Starting phenix.real_space_refine on Thu Jul 2 19:42:30 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcc_36157/07_2026/8jcc_36157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcc_36157/07_2026/8jcc_36157.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.42 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8jcc_36157/07_2026/8jcc_36157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcc_36157/07_2026/8jcc_36157.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8jcc_36157/07_2026/8jcc_36157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcc_36157/07_2026/8jcc_36157.map" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 232 5.49 5 S 16 5.16 5 C 5770 2.51 5 N 1958 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "I" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2391 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "J" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2365 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Time building chain proxies: 2.11, per 1000 atoms: 0.20 Number of scatterers: 10358 At special positions: 0 Unit cell: (83.74, 114.48, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 232 15.00 O 2382 8.00 N 1958 7.00 C 5770 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 Time building additional restraints: 0.90 Conformation dependent library (CDL) restraints added in 227.8 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 75.7% alpha, 3.1% beta 114 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 1.40 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.894A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.911A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 31 through 42 removed outlier: 4.044A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.968A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.650A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.343A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.608A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 76 through 105 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.578A pdb=" N ALA D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.801A pdb=" N LYS D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 removed outlier: 3.729A pdb=" N ALA D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.005A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.611A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.843A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.683A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.628A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 76 through 105 removed outlier: 3.523A pdb=" N THR H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 123 removed outlier: 3.598A pdb=" N VAL H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 144 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.641A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.378A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.671A pdb=" N ARG C 42 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.839A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.443A pdb=" N ARG G 42 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 379 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 297 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 1.76 Time building geometry restraints manager: 1.19 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: 1956 1.33 - 1.45: 3509 1.45 - 1.57: 5046 1.57 - 1.69: 462 1.69 - 1.81: 28 Bond restraints: 11001 Sorted by residual: bond pdb=" C3' DA I -38 " pdb=" C2' DA I -38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.17e+01 bond pdb=" C3' DC I 40 " pdb=" C2' DC I 40 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DC J 21 " pdb=" C2' DC J 21 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DC J 4 " pdb=" C2' DC J 4 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.11e+01 bond pdb=" C3' DG I -22 " pdb=" C2' DG I -22 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.07e+01 ... (remaining 10996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15219 1.88 - 3.76: 591 3.76 - 5.64: 26 5.64 - 7.52: 4 7.52 - 9.40: 3 Bond angle restraints: 15843 Sorted by residual: angle pdb=" N3 DT J -42 " pdb=" C4 DT J -42 " pdb=" O4 DT J -42 " ideal model delta sigma weight residual 119.90 122.64 -2.74 6.00e-01 2.78e+00 2.08e+01 angle pdb=" N3 DT I 31 " pdb=" C4 DT I 31 " pdb=" O4 DT I 31 " ideal model delta sigma weight residual 119.90 122.49 -2.59 6.00e-01 2.78e+00 1.87e+01 angle pdb=" O4' DG I -35 " pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 106.00 103.43 2.57 6.00e-01 2.78e+00 1.84e+01 angle pdb=" N3 DT I -50 " pdb=" C4 DT I -50 " pdb=" O4 DT I -50 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 angle pdb=" N3 DT I -39 " pdb=" C4 DT I -39 " pdb=" O4 DT I -39 " ideal model delta sigma weight residual 119.90 122.46 -2.56 6.00e-01 2.78e+00 1.82e+01 ... (remaining 15838 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.78: 4792 35.78 - 71.55: 1192 71.55 - 107.33: 16 107.33 - 143.10: 2 143.10 - 178.88: 1 Dihedral angle restraints: 6003 sinusoidal: 3967 harmonic: 2036 Sorted by residual: dihedral pdb=" C4' DT I -17 " pdb=" C3' DT I -17 " pdb=" O3' DT I -17 " pdb=" P DT I -16 " ideal model delta sinusoidal sigma weight residual 220.00 41.12 178.88 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DC J 4 " pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " pdb=" P DC J 5 " ideal model delta sinusoidal sigma weight residual 220.00 88.74 131.26 1 3.50e+01 8.16e-04 1.30e+01 dihedral pdb=" C4' DA I -38 " pdb=" C3' DA I -38 " pdb=" O3' DA I -38 " pdb=" P DG I -37 " ideal model delta sinusoidal sigma weight residual 220.00 97.11 122.89 1 3.50e+01 8.16e-04 1.21e+01 ... (remaining 6000 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 1230 0.041 - 0.082: 430 0.082 - 0.122: 144 0.122 - 0.163: 10 0.163 - 0.204: 1 Chirality restraints: 1815 Sorted by residual: chirality