Starting phenix.real_space_refine on Thu Aug 6 07:54:11 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.cif" model { file = "/net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sna_40618/08_2026/8sna_40618.map" } resolution = 4.0 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= 0.000 sd= 0.003 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8264 2.51 5 N 2710 2.21 5 O 3288 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 21 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: 14591 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 682 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 52.091 72.096 45.471 1.00130.70 S ATOM 12446 SG CYS K 51 50.512 68.670 45.375 1.00137.26 S ATOM 12470 SG CYS K 54 52.924 69.743 42.642 1.00135.51 S ATOM 12187 SG CYS K 16 41.580 66.180 52.218 1.00144.97 S ATOM 12205 SG CYS K 19 40.762 63.036 54.186 1.00143.14 S ATOM 12335 SG CYS K 36 43.515 65.426 55.432 1.00132.02 S ATOM 12357 SG CYS K 39 43.985 63.037 52.593 1.00138.90 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 2.97, per 1000 atoms: 0.20 Number of scatterers: 14591 At special positions: 0 Unit cell: (128.816, 130.144, 124.832, 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) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3288 8.00 N 2710 7.00 C 8264 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 Number of custom bonds: simple=0, symmetry=0 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 1.10 Conformation dependent library (CDL) restraints added in 496.8 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2026 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 62.7% alpha, 5.4% beta 135 base pairs and 239 stacking pairs defined. Time for finding SS restraints: 1.76 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.593A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.561A pdb=" N ARG A 131 " --> pdb=" O ALA A 127 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.868A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.106A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.647A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.614A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 removed outlier: 3.613A pdb=" N LYS C 95 " --> pdb=" O GLU C 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.558A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.716A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.716A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.647A 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 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.936A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.721A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.526A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 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 removed outlier: 3.635A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.530A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.695A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 Processing helix chain 'K' and resid 58 through 68 removed outlier: 3.533A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 4.279A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.596A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.582A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 3.884A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) 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 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.796A 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 'B' and resid 96 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.784A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.362A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.520A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.559A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 499 hydrogen bonds defined for protein. 1462 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 239 stacking parallelities Total time for adding SS restraints: 2.13 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3554 1.34 - 1.46: 4330 1.46 - 1.58: 6943 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15462 Sorted by residual: bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.516 1.547 -0.031 8.00e-03 1.56e+04 1.49e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.09e+01 bond pdb=" C3' DG I -41 " pdb=" C2' DG I -41 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.01e+01 ... (remaining 15457 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.99: 21368 1.99 - 3.98: 758 3.98 - 5.97: 27 5.97 - 7.96: 1 7.96 - 9.95: 2 Bond angle restraints: 22156 Sorted by residual: angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 102.76 3.24 6.00e-01 2.78e+00 2.91e+01 angle pdb=" O4' DC J -71 " pdb=" C4' DC J -71 " pdb=" C3' DC J -71 " ideal model delta sigma weight residual 106.00 103.22 2.78 6.00e-01 2.78e+00 2.14e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.66 -2.76 6.00e-01 2.78e+00 2.11e+01 angle pdb=" O4' DA I -35 " pdb=" C4' DA I -35 " pdb=" C3' DA I -35 " ideal model delta sigma weight residual 106.00 103.32 2.68 6.00e-01 2.78e+00 2.00e+01 angle pdb=" N3 DT J 31 " pdb=" C4 DT J 31 " pdb=" O4 DT J 31 " ideal model delta sigma weight residual 119.90 122.55 -2.65 6.00e-01 2.78e+00 1.95e+01 ... (remaining 22151 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.45: 7269 35.45 - 70.90: 1314 70.90 - 106.36: 17 106.36 - 141.81: 0 141.81 - 177.26: 2 Dihedral angle restraints: 