Starting phenix.real_space_refine on Thu Aug 6 20:46:40 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u13_41800/08_2026/8u13_41800.map" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 293 5.49 5 S 25 5.16 5 C 7139 2.51 5 N 2408 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 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: 12825 Number of models: 1 Model: "" Number of chains: 12 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: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "H" Number of atoms: 737 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: 735 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: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "C" 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: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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 10617 SG CYS K 31 27.021 59.998 74.288 1.00394.38 S ATOM 10767 SG CYS K 51 26.391 63.713 73.415 1.00417.10 S ATOM 10791 SG CYS K 54 27.019 62.691 77.048 1.00421.64 S ATOM 10508 SG CYS K 16 19.411 66.329 66.379 1.00424.33 S ATOM 10526 SG CYS K 19 18.344 69.167 64.157 1.00433.92 S ATOM 10656 SG CYS K 36 20.356 66.435 62.624 1.00418.58 S ATOM 10678 SG CYS K 39 21.999 68.761 65.379 1.00418.47 S Time building chain proxies: 3.04, per 1000 atoms: 0.24 Number of scatterers: 12825 At special positions: 0 Unit cell: (103.788, 117.146, 117.146, 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 25 16.00 P 293 15.00 O 2958 8.00 N 2408 7.00 C 7139 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: 1.11 Conformation dependent library (CDL) restraints added in 352.3 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 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " 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 " Number of angles added : 9 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 68.9% alpha, 2.6% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 2.26 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.756A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.685A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.498A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.528A 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 Processing helix chain 'E' and resid 44 through 56 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.657A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.654A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 36 through 45 Processing helix chain 'K' and resid 58 through 68 removed outlier: 4.417A 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: 4.140A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'G' and resid 16 through 21 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: 3.543A 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 sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.449A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.545A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.565A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.296A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.579A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 432 hydrogen bonds defined for protein. 1273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 2.60 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2525 1.33 - 1.45: 4369 1.45 - 1.57: 6137 1.57 - 1.69: 584 1.69 - 1.81: 36 Bond restraints: 13651 Sorted by residual: bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.22e+01 bond pdb=" C3' DG J -49 " pdb=" C2' DG J -49 " ideal model delta sigma weight residual 1.516 1.544 -0.028 8.00e-03 1.56e+04 1.21e+01 bond pdb=" C3' DG I -11 " pdb=" C2' DG I -11 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.08e+01 bond pdb=" C3' DT J 5 " pdb=" C2' DT J 5 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.03e+01 bond pdb=" C3' DG I -41 " pdb=" C2' DG I -41 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 ... (remaining 13646 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 18461 1.60 - 3.20: 1142 3.20 - 4.79: 60 4.79 - 6.39: 22 6.39 - 7.99: 7 Bond angle restraints: 19692 Sorted by residual: angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.54 -2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J 5 " pdb=" C4 DT J 5 " pdb=" O4 DT J 5 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.48 -2.58 6.00e-01 2.78e+00 1.85e+01 angle pdb=" N3 DT I -42 " pdb=" C4 DT I -42 " pdb=" O4 DT I -42 " ideal model delta sigma weight residual 119.90 122.47 -2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I -17 " pdb=" C4 DT I -17 " pdb=" O4 DT I -17 " ideal model delta sigma weight residual 119.90 122.45 -2.55 6.00e-01 2.78e+00 1.81e+01 ... (remaining 19687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 6095 34.48 - 68.96: 1363 68.96 - 103.44: 29 103.44 - 137.92: 0 137.92 - 172.40: 2 Dihedral angle restraints: 7489 sinusoidal: 4990 harmonic: 2499 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+01 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 220.00 47.60 172.40 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7486 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1590 0.045 - 0.091: 509 0.091 - 0.136: 137 0.136 - 0.181: 3 0.181 - 0.226: 2 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 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 -2.52 -0.21 2.00e-01 2.50e+01 1.07e+00 chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 ... (remaining 2238 not shown) Planarity restraints: 1477 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 129 " 0.169 9.50e-02 1.11e+02 7.58e-02 3.72e+00 pdb=" NE ARG E 129 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 129 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" CD GLU H 113 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.022 2.00e-02 2.50e+03 9.15e-03 2.51e+00 pdb=" N9 DG I 48 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1474 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 483 2.70 - 3.25: 12231 3.25 - 3.80: 25255 3.80 - 4.35: 30112 4.35 - 4.90: 42904 Nonbonded interactions: 110985 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.145 3.120 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.153 2.496 nonbonded pdb=" OE1 GLU D 71 " pdb=" OH TYR C 39 " model vdw 2.180 3.040 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.240 3.040 nonbonded