pdb=" CB ILE H 110 " pdb=" CA ILE H 110 " pdb=" CG1 ILE H 110 " pdb=" CG2 ILE H 110 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" C3' DT I -17 " pdb=" C4' DT I -17 " pdb=" O3' DT I -17 " pdb=" C2' DT I -17 " both_signs ideal model delta sigma weight residual False -2.73 -2.57 -0.16 2.00e-01 2.50e+01 6.11e-01 chirality pdb=" C3' DC J 4 " pdb=" C4' DC J 4 " pdb=" O3' DC J 4 " pdb=" C2' DC J 4 " both_signs ideal model delta sigma weight residual False -2.73 -2.58 -0.15 2.00e-01 2.50e+01 5.35e-01 ... (remaining 1812 not shown) Planarity restraints: 1203 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " 0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO A 43 " -0.093 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -5 " 0.025 2.00e-02 2.50e+03 1.08e-02 3.49e+00 pdb=" N9 DG I -5 " -0.024 2.00e-02 2.50e+03 pdb=" C8 DG I -5 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG I -5 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I -5 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I -5 " 0.005 2.00e-02 2.50e+03 pdb=" O6 DG I -5 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DG I -5 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -5 " -0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -5 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -5 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I -5 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I -35 " -0.024 2.00e-02 2.50e+03 9.74e-03 2.84e+00 pdb=" N9 DG I -35 " 0.020 2.00e-02 2.50e+03 pdb=" C8 DG I -35 " 0.006 2.00e-02 2.50e+03 pdb=" N7 DG I -35 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DG I -35 " -0.002 2.00e-02 2.50e+03 pdb=" O6 DG I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DG I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DG I -35 " 0.000 2.00e-02 2.50e+03 pdb=" N2 DG I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N3 DG I -35 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DG I -35 " 0.002 2.00e-02 2.50e+03 ... (remaining 1200 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1893 2.78 - 3.31: 9631 3.31 - 3.84: 20427 3.84 - 4.37: 23005 4.37 - 4.90: 33585 Nonbonded interactions: 88541 Sorted by model distance: nonbonded pdb=" O ILE C 78 " pdb=" OG SER D 76 " model vdw 2.246 3.040 nonbonded pdb=" OG SER H 57 " pdb=" OD2 ASP H 84 " model vdw 2.260 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 89 " model vdw 2.274 3.040 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.284 3.040 nonbonded pdb=" OG SER D 85 " pdb=" O GLY F 101 " model vdw 2.290 3.040 ... (remaining 88536 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 'B' selection = (chain 'F' and resid 23 through 101) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 15 through 105) } ncs_group { reference = chain 'D' selection = (chain 'H' and resid 56 through 147) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.660 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 10.920 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7686 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 0.037 11001 Z= 0.510 Angle : 0.742 9.395 15843 Z= 0.627 Chirality : 0.045 0.204 1815 Planarity : 0.004 0.054 1203 Dihedral : 28.833 178.878 4687 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.34 % Allowed : 31.62 % Favored : 68.03 % 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: 1.53 (0.32), residues: 691 helix: 1.75 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 103 TYR 0.011 0.001 TYR D 145 PHE 0.007 0.001 PHE D 58 TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS H 70 Details of bonding type rmsd/Z covalent geometry : bond 0.00622 / 0.51 (11001) covalent geometry : angle 0.74208 / 0.63 (15843) hydrogen bonds : bond 0.11443 / 8.33 ( 676) hydrogen bonds : angle 4.05117 / 3.01 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.224 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7118 (t0) cc_final: 0.6514 (t0) REVERT: C 57 TYR cc_start: 0.7832 (t80) cc_final: 0.7582 (t80) REVERT: G 61 GLU cc_start: 0.6135 (tt0) cc_final: 0.5170 (tt0) REVERT: H 108 GLN cc_start: 0.7506 (pt0) cc_final: 0.6928 (pt0) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.1269 time to fit residues: 53.2428 Evaluate side-chains 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 255 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 0.6980 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.2980 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 30.0000 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 84 GLN C 94 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.035284 restraints weight = 56441.049| |-----------------------------------------------------------------------------| r_work (start): 0.2647 rms_B_bonded: 3.58 r_work (final): 0.2647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 11001 Z= 0.173 Angle : 0.708 7.895 15843 Z= 0.407 Chirality : 0.045 0.380 1815 Planarity : 0.006 0.053 1203 Dihedral : 30.683 177.795 3304 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 7.01 % Allowed : 34.02 % Favored : 58.97 % 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: 1.47 (0.32), residues: 691 helix: 1.61 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 35 TYR 0.019 0.002 TYR B 98 PHE 0.023 0.002 PHE D 62 TRP 0.006 0.001 TRP H 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00314 / 0.17 (11001) covalent geometry : angle 0.70772 / 0.41 (15843) hydrogen bonds : bond 0.04883 / 3.26 ( 676) hydrogen bonds : angle 3.50021 / 2.57 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 264 time to evaluate : 0.273 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9431 (tt0) cc_final: 0.8674 (tp30) REVERT: A 68 GLN cc_start: 0.9390 (tt0) cc_final: 0.9130 (tt0) REVERT: B 63 GLU cc_start: 0.8908 (OUTLIER) cc_final: 0.8493 (mp0) REVERT: B 79 LYS cc_start: 0.8892 (mtpt) cc_final: 0.8638 (mtmm) REVERT: C 25 PHE cc_start: 0.8744 (m-10) cc_final: 0.8338 (m-80) REVERT: C 35 ARG cc_start: 