8602 sinusoidal: 5466 harmonic: 3136 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 37.26 -177.26 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 72.91 147.09 1 3.50e+01 8.16e-04 1.44e+01 dihedral pdb=" CG ARG A 128 " pdb=" CD ARG A 128 " pdb=" NE ARG A 128 " pdb=" CZ ARG A 128 " ideal model delta sinusoidal sigma weight residual -90.00 -133.54 43.54 2 1.50e+01 4.44e-03 1.01e+01 ... (remaining 8599 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1435 0.031 - 0.061: 684 0.061 - 0.092: 237 0.092 - 0.123: 146 0.123 - 0.153: 12 Chirality restraints: 2514 Sorted by residual: chirality pdb=" C3' DG J -70 " pdb=" C4' DG J -70 " pdb=" O3' DG J -70 " pdb=" C2' DG J -70 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" C3' DT J -17 " pdb=" C4' DT J -17 " pdb=" O3' DT J -17 " pdb=" C2' DT J -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.76e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.74e-01 ... (remaining 2511 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " -0.025 2.00e-02 2.50e+03 1.05e-02 3.33e+00 pdb=" N9 DG I 47 " 0.023 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " -0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " 0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.024 2.00e-02 2.50e+03 1.02e-02 2.84e+00 pdb=" N9 DA I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.026 5.00e-02 4.00e+02 4.00e-02 2.56e+00 pdb=" N PRO G 80 " 0.069 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.020 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.022 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 414 2.68 - 3.24: 13010 3.24 - 3.79: 26178 3.79 - 4.35: 32343 4.35 - 4.90: 47562 Nonbonded interactions: 119507 Sorted by model distance: nonbonded pdb=" OE2 GLU K 45 " pdb=" NZ LYS K 46 " model vdw 2.125 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.138 2.496 nonbonded pdb=" OE2 GLU C 61 " pdb=" NH1 ARG K 63 " model vdw 2.194 3.120 nonbonded pdb=" OH TYR A 99 " pdb=" OE1 GLU A 133 " model vdw 2.204 3.040 nonbonded pdb=" O PRO L 40 " pdb=" OG SER L 43 " model vdw 2.222 3.040 ... (remaining 119502 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' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.25 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: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.160 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 15.300 Find NCS groups from input model: 0.180 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8574 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 0.034 15472 Z= 0.483 Angle : 0.730 9.951 22171 Z= 0.617 Chirality : 0.044 0.153 2514 Planarity : 0.004 0.058 1792 Dihedral : 25.679 177.259 6570 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.91 (0.27), residues: 1056 helix: 2.26 (0.21), residues: 639 sheet: 0.73 (0.81), residues: 48 loop : -0.45 (0.33), residues: 369 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 86 TYR 0.023 0.002 TYR H 40 PHE 0.007 0.001 PHE L 62 TRP 0.017 0.002 TRP L 33 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00560 / 0.48 (15462) covalent geometry : angle 0.72533 / 0.62 (22156) hydrogen bonds : bond 0.10479 / 7.06 ( 846) hydrogen bonds : angle 4.29032 / 3.11 ( 2152) metal coordination : bond 0.00789 / 0.38 ( 8) metal coordination : angle 4.14638 / 2.10 ( 9) link_TRANS : bond 0.00231 / 0.11 ( 2) link_TRANS : angle 0.35621 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 247 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 18 SER cc_start: 0.7819 (m) cc_final: 0.7513 (p) REVERT: C 111 ILE cc_start: 0.9141 (mt) cc_final: 0.8919 (tt) REVERT: D 33 ARG cc_start: 0.8569 (ttm110) cc_final: 0.7927 (mtp-110) REVERT: D 59 MET cc_start: 0.9391 (tpp) cc_final: 0.8977 (tpp) REVERT: D 116 LYS cc_start: 0.9335 (tmtt) cc_final: 0.8994 (tttp) REVERT: E 94 GLU cc_start: 0.8146 (mm-30) cc_final: 0.7906 (mm-30) REVERT: G 39 TYR cc_start: 0.8796 (m-80) cc_final: 0.8453 (m-80) REVERT: G 56 GLU cc_start: 0.8353 (tt0) cc_final: 0.7969 (tt0) REVERT: G 84 GLN cc_start: 0.9562 (tp-100) cc_final: 0.9356 (tp-100) REVERT: H 120 LYS cc_start: 0.9184 (tttm) cc_final: 0.8905 (ttmt) REVERT: K 39 CYS cc_start: 0.3630 (m) cc_final: 0.2815 (m) REVERT: L 86 LEU cc_start: 0.8696 (tp) cc_final: 0.8404 (tp) REVERT: L 97 LEU cc_start: 0.8363 (mt) cc_final: 0.8086 (mt) outliers start: 0 outliers final: 0 residues processed: 247 average time/residue: 0.1306 time to fit residues: 45.7109 Evaluate side-chains 193 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 193 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 10.0000 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 124 optimal weight: 2.9990 chunk 103 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 122 optimal weight: 10.0000 chunk 91 optimal weight: 9.9990 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN H 49 HIS ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN M 62 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.117143 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.077609 restraints weight = 47488.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.078121 restraints weight = 35571.614| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2978 r_free = 0.2978 target = 0.077675 restraints weight = 40419.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.078069 restraints weight = 24280.