Starting phenix.real_space_refine on Fri Aug 7 11:27:06 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ruq_19514/08_2026/8ruq_19514.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ruq_19514/08_2026/8ruq_19514.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8ruq_19514/08_2026/8ruq_19514.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ruq_19514/08_2026/8ruq_19514.map" model { file = "/net/cci-nas-00/data/ceres_data/8ruq_19514/08_2026/8ruq_19514.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ruq_19514/08_2026/8ruq_19514.cif" } resolution = 2.29 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= 0.004 sd= 0.040 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 35 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians P 293 5.49 5 S 12 5.16 5 C 6715 2.51 5 N 2289 2.21 5 O 2838 1.98 5 H 9671 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 21818 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 1634 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1634 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1303 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "C" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1676 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 1472 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1472 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "E" Number of atoms: 1622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 1622 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'ASP:plan': 2, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "F" Number of atoms: 1303 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 1303 Classifications: {'peptide': 80} Link IDs: {'PTRANS': 1, 'TRANS': 78} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "G" Number of atoms: 1691 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1691 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 11 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "H" Number of atoms: 1444 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 1444 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 23 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 21 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "I" Number of atoms: 4679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4679 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4632 Classifications: {'DNA': 147} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 146} Chain: "L" Number of atoms: 362 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 362 Classifications: {'peptide': 22} Link IDs: {'PTRANS': 1, 'TRANS': 20} Time building chain proxies: 3.19, per 1000 atoms: 0.15 Number of scatterers: 21818 At special positions: 0 Unit cell: (78.02, 129.48, 123.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 12 16.00 P 293 15.00 O 2838 8.00 N 2289 7.00 C 6715 6.00 H 9671 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 371.4 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1474 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 10 sheets defined 72.1% alpha, 3.1% beta 147 base pairs and 267 stacking pairs defined. Time for finding SS restraints: 3.74 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.518A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.702A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.537A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.978A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.558A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.623A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.501A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.939A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.679A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 104 through 124 removed outlier: 3.665A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 9 through 23 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.009A 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 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.176A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.767A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.913A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.158A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 413 hydrogen bonds defined for protein. 1212 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 377 hydrogen bonds 754 hydrogen bond angles 0 basepair planarities 147 basepair parallelities 267 stacking parallelities Total time for adding SS restraints: 4.82 Time building geometry restraints manager: 2.