: 0.7164 (tp-100) cc_final: 0.6796 (tp-100) REVERT: M 43 LEU cc_start: 0.7639 (mm) cc_final: 0.7233 (mm) REVERT: K 1630 ARG cc_start: 0.5934 (tpm170) cc_final: 0.5670 (tpm170) outliers start: 0 outliers final: 0 residues processed: 350 average time/residue: 0.1238 time to fit residues: 61.4127 Evaluate side-chains 273 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 273 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 48 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 25 optimal weight: 0.3980 chunk 64 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 14 optimal weight: 8.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 5.9990 overall best weight: 1.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN D 106 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.049745 restraints weight = 62344.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.051313 restraints weight = 36030.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.052354 restraints weight = 25170.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.053047 restraints weight = 20010.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.053439 restraints weight = 17259.722| |-----------------------------------------------------------------------------| r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 moved from start: 0.6478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 14595 Z= 0.165 Angle : 0.658 12.323 20918 Z= 0.373 Chirality : 0.037 0.177 2380 Planarity : 0.005 0.072 1650 Dihedral : 30.248 163.004 4276 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.42 % Allowed : 3.76 % Favored : 95.82 % Rotamer: Outliers : 0.00 % Allowed : 2.29 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.18 (0.26), residues: 958 helix: 1.05 (0.21), residues: 579 sheet: -2.43 (0.62), residues: 50 loop : -1.08 (0.34), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 20 TYR 0.017 0.002 TYR D 37 PHE 0.014 0.002 PHE B 61 HIS 0.015 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00359 (14595) covalent geometry : angle 0.65757 (20918) hydrogen bonds : bond 0.04311 ( 697) hydrogen bonds : angle 3.71780 ( 1766) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 341 time to evaluate : 0.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8502 (tp30) cc_final: 0.7978 (mm-30) REVERT: A 54 TYR cc_start: 0.8245 (m-10) cc_final: 0.7559 (m-10) REVERT: A 56 LYS cc_start: 0.9599 (tptm) cc_final: 0.9324 (tttt) REVERT: A 57 SER cc_start: 0.9314 (m) cc_final: 0.9016 (m) REVERT: A 76 GLN cc_start: 0.9467 (tt0) cc_final: 0.8812 (pt0) REVERT: A 93 GLN cc_start: 0.8874 (tm-30) cc_final: 0.8483 (tm-30) REVERT: A 94 GLU cc_start: 0.9187 (tt0) cc_final: 0.8949 (tt0) REVERT: A 105 GLU cc_start: 0.8735 (tp30) cc_final: 0.8293 (tm-30) REVERT: B 22 LEU cc_start: -0.0668 (tp) cc_final: -0.0980 (mp) REVERT: B 26 ILE cc_start: 0.9303 (tt) cc_final: 0.9045 (tt) REVERT: B 30 THR cc_start: 0.9133 (p) cc_final: 0.8647 (t) REVERT: B 85 ASP cc_start: 0.8913 (m-30) cc_final: 0.8700 (m-30) REVERT: C 39 TYR cc_start: 0.8858 (m-80) cc_final: 0.8566 (m-80) REVERT: C 56 GLU cc_start: 0.8815 (tt0) cc_final: 0.8041 (tt0) REVERT: C 64 GLU cc_start: 0.8987 (tm-30) cc_final: 0.8578 (tp30) REVERT: C 72 ASP cc_start: 0.9435 (m-30) cc_final: 0.9212 (m-30) REVERT: C 78 ILE cc_start: 0.9420 (mm) cc_final: 0.9069 (mm) REVERT: C 79 ILE cc_start: 0.9543 (tt) cc_final: 0.9335 (mm) REVERT: D 58 ILE cc_start: 0.9679 (mm) cc_final: 0.9456 (mt) REVERT: E 50 GLU cc_start: 0.8468 (tp30) cc_final: 0.7349 (tp30) REVERT: E 57 SER cc_start: 0.9375 (m) cc_final: 0.8980 (m) REVERT: E 76 GLN cc_start: 0.9065 (tt0) cc_final: 0.8343 (pt0) REVERT: E 80 THR cc_start: 0.8423 (p) cc_final: 0.8200 (p) REVERT: E 97 GLU cc_start: 0.8995 (mm-30) cc_final: 0.8675 (mm-30) REVERT: E 105 GLU cc_start: 0.9095 (mm-30) cc_final: 0.8874 (tp30) REVERT: E 125 GLN cc_start: 0.9607 (mt0) cc_final: 0.8804 (mm110) REVERT: F 44 LYS cc_start: 0.9471 (tttt) cc_final: 0.8868 (mtmt) REVERT: F 84 MET cc_start: 0.8857 (tpp) cc_final: 0.8588 (tpt) REVERT: F 85 ASP cc_start: 0.8870 (m-30) cc_final: 0.8667 (m-30) REVERT: F 88 TYR cc_start: 0.9251 (m-10) cc_final: 0.8892 (m-80) REVERT: F 98 TYR cc_start: 0.8826 (m-80) cc_final: 0.8426 (m-80) REVERT: G 56 GLU cc_start: 0.9167 (tt0) cc_final: 0.8523 (mt-10) REVERT: G 64 GLU cc_start: 0.8929 (tp30) cc_final: 0.8356 (tp30) REVERT: G 72 ASP cc_start: 0.9524 (m-30) cc_final: 0.9127 (m-30) REVERT: G 74 LYS cc_start: 0.9498 (mtmm) cc_final: 0.8488 (tppt) REVERT: H 51 ILE cc_start: 0.8480 (mm) cc_final: 0.8088 (tp) REVERT: H 92 GLN cc_start: 0.9563 (tt0) cc_final: 0.8520 (tp40) REVERT: H 108 VAL cc_start: 0.9360 (t) cc_final: 0.9099 (t) REVERT: H 110 GLU cc_start: 0.9382 (mm-30) cc_final: 0.9043 (mm-30) REVERT: O 17 VAL cc_start: 0.7907 (m) cc_final: 0.7687 (m) REVERT: O 42 ARG cc_start: 0.6463 (tpt-90) cc_final: 0.6192 (tpt170) REVERT: M 23 ILE cc_start: 0.8847 (mm) cc_final: 0.8511 (mm) REVERT: M 52 ASP cc_start: 0.7618 (m-30) cc_final: 0.7350 (m-30) outliers start: 0 outliers final: 0 residues processed: 341 average time/residue: 0.1208 time to fit residues: 59.3568 Evaluate side-chains 275 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 275 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 23 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 4 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 24 optimal weight: 7.9990 chunk 62 optimal weight: 3.9990 chunk 55 optimal weight: 9.9990 chunk 70 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 overall best weight: 7.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 106 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.062963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.046064 restraints weight = 65554.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.047429 restraints weight = 39812.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2810 r_free = 0.2810 target = 0.048341 restraints weight = 28777.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.048945 restraints weight = 23416.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.049314 restraints weight = 20597.270| |-----------------------------------------------------------------------------| r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.6916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.075 14595 Z= 0.298 Angle : 0.742 13.238 20918 Z= 0.423 Chirality : 0.041 0.217 2380 Planarity : 0.006 0.099 1650 Dihedral : 30.145 166.493 4276 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.42 % Allowed : 4.38 % Favored : 95.20 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.26), residues: 958 helix: 0.69 (0.20), residues: 577 sheet: -2.43 (0.61), residues: 50 loop : -1.21 (0.33), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 20 TYR 0.026 0.003 TYR G 39 PHE 0.016 0.003 PHE E 104 HIS 0.017 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00652 (14595) covalent geometry : angle 0.74178 (20918) hydrogen bonds : bond 0.05834 ( 697) hydrogen bonds : angle 4.22479 ( 