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.078678 restraints weight = 21216.382| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2951 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2951 r_free = 0.2951 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (15 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8561 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15472 Z= 0.235 Angle : 0.719 17.126 22171 Z= 0.401 Chirality : 0.046 0.268 2514 Planarity : 0.005 0.042 1792 Dihedral : 29.063 175.095 4410 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.17 % Allowed : 11.40 % Favored : 86.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.72 (0.27), residues: 1056 helix: 2.14 (0.21), residues: 649 sheet: 0.62 (0.80), residues: 48 loop : -0.67 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG D 33 TYR 0.023 0.002 TYR B 88 PHE 0.011 0.002 PHE E 104 TRP 0.012 0.002 TRP L 33 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00507 / 0.23 (15462) covalent geometry : angle 0.69770 / 0.40 (22156) hydrogen bonds : bond 0.05704 / 3.84 ( 846) hydrogen bonds : angle 3.89486 / 2.82 ( 2152) metal coordination : bond 0.00987 / 0.50 ( 8) metal coordination : angle 8.60747 / 4.35 ( 9) link_TRANS : bond 0.00206 / 0.11 ( 2) link_TRANS : angle 0.47176 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 197 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8569 (pp30) cc_final: 0.8347 (pp30) REVERT: A 93 GLN cc_start: 0.8987 (tt0) cc_final: 0.8764 (tt0) REVERT: B 59 LYS cc_start: 0.8955 (ttmt) cc_final: 0.8661 (ttmm) REVERT: C 18 SER cc_start: 0.7956 (m) cc_final: 0.7732 (p) REVERT: D 59 MET cc_start: 0.9418 (tpp) cc_final: 0.9023 (tpp) REVERT: D 113 GLU cc_start: 0.8390 (tp30) cc_final: 0.7995 (tm-30) REVERT: E 94 GLU cc_start: 0.8291 (mm-30) cc_final: 0.8086 (mm-30) REVERT: F 52 GLU cc_start: 0.7913 (tp30) cc_final: 0.7674 (mm-30) REVERT: F 88 TYR cc_start: 0.7778 (m-80) cc_final: 0.7180 (m-10) REVERT: G 56 GLU cc_start: 0.8267 (tt0) cc_final: 0.7953 (tt0) REVERT: G 84 GLN cc_start: 0.9601 (tp-100) cc_final: 0.9316 (tp-100) REVERT: H 71 GLU cc_start: 0.8567 (tp30) cc_final: 0.8333 (tp30) REVERT: H 83 TYR cc_start: 0.7927 (m-80) cc_final: 0.7605 (m-80) REVERT: H 120 LYS cc_start: 0.9102 (tttm) cc_final: 0.8832 (ttmt) REVERT: K 35 LEU cc_start: 0.7570 (tp) cc_final: 0.7288 (mp) REVERT: K 46 LYS cc_start: 0.8695 (OUTLIER) cc_final: 0.8263 (ptpp) REVERT: L 97 LEU cc_start: 0.8447 (mt) cc_final: 0.8182 (mt) outliers start: 20 outliers final: 13 residues processed: 204 average time/residue: 0.1291 time to fit residues: 36.9903 Evaluate side-chains 192 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 178 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain M residue 5 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 8 optimal weight: 0.6980 chunk 106 optimal weight: 8.9990 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.5980 chunk 128 optimal weight: 10.0000 chunk 83 optimal weight: 10.0000 chunk 55 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 20.0000 chunk 39 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 47 GLN E 108 ASN F 25 ASN L 7 ASN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.118622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.079215 restraints weight = 47737.339| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.079336 restraints weight = 37071.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.079392 restraints weight = 41230.433| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.079763 restraints weight = 25890.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.080485 restraints weight = 22582.089| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2982 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2982 r_free = 0.2982 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.2982 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1184 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 15472 Z= 0.159 Angle : 0.646 14.232 22171 Z= 0.367 Chirality : 0.043 0.256 2514 Planarity : 0.004 0.063 1792 Dihedral : 29.176 175.485 4410 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 1.95 % Allowed : 15.42 % Favored : 82.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.85 (0.27), residues: 1056 helix: 2.26 (0.21), residues: 650 sheet: 0.63 (0.81), residues: 47 loop : -0.66 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 33 TYR 0.030 0.002 TYR D 83 PHE 0.008 0.001 PHE A 67 TRP 0.010 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00293 / 0.16 (15462) covalent geometry : angle 0.62573 / 0.37 (22156) hydrogen bonds : bond 0.04995 / 3.35 ( 846) hydrogen bonds : angle 3.52354 / 2.54 ( 2152) metal coordination : bond 0.02012 / 1.16 ( 8) metal coordination : angle 7.94571 / 3.95 ( 9) link_TRANS : bond 0.00129 / 0.07 ( 2) link_TRANS : angle 0.40356 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 202 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 76 GLN cc_start: 0.8512 (pp30) cc_final: 0.8306 (pp30) REVERT: A 93 GLN cc_start: 0.8923 (tt0) cc_final: 0.8699 (tt0) REVERT: B 88 TYR cc_start: 0.7828 (m-10) cc_final: 0.6522 (m-10) REVERT: C 18 SER cc_start: 0.8038 (m) cc_final: 0.7756 (p) REVERT: C 29 ARG cc_start: 0.8327 (ttm170) cc_final: 0.7896 (ttm170) REVERT: D 35 GLU cc_start: 0.8493 (tp30) cc_final: 0.7771 (mm-30) REVERT: D 59 MET cc_start: 0.9367 (tpp) cc_final: 0.9018 (tpp) REVERT: D 83 TYR cc_start: 0.8354 (m-10) cc_final: 0.7909 (m-80) REVERT: E 94 GLU cc_start: 0.8264 (mm-30) cc_final: 0.8024 (mm-30) REVERT: G 56 GLU cc_start: 0.8336 (tt0) cc_final: 0.7985 (tt0) REVERT: H 71 GLU cc_start: 0.8640 (tp30) cc_final: 0.8365 (tp30) REVERT: H 120 LYS cc_start: 0.9075 (tttm) cc_final: 0.8784 (ttmt) REVERT: K 18 ILE cc_start: 0.8219 (OUTLIER) cc_final: 0.7813 (pt) REVERT: K 35 LEU cc_start: 0.7243 (tp) cc_final: 0.6769 (tp) REVERT: L 86 LEU cc_start: 0.8590 (tp) cc_final: 0.8173 (tt) REVERT: L 97 LEU cc_start: 0.8466 (mt) cc_final: 0.8099 (mt) REVERT: L 147 MET cc_start: 0.6740 (tpt) cc_final: 0.6078 (tpp) REVERT: M 27 LYS cc_start: 0.9156 (ptmm) cc_final: 0.8832 (pttm) outliers start: 18 outliers final: 12 residues processed: 210 average time/residue: 0.1226 time to fit residues: 36.9429 Evaluate side-chains 201 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 188 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain L residue 33 TRP Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 78 optimal weight: 10.0000 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 64 optimal weight: 0.6980 chunk 127 optimal weight: 9.9990 chunk 4 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 42 optimal weight: 0.5980 chunk 125 optimal weight: 0.0770 chunk 70 optimal weight: 0.3980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 25 ASN K 15 GLN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 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 = 0.3724 r_free = 0.3724 target = 0.119629 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.081992 restraints weight = 53645.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.083057 restraints weight = 42189.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.082544 restraints weight = 42017.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3069 r_free = 0.3069 target = 0.082796 restraints weight = 25730.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.083160 restraints weight = 22342.777| |-----------------------------------------------------------------------------| r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3023 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3023 r_free = 0.3023 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3023 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.048 15472 Z= 0.139 Angle : 0.607 11.724 22171 Z= 0.349 Chirality : 0.041 0.257 2514 Planarity : 0.004 0.043 1792 Dihedral : 29.277 174.842 4410 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 8.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.28 % Allowed : 16.40 % Favored : 81.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.97 (0.27), residues: 1056 helix: 2.35 (0.21), residues: 649 sheet: 0.59 (0.75), residues: 49 loop : -0.59 (0.32), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 33 TYR 0.025 0.002 TYR H 40 PHE 0.010 0.001 PHE L 31 TRP 0.007 0.001 TRP K 77 HIS 0.003 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00238 / 0.14 (15462) covalent geometry : angle 0.59404 / 0.35 (22156) hydrogen bonds : bond 0.04566 / 3.07 ( 846) hydrogen bonds : angle 3.41236 / 2.45 ( 2152) metal coordination : bond 0.02000 / 0.78 ( 8) metal coordination : angle 6.28796 / 3.12 ( 9) link_TRANS : bond 0.00023 / 0.01 ( 2) link_TRANS : angle 0.29922 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7799 (m-10) cc_final: 0.7278 (m-80) REVERT: C 18 SER cc_start: 0.8014 (m) cc_final: 0.7732 (p) REVERT: C 29 ARG cc_start: 0.8204 (ttm170) cc_final: 0.7694 (ttm170) REVERT: D 35 GLU cc_start: 0.8484 (tp30) cc_final: 0.7646 (mm-30) REVERT: D 59 MET cc_start: 0.9344 (tpp) cc_final: 0.8946 (tpp) REVERT: E 94 GLU cc_start: 0.8173 (mm-30) cc_final: 0.7958 (mm-30) REVERT: E 125 GLN cc_start: 0.7939 (OUTLIER) cc_final: 0.7573 (mm-40) REVERT: F 88 TYR cc_start: 0.7697 (m-80) cc_final: 0.7392 (m-80) REVERT: G 56 GLU cc_start: 0.8315 (tt0) cc_final: 0.7771 (tt0) REVERT: G 57 TYR cc_start: 0.9105 (t80) cc_final: 0.8868 (t80) REVERT: H 59 MET cc_start: 0.9058 (tpt) cc_final: 0.8777 (tpp) REVERT: K 21 GLU cc_start: 0.7418 (pp20) cc_final: 0.7097 (pp20) REVERT: K 40 PHE cc_start: 0.8753 (t80) cc_final: 0.8536 (t80) REVERT: K 46 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.7953 (mtmm) REVERT: L 1 MET cc_start: 0.8313 (mpp) cc_final: 0.8019 (mpp) REVERT: M 27 LYS cc_start: 0.9123 (ptmm) cc_final: 0.8777 (pttm) outliers start: 21 outliers final: 15 residues processed: 208 average time/residue: 0.1181 time to fit residues: 34.9755 Evaluate side-chains 208 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 191 time to evaluate : 0.323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 37 LYS Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 33 TRP Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.5980 chunk 49 optimal weight: 0.5980 chunk 55 optimal weight: 0.7980 chunk 12 optimal weight: 0.4980 chunk 57 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 104 optimal weight: 5.9990 chunk 90 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 25 ASN L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.120312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.070078 restraints weight = 63222.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072491 restraints weight = 32047.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.072813 restraints weight = 20773.256| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.073803 restraints weight = 16721.