0.9497 (ttm110) cc_final: 0.8795 (mtt90) REVERT: C 38 ASN cc_start: 0.9044 (t0) cc_final: 0.8709 (t0) REVERT: C 39 TYR cc_start: 0.8300 (m-80) cc_final: 0.8065 (m-80) REVERT: C 71 ARG cc_start: 0.8493 (mtm-85) cc_final: 0.8207 (mtm-85) REVERT: C 84 GLN cc_start: 0.9537 (tt0) cc_final: 0.9237 (tt0) REVERT: C 88 ARG cc_start: 0.9327 (ttm110) cc_final: 0.8742 (ttm110) REVERT: C 99 ARG cc_start: 0.9001 (mmm160) cc_final: 0.8633 (mmp80) REVERT: C 104 GLN cc_start: 0.8452 (mp10) cc_final: 0.7879 (mp10) REVERT: D 67 LYS cc_start: 0.9526 (tttt) cc_final: 0.9319 (tttt) REVERT: E 105 GLU cc_start: 0.9151 (tp30) cc_final: 0.8708 (tp30) REVERT: E 120 MET cc_start: 0.8776 (OUTLIER) cc_final: 0.8554 (mmm) REVERT: E 128 ARG cc_start: 0.9558 (mtp-110) cc_final: 0.8880 (mmm-85) REVERT: F 30 THR cc_start: 0.9010 (OUTLIER) cc_final: 0.8680 (p) REVERT: F 84 MET cc_start: 0.9234 (mmm) cc_final: 0.8942 (mmm) REVERT: F 88 TYR cc_start: 0.9736 (m-10) cc_final: 0.9509 (m-10) REVERT: G 41 GLU cc_start: 0.9078 (mt-10) cc_final: 0.8770 (mt-10) REVERT: G 56 GLU cc_start: 0.8775 (tt0) cc_final: 0.8474 (tt0) REVERT: G 57 TYR cc_start: 0.8730 (t80) cc_final: 0.8426 (t80) REVERT: G 87 ILE cc_start: 0.9358 (tt) cc_final: 0.9157 (tp) REVERT: G 94 ASN cc_start: 0.9433 (t0) cc_final: 0.9088 (t0) REVERT: H 114 GLU cc_start: 0.9138 (mp0) cc_final: 0.8690 (mp0) REVERT: H 129 LYS cc_start: 0.8958 (mtmm) cc_final: 0.8547 (mtmm) REVERT: H 132 GLU cc_start: 0.8822 (tt0) cc_final: 0.8277 (tm-30) outliers start: 41 outliers final: 16 residues processed: 288 average time/residue: 0.1180 time to fit residues: 44.4037 Evaluate side-chains 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 0.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 56 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 52 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN F 25 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.049407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.034995 restraints weight = 57581.823| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.59 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8604 moved from start: 0.2387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11001 Z= 0.166 Angle : 0.688 10.621 15843 Z= 0.396 Chirality : 0.044 0.352 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.745 175.802 3302 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.47 % Allowed : 34.87 % Favored : 59.66 % 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: 1.60 (0.32), residues: 691 helix: 1.78 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.38 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 77 TYR 0.011 0.002 TYR D 61 PHE 0.018 0.001 PHE D 62 TRP 0.006 0.001 TRP D 113 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.17 (11001) covalent geometry : angle 0.68813 / 0.40 (15843) hydrogen bonds : bond 0.04365 / 2.91 ( 676) hydrogen bonds : angle 3.42580 / 2.53 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9158 (tt0) cc_final: 0.8733 (tp30) REVERT: B 84 MET cc_start: 0.8832 (tpp) cc_final: 0.8192 (mmm) REVERT: B 98 TYR cc_start: 0.9049 (m-10) cc_final: 0.8848 (m-10) REVERT: C 25 PHE cc_start: 0.8712 (m-10) cc_final: 0.8281 (m-80) REVERT: C 35 ARG cc_start: 0.9507 (ttm110) cc_final: 0.9245 (ttm110) REVERT: C 38 ASN cc_start: 0.9045 (t0) cc_final: 0.8604 (t0) REVERT: C 57 TYR cc_start: 0.8301 (t80) cc_final: 0.7846 (t80) REVERT: C 61 GLU cc_start: 0.8957 (tt0) cc_final: 0.8562 (tt0) REVERT: C 71 ARG cc_start: 0.8419 (mtm-85) cc_final: 0.8147 (mtm-85) REVERT: C 84 GLN cc_start: 0.9612 (tt0) cc_final: 0.9197 (tt0) REVERT: C 88 ARG cc_start: 0.9329 (ttm110) cc_final: 0.8727 (ttm110) REVERT: C 89 ASN cc_start: 0.9370 (m-40) cc_final: 0.9046 (m110) REVERT: C 99 ARG cc_start: 0.9019 (mmm160) cc_final: 0.8536 (mmp80) REVERT: C 104 GLN cc_start: 0.8577 (mp10) cc_final: 0.7994 (mp10) REVERT: D 103 ARG cc_start: 0.8789 (mtm110) cc_final: 0.8492 (mtm-85) REVERT: D 137 LYS cc_start: 0.9297 (mtmm) cc_final: 0.8971 (mtmm) REVERT: E 105 GLU cc_start: 0.9051 (tp30) cc_final: 0.8477 (tp30) REVERT: E 128 ARG cc_start: 0.9384 (mtp-110) cc_final: 0.9090 (mmm-85) REVERT: E 133 GLU cc_start: 0.8351 (pm20) cc_final: 0.7805 (pm20) REVERT: G 56 GLU cc_start: 0.8846 (tt0) cc_final: 0.8240 (tt0) REVERT: G 57 TYR cc_start: 0.8738 (t80) cc_final: 0.8446 (t80) REVERT: G 85 LEU cc_start: 0.9644 (OUTLIER) cc_final: 0.9432 (mm) REVERT: G 87 ILE cc_start: 0.9507 (tt) cc_final: 0.9277 (tp) REVERT: G 94 ASN cc_start: 0.9439 (t0) cc_final: 0.9142 (t0) REVERT: H 77 ARG cc_start: 0.9038 (ttm110) cc_final: 0.8460 (ptp-110) REVERT: H 78 GLU cc_start: 0.9368 (mp0) cc_final: 0.8847 (mp0) REVERT: H 89 ASP cc_start: 0.9225 (t0) cc_final: 0.8751 (t0) REVERT: H 114 GLU cc_start: 0.9085 (mp0) cc_final: 0.8563 (mp0) REVERT: H 129 LYS cc_start: 0.8992 (mtmm) cc_final: 0.8537 (mtmm) REVERT: H 132 GLU cc_start: 0.8810 (tt0) cc_final: 0.8230 (tm-30) REVERT: H 141 ARG cc_start: 0.9440 (mmm-85) cc_final: 0.9238 (mmm-85) REVERT: H 142 THR cc_start: 0.9591 (OUTLIER) cc_final: 0.9253 (p) outliers start: 32 outliers final: 16 residues processed: 266 average time/residue: 0.1138 time to fit residues: 39.9663 Evaluate side-chains 270 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 252 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 20.0000 chunk 1 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 30.0000 chunk 26 optimal weight: 1.9990 chunk 79 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 38 optimal weight: 0.8980 chunk 14 optimal weight: 8.9990 chunk 75 optimal weight: 20.0000 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 55 GLN A 108 ASN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.049473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2703 r_free = 0.2703 target = 0.034880 restraints weight = 57994.611| |-----------------------------------------------------------------------------| r_work (start): 0.2642 rms_B_bonded: 3.66 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11001 Z= 0.164 Angle : 0.667 8.287 15843 Z= 0.387 Chirality : 0.044 0.350 1815 Planarity : 0.005 0.051 1203 Dihedral : 30.793 176.596 3302 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.98 % Allowed : 35.90 % Favored : 58.