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 9669 1.03 - 1.22: 108 1.22 - 1.42: 5673 1.42 - 1.61: 7158 1.61 - 1.80: 23 Bond restraints: 22631 Sorted by residual: bond pdb=" C3' DC I 33 " pdb=" C2' DC I 33 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 bond pdb=" C3' DC I 143 " pdb=" C2' DC I 143 " ideal model delta sigma weight residual 1.516 1.539 -0.023 8.00e-03 1.56e+04 8.49e+00 bond pdb=" C1' DT J 263 " pdb=" N1 DT J 263 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.35e+00 bond pdb=" C1' DT I 140 " pdb=" N1 DT I 140 " ideal model delta sigma weight residual 1.468 1.508 -0.040 1.40e-02 5.10e+03 8.10e+00 bond pdb=" C3' DC J 238 " pdb=" C2' DC J 238 " ideal model delta sigma weight residual 1.516 1.538 -0.022 8.00e-03 1.56e+04 7.59e+00 ... (remaining 22626 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.23: 36798 1.23 - 2.46: 3718 2.46 - 3.69: 462 3.69 - 4.91: 16 4.91 - 6.14: 2 Bond angle restraints: 40996 Sorted by residual: angle pdb=" N3 DT I 49 " pdb=" C4 DT I 49 " pdb=" O4 DT I 49 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I 23 " pdb=" C4 DT I 23 " pdb=" O4 DT I 23 " ideal model delta sigma weight residual 119.90 122.60 -2.70 6.00e-01 2.78e+00 2.02e+01 angle pdb=" N3 DT J 258 " pdb=" C4 DT J 258 " pdb=" O4 DT J 258 " ideal model delta sigma weight residual 119.90 122.58 -2.68 6.00e-01 2.78e+00 1.99e+01 angle pdb=" N3 DT J 178 " pdb=" C4 DT J 178 " pdb=" O4 DT J 178 " ideal model delta sigma weight residual 119.90 122.57 -2.67 6.00e-01 2.78e+00 1.97e+01 angle pdb=" N3 DT J 254 " pdb=" C4 DT J 254 " pdb=" O4 DT J 254 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.86e+01 ... (remaining 40991 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.88: 7681 33.88 - 67.75: 1712 67.75 - 101.63: 20 101.63 - 135.50: 0 135.50 - 169.38: 1 Dihedral angle restraints: 9414 sinusoidal: 6877 harmonic: 2537 Sorted by residual: dihedral pdb=" C4' DG I 36 " pdb=" C3' DG I 36 " pdb=" O3' DG I 36 " pdb=" P DG I 37 " ideal model delta sinusoidal sigma weight residual 220.00 50.62 169.38 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" CG ARG A 52 " pdb=" CD ARG A 52 " pdb=" NE ARG A 52 " pdb=" CZ ARG A 52 " ideal model delta sinusoidal sigma weight residual 180.00 136.33 43.67 2 1.50e+01 4.44e-03 1.02e+01 dihedral pdb=" CB GLU H 76 " pdb=" CG GLU H 76 " pdb=" CD GLU H 76 " pdb=" OE1 GLU H 76 " ideal model delta sinusoidal sigma weight residual 0.00 85.31 -85.31 1 3.00e+01 1.11e-03 9.79e+00 ... (remaining 9411 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1490 0.038 - 0.076: 313 0.076 - 0.114: 89 0.114 - 0.152: 198 0.152 - 0.190: 62 Chirality restraints: 2152 Sorted by residual: chirality pdb=" C3' DA J 206 " pdb=" C4' DA J 206 " pdb=" O3' DA J 206 " pdb=" C2' DA J 206 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 9.07e-01 chirality pdb=" C3' DG I 52 " pdb=" C4' DG I 52 " pdb=" O3' DG I 52 " pdb=" C2' DG I 52 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.76e-01 chirality pdb=" C3' DC I 21 " pdb=" C4' DC I 21 " pdb=" O3' DC I 21 " pdb=" C2' DC I 21 " both_signs ideal model delta sigma weight residual False -2.73 -2.54 -0.19 2.00e-01 2.50e+01 8.75e-01 ... (remaining 2149 not shown) Planarity restraints: 2337 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I 87 " 0.025 2.00e-02 2.50e+03 1.06e-02 3.38e+00 pdb=" N1 DT I 87 " -0.025 2.00e-02 2.50e+03 pdb=" C2 DT I 87 " -0.004 2.00e-02 2.50e+03 pdb=" O2 DT I 87 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DT I 87 " 0.000 2.00e-02 2.50e+03 pdb=" C4 DT I 87 " 0.001 2.00e-02 2.50e+03 pdb=" O4 DT I 87 " 0.006 2.00e-02 2.50e+03 pdb=" C5 DT I 87 " 0.001 2.00e-02 2.50e+03 pdb=" C7 DT I 87 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DT I 87 " -0.002 2.00e-02 2.50e+03 pdb=" H3 DT I 87 " 0.003 2.00e-02 2.50e+03 pdb=" H6 DT I 87 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 120 " -0.025 2.00e-02 2.50e+03 1.01e-02 3.30e+00 pdb=" N9 DA I 120 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" N7 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" C5 DA I 120 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 120 " -0.003 2.00e-02 2.50e+03 pdb=" N6 DA I 120 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I 120 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 120 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I 120 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 120 " 0.002 2.00e-02 2.50e+03 pdb=" H8 DA I 120 " 0.000 2.00e-02 2.50e+03 pdb=" H2 DA I 120 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I 99 " -0.024 2.00e-02 2.50e+03 9.94e-03 3.21e+00 pdb=" N9 DA I 99 " 0.025 2.00e-02 2.50e+03 pdb=" C8 DA I 99 " 0.001 2.00e-02 2.50e+03 pdb=" N7 DA I 99 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I 99 " -0.000 2.00e-02 2.50e+03 pdb=" C6 DA I 99 " -0.004 2.00e-02 2.50e+03 pdb=" N6 DA I 99 " -0.006 2.00e-02 2.50e+03 pdb=" N1 DA I 99 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I 99 " 0.000 2.00e-02 2.50e+03 pdb=" N3 DA I 99 " 0.003 2.00e-02 2.50e+03 pdb=" C4 DA I 99 " 0.002 2.00e-02 2.50e+03 pdb=" H8 DA I 99 " 0.001 2.00e-02 2.50e+03 pdb=" H2 DA I 99 " 0.003 2.00e-02 2.50e+03 ... (remaining 2334 not shown) Histogram of nonbonded interaction distances: 1.41 - 2.05: 195 2.05 - 2.69: 27770 2.69 - 3.33: 56544 3.33 - 3.96: 80966 3.96 - 4.60: 124126 Nonbonded interactions: 