1766) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 316 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8493 (tp30) cc_final: 0.8229 (mm-30) REVERT: A 56 LYS cc_start: 0.9569 (tptm) cc_final: 0.9285 (ttpt) REVERT: A 57 SER cc_start: 0.9418 (m) cc_final: 0.9190 (m) REVERT: A 76 GLN cc_start: 0.9389 (tt0) cc_final: 0.8676 (pt0) REVERT: A 80 THR cc_start: 0.8644 (p) cc_final: 0.8239 (p) REVERT: A 81 ASP cc_start: 0.8910 (p0) cc_final: 0.8709 (p0) REVERT: A 93 GLN cc_start: 0.8566 (tm-30) cc_final: 0.8042 (tm-30) REVERT: A 94 GLU cc_start: 0.9079 (tt0) cc_final: 0.8548 (tt0) REVERT: A 105 GLU cc_start: 0.8709 (tp30) cc_final: 0.8282 (tm-30) REVERT: A 120 MET cc_start: 0.8978 (ptp) cc_final: 0.8668 (ptp) REVERT: B 30 THR cc_start: 0.9216 (p) cc_final: 0.8858 (t) REVERT: B 53 GLU cc_start: 0.8303 (tp30) cc_final: 0.7978 (tp30) REVERT: B 85 ASP cc_start: 0.8877 (m-30) cc_final: 0.8658 (m-30) REVERT: C 56 GLU cc_start: 0.9029 (tt0) cc_final: 0.8365 (tt0) REVERT: C 64 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8307 (tm-30) REVERT: C 72 ASP cc_start: 0.9397 (m-30) cc_final: 0.9092 (m-30) REVERT: C 79 ILE cc_start: 0.9640 (tt) cc_final: 0.9385 (mm) REVERT: D 45 VAL cc_start: 0.8794 (m) cc_final: 0.8509 (p) REVERT: D 83 ARG cc_start: 0.8999 (mmt-90) cc_final: 0.8666 (mmm-85) REVERT: E 50 GLU cc_start: 0.8324 (tp30) cc_final: 0.7419 (tp30) REVERT: E 54 TYR cc_start: 0.8207 (m-10) cc_final: 0.7827 (m-10) REVERT: E 57 SER cc_start: 0.9437 (m) cc_final: 0.9131 (m) REVERT: E 73 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8587 (tm-30) REVERT: E 105 GLU cc_start: 0.9033 (mm-30) cc_final: 0.8612 (tp30) REVERT: E 123 ASP cc_start: 0.8834 (m-30) cc_final: 0.8479 (m-30) REVERT: E 125 GLN cc_start: 0.9601 (mt0) cc_final: 0.9196 (mm-40) REVERT: F 43 VAL cc_start: 0.9371 (t) cc_final: 0.8844 (p) REVERT: F 44 LYS cc_start: 0.9498 (tttt) cc_final: 0.8850 (mtmt) REVERT: F 46 ILE cc_start: 0.9211 (pt) cc_final: 0.8761 (tp) REVERT: F 52 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8689 (tm-30) REVERT: F 84 MET cc_start: 0.8671 (tpp) cc_final: 0.8404 (tpt) REVERT: F 88 TYR cc_start: 0.9235 (m-10) cc_final: 0.8742 (m-80) REVERT: G 56 GLU cc_start: 0.9170 (tt0) cc_final: 0.8784 (mt-10) REVERT: G 64 GLU cc_start: 0.8903 (tp30) cc_final: 0.8423 (tp30) REVERT: G 72 ASP cc_start: 0.9490 (m-30) cc_final: 0.9117 (m-30) REVERT: G 74 LYS cc_start: 0.9547 (mtmm) cc_final: 0.8566 (tppt) REVERT: G 116 LEU cc_start: 0.9206 (mm) cc_final: 0.8827 (mm) REVERT: G 118 LYS cc_start: 0.8608 (mmmt) cc_final: 0.8317 (mmmt) REVERT: H 86 ILE cc_start: 0.9049 (tp) cc_final: 0.8822 (tt) REVERT: H 91 ILE cc_start: 0.9804 (mp) cc_final: 0.9279 (tt) REVERT: H 92 GLN cc_start: 0.9623 (tt0) cc_final: 0.8719 (tp40) REVERT: H 106 HIS cc_start: 0.7634 (m90) cc_final: 0.6761 (m90) REVERT: H 110 GLU cc_start: 0.9285 (mm-30) cc_final: 0.8979 (mm-30) REVERT: L 1621 ASN cc_start: 0.7318 (p0) cc_final: 0.6870 (p0) REVERT: O 4 PHE cc_start: 0.8391 (m-10) cc_final: 0.8154 (m-10) REVERT: O 17 VAL cc_start: 0.8461 (m) cc_final: 0.7583 (p) REVERT: O 23 ILE cc_start: 0.9018 (mp) cc_final: 0.8723 (mp) REVERT: O 67 LEU cc_start: 0.8759 (tp) cc_final: 0.8494 (tp) REVERT: M 18 GLU cc_start: 0.6974 (mm-30) cc_final: 0.6717 (mm-30) REVERT: M 42 ARG cc_start: 0.6695 (mtp180) cc_final: 0.6333 (mpp-170) outliers start: 0 outliers final: 0 residues processed: 316 average time/residue: 0.1047 time to fit residues: 47.8558 Evaluate side-chains 259 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 259 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 119 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 0.9980 chunk 99 optimal weight: 10.0000 chunk 59 optimal weight: 0.9990 chunk 100 optimal weight: 10.0000 chunk 55 optimal weight: 8.9990 chunk 27 optimal weight: 8.9990 chunk 122 optimal weight: 1.9990 chunk 66 optimal weight: 5.9990 chunk 60 optimal weight: 3.