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.073614 restraints weight = 14021.340| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2849 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2849 r_free = 0.2849 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2849 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.1581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 15472 Z= 0.137 Angle : 0.603 12.772 22171 Z= 0.344 Chirality : 0.041 0.257 2514 Planarity : 0.004 0.047 1792 Dihedral : 29.327 174.500 4410 Min Nonbonded Distance : 2.074 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.39 % Allowed : 16.83 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 2.01 (0.26), residues: 1056 helix: 2.41 (0.21), residues: 650 sheet: 0.37 (0.72), residues: 49 loop : -0.58 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG G 20 TYR 0.021 0.002 TYR F 88 PHE 0.010 0.001 PHE L 51 TRP 0.008 0.001 TRP L 33 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00234 / 0.14 (15462) covalent geometry : angle 0.59032 / 0.34 (22156) hydrogen bonds : bond 0.04421 / 2.98 ( 846) hydrogen bonds : angle 3.39189 / 2.42 ( 2152) metal coordination : bond 0.01568 / 0.66 ( 8) metal coordination : angle 6.04862 / 3.11 ( 9) link_TRANS : bond 0.00026 / 0.01 ( 2) link_TRANS : angle 0.34336 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 206 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.7958 (m-10) cc_final: 0.7544 (m-10) REVERT: C 18 SER cc_start: 0.8321 (m) cc_final: 0.8087 (p) REVERT: C 29 ARG cc_start: 0.8325 (ttm170) cc_final: 0.7961 (ttm170) REVERT: D 35 GLU cc_start: 0.8466 (tp30) cc_final: 0.7730 (mm-30) REVERT: D 59 MET cc_start: 0.9358 (tpp) cc_final: 0.8861 (tpp) REVERT: E 94 GLU cc_start: 0.8235 (mm-30) cc_final: 0.7988 (mm-30) REVERT: E 125 GLN cc_start: 0.8137 (OUTLIER) cc_final: 0.7886 (mm-40) REVERT: G 56 GLU cc_start: 0.8497 (tt0) cc_final: 0.8086 (tt0) REVERT: G 57 TYR cc_start: 0.9124 (t80) cc_final: 0.8880 (t80) REVERT: K 46 LYS cc_start: 0.8131 (OUTLIER) cc_final: 0.7423 (mtmm) REVERT: L 86 LEU cc_start: 0.8481 (tp) cc_final: 0.8223 (tt) REVERT: L 147 MET cc_start: 0.7779 (tpt) cc_final: 0.7333 (tpp) REVERT: M 27 LYS cc_start: 0.9400 (ptmm) cc_final: 0.9129 (pttm) outliers start: 22 outliers final: 12 residues processed: 215 average time/residue: 0.1202 time to fit residues: 36.4825 Evaluate side-chains 206 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 192 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 61 optimal weight: 0.9990 chunk 106 optimal weight: 9.9990 chunk 30 optimal weight: 1.9990 chunk 110 optimal weight: 1.9990 chunk 128 optimal weight: 0.0040 chunk 7 optimal weight: 0.9990 chunk 100 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 112 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 107 optimal weight: 5.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.119716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.071185 restraints weight = 62687.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.2893 r_free = 0.2893 target = 0.072442 restraints weight = 33379.895| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.074227 restraints weight = 19627.845| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.074214 restraints weight = 17517.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.074037 restraints weight = 14472.349| |-----------------------------------------------------------------------------| r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2887 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2887 r_free = 0.2887 target_work(ls_wunit_k1) = 0.071 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2887 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15472 Z= 0.147 Angle : 0.615 12.349 22171 Z= 0.347 Chirality : 0.041 0.261 2514 Planarity : 0.004 0.052 1792 Dihedral : 29.367 174.089 4410 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.28 % Allowed : 18.57 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.98 (0.26), residues: 1056 helix: 2.40 (0.21), residues: 650 sheet: 0.11 (0.70), residues: 49 loop : -0.59 (0.32), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 33 TYR 0.031 0.002 TYR F 88 PHE 0.007 0.001 PHE H 70 TRP 0.007 0.001 TRP L 33 HIS 0.003 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00275 / 0.15 (15462) covalent geometry : angle 0.60543 / 0.35 (22156) hydrogen bonds : bond 0.04448 / 3.00 ( 846) hydrogen bonds : angle 3.40043 / 2.43 ( 2152) metal coordination : bond 0.01413 / 0.60 ( 8) metal coordination : angle 5.31545 / 2.81 ( 9) link_TRANS : bond 0.00058 / 0.03 ( 2) link_TRANS : angle 0.34782 / 0.15 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 195 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8029 (m-10) cc_final: 0.7455 (m-10) REVERT: C 18 SER cc_start: 0.8352 (m) cc_final: 0.8123 (p) REVERT: D 59 MET cc_start: 0.9342 (tpp) cc_final: 0.8807 (tpp) REVERT: E 94 GLU cc_start: 0.8149 (mm-30) cc_final: 0.7880 (mm-30) REVERT: E 125 GLN cc_start: 0.8169 (OUTLIER) cc_final: 0.7893 (mm-40) REVERT: G 56 GLU cc_start: 0.8456 (tt0) cc_final: 0.8065 (tt0) REVERT: G 57 TYR cc_start: 0.9117 (t80) cc_final: 0.8885 (t80) REVERT: K 46 LYS cc_start: 0.8291 (OUTLIER) cc_final: 0.7540 (mtmm) REVERT: L 5 ARG cc_start: 0.8408 (tmt-80) cc_final: 0.8032 (tmt170) REVERT: L 30 MET cc_start: 0.8684 (tpp) cc_final: 0.8443 (tpp) REVERT: L 86 LEU cc_start: 0.8574 (tp) cc_final: 0.8366 (tt) REVERT: L 147 MET cc_start: 0.7630 (tpt) cc_final: 0.7069 (tpp) REVERT: M 27 LYS cc_start: 0.9407 (ptmm) cc_final: 0.9133 (pttm) outliers start: 21 outliers final: 14 residues processed: 205 average time/residue: 0.1331 time to fit residues: 38.3974 Evaluate side-chains 203 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 187 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 18 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 34 optimal weight: 0.9990 chunk 40 optimal weight: 3.9990 chunk 79 optimal weight: 9.9990 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.7980 chunk 104 optimal weight: 9.9990 chunk 128 optimal weight: 9.9990 chunk 42 optimal weight: 2.9990 chunk 94 optimal weight: 10.0000 chunk 96 optimal weight: 9.9990 chunk 108 optimal weight: 6.9990 overall best weight: 1.