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.63 (0.32), residues: 691 helix: 1.78 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 77 TYR 0.014 0.002 TYR C 39 PHE 0.014 0.001 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (11001) covalent geometry : angle 0.66651 / 0.39 (15843) hydrogen bonds : bond 0.04180 / 2.76 ( 676) hydrogen bonds : angle 3.38234 / 2.50 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 249 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9268 (OUTLIER) cc_final: 0.8895 (mm) REVERT: A 68 GLN cc_start: 0.9398 (tt0) cc_final: 0.9191 (tt0) REVERT: A 94 GLU cc_start: 0.9268 (tp30) cc_final: 0.8997 (tp30) REVERT: A 105 GLU cc_start: 0.9240 (tt0) cc_final: 0.8685 (tp30) REVERT: B 53 GLU cc_start: 0.8890 (tt0) cc_final: 0.8620 (tt0) REVERT: B 63 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8651 (mt-10) REVERT: B 84 MET cc_start: 0.8874 (tpp) cc_final: 0.8121 (mmm) REVERT: B 98 TYR cc_start: 0.9092 (m-10) cc_final: 0.8882 (m-10) REVERT: C 25 PHE cc_start: 0.8756 (m-10) cc_final: 0.8270 (m-80) REVERT: C 38 ASN cc_start: 0.9128 (t0) cc_final: 0.8623 (t0) REVERT: C 57 TYR cc_start: 0.8244 (t80) cc_final: 0.7754 (t80) REVERT: C 61 GLU cc_start: 0.8968 (tt0) cc_final: 0.8523 (tt0) REVERT: C 84 GLN cc_start: 0.9587 (tt0) cc_final: 0.9207 (tt0) REVERT: C 88 ARG cc_start: 0.9375 (ttm110) cc_final: 0.8673 (ttm110) REVERT: C 94 ASN cc_start: 0.9269 (OUTLIER) cc_final: 0.8950 (t0) REVERT: C 99 ARG cc_start: 0.9059 (mmm160) cc_final: 0.8597 (mmp80) REVERT: C 104 GLN cc_start: 0.8609 (mp10) cc_final: 0.7950 (mp10) REVERT: D 67 LYS cc_start: 0.9544 (tttt) cc_final: 0.9332 (tttt) REVERT: D 103 ARG cc_start: 0.8829 (mtm110) cc_final: 0.8484 (mtm-85) REVERT: D 137 LYS cc_start: 0.9288 (mtmm) cc_final: 0.8948 (mtmm) REVERT: E 105 GLU cc_start: 0.9091 (tp30) cc_final: 0.8429 (tp30) REVERT: E 128 ARG cc_start: 0.9324 (mtp-110) cc_final: 0.8961 (mmm-85) REVERT: E 133 GLU cc_start: 0.8252 (pm20) cc_final: 0.7722 (pm20) REVERT: F 50 ILE cc_start: 0.9472 (mm) cc_final: 0.9071 (mm) REVERT: G 39 TYR cc_start: 0.9531 (m-80) cc_final: 0.9171 (m-80) REVERT: G 56 GLU cc_start: 0.8847 (tt0) cc_final: 0.8284 (tt0) REVERT: G 57 TYR cc_start: 0.8685 (t80) cc_final: 0.8398 (t80) REVERT: G 64 GLU cc_start: 0.9038 (tm-30) cc_final: 0.8461 (tm-30) REVERT: G 68 ASN cc_start: 0.9207 (m-40) cc_final: 0.8600 (m110) REVERT: G 85 LEU cc_start: 0.9605 (OUTLIER) cc_final: 0.9386 (mm) REVERT: G 87 ILE cc_start: 0.9466 (tt) cc_final: 0.9184 (tp) REVERT: G 94 ASN cc_start: 0.9397 (t0) cc_final: 0.9095 (t0) REVERT: H 84 ASP cc_start: 0.9103 (OUTLIER) cc_final: 0.8652 (m-30) REVERT: H 89 ASP cc_start: 0.9274 (t0) cc_final: 0.8726 (t0) REVERT: H 114 GLU cc_start: 0.9041 (mp0) cc_final: 0.8527 (mp0) REVERT: H 129 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8603 (mtmm) REVERT: H 141 ARG cc_start: 0.9439 (mmm-85) cc_final: 0.9098 (mmm-85) REVERT: H 142 THR cc_start: 0.9548 (OUTLIER) cc_final: 0.9191 (p) outliers start: 35 outliers final: 18 residues processed: 263 average time/residue: 0.1182 time to fit residues: 41.1906 Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.196 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 20.0000 chunk 47 optimal weight: 2.9990 chunk 16 optimal weight: 10.0000 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 14 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 66 optimal weight: 7.9990 chunk 12 optimal weight: 10.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.048854 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.034363 restraints weight = 58546.161| |-----------------------------------------------------------------------------| r_work (start): 0.2632 rms_B_bonded: 3.62 r_work (final): 0.2632 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 11001 Z= 0.187 Angle : 0.684 10.915 15843 Z= 0.395 Chirality : 0.043 0.294 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.828 177.060 3302 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.13 % Allowed : 38.29 % Favored : 56.58 % 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: 1.65 (0.32), residues: 691 helix: 1.79 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.33 (0.42), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 42 TYR 0.021 0.002 TYR F 98 PHE 0.011 0.001 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00359 / 0.19 (11001) covalent geometry : angle 0.68440 / 0.39 (15843) hydrogen bonds : bond 0.04270 / 2.83 ( 676) hydrogen bonds : angle 3.42725 / 2.52 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 246 time to evaluate : 0.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9267 (OUTLIER) cc_final: 0.8913 (mm) REVERT: A 94 GLU cc_start: 0.9180 (tp30) cc_final: 0.8913 (tp30) REVERT: A 105 GLU cc_start: 0.9260 (tt0) cc_final: 0.8714 (tp30) REVERT: B 63 GLU cc_start: 0.9032 (mt-10) cc_final: 0.8592 (mt-10) REVERT: B 84 MET cc_start: 0.8847 (tpp) cc_final: 0.8115 (mmm) REVERT: B 98 TYR cc_start: 0.9157 (m-10) cc_final: 0.8951 (m-10) REVERT: C 25 PHE cc_start: 0.8759 (m-10) cc_final: 0.8252 (m-80) REVERT: C 35 ARG cc_start: 0.9536 (ttm-80) cc_final: 0.9232 (ttm110) REVERT: C 38 ASN cc_start: 0.9173 (t0) cc_final: 0.8647 (t0) REVERT: C 57 TYR cc_start: 0.8287 (t80) cc_final: 0.7747 (t80) REVERT: C 61 GLU cc_start: 0.9003 (tt0) cc_final: 0.8557 (tt0) REVERT: C 89 ASN cc_start: 0.9374 (m-40) cc_final: 0.9112 (m110) REVERT: C 94 ASN cc_start: 0.9277 (OUTLIER) cc_final: 0.8990 (t0) REVERT: C 99 ARG cc_start: 0.9049 (mmm160) cc_final: 0.8599 (mmp80) REVERT: C 104 GLN cc_start: 0.8641 (mp10) cc_final: 0.7942 (mp10) REVERT: D 67 LYS cc_start: 0.9563 (tttt) cc_final: 0.9341 (tttt) REVERT: D 103 ARG cc_start: 0.8842 (mtm110) cc_final: 0.8492 (mtm-85) REVERT: D 107 ARG cc_start: 0.8854 (mtp85) cc_final: 0.8401 (mtp85) REVERT: D 114 GLU cc_start: 0.9365 (mp0) cc_final: 0.8602 (mm-30) REVERT: D 137 LYS cc_start: 0.9320 (mtmm) cc_final: 0.8952 (mtmm) REVERT: E 105 GLU cc_start: 0.9057 (tp30) cc_final: 0.8368 (tp30) REVERT: E 128 ARG cc_start: 0.9343 (mtp-110) cc_final: 0.8670 (mmm-85) REVERT: E 133 GLU cc_start: 0.8260 (pm20) cc_final: 0.7511 (pm20) REVERT: F 50 ILE cc_start: 0.9538 (mm) cc_final: 0.9124 (mm) REVERT: G 39 TYR cc_start: 0.9560 (m-80) cc_final: 0.9180 (m-80) REVERT: G 56 GLU cc_start: 0.8899 (tt0) cc_final: 0.8280 (tt0) REVERT: G 57 TYR cc_start: 0.8716 (t80) cc_final: 0.8439 (t80) REVERT: G 64 GLU cc_start: 0.9050 (tm-30) cc_final: 0.8315 (tm-30) REVERT: G 68 ASN cc_start: 0.9222 (m-40) cc_final: 0.8660 (m-40) REVERT: G 87 ILE cc_start: 0.9467 (tt) cc_final: 0.9199 (tp) REVERT: H 68 GLN cc_start: 0.9315 (tm-30) cc_final: 0.9113 (tm-30) REVERT: H 84 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8640 (m-30) REVERT: H 89 ASP cc_start: 0.9244 (t0) cc_final: 0.8728 (t0) REVERT: H 114 GLU cc_start: 0.9089 (mp0) cc_final: 0.8500 (mp0) REVERT: H 129 LYS cc_start: 0.9005 (OUTLIER) cc_final: 0.8618 (mtmm) REVERT: H 141 ARG cc_start: 0.9467 (mmm-85) cc_final: 0.9180 (mmm-85) REVERT: H 142 THR cc_start: 0.9561 (OUTLIER) cc_final: 0.9212 (p) outliers start: 30 outliers final: 18 residues processed: 260 average time/residue: 0.1159 time to fit residues: 40.0681 Evaluate side-chains 261 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 238 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 86 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 9.9990 chunk 51 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN E 108 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.047976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.034302 restraints weight = 57979.736| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 3.60 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.2877 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 11001 Z= 0.199 Angle : 0.692 9.820 15843 Z= 0.398 Chirality : 0.044 0.262 1815 Planarity : 0.007 0.180 1203 Dihedral : 30.873 177.814 3302 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 7.01 % Allowed : 36.07 % Favored : 56.92 % 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: 1.65 (0.32), residues: 691 helix: 1.80 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.38 (0.42), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.028 0.001 ARG E 134 TYR 0.038 0.002 TYR F 98 PHE 0.011 0.001 PHE G 25 TRP 0.003 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.20 (11001) covalent geometry : angle 0.69239 / 0.40 (15843) hydrogen bonds : bond 0.04334 / 2.86 ( 676) hydrogen bonds : angle 3.45136 / 2.55 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 234 time to evaluate : 0.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9219 (tt0) cc_final: 0.8708 (tp30) REVERT: B 63 GLU cc_start: 0.8997 (mt-10) cc_final: 0.8491 (mt-10) REVERT: B 84 MET cc_start: 0.8881 (tpp) cc_final: 0.8169 (mmm) REVERT: B 98 TYR cc_start: 0.9186 (m-10) cc_final: 0.8971 (m-10) REVERT: C 25 PHE cc_start: 0.8758 (m-10) cc_final: 0.8268 (m-80) REVERT: C 35 ARG cc_start: 0.9530 (ttm-80) cc_final: 0.9229 (ttm110) REVERT: C 38 ASN cc_start: 0.9211 (t0) cc_final: 0.8629 (t0) REVERT: C 57 TYR cc_start: 0.8380 (t80) cc_final: 0.7835 (t80) REVERT: C 61 GLU cc_start: 0.8996 (tt0) cc_final: 0.8618 (tt0) REVERT: C 89 ASN cc_start: 0.9423 (m-40) cc_final: 0.9154 (m110) REVERT: C 92 GLU cc_start: 0.9317 (tm-30) cc_final: 0.9017 (pp20) REVERT: C 94 ASN cc_start: 0.9437 (OUTLIER) cc_final: 0.8794 (m110) REVERT: C 99 ARG cc_start: 0.9012 (mmm160) cc_final: 0.8626 (mmp80) REVERT: C 104 GLN cc_start: 0.8617 (mp10) cc_final: 0.7986 (mp10) REVERT: D 67 LYS cc_start: 0.9553 (tttt) cc_final: 0.9327 (tttt) REVERT: D 83 MET cc_start: 0.9351 (tpp) cc_final: 0.8880 (mpp) REVERT: D 103 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8477 (mtm-85) REVERT: D 107 ARG cc_start: 0.8896 (mtp85) cc_final: 0.8308 (mtp85) REVERT: D 108 GLN cc_start: 0.8072 (pm20) cc_final: 0.7592 (pm20) REVERT: D 114 GLU cc_start: 0.9342 (OUTLIER) cc_final: 0.8578 (mm-30) REVERT: D 137 LYS cc_start: 0.9332 (mtmm) cc_final: 0.8935 (mtmm) REVERT: E 105 GLU cc_start: 0.9040 (tp30) cc_final: 0.8343 (tp30) REVERT: E 128 ARG cc_start: 0.9496 (mtp-110) cc_final: 0.9153 (mmm-85) REVERT: E 133 GLU cc_start: 0.8666 (pm20) cc_final: 0.8135 (pm20) REVERT: F 50 ILE cc_start: 0.9576 (mm) cc_final: 0.9144 (mm) REVERT: G 56 GLU cc_start: 0.8929 (tt0) cc_final: 0.8351 (tt0) REVERT: G 57 TYR cc_start: 0.8738 (t80) cc_final: 0.8488 (t80) REVERT: G 64 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8251 (tm-30) REVERT: G 68 ASN cc_start: 0.9206 (m-40) cc_final: 0.8629 (m-40) REVERT: G 84 GLN cc_start: 0.9425 (OUTLIER) cc_final: 0.8917 (tp40) REVERT: G 87 ILE cc_start: 0.9563 (tt) cc_final: 0.9287 (tp) REVERT: G 93 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9296 (mm) REVERT: G 94 ASN cc_start: 0.9407 (t0) cc_final: 0.9155 (t0) REVERT: H 68 GLN cc_start: 0.9334 (tm-30) cc_final: 0.9093 (tm-30) REVERT: H 84 ASP cc_start: 0.9137 (OUTLIER) cc_final: 0.8621 (m-30) REVERT: H 89 ASP cc_start: 0.9284 (t0) cc_final: 0.8774 (t0) REVERT: H 107 ARG cc_start: 0.9070 (mmm-85) cc_final: 0.8810 (mmm-85) REVERT: H 114 GLU cc_start: 0.9037 (mp0) cc_final: 0.8499 (mp0) REVERT: H 129 LYS cc_start: 0.9042 (OUTLIER) cc_final: 0.8641 (mtmm) REVERT: H 141 ARG cc_start: 0.9460 (mmm-85) cc_final: 0.9126 (mmm-85) REVERT: H 142 THR cc_start: 0.9595 (OUTLIER) cc_final: 0.9243 (p) outliers start: 41 outliers final: 27 residues processed: 252 average time/residue: 0.1140 time to fit residues: 37.7670 Evaluate side-chains 266 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 232 time to evaluate : 0.166 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 57 SER Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 7.9990 chunk 55 optimal weight: 10.0000 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 4.9990 chunk 58 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 65 optimal weight: 9.