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 94 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.064713 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.047751 restraints weight = 64531.909| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.049141 restraints weight = 39222.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2859 r_free = 0.2859 target = 0.050110 restraints weight = 28330.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.050703 restraints weight = 22979.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.051149 restraints weight = 20260.601| |-----------------------------------------------------------------------------| r_work (final): 0.2876 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.7100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 14595 Z= 0.178 Angle : 0.676 9.837 20918 Z= 0.383 Chirality : 0.038 0.253 2380 Planarity : 0.005 0.093 1650 Dihedral : 30.120 168.480 4276 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.07 % Favored : 95.62 % Rotamer: Outliers : 0.12 % Allowed : 1.33 % Favored : 98.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.03 (0.26), residues: 958 helix: 0.93 (0.21), residues: 578 sheet: -1.76 (0.70), residues: 44 loop : -1.27 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG K1627 TYR 0.018 0.002 TYR D 37 PHE 0.016 0.002 PHE G 25 HIS 0.005 0.001 HIS H 106 Details of bonding type rmsd covalent geometry : bond 0.00400 (14595) covalent geometry : angle 0.67632 (20918) hydrogen bonds : bond 0.04451 ( 697) hydrogen bonds : angle 3.81692 ( 1766) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 333 time to evaluate : 0.285 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8460 (tp30) cc_final: 0.8136 (mm-30) REVERT: A 56 LYS cc_start: 0.9575 (tptm) cc_final: 0.9258 (ttpt) REVERT: A 57 SER cc_start: 0.9366 (m) cc_final: 0.9010 (m) REVERT: A 76 GLN cc_start: 0.9183 (tt0) cc_final: 0.8804 (pt0) REVERT: A 80 THR cc_start: 0.8891 (p) cc_final: 0.8487 (p) REVERT: A 93 GLN cc_start: 0.8581 (tm-30) cc_final: 0.8285 (tm-30) REVERT: A 94 GLU cc_start: 0.8998 (tt0) cc_final: 0.8715 (tt0) REVERT: A 105 GLU cc_start: 0.8611 (tp30) cc_final: 0.8186 (tm-30) REVERT: A 120 MET cc_start: 0.9007 (ptp) cc_final: 0.8709 (ptp) REVERT: A 130 ILE cc_start: 0.8915 (mp) cc_final: 0.8530 (tp) REVERT: B 30 THR cc_start: 0.9129 (p) cc_final: 0.8857 (t) REVERT: B 84 MET cc_start: 0.8599 (mmt) cc_final: 0.8293 (mmp) REVERT: B 85 ASP cc_start: 0.8928 (m-30) cc_final: 0.8703 (m-30) REVERT: C 39 TYR cc_start: 0.8990 (m-80) cc_final: 0.8542 (m-80) REVERT: C 56 GLU cc_start: 0.8895 (tt0) cc_final: 0.8152 (tt0) REVERT: C 64 GLU cc_start: 0.8901 (tm-30) cc_final: 0.8594 (tp30) REVERT: C 72 ASP cc_start: 0.9404 (m-30) cc_final: 0.9193 (m-30) REVERT: C 78 ILE cc_start: 0.9470 (mm) cc_final: 0.9135 (mm) REVERT: C 79 ILE cc_start: 0.9610 (tt) cc_final: 0.9396 (mm) REVERT: D 56 MET cc_start: 0.8557 (tpp) cc_final: 0.8177 (tpp) REVERT: D 58 ILE cc_start: 0.9686 (mm) cc_final: 0.9452 (mt) REVERT: D 83 ARG cc_start: 0.8641 (mmt-90) cc_final: 0.8254 (mmm-85) REVERT: D 99 LEU cc_start: 0.9489 (mt) cc_final: 0.8928 (tt) REVERT: E 57 SER cc_start: 