289601 Sorted by model distance: nonbonded pdb=" OE1 GLU G 91 " pdb=" H GLU G 91 " model vdw 1.413 2.450 nonbonded pdb=" OE1 GLU A 59 " pdb=" H GLU A 59 " model vdw 1.503 2.450 nonbonded pdb=" OE1 GLU E 59 " pdb=" H GLU E 59 " model vdw 1.665 2.450 nonbonded pdb=" OE1 GLU G 92 " pdb="HH11 ARG L 9 " model vdw 1.666 2.450 nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.699 2.450 ... (remaining 289596 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 37 and (name N or name CA or name C or name O or name CB \ or name HA )) or resid 38 through 76 or (resid 77 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 78 through 80 or (resid \ 81 and (name N or name CA or name C or name O or name CB or name H or name HA ) \ ) or resid 82 through 134)) selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 11 through 40 or (resid 41 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 42 through 118)) selection = (chain 'G' and (resid 11 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 75 through 90 or (resid \ 91 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 92 through 118)) } ncs_group { reference = (chain 'D' and (resid 31 through 50 or (resid 51 and (name N or name CA or name \ C or name O or name CB or name H or name HA )) or resid 52 through 56 or (resid \ 57 and (name N or name CA or name C or name O or name CB or name H or name HA )) \ or resid 58 through 70 or (resid 71 and (name N or name CA or name C or name O \ or name CB or name H or name HA )) or resid 72 through 125)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.110 Extract box with map and model: 0.270 Check model and map are aligned: 0.050 Set scattering table: 0.020 Process input model: 22.460 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.070 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:6.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8804 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 : 0.006 0.040 12960 Z= 0.535 Angle : 0.760 6.142 18779 Z= 0.664 Chirality : 0.059 0.190 2152 Planarity : 0.004 0.041 1358 Dihedral : 28.426 169.376 5559 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer: Outliers : 0.64 % Allowed : 16.88 % Favored : 82.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.96 (0.30), residues: 766 helix: 2.97 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.008 0.001 TYR B 51 PHE 0.007 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00619 / 0.54 (12960) covalent geometry : angle 0.75986 / 0.66 (18779) hydrogen bonds : bond 0.10466 / 7.09 ( 790) hydrogen bonds : angle 3.38092 / 2.42 ( 1966) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.599 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 80 average time/residue: 1.8083 time to fit residues: 152.9822 Evaluate side-chains 77 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 73 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 SER Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 49 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 49 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.054968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.043139 restraints weight = 78002.023| |-----------------------------------------------------------------------------| r_work (start): 0.2813 rms_B_bonded: 1.28 r_work: 0.2638 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2516 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8887 moved from start: 0.0420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 12960 Z= 0.180 Angle : 0.609 6.695 18779 Z= 0.387 Chirality : 0.039 0.259 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.766 172.693 4085 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 2.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 0.96 % Allowed : 16.72 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.93 (0.30), residues: 766 helix: 2.91 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.008 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00313 / 0.18 (12960) covalent geometry : angle 0.60897 / 0.39 (18779) hydrogen bonds : bond 0.05864 / 4.01 ( 790) hydrogen bonds : angle 3.10808 / 2.17 ( 1966) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.461 Fit side-chains REVERT: C 95 LYS cc_start: 0.9397 (OUTLIER) cc_final: 0.9100 (ttpt) outliers start: 6 outliers final: 3 residues processed: 82 average time/residue: 1.7109 time to fit residues: 148.4156 Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 75 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 94 optimal weight: 6.9990 chunk 29 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 93 optimal weight: 7.9990 chunk 83 optimal weight: 7.9990 chunk 65 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.055347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.043269 restraints weight = 77871.478| |-----------------------------------------------------------------------------| r_work (start): 0.2816 rms_B_bonded: 1.31 r_work: 0.2640 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2519 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.2519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8906 moved from start: 0.0544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 12960 Z= 0.185 Angle : 0.591 7.023 18779 Z= 0.377 Chirality : 0.038 0.264 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.853 171.928 4083 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 2.