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 25 ASN H 84 ASN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS ** M 31 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 = 0.3685 r_free = 0.3685 target = 0.117003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2784 r_free = 0.2784 target = 0.067253 restraints weight = 52954.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.068837 restraints weight = 28426.518| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.069614 restraints weight = 17369.962| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.069956 restraints weight = 15806.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.2846 r_free = 0.2846 target = 0.069859 restraints weight = 14315.039| |-----------------------------------------------------------------------------| r_work (final): 0.2807 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8715 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 15472 Z= 0.219 Angle : 0.683 12.296 22171 Z= 0.372 Chirality : 0.043 0.279 2514 Planarity : 0.005 0.063 1792 Dihedral : 29.461 173.102 4410 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.28 % Allowed : 19.87 % Favored : 77.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.75 (0.26), residues: 1056 helix: 2.23 (0.21), residues: 650 sheet: -0.30 (0.69), residues: 49 loop : -0.67 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 33 TYR 0.022 0.002 TYR D 83 PHE 0.011 0.002 PHE M 4 TRP 0.008 0.001 TRP L 33 HIS 0.006 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.22 (15462) covalent geometry : angle 0.66770 / 0.37 (22156) hydrogen bonds : bond 0.05124 / 3.42 ( 846) hydrogen bonds : angle 3.68577 / 2.66 ( 2152) metal coordination : bond 0.01515 / 0.63 ( 8) metal coordination : angle 7.15064 / 3.76 ( 9) link_TRANS : bond 0.00233 / 0.12 ( 2) link_TRANS : angle 0.48543 / 0.20 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 192 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.9084 (tt0) cc_final: 0.8860 (tt0) REVERT: B 88 TYR cc_start: 0.8266 (m-10) cc_final: 0.7664 (m-10) REVERT: D 35 GLU cc_start: 0.8423 (tp30) cc_final: 0.8034 (mm-30) REVERT: D 51 ASP cc_start: 0.7693 (p0) cc_final: 0.7453 (p0) REVERT: D 59 MET cc_start: 0.9439 (tpp) cc_final: 0.8896 (tpp) REVERT: E 94 GLU cc_start: 0.8263 (mm-30) cc_final: 0.8040 (mm-30) REVERT: F 74 GLU cc_start: 0.8648 (mm-30) cc_final: 0.8399 (mm-30) REVERT: G 56 GLU cc_start: 0.8606 (tt0) cc_final: 0.8176 (tt0) REVERT: G 57 TYR cc_start: 0.9167 (t80) cc_final: 0.8941 (t80) REVERT: K 21 GLU cc_start: 0.7623 (pp20) cc_final: 0.7405 (pp20) REVERT: K 46 LYS cc_start: 0.8056 (OUTLIER) cc_final: 0.7358 (mtmm) REVERT: L 5 ARG cc_start: 0.8505 (tmt-80) cc_final: 0.8009 (tmt170) REVERT: L 9 GLU cc_start: 0.7522 (mm-30) cc_final: 0.7317 (mm-30) REVERT: L 136 ARG cc_start: 0.9579 (OUTLIER) cc_final: 0.9365 (ttp80) REVERT: M 6 LYS cc_start: 0.8904 (mptt) cc_final: 0.8673 (mptt) REVERT: M 24 GLU cc_start: 0.9590 (tm-30) cc_final: 0.9348 (tp30) outliers start: 21 outliers final: 15 residues processed: 204 average time/residue: 0.1324 time to fit residues: 38.7450 Evaluate side-chains 201 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 46 LYS Chi-restraints excluded: chain K residue 70 SER Chi-restraints excluded: chain L residue 53 THR Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 75 optimal weight: 9.9990 chunk 110 optimal weight: 8.9990 chunk 51 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 chunk 52 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 80 optimal weight: 9.9990 chunk 104 optimal weight: 0.0670 chunk 121 optimal weight: 10.0000 chunk 29 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.5718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 47 GLN F 25 ASN H 84 ASN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3728 r_free = 0.3728 target = 0.119888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.076396 restraints weight = 37406.591| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077092 restraints weight = 27335.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.076848 restraints weight = 24623.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.077132 restraints weight = 20915.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.077216 restraints weight = 18609.542| |-----------------------------------------------------------------------------| r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2949 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2949 r_free = 0.2949 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.2949 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15472 Z= 0.140 Angle : 0.622 13.009 22171 Z= 0.350 Chirality : 0.042 0.264 2514 Planarity : 0.004 0.057 1792 Dihedral : 29.392 174.133 4410 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.63 % Allowed : 20.85 % Favored : 77.