0.9386 (m) cc_final: 0.9076 (m) REVERT: E 73 GLU cc_start: 0.8924 (tm-30) cc_final: 0.8569 (tm-30) REVERT: E 105 GLU cc_start: 0.9038 (mm-30) cc_final: 0.8815 (tp30) REVERT: E 123 ASP cc_start: 0.8676 (m-30) cc_final: 0.8463 (m-30) REVERT: E 125 GLN cc_start: 0.9553 (mt0) cc_final: 0.8688 (mm-40) REVERT: F 43 VAL cc_start: 0.9375 (t) cc_final: 0.8883 (p) REVERT: F 44 LYS cc_start: 0.9477 (tttt) cc_final: 0.8929 (mtmt) REVERT: F 46 ILE cc_start: 0.9236 (pt) cc_final: 0.8761 (tp) REVERT: F 52 GLU cc_start: 0.8914 (mm-30) cc_final: 0.8673 (tm-30) REVERT: F 88 TYR cc_start: 0.9221 (m-10) cc_final: 0.8798 (m-80) REVERT: G 39 TYR cc_start: 0.9184 (m-80) cc_final: 0.8708 (m-80) REVERT: G 56 GLU cc_start: 0.9128 (tt0) cc_final: 0.8624 (mt-10) REVERT: G 64 GLU cc_start: 0.8953 (tp30) cc_final: 0.8456 (tp30) REVERT: G 72 ASP cc_start: 0.9536 (m-30) cc_final: 0.9139 (m-30) REVERT: G 74 LYS cc_start: 0.9487 (mtmm) cc_final: 0.8454 (tppt) REVERT: G 116 LEU cc_start: 0.9164 (mm) cc_final: 0.8798 (mm) REVERT: H 51 ILE cc_start: 0.8477 (mm) cc_final: 0.8210 (tp) REVERT: H 86 ILE cc_start: 0.9070 (tp) cc_final: 0.8739 (tt) REVERT: H 92 GLN cc_start: 0.9548 (tt0) cc_final: 0.8755 (tp40) REVERT: H 110 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8892 (mm-30) REVERT: O 17 VAL cc_start: 0.8399 (m) cc_final: 0.7612 (p) REVERT: O 23 ILE cc_start: 0.8874 (mp) cc_final: 0.8657 (mp) REVERT: O 42 ARG cc_start: 0.6546 (tpt-90) cc_final: 0.6145 (tpt170) REVERT: M 18 GLU cc_start: 0.7065 (mm-30) cc_final: 0.6824 (mm-30) REVERT: M 45 PHE cc_start: 0.8090 (t80) cc_final: 0.7841 (t80) outliers start: 1 outliers final: 1 residues processed: 333 average time/residue: 0.1064 time to fit residues: 51.9457 Evaluate side-chains 275 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 274 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 74 optimal weight: 0.0670 chunk 87 optimal weight: 10.0000 chunk 62 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 49 optimal weight: 6.9990 chunk 90 optimal weight: 20.0000 chunk 47 optimal weight: 8.9990 chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 20.0000 chunk 83 optimal weight: 10.0000 chunk 38 optimal weight: 9.9990 overall best weight: 3.8126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 81 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 49 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.064177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2779 r_free = 0.2779 target = 0.047304 restraints weight = 63184.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2822 r_free = 0.2822 target = 0.048748 restraints weight = 37433.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.049715 restraints weight = 26540.239| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.050350 restraints weight = 21334.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.050720 restraints weight = 18577.382| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8409 moved from start: 0.7344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14595 Z= 0.202 Angle : 0.687 10.307 20918 Z= 0.388 Chirality : 0.039 0.306 2380 Planarity : 0.005 0.054 1650 Dihedral : 29.956 170.654 4276 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 14.99 Ramachandran Plot: Outliers : 0.31 % Allowed : 4.49 % Favored : 95.20 % Rotamer: Outliers : 0.12 % Allowed : 1.21 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.26), residues: 958 helix: 0.90 (0.21), residues: 580 sheet: -1.66 (0.70), residues: 44 loop : -1.30 (0.32), residues: 