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.80 % Allowed : 15.61 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.98 (0.30), residues: 766 helix: 2.95 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.87 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.008 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00332 / 0.19 (12960) covalent geometry : angle 0.59101 / 0.38 (18779) hydrogen bonds : bond 0.05573 / 3.81 ( 790) hydrogen bonds : angle 2.99680 / 2.10 ( 1966) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.487 Fit side-chains REVERT: C 95 LYS cc_start: 0.9408 (OUTLIER) cc_final: 0.9119 (ttpt) outliers start: 5 outliers final: 4 residues processed: 80 average time/residue: 1.8221 time to fit residues: 154.3143 Evaluate side-chains 79 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 74 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 93 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 99 optimal weight: 10.0000 chunk 58 optimal weight: 3.9990 chunk 52 optimal weight: 1.9990 chunk 90 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.054706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2835 r_free = 0.2835 target = 0.042548 restraints weight = 77507.965| |-----------------------------------------------------------------------------| r_work (start): 0.2798 rms_B_bonded: 1.27 r_work: 0.2620 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.2495 rms_B_bonded: 3.93 restraints_weight: 0.2500 r_work (final): 0.2495 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 12960 Z= 0.231 Angle : 0.619 7.836 18779 Z= 0.385 Chirality : 0.040 0.268 2152 Planarity : 0.004 0.045 1358 Dihedral : 30.913 172.443 4083 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.11 % Allowed : 15.29 % Favored : 83.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.95 (0.30), residues: 766 helix: 2.95 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.97 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00453 / 0.23 (12960) covalent geometry : angle 0.61925 / 0.38 (18779) hydrogen bonds : bond 0.06103 / 4.19 ( 790) hydrogen bonds : angle 3.00400 / 2.11 ( 1966) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.488 Fit side-chains REVERT: A 131 ARG cc_start: 0.9234 (OUTLIER) cc_final: 0.8369 (mtp85) REVERT: C 95 LYS cc_start: 0.9395 (OUTLIER) cc_final: 0.9095 (ttpt) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 1.9021 time to fit residues: 158.8692 Evaluate side-chains 78 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 79 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 100 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 73 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.054763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2834 r_free = 0.2834 target = 0.042543 restraints weight = 77290.194| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.29 r_work: 0.2621 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2497 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2497 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 12960 Z= 0.218 Angle : 0.621 8.574 18779 Z= 0.385 Chirality : 0.040 0.266 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.929 172.486 4083 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.27 % Allowed : 15.61 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.93 (0.30), residues: 766 helix: 2.94 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.97 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.007 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00424 / 0.22 (12960) covalent geometry : angle 0.62057 / 0.38 (18779) hydrogen bonds : bond 0.05981 / 4.10 ( 790) hydrogen bonds : angle 3.02038 / 2.12 ( 1966) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.491 Fit side-chains REVERT: A 131 ARG cc_start: 0.9237 (OUTLIER) cc_final: 0.8408 (mtp85) REVERT: C 95 LYS cc_start: 0.9394 (OUTLIER) cc_final: 0.9095 (ttpt) outliers start: 8 outliers final: 5 residues processed: 81 average time/residue: 1.7020 time to fit residues: 145.9867 Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 73 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 85 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 74 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 53 optimal weight: 4.9990 chunk 71 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.042825 restraints weight = 77854.301| |-----------------------------------------------------------------------------| r_work (start): 0.2804 rms_B_bonded: 1.29 r_work: 0.2626 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 12960 Z= 0.178 Angle : 0.614 8.136 18779 Z= 0.382 Chirality : 0.039 0.263 2152 Planarity : 0.004 0.040 1358 Dihedral : 30.934 172.238 4083 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.96 % Allowed : 16.24 % Favored : 82.