pdb=" NH2 ARG E 42 " pdb=" OP1 DG J -5 " model vdw 2.249 3.120 ... (remaining 110980 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 119) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 16.360 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.650 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 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 0.042 13661 Z= 0.493 Angle : 0.791 7.991 19707 Z= 0.656 Chirality : 0.046 0.226 2241 Planarity : 0.005 0.076 1475 Dihedral : 27.097 172.397 5871 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.28), residues: 842 helix: 1.16 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG C 99 TYR 0.021 0.002 TYR B 88 PHE 0.009 0.001 PHE G 25 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 Details of bonding type rmsd/Z covalent geometry : bond 0.00555 / 0.49 (13651) covalent geometry : angle 0.78814 / 0.66 (19692) hydrogen bonds : bond 0.10747 / 7.20 ( 791) hydrogen bonds : angle 4.26585 / 3.07 ( 1987) metal coordination : bond 0.00645 / 0.37 ( 8) metal coordination : angle 3.29907 / 1.75 ( 9) link_TRANS : bond 0.00262 / 0.13 ( 2) link_TRANS : angle 0.86790 / 0.43 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 347 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 125 GLN cc_start: 0.9259 (mp10) cc_final: 0.8944 (mp10) REVERT: B 23 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8125 (mmp80) REVERT: B 25 ASN cc_start: 0.8800 (m110) cc_final: 0.8441 (m110) REVERT: B 49 LEU cc_start: 0.9349 (pt) cc_final: 0.8361 (pt) REVERT: B 50 ILE cc_start: 0.9347 (tp) cc_final: 0.9046 (tp) REVERT: B 88 TYR cc_start: 0.8364 (m-80) cc_final: 0.8101 (m-80) REVERT: D 34 LYS cc_start: 0.8971 (mptt) cc_final: 0.8693 (mmtm) REVERT: D 57 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8598 (mmmm) REVERT: D 105 GLU cc_start: 0.8261 (tp30) cc_final: 0.7680 (tp30) REVERT: D 109 HIS cc_start: 0.8833 (m170) cc_final: 0.8628 (m170) REVERT: D 120 LYS cc_start: 0.9231 (tttp) cc_final: 0.8841 (ttmm) REVERT: E 53 ARG cc_start: 0.8788 (tmt-80) cc_final: 0.8330 (tmt-80) REVERT: E 54 TYR cc_start: 0.7863 (m-80) cc_final: 0.7640 (m-80) REVERT: E 57 SER cc_start: 0.7527 (p) cc_final: 0.6920 (p) REVERT: E 59 GLU cc_start: 0.8178 (pm20) cc_final: 0.7882 (pm20) REVERT: E 60 LEU cc_start: 0.8664 (mm) cc_final: 0.8014 (mm) REVERT: E 68 GLN cc_start: 0.8675 (pp30) cc_final: 0.8322 (pp30) REVERT: E 81 ASP cc_start: 0.8075 (m-30) cc_final: 0.7857 (m-30) REVERT: E 92 LEU cc_start: 0.9668 (mt) cc_final: 0.9463 (mt) REVERT: E 125 GLN cc_start: 0.8554 (mp10) cc_final: 0.8005 (mp10) REVERT: F 49 LEU cc_start: 0.8913 (mm) cc_final: 0.8194 (mm) REVERT: H 68 ASP cc_start: 0.8399 (t70) cc_final: 0.8063 (t0) REVERT: H 83 TYR cc_start: 0.8409 (m-10) cc_final: 0.7687 (m-10) REVERT: H 86 ARG cc_start: 0.9040 (mmt-90) cc_final: 0.8331 (mtt-85) REVERT: C 84 GLN cc_start: 0.9171 (tm-30) cc_final: 0.8811 (tp-100) REVERT: G 61 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7762 (mm-30) REVERT: G 68 ASN cc_start: 0.8959 (m-40) cc_final: 0.8649 (m-40) REVERT: G 104 GLN cc_start: 0.8967 (mp10) cc_final: 0.8680 (mp10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.1391 time to fit residues: 66.3962 Evaluate side-chains 290 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 290 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 108 optimal weight: 10.0000 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 40.0000 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 65 optimal weight: 30.0000 chunk 62 optimal weight: 20.0000 chunk 51 optimal weight: 5.9990 chunk 100 optimal weight: 4.9990 chunk 106 optimal weight: 4.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN B 93 GLN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 82 HIS C 84 GLN C 89 ASN C 104 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.076120 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.051976 restraints weight = 65012.185| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053477 restraints weight = 29815.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.054465 restraints weight = 19690.236| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.3002 r_free = 0.3002 target = 0.055021 restraints weight = 15794.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.055324 restraints weight = 14128.001| |-----------------------------------------------------------------------------| r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2985 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2985 r_free = 0.2985 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2983 r_free = 0.2983 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (4 function evaluations) r_final: 0.2983 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8487 moved from start: 0.1319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 13661 Z= 0.193 Angle : 0.730 8.708 19707 Z= 0.417 Chirality : 0.045 0.422 2241 Planarity : 0.005 0.046 1475 Dihedral : 30.403 176.877 4161 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.44 % Allowed : 17.06 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.28), residues: 842 helix: 1.06 (0.21), residues: 586 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.026 0.002 TYR H 40 PHE 0.018 0.002 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.005 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00363 / 0.19 (13651) covalent geometry : angle 0.72508 / 0.42 (19692) hydrogen bonds : bond 0.05905 / 3.94 ( 791) hydrogen bonds : angle 3.88230 / 2.79 ( 1987) metal coordination : bond 0.00804 / 0.49 ( 8) metal coordination : angle 4.00707 / 2.30 ( 9) link_TRANS : bond 0.00066 / 0.03 ( 2) link_TRANS : angle 0.21552 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 314 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 289 time to evaluate : 0.345 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7868 (mt-10) cc_final: 0.7120 (mt-10) REVERT: A 125 GLN cc_start: 0.9422 (mp10) cc_final: 0.8933 (mp10) REVERT: B 23 ARG cc_start: 0.8572 (mmp80) cc_final: 0.8363 (mmp80) REVERT: B 25 ASN cc_start: 0.8821 (m110) cc_final: 0.8342 (m110) REVERT: B 63 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8362 (mp0) REVERT: B 88 TYR cc_start: 0.8746 (m-10) cc_final: 0.7712 (m-10) REVERT: D 31 ARG cc_start: 0.8060 (mmp80) cc_final: 0.7657 (mmp80) REVERT: D 34 LYS cc_start: 0.8960 (mptt) cc_final: 0.8694 (mmtm) REVERT: D 57 LYS cc_start: 0.9040 (mmtt) cc_final: 0.8626 (mmmm) REVERT: D 83 TYR cc_start: 0.8200 (m-10) cc_final: 0.7479 (m-10) REVERT: D 105 GLU cc_start: 0.8437 (tp30) cc_final: 0.7851 (tp30) REVERT: D 109 HIS cc_start: 0.9171 (m170) cc_final: 0.8841 (m170) REVERT: D 120 LYS cc_start: 0.9252 (tttp) cc_final: 0.8870 (ttmm) REVERT: E 60 LEU cc_start: 0.8887 (mm) cc_final: 0.8314 (mm) REVERT: E 64 LYS cc_start: 0.8931 (mmtt) cc_final: 0.8656 (mmtt) REVERT: E 68 GLN cc_start: 0.8893 (pp30) cc_final: 0.8674 (pp30) REVERT: E 81 ASP cc_start: 0.8241 (m-30) cc_final: 0.8007 (m-30) REVERT: E 97 GLU cc_start: 0.8554 (mt-10) cc_final: 0.8050 (mt-10) REVERT: E 125 GLN cc_start: 0.8818 (mp10) cc_final: 0.8386 (mp10) REVERT: F 53 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8319 (mt-10) REVERT: F 84 MET cc_start: 0.8831 (mmm) cc_final: 0.8552 (tpp) REVERT: H 68 ASP cc_start: 0.9027 (t70) cc_final: 0.8588 (t0) REVERT: H 83 TYR cc_start: 0.8408 (m-10) cc_final: 0.7795 (m-10) REVERT: H 86 ARG cc_start: 0.9142 (mmt-90) cc_final: 0.8246 (mtt-85) REVERT: H 120 LYS cc_start: 0.9354 (ttmt) cc_final: 0.8860 (tptt) REVERT: C 38 ASN cc_start: 0.8497 (t0) cc_final: 0.8253 (t0) REVERT: C 78 ILE cc_start: 0.8934 (mm) cc_final: 0.8691 (mm) REVERT: G 61 GLU cc_start: 0.8628 (mm-30) cc_final: 0.8413 (mm-30) REVERT: G 104 GLN cc_start: 0.9237 (mp10) cc_final: 0.8803 (mp10) outliers start: 25 outliers final: 15 residues processed: 299 average time/residue: 0.1335 time to fit residues: 55.1252 Evaluate side-chains 288 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 272 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 87 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 22 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 45 optimal weight: 7.9990 chunk 51 optimal weight: 3.9990 chunk 78 optimal weight: 20.0000 chunk 82 optimal weight: 40.0000 chunk 16 optimal weight: 0.9980 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 30.0000 chunk 103 optimal weight: 0.7980 overall best weight: 3.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN H 82 HIS H 84 ASN C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.074363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2874 r_free = 0.2874 target = 0.049930 restraints weight = 81958.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.051440 restraints weight = 34012.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.052477 restraints weight = 21286.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.053075 restraints weight = 16627.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2957 r_free = 0.2957 target = 0.053285 restraints weight = 14651.367| |-----------------------------------------------------------------------------| r_work (final): 0.2930 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13661 Z= 0.254 Angle : 0.731 8.448 19707 Z= 0.416 Chirality : 0.045 0.416 2241 Planarity : 0.005 0.035 1475 Dihedral : 30.613 178.719 4161 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 16.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.99 % Allowed : 19.81 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.28), residues: 842 helix: 1.04 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 99 TYR 0.031 0.003 TYR G 57 PHE 0.025 0.002 PHE E 67 TRP 0.008 0.002 TRP K 61 HIS 0.036 0.002 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00511 / 0.25 (13651) covalent geometry : angle 0.72477 / 0.42 (19692) hydrogen bonds : bond 0.06291 / 4.26 ( 791) hydrogen bonds : angle 3.91065 / 2.81 ( 1987) metal coordination : bond 0.00772 / 0.41 ( 8) metal coordination : angle 4.40228 / 2.48 ( 9) link_TRANS : bond 0.00268 / 0.14 ( 2) link_TRANS : angle 0.51102 / 0.25 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 273 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7926 (mt-10) cc_final: 0.6966 (mt-10) REVERT: A 92 LEU cc_start: 0.9476 (OUTLIER) cc_final: 0.9224 (mm) REVERT: A 93 GLN cc_start: 0.8446 (tt0) cc_final: 0.8153 (tp40) REVERT: A 125 GLN cc_start: 0.9412 (mp10) cc_final: 0.8882 (mp10) REVERT: B 23 ARG cc_start: 0.8659 (mmp80) cc_final: 0.8378 (mmp80) REVERT: B 25 ASN cc_start: 0.8848 (m110) cc_final: 0.8209 (m110) REVERT: B 63 GLU cc_start: 0.8639 (mp0) cc_final: 0.8385 (mp0) REVERT: B 88 TYR cc_start: 0.8871 (m-10) cc_final: 0.8577 (m-80) REVERT: D 34 LYS cc_start: 0.8981 (mptt) cc_final: 0.8730 (mmtm) REVERT: D 57 LYS cc_start: 0.9112 (mmtt) cc_final: 0.8673 (mmmm) REVERT: D 105 GLU cc_start: 0.8544 (tp30) cc_final: 0.7290 (tp30) REVERT: D 109 HIS cc_start: 0.9185 (m170) cc_final: 0.8877 (m170) REVERT: D 120 LYS cc_start: 0.9267 (tttp) cc_final: 0.8893 (ttmm) REVERT: E 60 LEU cc_start: 0.8892 (mm) cc_final: 0.8583 (mm) REVERT: E 68 GLN cc_start: 0.8939 (pp30) cc_final: 0.8620 (pp30) REVERT: E 81 ASP cc_start: 0.8266 (m-30) cc_final: 0.8034 (m-30) REVERT: E 120 MET cc_start: 0.8321 (mtt) cc_final: 0.7763 (mtt) REVERT: E 125 GLN cc_start: 0.8900 (mp10) cc_final: 0.8609 (mp10) REVERT: F 31 LYS cc_start: 0.9268 (tppp) cc_final: 0.9061 (tppp) REVERT: H 68 ASP cc_start: 0.9083 (t70) cc_final: 0.8685 (t0) REVERT: H 83 TYR cc_start: 0.8471 (m-10) cc_final: 0.7905 (m-10) REVERT: H 85 LYS cc_start: 0.9484 (mptt) cc_final: 0.9254 (mmmm) REVERT: H 86 ARG cc_start: 0.9158 (mmt-90) cc_final: 0.8247 (mtt-85) REVERT: H 120 LYS cc_start: 0.9380 (ttmt) cc_final: 0.8848 (tptt) REVERT: C 24 GLN cc_start: 0.8517 (pm20) cc_final: 0.8231 (pm20) REVERT: C 38 ASN cc_start: 0.8555 (t0) cc_final: 0.8335 (t0) REVERT: C 78 ILE cc_start: 0.8991 (mm) cc_final: 0.8745 (mm) REVERT: C 91 GLU cc_start: 0.9177 (tp30) cc_final: 0.8903 (tp30) REVERT: C 92 GLU cc_start: 0.8832 (mt-10) cc_final: 0.8075 (mp0) REVERT: G 90 ASP cc_start: 0.8790 (t0) cc_final: 0.8303 (t0) REVERT: G 104 GLN cc_start: 0.9285 (mp10) cc_final: 0.8862 (mp10) outliers start: 29 outliers final: 19 residues processed: 288 average time/residue: 0.1275 time to fit residues: 50.6096 Evaluate side-chains 282 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 262 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 37 TYR Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 82 HIS Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 80 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 71 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 chunk 55 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 17 optimal weight: 5.9990 chunk 85 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 50 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 82 HIS K 41 GLN C 73 ASN C 84 GLN G 24 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3486 r_free = 0.3486 target = 0.075194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.050584 restraints weight = 77764.