334 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG K1627 TYR 0.022 0.002 TYR F 98 PHE 0.018 0.002 PHE G 25 HIS 0.006 0.001 HIS C 82 Details of bonding type rmsd covalent geometry : bond 0.00450 (14595) covalent geometry : angle 0.68688 (20918) hydrogen bonds : bond 0.04641 ( 697) hydrogen bonds : angle 3.87805 ( 1766) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 320 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8507 (tp30) cc_final: 0.8230 (mm-30) REVERT: A 56 LYS cc_start: 0.9575 (tptm) cc_final: 0.9258 (ttpt) REVERT: A 57 SER cc_start: 0.9339 (m) cc_final: 0.9000 (m) REVERT: A 76 GLN cc_start: 0.9183 (tt0) cc_final: 0.8966 (pt0) REVERT: A 80 THR cc_start: 0.8922 (p) cc_final: 0.8534 (p) REVERT: A 93 GLN cc_start: 0.8762 (tm-30) cc_final: 0.8526 (tm-30) REVERT: A 94 GLU cc_start: 0.9178 (tt0) cc_final: 0.8887 (tt0) REVERT: A 105 GLU cc_start: 0.8816 (tp30) cc_final: 0.8315 (tm-30) REVERT: A 120 MET cc_start: 0.8975 (ptp) cc_final: 0.8633 (ptp) REVERT: A 130 ILE cc_start: 0.8826 (mp) cc_final: 0.8418 (tp) REVERT: B 30 THR cc_start: 0.9139 (p) cc_final: 0.8820 (t) REVERT: B 84 MET cc_start: 0.8700 (mmt) cc_final: 0.8373 (mmp) REVERT: C 39 TYR cc_start: 0.9053 (m-80) cc_final: 0.8569 (m-80) REVERT: C 56 GLU cc_start: 0.8980 (tt0) cc_final: 0.8254 (tt0) REVERT: C 64 GLU cc_start: 0.9081 (tm-30) cc_final: 0.8637 (tp30) REVERT: C 72 ASP cc_start: 0.9410 (m-30) cc_final: 0.9191 (m-30) REVERT: D 56 MET cc_start: 0.8648 (tpp) cc_final: 0.8231 (tpp) REVERT: D 58 ILE cc_start: 0.9658 (mm) cc_final: 0.9435 (mt) REVERT: D 83 ARG cc_start: 0.8693 (mmt-90) cc_final: 0.8295 (mmm-85) REVERT: D 99 LEU cc_start: 0.9484 (mt) cc_final: 0.8907 (tt) REVERT: E 57 SER cc_start: 0.9361 (m) cc_final: 0.9093 (m) REVERT: E 73 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8598 (tm-30) REVERT: E 97 GLU cc_start: 0.8685 (mm-30) cc_final: 0.8384 (mm-30) REVERT: E 125 GLN cc_start: 0.9570 (mt0) cc_final: 0.8748 (mm-40) REVERT: F 43 VAL cc_start: 0.9388 (t) cc_final: 0.8879 (p) REVERT: F 44 LYS cc_start: 0.9463 (tttt) cc_final: 0.8890 (mtmt) REVERT: F 46 ILE cc_start: 0.9205 (pt) cc_final: 0.8719 (tp) REVERT: F 52 GLU cc_start: 0.8948 (mm-30) cc_final: 0.8732 (tm-30) REVERT: G 39 TYR cc_start: 0.9220 (m-80) cc_final: 0.8567 (m-80) REVERT: G 56 GLU cc_start: 0.9139 (tt0) cc_final: 0.8644 (tt0) REVERT: G 64 GLU cc_start: 0.8988 (tp30) cc_final: 0.8465 (tp30) REVERT: G 72 ASP cc_start: 0.9549 (m-30) cc_final: 0.9152 (m-30) REVERT: G 74 LYS cc_start: 0.9493 (mtmm) cc_final: 0.8432 (tppt) REVERT: G 116 LEU cc_start: 0.9162 (mm) cc_final: 0.8841 (mm) REVERT: H 51 ILE cc_start: 0.8483 (mm) cc_final: 0.8250 (tp) REVERT: H 110 GLU cc_start: 0.9244 (mm-30) cc_final: 0.8885 (mm-30) REVERT: L 1621 ASN cc_start: 0.6634 (p0) cc_final: 0.5874 (t0) REVERT: O 4 PHE cc_start: 0.8449 (m-10) cc_final: 0.8211 (m-10) REVERT: O 17 VAL cc_start: 0.8328 (m) cc_final: 0.7678 (p) REVERT: O 23 ILE cc_start: 0.8866 (mp) cc_final: 0.8658 (mp) REVERT: O 42 ARG cc_start: 0.6444 (tpt-90) cc_final: 0.6079 (tpt170) REVERT: M 18 GLU cc_start: 0.7107 (mm-30) cc_final: 0.6875 (mm-30) REVERT: M 23 ILE cc_start: 0.8765 (mm) cc_final: 0.8554 (mm) outliers start: 1 outliers final: 0 residues processed: 320 average time/residue: 0.1116 time to fit residues: 52.0155 Evaluate side-chains 267 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 267 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 80 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 chunk 64 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 94 optimal weight: 10.0000 chunk 46 optimal weight: 7.9990 chunk 118 optimal weight: 0.7980 chunk 87 optimal weight: 10.0000 chunk 2 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 overall best weight: 4.