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.91 (0.30), residues: 766 helix: 2.92 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.97 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00318 / 0.18 (12960) covalent geometry : angle 0.61364 / 0.38 (18779) hydrogen bonds : bond 0.05797 / 3.98 ( 790) hydrogen bonds : angle 3.00995 / 2.11 ( 1966) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.480 Fit side-chains REVERT: A 131 ARG cc_start: 0.9232 (OUTLIER) cc_final: 0.8402 (mtp85) REVERT: C 95 LYS cc_start: 0.9396 (OUTLIER) cc_final: 0.9098 (ttpt) outliers start: 6 outliers final: 4 residues processed: 78 average time/residue: 1.6665 time to fit residues: 137.3526 Evaluate side-chains 80 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 6.9990 chunk 85 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 90 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 24 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 77 optimal weight: 7.9990 overall best weight: 1.8586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.054923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.042852 restraints weight = 77726.144| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 1.28 r_work: 0.2627 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2503 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.2503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8894 moved from start: 0.0650 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 12960 Z= 0.193 Angle : 0.610 7.755 18779 Z= 0.380 Chirality : 0.039 0.263 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.940 172.352 4083 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.93 (0.30), residues: 766 helix: 2.93 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.96 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.19 (12960) covalent geometry : angle 0.60952 / 0.38 (18779) hydrogen bonds : bond 0.05773 / 3.96 ( 790) hydrogen bonds : angle 3.00760 / 2.11 ( 1966) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.466 Fit side-chains REVERT: A 131 ARG cc_start: 0.9233 (OUTLIER) cc_final: 0.8422 (mtp85) REVERT: C 95 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9100 (ttpt) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 1.7595 time to fit residues: 146.8847 Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 100 optimal weight: 5.9990 chunk 58 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 79 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 78 optimal weight: 6.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.055001 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.042959 restraints weight = 77694.709| |-----------------------------------------------------------------------------| r_work (start): 0.2808 rms_B_bonded: 1.28 r_work: 0.2631 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2508 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.2508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8892 moved from start: 0.0672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 12960 Z= 0.170 Angle : 0.607 7.666 18779 Z= 0.379 Chirality : 0.038 0.261 2152 Planarity : 0.004 0.040 1358 Dihedral : 30.942 172.209 4083 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 2.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.92 (0.30), residues: 766 helix: 2.93 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.95 (0.36), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 (12960) covalent geometry : angle 0.60658 / 0.38 (18779) hydrogen bonds : bond 0.05659 / 3.88 ( 790) hydrogen bonds : angle 3.00818 / 2.12 ( 1966) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 82 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.460 Fit side-chains REVERT: A 131 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8437 (mtp85) REVERT: C 95 LYS cc_start: 0.9398 (OUTLIER) cc_final: 0.9099 (ttpt) outliers start: 7 outliers final: 5 residues processed: 80 average time/residue: 1.6848 time to fit residues: 142.4512 Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 38 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 65 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 55 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.054907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.042734 restraints weight = 78861.179| |-----------------------------------------------------------------------------| r_work (start): 0.2796 rms_B_bonded: 1.28 r_work: 0.2619 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2499 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8898 moved from start: 0.0695 