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.052149 restraints weight = 32590.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053177 restraints weight = 20767.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.053775 restraints weight = 16389.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.054005 restraints weight = 14530.060| |-----------------------------------------------------------------------------| r_work (final): 0.2953 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13661 Z= 0.189 Angle : 0.696 9.761 19707 Z= 0.398 Chirality : 0.043 0.414 2241 Planarity : 0.005 0.037 1475 Dihedral : 30.616 178.655 4161 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.71 % Allowed : 22.83 % Favored : 73.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.54 (0.28), residues: 842 helix: 1.11 (0.21), residues: 587 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 92 TYR 0.029 0.002 TYR G 57 PHE 0.013 0.002 PHE E 67 TRP 0.008 0.002 TRP K 77 HIS 0.024 0.002 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.19 (13651) covalent geometry : angle 0.68870 / 0.40 (19692) hydrogen bonds : bond 0.05396 / 3.60 ( 791) hydrogen bonds : angle 3.74780 / 2.68 ( 1987) metal coordination : bond 0.00659 / 0.31 ( 8) metal coordination : angle 4.77860 / 2.82 ( 9) link_TRANS : bond 0.00110 / 0.06 ( 2) link_TRANS : angle 0.17625 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 278 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7567 (mt-10) REVERT: A 92 LEU cc_start: 0.9457 (OUTLIER) cc_final: 0.9209 (mm) REVERT: A 93 GLN cc_start: 0.8407 (tt0) cc_final: 0.8170 (tp40) REVERT: A 125 GLN cc_start: 0.9354 (mp10) cc_final: 0.8870 (mp10) REVERT: B 23 ARG cc_start: 0.8662 (mmp80) cc_final: 0.8222 (mmp80) REVERT: B 88 TYR cc_start: 0.8887 (m-10) cc_final: 0.8573 (m-80) REVERT: D 34 LYS cc_start: 0.9000 (mptt) cc_final: 0.8721 (mmtm) REVERT: D 57 LYS cc_start: 0.9072 (mmtt) cc_final: 0.8638 (mmmm) REVERT: D 76 GLU cc_start: 0.9319 (tp30) cc_final: 0.9053 (tp30) REVERT: D 105 GLU cc_start: 0.8508 (tp30) cc_final: 0.7258 (tp30) REVERT: D 109 HIS cc_start: 0.9143 (m170) cc_final: 0.8833 (m170) REVERT: D 120 LYS cc_start: 0.9261 (tttp) cc_final: 0.8879 (ttmm) REVERT: E 60 LEU cc_start: 0.8913 (mm) cc_final: 0.8380 (mm) REVERT: E 68 GLN cc_start: 0.8914 (pp30) cc_final: 0.8657 (pp30) REVERT: E 81 ASP cc_start: 0.8223 (m-30) cc_final: 0.7954 (m-30) REVERT: E 97 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8018 (mt-10) REVERT: E 120 MET cc_start: 0.8371 (mtt) cc_final: 0.7905 (mtt) REVERT: E 125 GLN cc_start: 0.8937 (OUTLIER) cc_final: 0.8570 (mp10) REVERT: F 31 LYS cc_start: 0.9246 (tppp) cc_final: 0.9031 (tppp) REVERT: H 33 ARG cc_start: 0.8728 (tpp-160) cc_final: 0.8443 (tpp80) REVERT: H 68 ASP cc_start: 0.9036 (t70) cc_final: 0.8667 (t0) REVERT: H 83 TYR cc_start: 0.8428 (m-10) cc_final: 0.7915 (m-10) REVERT: H 85 LYS cc_start: 0.9499 (mptt) cc_final: 0.9285 (mmmm) REVERT: H 86 ARG cc_start: 0.9128 (mmt-90) cc_final: 0.8232 (mtt-85) REVERT: C 38 ASN cc_start: 0.8349 (t0) cc_final: 0.8093 (t0) REVERT: C 78 ILE cc_start: 0.8973 (mm) cc_final: 0.8737 (mm) REVERT: C 91 GLU cc_start: 0.9154 (tp30) cc_final: 0.8858 (tp30) REVERT: C 92 GLU cc_start: 0.8811 (mt-10) cc_final: 0.8035 (mp0) REVERT: C 104 GLN cc_start: 0.8486 (mm-40) cc_final: 0.8242 (mp10) REVERT: G 24 GLN cc_start: 0.8592 (tt0) cc_final: 0.8384 (tt0) REVERT: G 56 GLU cc_start: 0.9165 (OUTLIER) cc_final: 0.8556 (tt0) REVERT: G 90 ASP cc_start: 0.8776 (t0) cc_final: 0.8204 (t0) REVERT: G 104 GLN cc_start: 0.9242 (mp10) cc_final: 0.8802 (mp10) outliers start: 27 outliers final: 13 residues processed: 290 average time/residue: 0.1281 time to fit residues: 50.9369 Evaluate side-chains 285 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 269 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 69 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 19 optimal weight: 9.9990 chunk 102 optimal weight: 0.7980 chunk 106 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 60 optimal weight: 20.0000 chunk 35 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 84 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.075389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.051030 restraints weight = 64371.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.052578 restraints weight = 29560.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 55)----------------| | r_work = 0.2965 r_free = 0.2965 target = 0.053551 restraints weight = 19597.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053832 restraints weight = 15806.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2986 r_free = 0.2986 target = 0.054219 restraints weight = 14589.430| |-----------------------------------------------------------------------------| r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2961 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2961 r_free = 0.2961 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2961 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8519 moved from start: 0.1921 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13661 Z= 0.181 Angle : 0.699 11.882 19707 Z= 0.398 Chirality : 0.044 0.409 2241 Planarity : 0.005 0.041 1475 Dihedral : 30.587 179.408 4161 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.44 % Allowed : 24.62 % Favored : 71.