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.048692 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.034184 restraints weight = 57575.301| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 3.70 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8600 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 11001 Z= 0.173 Angle : 0.703 11.237 15843 Z= 0.398 Chirality : 0.043 0.262 1815 Planarity : 0.005 0.075 1203 Dihedral : 30.884 178.472 3302 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.32 % Allowed : 38.12 % Favored : 55.56 % 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: 1.66 (0.32), residues: 691 helix: 1.81 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.42 (0.41), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG E 134 TYR 0.042 0.002 TYR F 98 PHE 0.010 0.001 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.17 (11001) covalent geometry : angle 0.70335 / 0.40 (15843) hydrogen bonds : bond 0.04082 / 2.68 ( 676) hydrogen bonds : angle 3.36987 / 2.49 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 271 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 234 time to evaluate : 0.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9284 (tt0) cc_final: 0.8714 (tp30) REVERT: B 63 GLU cc_start: 0.9021 (mt-10) cc_final: 0.8475 (mt-10) REVERT: B 84 MET cc_start: 0.8864 (tpp) cc_final: 0.8023 (mmm) REVERT: C 25 PHE cc_start: 0.8766 (m-10) cc_final: 0.8266 (m-80) REVERT: C 35 ARG cc_start: 0.9545 (ttm-80) cc_final: 0.9221 (ttm110) REVERT: C 38 ASN cc_start: 0.9256 (t0) cc_final: 0.8656 (t0) REVERT: C 57 TYR cc_start: 0.8268 (t80) cc_final: 0.7682 (t80) REVERT: C 61 GLU cc_start: 0.9061 (tt0) cc_final: 0.8610 (tt0) REVERT: C 68 ASN cc_start: 0.9319 (m-40) cc_final: 0.8839 (m-40) REVERT: C 72 ASP cc_start: 0.9589 (t0) cc_final: 0.9273 (m-30) REVERT: C 89 ASN cc_start: 0.9384 (m-40) cc_final: 0.9100 (m110) REVERT: C 92 GLU cc_start: 0.9389 (tm-30) cc_final: 0.9186 (pp20) REVERT: C 94 ASN cc_start: 0.9340 (OUTLIER) cc_final: 0.8805 (m-40) REVERT: C 99 ARG cc_start: 0.9020 (mmm160) cc_final: 0.8623 (mmp80) REVERT: C 104 GLN cc_start: 0.8631 (mp10) cc_final: 0.7994 (mp10) REVERT: D 67 LYS cc_start: 0.9561 (tttt) cc_final: 0.9337 (tttt) REVERT: D 83 MET cc_start: 0.9331 (tpp) cc_final: 0.8838 (mpp) REVERT: D 103 ARG cc_start: 0.8819 (mtm110) cc_final: 0.8405 (mtm-85) REVERT: D 107 ARG cc_start: 0.8841 (mtp85) cc_final: 0.8379 (mtp85) REVERT: D 114 GLU cc_start: 0.9354 (OUTLIER) cc_final: 0.8624 (mm-30) REVERT: D 126 GLN cc_start: 0.8402 (tp-100) cc_final: 0.8154 (tp-100) REVERT: D 127 MET cc_start: 0.9470 (mtm) cc_final: 0.9108 (mtm) REVERT: D 137 LYS cc_start: 0.9347 (mtmm) cc_final: 0.8940 (mtmm) REVERT: E 105 GLU cc_start: 0.9104 (tp30) cc_final: 0.8357 (tp30) REVERT: E 128 ARG cc_start: 0.9499 (mtp-110) cc_final: 0.9240 (mmm-85) REVERT: F 50 ILE cc_start: 0.9511 (mm) cc_final: 0.9056 (mm) REVERT: G 56 GLU cc_start: 0.8924 (tt0) cc_final: 0.8351 (tt0) REVERT: G 57 TYR cc_start: 0.8715 (t80) cc_final: 0.8458 (t80) REVERT: G 64 GLU cc_start: 0.9116 (tm-30) cc_final: 0.8326 (tm-30) REVERT: G 68 ASN cc_start: 0.9235 (m-40) cc_final: 0.8652 (m-40) REVERT: G 84 GLN cc_start: 0.9366 (OUTLIER) cc_final: 0.8874 (tp40) REVERT: G 87 ILE cc_start: 0.9487 (tt) cc_final: 0.9202 (tp) REVERT: G 93 LEU cc_start: 0.9499 (OUTLIER) cc_final: 0.9239 (mm) REVERT: G 94 ASN cc_start: 0.9376 (t0) cc_final: 0.9114 (t0) REVERT: H 68 GLN cc_start: 0.9430 (tm-30) cc_final: 0.9162 (tm-30) REVERT: H 84 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8596 (m-30) REVERT: H 89 ASP cc_start: 0.9286 (t0) cc_final: 0.8743 (t0) REVERT: H 114 GLU cc_start: 0.9079 (mp0) cc_final: 0.8484 (mp0) REVERT: H 129 LYS cc_start: 0.9010 (OUTLIER) cc_final: 0.8635 (mtmm) REVERT: H 141 ARG cc_start: 0.9480 (mmm-85) cc_final: 0.9126 (mmm-85) REVERT: H 142 THR cc_start: 0.9547 (OUTLIER) cc_final: 0.9192 (p) outliers start: 37 outliers final: 24 residues processed: 250 average time/residue: 0.1142 time to fit residues: 37.8973 Evaluate side-chains 267 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 236 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 50.0000 chunk 3 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 21 optimal weight: 5.9990 chunk 68 optimal weight: 30.0000 chunk 4 optimal weight: 2.9990 chunk 75 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 chunk 5 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 108 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.047925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.033868 restraints weight = 57887.087| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.56 r_work (final): 0.2673 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 11001 Z= 0.207 Angle : 0.723 9.559 15843 Z= 0.410 Chirality : 0.043 0.265 1815 Planarity : 0.005 0.050 1203 Dihedral : 30.915 178.639 3302 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.98 % Allowed : 38.63 % Favored : 55.38 % 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: 1.57 (0.32), residues: 691 helix: 1.75 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.44 (0.42), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 71 TYR 0.046 0.002 TYR F 98 PHE 0.010 0.001 PHE D 62 TRP 0.003 0.001 TRP D 113 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00406 / 0.21 (11001) covalent geometry : angle 0.72285 / 0.41 (15843) hydrogen bonds : bond 0.04386 / 2.88 ( 676) hydrogen bonds : angle 3.50505 / 2.58 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 233 time to evaluate : 0.274 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9223 (tt0) cc_final: 0.8708 (tp30) REVERT: B 63 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8465 (mt-10) REVERT: B 84 MET cc_start: 