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 12960 Z= 0.201 Angle : 0.603 7.642 18779 Z= 0.377 Chirality : 0.039 0.266 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.977 172.225 4083 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 1.11 % Allowed : 15.76 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.99 (0.30), residues: 766 helix: 2.98 (0.22), residues: 556 sheet: None (None), residues: 0 loop : -0.95 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.007 0.001 PHE F 61 HIS 0.002 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (12960) covalent geometry : angle 0.60285 / 0.38 (18779) hydrogen bonds : bond 0.05630 / 3.86 ( 790) hydrogen bonds : angle 2.97302 / 2.09 ( 1966) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.411 Fit side-chains REVERT: A 131 ARG cc_start: 0.9241 (OUTLIER) cc_final: 0.8405 (mtp85) REVERT: C 95 LYS cc_start: 0.9414 (OUTLIER) cc_final: 0.9122 (ttpt) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 1.6713 time to fit residues: 139.4950 Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.560 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 99 optimal weight: 10.0000 chunk 75 optimal weight: 8.9990 chunk 82 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 39 optimal weight: 0.4980 chunk 64 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 68 optimal weight: 0.9990 overall best weight: 1.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042902 restraints weight = 78901.881| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.28 r_work: 0.2624 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2502 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.2502 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 12960 Z= 0.173 Angle : 0.603 8.003 18779 Z= 0.376 Chirality : 0.038 0.264 2152 Planarity : 0.004 0.041 1358 Dihedral : 30.982 171.973 4083 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 2.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.98 (0.30), residues: 766 helix: 2.97 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12960) covalent geometry : angle 0.60294 / 0.38 (18779) hydrogen bonds : bond 0.05518 / 3.78 ( 790) hydrogen bonds : angle 2.97074 / 2.09 ( 1966) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 74 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 37 is missing expected H atoms. Skipping. Residue LYS 13 is missing expected H atoms. Skipping. Residue LYS 31 is missing expected H atoms. Skipping. Residue LYS 34 is missing expected H atoms. Skipping. Residue LYS 57 is missing expected H atoms. Skipping. Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.452 Fit side-chains REVERT: A 131 ARG cc_start: 0.9236 (OUTLIER) cc_final: 0.8417 (mtp85) REVERT: C 95 LYS cc_start: 0.9415 (OUTLIER) cc_final: 0.9121 (ttpt) outliers start: 7 outliers final: 5 residues processed: 79 average time/residue: 1.7383 time to fit residues: 145.0960 Evaluate side-chains 81 residues out of total 654 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 74 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 131 ARG Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain L residue 8 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 27 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 95 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 13 optimal weight: 2.9990 chunk 93 optimal weight: 7.9990 chunk 14 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 91 optimal weight: 7.9990 chunk 6 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.055034 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2849 r_free = 0.2849 target = 0.042867 restraints weight = 78286.619| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 1.28 r_work: 0.2624 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2505 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.2505 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8895 moved from start: 0.0702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 12960 Z= 0.184 Angle : 0.601 8.511 18779 Z= 0.375 Chirality : 0.038 0.263 2152 Planarity : 0.004 0.042 1358 Dihedral : 30.984 172.072 4083 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 2.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 1.11 % Allowed : 15.92 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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 are not related in a simple way. whole: 2.99 (0.30), residues: 766 helix: 2.98 (0.21), residues: 556 sheet: None (None), residues: 0 loop : -0.94 (0.35), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.009 0.001 TYR B 51 PHE 0.006 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00338 / 0.18 (12960) covalent geometry : angle 0.60121 / 0.38 (18779) hydrogen bonds : bond 0.05511 / 3.77 ( 790) hydrogen bonds : angle 2.96770 / 2.09 ( 1966) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7732.07 seconds wall clock time: 131 minutes 12.60 seconds (7872.60 seconds total)