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.66 (0.28), residues: 842 helix: 1.22 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 92 TYR 0.026 0.002 TYR H 40 PHE 0.008 0.002 PHE A 67 TRP 0.008 0.002 TRP K 77 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.18 (13651) covalent geometry : angle 0.68933 / 0.40 (19692) hydrogen bonds : bond 0.05258 / 3.49 ( 791) hydrogen bonds : angle 3.70239 / 2.64 ( 1987) metal coordination : bond 0.00714 / 0.29 ( 8) metal coordination : angle 5.41493 / 3.18 ( 9) link_TRANS : bond 0.00099 / 0.05 ( 2) link_TRANS : angle 0.16785 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 280 time to evaluate : 0.276 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7834 (mt-10) cc_final: 0.7595 (mt-10) REVERT: A 125 GLN cc_start: 0.9328 (mp10) cc_final: 0.8840 (mp10) REVERT: B 88 TYR cc_start: 0.8828 (m-10) cc_final: 0.8584 (m-80) REVERT: D 34 LYS cc_start: 0.9013 (mptt) cc_final: 0.8722 (mmtm) REVERT: D 57 LYS cc_start: 0.9083 (mmtt) cc_final: 0.8641 (mmmm) REVERT: D 105 GLU cc_start: 0.8503 (tp30) cc_final: 0.7253 (tp30) REVERT: D 109 HIS cc_start: 0.9148 (m170) cc_final: 0.8837 (m170) REVERT: D 120 LYS cc_start: 0.9268 (tttp) cc_final: 0.8874 (ttmm) REVERT: E 60 LEU cc_start: 0.8904 (mm) cc_final: 0.8412 (mm) REVERT: E 68 GLN cc_start: 0.8911 (pp30) cc_final: 0.8581 (pp30) REVERT: E 81 ASP cc_start: 0.8222 (m-30) cc_final: 0.7946 (m-30) REVERT: E 97 GLU cc_start: 0.8507 (mt-10) cc_final: 0.8141 (mt-10) REVERT: H 33 ARG cc_start: 0.8735 (tpp-160) cc_final: 0.8444 (tpp80) REVERT: H 68 ASP cc_start: 0.9041 (t70) cc_final: 0.8668 (t0) REVERT: H 83 TYR cc_start: 0.8342 (m-10) cc_final: 0.7788 (m-10) REVERT: H 85 LYS cc_start: 0.9528 (mptt) cc_final: 0.9317 (mmmm) REVERT: H 86 ARG cc_start: 0.9123 (mmt-90) cc_final: 0.8252 (mtt-85) REVERT: C 38 ASN cc_start: 0.8305 (t0) cc_final: 0.8057 (t0) REVERT: C 78 ILE cc_start: 0.8988 (mm) cc_final: 0.8742 (mm) REVERT: C 91 GLU cc_start: 0.9206 (tp30) cc_final: 0.8867 (tp30) REVERT: C 92 GLU cc_start: 0.8825 (mt-10) cc_final: 0.8044 (mp0) REVERT: C 104 GLN cc_start: 0.8543 (mm-40) cc_final: 0.8295 (mp10) REVERT: G 90 ASP cc_start: 0.8767 (t0) cc_final: 0.8223 (t0) REVERT: G 104 GLN cc_start: 0.9220 (mp10) cc_final: 0.8779 (mp10) outliers start: 25 outliers final: 18 residues processed: 292 average time/residue: 0.1273 time to fit residues: 51.0444 Evaluate side-chains 296 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 278 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 6 optimal weight: 5.9990 chunk 68 optimal weight: 20.0000 chunk 95 optimal weight: 2.9990 chunk 64 optimal weight: 20.0000 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.0870 chunk 49 optimal weight: 0.8980 chunk 57 optimal weight: 20.0000 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 100 optimal weight: 4.9990 overall best weight: 2.3964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN B 93 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.075108 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.050348 restraints weight = 78984.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.052039 restraints weight = 32894.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.053094 restraints weight = 20768.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 48)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.053695 restraints weight = 16273.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053878 restraints weight = 14369.985| |-----------------------------------------------------------------------------| r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13661 Z= 0.196 Angle : 0.709 9.921 19707 Z= 0.401 Chirality : 0.044 0.405 2241 Planarity : 0.005 0.047 1475 Dihedral : 30.618 179.951 4161 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.30 % Allowed : 24.48 % Favored : 72.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.28), residues: 842 helix: 1.21 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 92 TYR 0.026 0.002 TYR H 40 PHE 0.010 0.002 PHE A 67 TRP 0.007 0.001 TRP K 77 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00387 / 0.20 (13651) covalent geometry : angle 0.70213 / 0.40 (19692) hydrogen bonds : bond 0.05361 / 3.59 ( 791) hydrogen bonds : angle 3.72600 / 2.66 ( 1987) metal coordination : bond 0.00677 / 0.30 ( 8) metal coordination : angle 4.59364 / 2.73 ( 9) link_TRANS : bond 0.00315 / 0.15 ( 2) link_TRANS : angle 0.19172 / 0.09 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 300 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 276 time to evaluate : 0.336 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7816 (mt-10) cc_final: 0.7424 (mp0) REVERT: A 93 GLN cc_start: 0.8820 (tp40) cc_final: 0.8541 (tp40) REVERT: A 125 GLN cc_start: 0.9330 (mp10) cc_final: 0.8830 (mp10) REVERT: B 88 TYR cc_start: 0.8812 (m-10) cc_final: 0.8569 (m-80) REVERT: D 34 LYS cc_start: 0.9022 (mptt) cc_final: 0.8732 (mmtm) REVERT: D 57 LYS cc_start: 0.9091 (mmtt) cc_final: 0.8658 (mmmm) REVERT: D 79 ARG cc_start: 0.8456 (mtp-110) cc_final: 0.7970 (mtm110) REVERT: D 105 GLU cc_start: 0.8522 (tp30) cc_final: 0.7316 (tp30) REVERT: D 120 LYS cc_start: 0.9268 (tttp) cc_final: 0.8879 (ttmm) REVERT: E 60 LEU cc_start: 0.8886 (mm) cc_final: 0.8435 (mm) REVERT: E 68 GLN cc_start: 0.8943 (pp30) cc_final: 0.8635 (pp30) REVERT: E 81 ASP cc_start: 0.8225 (m-30) cc_final: 0.7946 (m-30) REVERT: E 97 GLU cc_start: 0.8466 (mt-10) cc_final: 0.8187 (mt-10) REVERT: E 120 MET cc_start: 0.8401 (mmm) cc_final: 0.7943 (mtp) REVERT: H 33 ARG cc_start: 0.8728 (tpp-160) cc_final: 0.8518 (tpp80) REVERT: H 68 ASP cc_start: 0.9033 (t70) cc_final: 0.8684 (t0) REVERT: H 83 TYR cc_start: 0.8283 (m-10) cc_final: 0.7825 (m-10) REVERT: H 85 LYS cc_start: 0.9530 (mptt) cc_final: 0.9322 (mmmm) REVERT: H 86 ARG cc_start: 0.9139 (mmt-90) cc_final: 0.8250 (mtt-85) REVERT: H 92 ARG cc_start: 0.9288 (ptm-80) cc_final: 0.8995 (ptm160) REVERT: C 38 ASN cc_start: 0.8341 (t0) cc_final: 0.8041 (t0) REVERT: C 78 ILE cc_start: 0.9006 (mm) cc_final: 0.8774 (mm) REVERT: C 91 GLU cc_start: 0.9222 (tp30) cc_final: 0.8829 (tp30) REVERT: C 92 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8029 (mp0) REVERT: G 56 GLU cc_start: 0.9150 (OUTLIER) cc_final: 0.8919 (tt0) REVERT: G 90 ASP cc_start: 0.8854 (t0) cc_final: 0.8340 (t0) REVERT: G 104 GLN cc_start: 0.9219 (mp10) cc_final: 0.8772 (mp10) outliers start: 24 outliers final: 18 residues processed: 283 average time/residue: 0.1376 time to fit residues: 53.0758 Evaluate side-chains 288 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 269 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 86 optimal weight: 20.0000 chunk 103 optimal weight: 3.9990 chunk 55 optimal weight: 20.0000 chunk 7 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 62 optimal weight: 20.0000 chunk 101 optimal weight: 0.7980 chunk 107 optimal weight: 0.8980 chunk 71 optimal weight: 20.0000 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.076045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.051838 restraints weight = 108689.118| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.2984 r_free = 0.2984 target = 0.053767 restraints weight = 38855.948| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.054567 restraints weight = 21411.