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 68 GLN C 38 ASN C 94 ASN D 106 HIS E 68 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.063642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.046836 restraints weight = 63331.947| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.048376 restraints weight = 36498.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.049389 restraints weight = 25351.340| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.050066 restraints weight = 20065.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.050500 restraints weight = 17300.464| |-----------------------------------------------------------------------------| r_work (final): 0.2864 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.7608 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 14595 Z= 0.214 Angle : 0.700 10.636 20918 Z= 0.395 Chirality : 0.039 0.247 2380 Planarity : 0.005 0.062 1650 Dihedral : 29.889 172.949 4276 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.31 % Allowed : 5.01 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 0.72 % Favored : 99.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.26), residues: 958 helix: 0.81 (0.21), residues: 582 sheet: -1.55 (0.72), residues: 44 loop : -1.31 (0.32), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 72 TYR 0.034 0.003 TYR B 98 PHE 0.015 0.002 PHE G 25 HIS 0.014 0.002 HIS D 106 Details of bonding type rmsd covalent geometry : bond 0.00477 (14595) covalent geometry : angle 0.69979 (20918) hydrogen bonds : bond 0.04643 ( 697) hydrogen bonds : angle 3.97595 ( 1766) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1916 Ramachandran restraints generated. 958 Oldfield, 0 Emsley, 958 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 327 time to evaluate : 0.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 39 HIS cc_start: 0.7052 (t-90) cc_final: 0.6783 (t70) REVERT: A 50 GLU cc_start: 0.8562 (tp30) cc_final: 0.8237 (mm-30) REVERT: A 56 LYS cc_start: 0.9562 (tptm) cc_final: 0.9230 (ttpt) REVERT: A 57 SER cc_start: 0.9287 (m) cc_final: 0.8981 (m) REVERT: A 76 GLN cc_start: 0.9275 (tt0) cc_final: 0.8688 (pt0) REVERT: A 81 ASP cc_start: 0.8778 (p0) cc_final: 0.8529 (p0) REVERT: A 93 GLN cc_start: 0.8682 (tm-30) cc_final: 0.8386 (tm-30) REVERT: A 94 GLU cc_start: 0.9108 (tt0) cc_final: 0.8724 (tt0) REVERT: A 130 ILE cc_start: 0.8838 (mp) cc_final: 0.8536 (tp) REVERT: B 30 THR cc_start: 0.9188 (p) cc_final: 0.8881 (t) REVERT: B 44 LYS cc_start: 0.9578 (mtpp) cc_final: 0.9188 (mttt) REVERT: B 85 ASP cc_start: 0.8845 (m-30) cc_final: 0.8589 (m-30) REVERT: C 39 TYR cc_start: 0.9192 (m-80) cc_final: 0.8712 (m-80) REVERT: C 56 GLU cc_start: 0.9015 (tt0) cc_final: 0.8130 (tt0) REVERT: C 64 GLU cc_start: 0.9036 (tm-30) cc_final: 0.8711 (tp30) REVERT: C 72 ASP cc_start: 0.9415 (m-30) cc_final: 0.9193 (m-30) REVERT: C 78 ILE cc_start: 0.9452 (mm) cc_final: 0.9159 (mm) REVERT: D 56 MET cc_start: 0.8673 (tpp) cc_final: 0.8242 (tpp) REVERT: D 83 ARG cc_start: 0.8747 (mmt-90) cc_final: 0.8382 (mmm-85) REVERT: D 99 LEU cc_start: 0.9520 (mt) cc_final: 0.8939 (tt) REVERT: E 57 SER cc_start: 0.9395 (m) cc_final: 0.9109 (m) REVERT: E 73 GLU cc_start: 0.9008 (tm-30) cc_final: 0.8682 (tm-30) REVERT: E 125 GLN cc_start: 0.9500 (mt0) cc_final: 