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.86 (0.26), residues: 1056 helix: 2.35 (0.21), residues: 651 sheet: -0.19 (0.69), residues: 49 loop : -0.69 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG D 33 TYR 0.020 0.001 TYR F 88 PHE 0.008 0.001 PHE A 67 TRP 0.007 0.001 TRP L 33 HIS 0.004 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00253 / 0.14 (15462) covalent geometry : angle 0.60789 / 0.35 (22156) hydrogen bonds : bond 0.04556 / 3.06 ( 846) hydrogen bonds : angle 3.40414 / 2.44 ( 2152) metal coordination : bond 0.01330 / 0.58 ( 8) metal coordination : angle 6.68513 / 3.55 ( 9) link_TRANS : bond 0.00015 / 0.01 ( 2) link_TRANS : angle 0.37798 / 0.16 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 198 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8742 (tt0) cc_final: 0.8520 (tt0) REVERT: B 88 TYR cc_start: 0.8230 (m-10) cc_final: 0.7620 (m-10) REVERT: C 29 ARG cc_start: 0.8473 (ttm170) cc_final: 0.8267 (ttm170) REVERT: D 51 ASP cc_start: 0.7631 (p0) cc_final: 0.7369 (p0) REVERT: D 59 MET cc_start: 0.9409 (tpp) cc_final: 0.8927 (tpp) REVERT: E 94 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7875 (mm-30) REVERT: G 56 GLU cc_start: 0.8478 (tt0) cc_final: 0.8035 (tt0) REVERT: G 57 TYR cc_start: 0.9105 (t80) cc_final: 0.8871 (t80) REVERT: K 21 GLU cc_start: 0.7328 (pp20) cc_final: 0.6909 (pp20) REVERT: M 27 LYS cc_start: 0.8819 (ptmt) cc_final: 0.8607 (ptpt) outliers start: 15 outliers final: 13 residues processed: 203 average time/residue: 0.1362 time to fit residues: 39.0100 Evaluate side-chains 199 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 186 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 22 ILE Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 1.9990 chunk 79 optimal weight: 9.9990 chunk 51 optimal weight: 0.8980 chunk 85 optimal weight: 20.0000 chunk 113 optimal weight: 30.0000 chunk 119 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 86 optimal weight: 20.0000 chunk 102 optimal weight: 30.0000 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 47 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.119804 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.080337 restraints weight = 45011.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.079557 restraints weight = 37747.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.080847 restraints weight = 30462.055| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.081031 restraints weight = 23150.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.081324 restraints weight = 23784.912| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3003 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3003 r_free = 0.3003 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3003 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8496 moved from start: 0.1945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 15472 Z= 0.151 Angle : 0.645 13.275 22171 Z= 0.357 Chirality : 0.041 0.263 2514 Planarity : 0.004 0.060 1792 Dihedral : 29.419 173.572 4410 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.95 % Allowed : 21.17 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.82 (0.26), residues: 1056 helix: 2.33 (0.21), residues: 651 sheet: -0.44 (0.68), residues: 49 loop : -0.71 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG L 5 TYR 0.012 0.001 TYR D 83 PHE 0.019 0.001 PHE M 4 TRP 0.007 0.001 TRP L 33 HIS 0.007 0.001 HIS M 68 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.15 (15462) covalent geometry : angle 0.63132 / 0.36 (22156) hydrogen bonds : bond 0.04538 / 3.04 ( 846) hydrogen bonds : angle 3.43492 / 2.46 ( 2152) metal coordination : bond 0.01144 / 0.49 ( 8) metal coordination : angle 6.69627 / 3.57 ( 9) link_TRANS : bond 0.00062 / 0.03 ( 2) link_TRANS : angle 0.40344 / 0.17 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 185 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8793 (tt0) cc_final: 0.8577 (tt0) REVERT: B 88 TYR cc_start: 0.8201 (m-10) cc_final: 0.7619 (m-10) REVERT: D 35 GLU cc_start: 0.8412 (tp30) cc_final: 0.8090 (mm-30) REVERT: D 51 ASP cc_start: 0.7488 (p0) cc_final: 0.7209 (p0) REVERT: D 59 MET cc_start: 0.9381 (tpp) cc_final: 0.8937 (tpp) REVERT: E 94 GLU cc_start: 0.8238 (mm-30) cc_final: 0.8008 (mm-30) REVERT: G 56 GLU cc_start: 0.8441 (tt0) cc_final: 0.8012 (tt0) REVERT: G 57 TYR cc_start: 0.9102 (t80) cc_final: 0.8858 (t80) REVERT: M 27 LYS cc_start: 0.8894 (ptmt) cc_final: 0.8636 (ptpt) outliers start: 18 outliers final: 16 residues processed: 193 average time/residue: 0.1301 time to fit residues: 35.8893 Evaluate side-chains 199 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 183 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 6 LYS Chi-restraints excluded: chain M residue 14 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 52 optimal weight: 0.9980 chunk 6 optimal weight: 0.9980 chunk 64 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 8.9990 chunk 83 optimal weight: 9.9990 chunk 75 optimal weight: 10.0000 chunk 61 optimal weight: 0.0670 chunk 92 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 overall best weight: 0.7918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 47 GLN H 84 ASN ** K 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN L 32 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.120013 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.072392 restraints weight = 47382.266| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.072643 restraints weight = 28886.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.072772 restraints weight = 20246.