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.054792 restraints weight = 16789.976| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.054992 restraints weight = 15622.573| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8514 moved from start: 0.2143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 13661 Z= 0.159 Angle : 0.692 9.530 19707 Z= 0.394 Chirality : 0.043 0.402 2241 Planarity : 0.004 0.046 1475 Dihedral : 30.511 179.733 4161 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 13.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.34 % Allowed : 26.82 % Favored : 70.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.71 (0.28), residues: 842 helix: 1.25 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 92 TYR 0.036 0.003 TYR G 57 PHE 0.008 0.001 PHE E 67 TRP 0.007 0.001 TRP K 77 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.16 (13651) covalent geometry : angle 0.68605 / 0.39 (19692) hydrogen bonds : bond 0.04816 / 3.15 ( 791) hydrogen bonds : angle 3.59180 / 2.57 ( 1987) metal coordination : bond 0.00599 / 0.27 ( 8) metal coordination : angle 4.42660 / 2.66 ( 9) link_TRANS : bond 0.00081 / 0.04 ( 2) link_TRANS : angle 0.20010 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 290 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7482 (mp0) REVERT: A 90 MET cc_start: 0.8924 (mmp) cc_final: 0.8700 (mmp) REVERT: A 93 GLN cc_start: 0.8829 (tp40) cc_final: 0.8538 (tp40) REVERT: A 125 GLN cc_start: 0.9305 (mp10) cc_final: 0.8816 (mp10) REVERT: B 23 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8219 (mmp80) REVERT: D 34 LYS cc_start: 0.8991 (mptt) cc_final: 0.8711 (mmtm) REVERT: D 57 LYS cc_start: 0.9077 (mmtt) cc_final: 0.8620 (mmmm) REVERT: D 59 MET cc_start: 0.9261 (tpp) cc_final: 0.9035 (tpp) REVERT: D 79 ARG cc_start: 0.8447 (mtp-110) cc_final: 0.8002 (mtm110) REVERT: D 96 THR cc_start: 0.9551 (m) cc_final: 0.9342 (p) REVERT: D 105 GLU cc_start: 0.8481 (tp30) cc_final: 0.6886 (tp30) REVERT: D 108 LYS cc_start: 0.9454 (ttpt) cc_final: 0.9208 (ttpp) REVERT: D 120 LYS cc_start: 0.9264 (tttp) cc_final: 0.8868 (ttmm) REVERT: E 60 LEU cc_start: 0.8921 (mm) cc_final: 0.8442 (mm) REVERT: E 67 PHE cc_start: 0.9151 (t80) cc_final: 0.8892 (t80) REVERT: E 68 GLN cc_start: 0.8881 (pp30) cc_final: 0.8533 (pp30) REVERT: E 81 ASP cc_start: 0.8171 (m-30) cc_final: 0.7880 (m-30) REVERT: E 97 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8183 (mt-10) REVERT: E 120 MET cc_start: 0.8448 (mmm) cc_final: 0.7906 (mtp) REVERT: H 68 ASP cc_start: 0.9043 (t70) cc_final: 0.8698 (t0) REVERT: H 83 TYR cc_start: 0.8377 (m-10) cc_final: 0.7950 (m-10) REVERT: H 85 LYS cc_start: 0.9531 (mptt) cc_final: 0.9311 (mmmm) REVERT: H 86 ARG cc_start: 0.9121 (mmt-90) cc_final: 0.8251 (mtt-85) REVERT: H 92 ARG cc_start: 0.9238 (ptm-80) cc_final: 0.8936 (ptm160) REVERT: C 38 ASN cc_start: 0.8176 (t0) cc_final: 0.7859 (t0) REVERT: C 78 ILE cc_start: 0.8970 (mm) cc_final: 0.8673 (mm) REVERT: C 84 GLN cc_start: 0.9206 (tm-30) cc_final: 0.8767 (tp-100) REVERT: C 91 GLU cc_start: 0.9215 (tp30) cc_final: 0.8788 (tp30) REVERT: C 92 GLU cc_start: 0.8840 (mt-10) cc_final: 0.8106 (mp0) REVERT: C 104 GLN cc_start: 0.8549 (mm-40) cc_final: 0.8267 (mp10) REVERT: G 90 ASP cc_start: 0.8904 (t0) cc_final: 0.8575 (t0) REVERT: G 104 GLN cc_start: 0.9183 (mp10) cc_final: 0.8674 (mp10) outliers start: 17 outliers final: 13 residues processed: 294 average time/residue: 0.1381 time to fit residues: 55.6105 Evaluate side-chains 285 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 272 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 92 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 39 optimal weight: 0.7980 chunk 86 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 68 optimal weight: 20.0000 chunk 58 optimal weight: 20.0000 chunk 77 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 84 GLN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.075428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.050985 restraints weight = 99453.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.052653 restraints weight = 37751.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2975 r_free = 0.2975 target = 0.053721 restraints weight = 22538.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 41)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.054411 restraints weight = 17339.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.054618 restraints weight = 14996.092| |-----------------------------------------------------------------------------| r_work (final): 0.2962 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2963 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2963 r_free = 0.2963 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2963 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 13661 Z= 0.176 Angle : 0.711 14.879 19707 Z= 0.399 Chirality : 0.043 0.395 2241 Planarity : 0.005 0.045 1475 Dihedral : 30.508 179.752 4161 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.16 % Allowed : 27.24 % Favored : 69.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.68 (0.28), residues: 842 helix: 1.21 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.25 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 79 TYR 0.026 0.003 TYR F 88 PHE 0.023 0.002 PHE H 65 TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (13651) covalent geometry : angle 0.70537 / 0.40 (19692) hydrogen bonds : bond 0.05056 / 3.36 ( 791) hydrogen bonds : angle 3.64180 / 2.60 ( 1987) metal coordination : bond 0.00611 / 0.28 ( 8) metal coordination : angle 4.25863 / 2.55 ( 9) link_TRANS : bond 0.00112 / 0.06 ( 2) link_TRANS : angle 0.20275 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 279 time to evaluate : 0.