0.8614 (mm-40) REVERT: F 43 VAL cc_start: 0.9407 (t) cc_final: 0.8913 (p) REVERT: F 44 LYS cc_start: 0.9437 (tttt) cc_final: 0.8816 (mtmt) REVERT: F 46 ILE cc_start: 0.9239 (pt) cc_final: 0.8661 (tp) REVERT: G 39 TYR cc_start: 0.9125 (m-80) cc_final: 0.8761 (m-80) REVERT: G 56 GLU cc_start: 0.9176 (tt0) cc_final: 0.8697 (tt0) REVERT: G 64 GLU cc_start: 0.9028 (tp30) cc_final: 0.8525 (tp30) REVERT: G 72 ASP cc_start: 0.9536 (m-30) cc_final: 0.9176 (m-30) REVERT: G 74 LYS cc_start: 0.9498 (mtmm) cc_final: 0.8383 (tppt) REVERT: H 54 LYS cc_start: 0.9597 (mmmm) cc_final: 0.9315 (mmmm) REVERT: H 92 GLN cc_start: 0.9430 (tt0) cc_final: 0.8377 (tp40) REVERT: H 110 GLU cc_start: 0.9269 (mm-30) cc_final: 0.8915 (mm-30) REVERT: L 1621 ASN cc_start: 0.6992 (p0) cc_final: 0.6525 (p0) REVERT: O 17 VAL cc_start: 0.8348 (m) cc_final: 0.7685 (p) REVERT: O 23 ILE cc_start: 0.8910 (mp) cc_final: 0.8617 (mp) REVERT: O 24 GLU cc_start: 0.8489 (pm20) cc_final: 0.8065 (pm20) REVERT: O 42 ARG cc_start: 0.6531 (tpt-90) cc_final: 0.6163 (tpt170) REVERT: O 67 LEU cc_start: 0.8760 (tp) cc_final: 0.8414 (tp) REVERT: M 52 ASP cc_start: 0.7887 (m-30) cc_final: 0.7586 (m-30) outliers start: 1 outliers final: 1 residues processed: 327 average time/residue: 0.1098 time to fit residues: 52.4505 Evaluate side-chains 264 residues out of total 829 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 263 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 87 optimal weight: 10.0000 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 0.0060 chunk 17 optimal weight: 3.9990 chunk 3 optimal weight: 6.9990 chunk 102 optimal weight: 10.0000 chunk 41 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.8000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS C 94 ASN D 81 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 94 ASN O 2 GLN ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 49 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.065128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.048476 restraints weight = 62703.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.049936 restraints weight = 36628.808| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.050920 restraints weight = 25857.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.051592 restraints weight = 20684.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.051996 restraints weight = 17904.972| |-----------------------------------------------------------------------------| r_work (final): 0.2911 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 moved from start: 0.7843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 14595 Z= 0.168 Angle : 0.691 8.785 20918 Z= 0.385 Chirality : 0.038 0.222 2380 Planarity : 0.005 0.066 1650 Dihedral : 29.796 174.984 4276 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.21 % Allowed : 5.11 % Favored : 94.68 % Rotamer: Outliers : 0.12 % Allowed : 0.36 % Favored : 99.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.09 (0.26), residues: 958 helix: 0.80 (0.21), residues: 583 sheet: -1.43 (0.73), residues: 44 loop : -1.34 (0.32), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 92 TYR 0.029 0.003 TYR B 98 PHE 0.016 0.002 PHE G 25 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00372 (14595) covalent geometry : angle 0.69081 (20918) hydrogen bonds : bond 0.04308 ( 697) hydrogen bonds : angle 3.79290 ( 1766) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2080.69 seconds wall clock time: 36 minutes 44.73 seconds (2204.73 seconds total)