0.8873 (tpp) cc_final: 0.8154 (mmm) REVERT: C 25 PHE cc_start: 0.8767 (m-10) cc_final: 0.8300 (m-80) REVERT: C 32 ARG cc_start: 0.8894 (ttp80) cc_final: 0.8584 (ttp80) REVERT: C 35 ARG cc_start: 0.9540 (ttm-80) cc_final: 0.9228 (ttm110) REVERT: C 38 ASN cc_start: 0.9300 (t0) cc_final: 0.8623 (t0) REVERT: C 57 TYR cc_start: 0.8392 (t80) cc_final: 0.7872 (t80) REVERT: C 61 GLU cc_start: 0.9049 (tt0) cc_final: 0.8630 (tt0) REVERT: C 68 ASN cc_start: 0.9354 (m-40) cc_final: 0.8906 (m-40) REVERT: C 72 ASP cc_start: 0.9573 (t0) cc_final: 0.9332 (m-30) REVERT: C 89 ASN cc_start: 0.9448 (m-40) cc_final: 0.9143 (m110) REVERT: C 94 ASN cc_start: 0.9417 (OUTLIER) cc_final: 0.8954 (m-40) REVERT: C 99 ARG cc_start: 0.8935 (mmm160) cc_final: 0.8548 (mmp80) REVERT: C 104 GLN cc_start: 0.8583 (mp10) cc_final: 0.8195 (mp10) REVERT: D 83 MET cc_start: 0.9393 (tpp) cc_final: 0.8872 (mpp) REVERT: D 103 ARG cc_start: 0.8830 (mtm110) cc_final: 0.8400 (mtm-85) REVERT: D 107 ARG cc_start: 0.8911 (mtp85) cc_final: 0.8439 (mtp85) REVERT: D 114 GLU cc_start: 0.9330 (OUTLIER) cc_final: 0.8673 (mm-30) REVERT: D 126 GLN cc_start: 0.8489 (tp-100) cc_final: 0.8272 (tp-100) REVERT: D 137 LYS cc_start: 0.9350 (mtmm) cc_final: 0.8922 (mtmm) REVERT: E 73 GLU cc_start: 0.8966 (tt0) cc_final: 0.8119 (tt0) REVERT: E 105 GLU cc_start: 0.9043 (tp30) cc_final: 0.8328 (tp30) REVERT: E 128 ARG cc_start: 0.9469 (mtp-110) cc_final: 0.9189 (mmm-85) REVERT: E 133 GLU cc_start: 0.8778 (pm20) cc_final: 0.7931 (pm20) REVERT: F 50 ILE cc_start: 0.9561 (mm) cc_final: 0.9105 (mm) REVERT: G 56 GLU cc_start: 0.8936 (tt0) cc_final: 0.8388 (tt0) REVERT: G 57 TYR cc_start: 0.8728 (t80) cc_final: 0.8500 (t80) REVERT: G 64 GLU cc_start: 0.9035 (tm-30) cc_final: 0.8232 (tm-30) REVERT: G 68 ASN cc_start: 0.9221 (m-40) cc_final: 0.8624 (m-40) REVERT: G 84 GLN cc_start: 0.9438 (OUTLIER) cc_final: 0.8935 (tp40) REVERT: G 94 ASN cc_start: 0.9425 (t0) cc_final: 0.9178 (t0) REVERT: H 68 GLN cc_start: 0.9402 (tm-30) cc_final: 0.9108 (tm-30) REVERT: H 84 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: H 89 ASP cc_start: 0.9300 (t0) cc_final: 0.8751 (t0) REVERT: H 108 GLN cc_start: 0.8969 (pt0) cc_final: 0.8239 (pt0) REVERT: H 114 GLU cc_start: 0.9020 (mp0) cc_final: 0.8487 (mp0) REVERT: H 129 LYS cc_start: 0.9030 (OUTLIER) cc_final: 0.8636 (mtmm) REVERT: H 141 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9135 (mmm-85) REVERT: H 142 THR cc_start: 0.9595 (OUTLIER) cc_final: 0.9237 (p) outliers start: 35 outliers final: 26 residues processed: 247 average time/residue: 0.1107 time to fit residues: 36.5927 Evaluate side-chains 263 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 231 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 70 HIS Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 84 GLN Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.0020 chunk 59 optimal weight: 7.9990 chunk 34 optimal weight: 0.0010 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 20.0000 chunk 69 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 chunk 53 optimal weight: 0.8980 chunk 55 optimal weight: 6.9990 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 4.9990 overall best weight: 1.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN C 94 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.048394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.034787 restraints weight = 57225.094| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.61 r_work (final): 0.2707 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11001 Z= 0.166 Angle : 0.736 11.771 15843 Z= 0.411 Chirality : 0.043 0.263 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.922 179.031 3302 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.30 % Allowed : 40.34 % Favored : 54.36 % 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: 1.53 (0.32), residues: 691 helix: 1.71 (0.23), residues: 535 sheet: None (None), residues: 0 loop : -1.46 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 103 TYR 0.018 0.002 TYR B 98 PHE 0.010 0.001 PHE E 84 TRP 0.004 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.17 (11001) covalent geometry : angle 0.73594 / 0.41 (15843) hydrogen bonds : bond 0.03990 / 2.60 ( 676) hydrogen bonds : angle 3.39759 / 2.49 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 241 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9385 (pt0) cc_final: 0.9045 (pp20) REVERT: A 64 LYS cc_start: 0.9221 (mttp) cc_final: 0.8956 (mmtm) REVERT: A 105 GLU cc_start: 0.9214 (tt0) cc_final: 0.8686 (tp30) REVERT: B 63 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8418 (mt-10) REVERT: B 79 LYS cc_start: 0.8898 (mtpt) cc_final: 0.8581 (mtpt) REVERT: B 84 MET cc_start: 0.8798 (tpp) cc_final: 0.7949 (mmm) REVERT: C 25 PHE cc_start: 0.8748 (m-10) cc_final: 0.8337 (m-80) REVERT: C 32 ARG cc_start: 0.8871 (ttp80) cc_final: 0.8545 (ttp80) REVERT: C 35 ARG cc_start: 0.9522 (ttm-80) cc_final: 0.9227 (ttm110) REVERT: C 38 ASN cc_start: 0.9245 (t0) cc_final: 0.8603 (t0) REVERT: C 57 TYR cc_start: 0.8449 (t80) cc_final: 0.7724 (t80) REVERT: C 61 GLU cc_start: 0.9055 (tt0) cc_final: 0.8538 (tt0) REVERT: C 72 ASP cc_start: 0.9438 (t0) cc_final: 0.9133 (m-30) REVERT: C 89 ASN cc_start: 0.9452 (m-40) cc_final: 0.9160 (m110) REVERT: C 94 ASN cc_start: 0.9412 (OUTLIER) cc_final: 0.8916 (m-40) REVERT: C 99 ARG cc_start: 0.8831 (mmm160) cc_final: 0.8484 (mmp80) REVERT: C 104 GLN cc_start: 0.8572 (mp10) cc_final: 0.8182 (mp10) REVERT: D 62 PHE cc_start: 0.9438 (m-80) cc_final: 0.9182 (m-80) REVERT: D 83 MET cc_start: 0.9409 (tpp) cc_final: 0.8823 (mpp) REVERT: D 103 ARG cc_start: 0.8813 (mtm110) cc_final: 0.8379 (mtm-85) REVERT: D 107 ARG cc_start: 0.8872 (mtp85) cc_final: 0.8444 (mtp85) REVERT: D 114 GLU cc_start: 0.9294 (OUTLIER) cc_final: 0.8652 (mm-30) REVERT: D 137 LYS cc_start: 0.9335 (mtmm) cc_final: 0.8951 (mtmm) REVERT: F 50 ILE cc_start: 0.9547 (mm) cc_final: 0.9087 (mm) REVERT: G 56 GLU cc_start: 