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7775 (mt-10) cc_final: 0.7483 (mp0) REVERT: A 93 GLN cc_start: 0.8878 (tp40) cc_final: 0.8534 (tp40) REVERT: A 125 GLN cc_start: 0.9308 (OUTLIER) cc_final: 0.8819 (mp10) REVERT: B 59 LYS cc_start: 0.9478 (ttmm) cc_final: 0.9187 (ttmm) REVERT: B 63 GLU cc_start: 0.8690 (mt-10) cc_final: 0.8487 (mt-10) REVERT: D 34 LYS cc_start: 0.8978 (mptt) cc_final: 0.8694 (mmtm) REVERT: D 57 LYS cc_start: 0.9088 (mmtt) cc_final: 0.8626 (mmmm) REVERT: D 59 MET cc_start: 0.9234 (tpp) cc_final: 0.8987 (tpp) REVERT: D 79 ARG cc_start: 0.8510 (mtp-110) cc_final: 0.8058 (mtm110) REVERT: D 92 ARG cc_start: 0.8868 (ttp80) cc_final: 0.8373 (ttp80) REVERT: D 96 THR cc_start: 0.9542 (m) cc_final: 0.9320 (p) REVERT: D 105 GLU cc_start: 0.8559 (tp30) cc_final: 0.6944 (tp30) REVERT: D 120 LYS cc_start: 0.9274 (tttp) cc_final: 0.8878 (ttmm) REVERT: E 60 LEU cc_start: 0.8937 (mm) cc_final: 0.8413 (mm) REVERT: E 68 GLN cc_start: 0.8910 (pp30) cc_final: 0.8585 (pp30) REVERT: E 81 ASP cc_start: 0.8104 (m-30) cc_final: 0.7827 (m-30) REVERT: E 97 GLU cc_start: 0.8423 (mt-10) cc_final: 0.8201 (mt-10) REVERT: E 120 MET cc_start: 0.8393 (mmm) cc_final: 0.7822 (mtp) REVERT: H 68 ASP cc_start: 0.9023 (t70) cc_final: 0.8696 (t0) REVERT: H 83 TYR cc_start: 0.8318 (m-10) cc_final: 0.7836 (m-10) REVERT: H 85 LYS cc_start: 0.9524 (mptt) cc_final: 0.9315 (mmmm) REVERT: H 86 ARG cc_start: 0.9132 (mmt-90) cc_final: 0.8251 (mtt-85) REVERT: C 38 ASN cc_start: 0.8191 (t0) cc_final: 0.7819 (t0) REVERT: C 78 ILE cc_start: 0.8979 (mm) cc_final: 0.8705 (mm) REVERT: C 91 GLU cc_start: 0.9248 (tp30) cc_final: 0.8897 (tp30) REVERT: C 92 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8079 (mp0) REVERT: G 38 ASN cc_start: 0.8300 (p0) cc_final: 0.8023 (p0) REVERT: G 90 ASP cc_start: 0.8839 (t0) cc_final: 0.8638 (t0) REVERT: G 104 GLN cc_start: 0.9195 (mp10) cc_final: 0.8670 (mp10) outliers start: 23 outliers final: 15 residues processed: 287 average time/residue: 0.1391 time to fit residues: 54.6579 Evaluate side-chains 287 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 271 time to evaluate : 0.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 63 optimal weight: 20.0000 chunk 24 optimal weight: 0.8980 chunk 67 optimal weight: 30.0000 chunk 101 optimal weight: 4.9990 chunk 61 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 77 optimal weight: 20.0000 chunk 12 optimal weight: 4.9990 chunk 95 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 28 optimal weight: 2.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.074393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.050065 restraints weight = 93185.263| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 53)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.051708 restraints weight = 36340.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.052781 restraints weight = 22169.764| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.053426 restraints weight = 17119.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.053595 restraints weight = 14964.285| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2931 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2931 r_free = 0.2931 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2931 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 13661 Z= 0.231 Angle : 0.746 13.395 19707 Z= 0.416 Chirality : 0.044 0.390 2241 Planarity : 0.005 0.045 1475 Dihedral : 30.618 179.489 4161 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 16.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.61 % Allowed : 28.47 % Favored : 68.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.64 (0.28), residues: 842 helix: 1.18 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 29 TYR 0.033 0.003 TYR F 88 PHE 0.025 0.002 PHE E 67 TRP 0.008 0.001 TRP K 61 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00474 / 0.23 (13651) covalent geometry : angle 0.74063 / 0.42 (19692) hydrogen bonds : bond 0.05631 / 3.80 ( 791) hydrogen bonds : angle 3.77577 / 2.70 ( 1987) metal coordination : bond 0.00764 / 0.35 ( 8) metal coordination : angle 4.10164 / 2.43 ( 9) link_TRANS : bond 0.00194 / 0.10 ( 2) link_TRANS : angle 0.30893 / 0.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 270 time to evaluate : 0.341 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7284 (mp0) REVERT: A 125 GLN cc_start: 0.9327 (mp10) cc_final: 0.8837 (mp10) REVERT: B 25 ASN cc_start: 0.8792 (m110) cc_final: 0.8213 (m110) REVERT: B 59 LYS cc_start: 0.9487 (ttmm) cc_final: 0.9211 (ttmm) REVERT: B 63 GLU cc_start: 0.8644 (mt-10) cc_final: 0.8372 (mt-10) REVERT: D 34 LYS cc_start: 0.8987 (mptt) cc_final: 0.8699 (mmtm) REVERT: D 57 LYS cc_start: 0.9108 (mmtt) cc_final: 0.8799 (mmmm) REVERT: D 76 GLU cc_start: 0.9263 (tp30) cc_final: 0.8697 (tp30) REVERT: D 79 ARG cc_start: 0.8588 (mtp-110) cc_final: 0.8344 (ttp-110) REVERT: D 96 THR cc_start: 0.9555 (m) cc_final: 0.9351 (p) REVERT: D 105 GLU cc_start: 0.8539 (tp30) cc_final: 0.7648 (tp30) REVERT: D 120 LYS cc_start: 0.9274 (tttp) cc_final: 0.8877 (ttmm) REVERT: E 60 LEU cc_start: 0.8865 (mm) cc_final: 0.8400 (mm) REVERT: E 68 GLN cc_start: 0.8998 (pp30) cc_final: 0.8642 (pp30) REVERT: E 81 ASP cc_start: 0.8096 (m-30) cc_final: 0.7822 (m-30) REVERT: E 97 GLU cc_start: 0.8451 (mt-10) cc_final: 0.8227 (mt-10) REVERT: E 120 MET cc_start: 0.8395 (mmm) cc_final: 0.7926 (mtp) REVERT: E 133 GLU cc_start: 0.7741 (OUTLIER) cc_final: 0.7262 (pm20) REVERT: H 68 ASP cc_start: 0.9073 (t70) cc_final: 0.8726 (t0) REVERT: H 83 TYR cc_start: 0.8326 (m-10) cc_final: 0.8056 (m-10) REVERT: H 85 LYS cc_start: 0.9539 (mptt) cc_final: 0.9337 (mmmm) REVERT: H 86 ARG cc_start: 0.9149 (mmt-90) cc_final: 0.8262 (mtt-85) REVERT: C 38 ASN cc_start: 0.8235 (t0) cc_final: 0.7815 (t0) REVERT: C 78 ILE cc_start: 0.9031 (mm) cc_final: 0.8759 (mm) REVERT: C 84 GLN cc_start: 0.9217 (tm-30) cc_final: 0.8813 (tp-100) REVERT: C 91 GLU cc_start: 0.9259 (tp30) cc_final: 0.8852 (tp30) REVERT: C 92 GLU cc_start: 0.8805 (mt-10) cc_final: 0.8119 (mp0) REVERT: G 38 ASN cc_start: 0.8418 (p0) cc_final: 0.8128 (p0) REVERT: G 90 ASP cc_start: 0.8841 (t0) cc_final: 0.8641 (t0) REVERT: G 104 GLN cc_start: 0.9225 (mp10) cc_final: 0.8722 (mp10) outliers start: 19 outliers final: 16 residues processed: 277 average time/residue: 0.1283 time to fit residues: 48.8755 Evaluate side-chains 282 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 265 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 61 optimal weight: 20.0000 chunk 12 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 74 optimal weight: 20.0000 chunk 71 optimal weight: 20.0000 chunk 19 optimal weight: 9.9990 chunk 30 optimal weight: 3.9990 chunk 92 optimal weight: 0.6980 chunk 66 optimal weight: 30.0000 chunk 26 optimal weight: 20.0000 chunk 85 optimal weight: 9.9990 overall best weight: 3.