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.073075 restraints weight = 20133.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.073074 restraints weight = 18851.832| |-----------------------------------------------------------------------------| r_work (final): 0.2859 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.069 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (10 function evaluations) r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2007 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15472 Z= 0.150 Angle : 0.646 13.768 22171 Z= 0.358 Chirality : 0.041 0.262 2514 Planarity : 0.004 0.063 1792 Dihedral : 29.424 173.511 4410 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 9.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.74 % Allowed : 21.39 % Favored : 76.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.79 (0.26), residues: 1056 helix: 2.31 (0.21), residues: 651 sheet: -0.46 (0.68), residues: 49 loop : -0.71 (0.31), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 33 TYR 0.011 0.001 TYR D 83 PHE 0.014 0.001 PHE M 4 TRP 0.005 0.001 TRP K 61 HIS 0.003 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00289 / 0.15 (15462) covalent geometry : angle 0.63262 / 0.36 (22156) hydrogen bonds : bond 0.04513 / 3.02 ( 846) hydrogen bonds : angle 3.44285 / 2.46 ( 2152) metal coordination : bond 0.00985 / 0.41 ( 8) metal coordination : angle 6.54667 / 3.50 ( 9) link_TRANS : bond 0.00042 / 0.02 ( 2) link_TRANS : angle 0.39795 / 0.16 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2112 Ramachandran restraints generated. 1056 Oldfield, 0 Emsley, 1056 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.395 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8912 (tt0) cc_final: 0.8674 (tt0) REVERT: B 88 TYR cc_start: 0.8266 (m-10) cc_final: 0.7686 (m-10) REVERT: D 35 GLU cc_start: 0.8387 (tp30) cc_final: 0.8016 (mm-30) REVERT: D 51 ASP cc_start: 0.7660 (p0) cc_final: 0.7394 (p0) REVERT: D 59 MET cc_start: 0.9391 (tpp) cc_final: 0.8853 (tpp) REVERT: E 94 GLU cc_start: 0.8161 (mm-30) cc_final: 0.7901 (mm-30) REVERT: G 56 GLU cc_start: 0.8518 (tt0) cc_final: 0.8110 (tt0) REVERT: G 57 TYR cc_start: 0.9156 (t80) cc_final: 0.8913 (t80) REVERT: G 84 GLN cc_start: 0.9570 (tp-100) cc_final: 0.9180 (tp-100) REVERT: H 59 MET cc_start: 0.9188 (tpt) cc_final: 0.8918 (tpp) REVERT: L 30 MET cc_start: 0.8465 (tpp) cc_final: 0.8177 (tpp) REVERT: M 27 LYS cc_start: 0.9078 (ptmt) cc_final: 0.8766 (ptpt) outliers start: 16 outliers final: 15 residues processed: 195 average time/residue: 0.1246 time to fit residues: 35.0310 Evaluate side-chains 197 residues out of total 919 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 182 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain C residue 15 CYS Chi-restraints excluded: chain C residue 95 LYS Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain K residue 39 CYS Chi-restraints excluded: chain L residue 37 ILE Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 5 VAL Chi-restraints excluded: chain M residue 6 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.5980 chunk 60 optimal weight: 0.6980 chunk 126 optimal weight: 9.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 45 optimal weight: 0.5980 chunk 128 optimal weight: 8.9990 chunk 125 optimal weight: 8.9990 chunk 108 optimal weight: 7.9990 chunk 93 optimal weight: 9.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN D 47 GLN K 15 GLN ** K 33 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 HIS L 55 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.118781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.070963 restraints weight = 46303.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.070618 restraints weight = 30296.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.070870 restraints weight = 21242.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.071206 restraints weight = 20339.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.071273 restraints weight = 18567.783| |-----------------------------------------------------------------------------| r_work (final): 0.2802 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2802 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2802 r_free = 0.2802 target_work(ls_wunit_k1) = 0.067 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2802 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8695 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 15472 Z= 0.196 Angle : 0.677 13.648 22171 Z= 0.368 Chirality : 0.042 0.272 2514 Planarity : 0.005 0.065 1792 Dihedral : 29.468 172.907 4410 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 1.85 % Allowed : 21.39 % Favored : 76.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.69 (0.26), residues: 1056 helix: 2.23 (0.21), residues: 650 sheet: -0.49 (0.70), residues: 49 loop : -0.77 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 33 TYR 0.015 0.002 TYR D 83 PHE 0.044 0.002 PHE M 4 TRP 0.007 0.001 TRP L 33 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00416 / 0.20 (15462) covalent geometry : angle 0.66351 / 0.37 (22156) hydrogen bonds : bond 0.04808 / 3.22 ( 846) hydrogen bonds : angle 3.58184 / 2.57 ( 2152) metal coordination : bond 0.00948 / 0.39 ( 8) metal coordination : angle 6.60950 / 3.50 ( 9) link_TRANS : bond 0.00185 / 0.10 ( 2) link_TRANS : angle 0.48325 / 0.19 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2317.02 seconds wall clock time: 40 minutes 33.40 seconds (2433.40 seconds total)