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.073567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2860 r_free = 0.2860 target = 0.049260 restraints weight = 75633.693| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.050838 restraints weight = 33131.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.051827 restraints weight = 21383.882| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.052409 restraints weight = 16986.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2946 r_free = 0.2946 target = 0.052657 restraints weight = 15081.992| |-----------------------------------------------------------------------------| r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2916 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2916 r_free = 0.2916 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2916 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.2578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13661 Z= 0.246 Angle : 0.763 13.890 19707 Z= 0.425 Chirality : 0.045 0.380 2241 Planarity : 0.005 0.062 1475 Dihedral : 30.745 179.444 4161 Min Nonbonded Distance : 2.041 Molprobity Statistics. All-atom Clashscore : 17.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 2.75 % Allowed : 29.02 % Favored : 68.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.49 (0.28), residues: 842 helix: 1.09 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 92 TYR 0.034 0.003 TYR F 88 PHE 0.028 0.002 PHE E 67 TRP 0.009 0.002 TRP K 61 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00505 / 0.25 (13651) covalent geometry : angle 0.75823 / 0.42 (19692) hydrogen bonds : bond 0.05921 / 4.01 ( 791) hydrogen bonds : angle 3.90133 / 2.79 ( 1987) metal coordination : bond 0.00783 / 0.38 ( 8) metal coordination : angle 4.22401 / 2.44 ( 9) link_TRANS : bond 0.00204 / 0.10 ( 2) link_TRANS : angle 0.36540 / 0.14 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 267 time to evaluate : 0.356 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9331 (mp10) cc_final: 0.8847 (mp10) REVERT: B 25 ASN cc_start: 0.8817 (m110) cc_final: 0.8369 (m-40) REVERT: B 59 LYS cc_start: 0.9501 (ttmm) cc_final: 0.9230 (ttmm) REVERT: B 77 LYS cc_start: 0.9163 (mmtt) cc_final: 0.8722 (mmtt) REVERT: B 84 MET cc_start: 0.8462 (tpp) cc_final: 0.8064 (tpp) REVERT: D 34 LYS cc_start: 0.9000 (mptt) cc_final: 0.8713 (mmtm) REVERT: D 57 LYS cc_start: 0.9128 (mmtt) cc_final: 0.8819 (mmmm) REVERT: D 76 GLU cc_start: 0.9256 (tp30) cc_final: 0.8708 (tp30) REVERT: D 79 ARG cc_start: 0.8564 (mtp-110) cc_final: 0.8361 (ttp-110) REVERT: D 92 ARG cc_start: 0.8826 (ttp80) cc_final: 0.8129 (ttp80) REVERT: D 96 THR cc_start: 0.9552 (m) cc_final: 0.9340 (p) REVERT: D 105 GLU cc_start: 0.8425 (tp30) cc_final: 0.7518 (tp30) REVERT: D 120 LYS cc_start: 0.9282 (tttp) cc_final: 0.8915 (ttmm) REVERT: E 60 LEU cc_start: 0.8894 (mm) cc_final: 0.8415 (mm) REVERT: E 68 GLN cc_start: 0.9007 (pp30) cc_final: 0.8621 (pp30) REVERT: E 97 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8238 (mt-10) REVERT: E 133 GLU cc_start: 0.7679 (OUTLIER) cc_final: 0.7223 (pm20) REVERT: H 68 ASP cc_start: 0.9090 (t70) cc_final: 0.8729 (t0) REVERT: H 83 TYR cc_start: 0.8337 (m-10) cc_final: 0.7940 (m-10) REVERT: H 85 LYS cc_start: 0.9547 (mptt) cc_final: 0.9342 (mmmm) REVERT: H 86 ARG cc_start: 0.9179 (mmt-90) cc_final: 0.8785 (ttm-80) REVERT: C 38 ASN cc_start: 0.8328 (t0) cc_final: 0.7894 (t0) REVERT: C 78 ILE cc_start: 0.9071 (mm) cc_final: 0.8789 (mm) REVERT: C 84 GLN cc_start: 0.9215 (tm-30) cc_final: 0.8795 (tp-100) REVERT: C 91 GLU cc_start: 0.9253 (tp30) cc_final: 0.8895 (tp30) REVERT: C 92 GLU cc_start: 0.8841 (mt-10) cc_final: 0.8207 (mp0) REVERT: G 38 ASN cc_start: 0.8564 (p0) cc_final: 0.8278 (p0) REVERT: G 104 GLN cc_start: 0.9256 (mp10) cc_final: 0.8768 (mp10) outliers start: 20 outliers final: 16 residues processed: 276 average time/residue: 0.1337 time to fit residues: 51.0451 Evaluate side-chains 280 residues out of total 723 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 263 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 58 LEU Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 73 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 31 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 98 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 84 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.075247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.050834 restraints weight = 87554.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 55)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.052512 restraints weight = 35141.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 58)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.053580 restraints weight = 21716.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.053929 restraints weight = 16838.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.2989 r_free = 0.2989 target = 0.054466 restraints weight = 15290.818| |-----------------------------------------------------------------------------| r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 13661 Z= 0.166 Angle : 0.735 13.642 19707 Z= 0.411 Chirality : 0.045 0.380 2241 Planarity : 0.005 0.043 1475 Dihedral : 30.593 179.765 4161 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 2.34 % Allowed : 29.85 % Favored : 67.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.52 (0.28), residues: 842 helix: 1.11 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.36 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 92 TYR 0.032 0.003 TYR F 88 PHE 0.016 0.002 PHE H 65 TRP 0.008 0.002 TRP K 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (13651) covalent geometry : angle 0.72999 / 0.41 (19692) hydrogen bonds : bond 0.04827 / 3.17 ( 791) hydrogen bonds : angle 3.68291 / 2.64 ( 1987) metal coordination : bond 0.00701 / 0.34 ( 8) metal coordination : angle 4.03499 / 2.41 ( 9) link_TRANS : bond 0.00061 / 0.03 ( 2) link_TRANS : angle 0.26842 / 0.10 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2585.37 seconds wall clock time: 45 minutes 5.85 seconds (2705.85 seconds total)