0.8912 (tt0) cc_final: 0.8369 (tt0) REVERT: G 57 TYR cc_start: 0.8707 (t80) cc_final: 0.8477 (t80) REVERT: G 64 GLU cc_start: 0.9031 (tm-30) cc_final: 0.8196 (tm-30) REVERT: G 68 ASN cc_start: 0.9177 (m-40) cc_final: 0.8554 (m-40) REVERT: G 94 ASN cc_start: 0.9437 (t0) cc_final: 0.9209 (t0) REVERT: H 68 GLN cc_start: 0.9405 (tm-30) cc_final: 0.9111 (tm-30) REVERT: H 84 ASP cc_start: 0.9089 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: H 89 ASP cc_start: 0.9291 (t0) cc_final: 0.8728 (t0) REVERT: H 107 ARG cc_start: 0.9107 (mmm-85) cc_final: 0.8870 (mmm-85) REVERT: H 114 GLU cc_start: 0.9015 (mp0) cc_final: 0.8473 (mp0) REVERT: H 129 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: H 132 GLU cc_start: 0.8769 (tt0) cc_final: 0.8457 (tp30) REVERT: H 141 ARG cc_start: 0.9451 (mmm-85) cc_final: 0.9104 (mmm-85) outliers start: 31 outliers final: 19 residues processed: 254 average time/residue: 0.1076 time to fit residues: 36.4545 Evaluate side-chains 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.278 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 4 optimal weight: 9.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 60 optimal weight: 0.0870 chunk 20 optimal weight: 5.9990 chunk 43 optimal weight: 6.9990 chunk 73 optimal weight: 30.0000 overall best weight: 2.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.047991 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2763 r_free = 0.2763 target = 0.034434 restraints weight = 57030.923| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.59 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.3229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.116 11001 Z= 0.186 Angle : 0.746 11.772 15843 Z= 0.416 Chirality : 0.043 0.265 1815 Planarity : 0.005 0.050 1203 Dihedral : 30.929 178.778 3302 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.27 % Allowed : 40.68 % Favored : 55.04 % 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: 1.55 (0.32), residues: 691 helix: 1.72 (0.23), residues: 535 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 77 TYR 0.016 0.002 TYR B 98 PHE 0.008 0.001 PHE D 62 TRP 0.003 0.000 TRP D 113 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (11001) covalent geometry : angle 0.74598 / 0.42 (15843) hydrogen bonds : bond 0.04150 / 2.70 ( 676) hydrogen bonds : angle 3.44903 / 2.52 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 231 time to evaluate : 0.282 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9213 (tt0) cc_final: 0.8697 (tp30) REVERT: B 63 GLU cc_start: 0.9001 (mt-10) cc_final: 0.8408 (mt-10) REVERT: B 79 LYS cc_start: 0.8899 (mtpt) cc_final: 0.8585 (mtpt) REVERT: B 84 MET cc_start: 0.8817 (tpp) cc_final: 0.8000 (mmm) REVERT: C 25 PHE cc_start: 0.8745 (m-10) cc_final: 0.8316 (m-80) REVERT: C 32 ARG cc_start: 0.8873 (ttp80) cc_final: 0.8552 (ttp80) REVERT: C 35 ARG cc_start: 0.9514 (ttm-80) cc_final: 0.9216 (ttm110) REVERT: C 38 ASN cc_start: 0.9267 (t0) cc_final: 0.8608 (t0) REVERT: C 57 TYR cc_start: 0.8434 (t80) cc_final: 0.8189 (t80) REVERT: C 72 ASP cc_start: 0.9419 (t0) cc_final: 0.9116 (m-30) REVERT: C 89 ASN cc_start: 0.9480 (m-40) cc_final: 0.9179 (m110) REVERT: C 94 ASN cc_start: 0.9384 (OUTLIER) cc_final: 0.8949 (m-40) REVERT: C 99 ARG cc_start: 0.8834 (mmm160) cc_final: 0.8538 (mmp80) REVERT: C 104 GLN cc_start: 0.8581 (mp10) cc_final: 0.8188 (mp10) REVERT: D 83 MET cc_start: 0.9420 (tpp) cc_final: 0.8886 (mpp) REVERT: D 103 ARG cc_start: 0.8812 (mtm110) cc_final: 0.8392 (mtm-85) REVERT: D 107 ARG cc_start: 0.8853 (mtp85) cc_final: 0.8385 (mtp85) REVERT: D 114 GLU cc_start: 0.9286 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: D 127 MET cc_start: 0.9405 (mtm) cc_final: 0.8758 (mpp) REVERT: D 137 LYS cc_start: 0.9338 (mtmm) cc_final: 0.8973 (mtmm) REVERT: F 50 ILE cc_start: 0.9588 (mm) cc_final: 0.9147 (mm) REVERT: G 56 GLU cc_start: 0.8907 (tt0) cc_final: 0.8367 (tt0) REVERT: G 57 TYR cc_start: 0.8703 (t80) cc_final: 0.8473 (t80) REVERT: G 64 GLU cc_start: 0.9056 (tm-30) cc_final: 0.8233 (tm-30) REVERT: G 68 ASN cc_start: 0.9195 (m-40) cc_final: 0.8574 (m-40) REVERT: G 94 ASN cc_start: 0.9444 (t0) cc_final: 0.9194 (t0) REVERT: H 68 GLN cc_start: 0.9431 (tm-30) cc_final: 0.9113 (tm-30) REVERT: H 84 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8516 (m-30) REVERT: H 89 ASP cc_start: 0.9319 (t0) cc_final: 0.8750 (t0) REVERT: H 114 GLU cc_start: 0.9045 (mp0) cc_final: 0.8507 (mp0) REVERT: H 129 LYS cc_start: 0.9043 (OUTLIER) cc_final: 0.8706 (mtmm) REVERT: H 132 GLU cc_start: 0.8789 (tt0) cc_final: 0.8459 (tp30) REVERT: H 141 ARG cc_start: 0.9477 (mmm-85) cc_final: 0.9087 (mmm-85) outliers start: 25 outliers final: 19 residues processed: 241 average time/residue: 0.1251 time to fit residues: 39.9298 Evaluate side-chains 251 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 228 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 5.9990 chunk 83 optimal weight: 30.0000 chunk 4 optimal weight: 5.9990 chunk 69 optimal weight: 30.0000 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 30 optimal weight: 0.0270 overall best weight: 3.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN H 108 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.047392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.033804 restraints weight = 58737.728| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.60 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.3297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 11001 Z= 0.207 Angle : 0.754 11.547 15843 Z= 0.420 Chirality : 0.043 0.266 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.977 178.807 3302 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.96 % Allowed : 39.83 % Favored : 55.21 % 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: 1.57 (0.32), residues: 691 helix: 1.74 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.43 (0.43), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 141 TYR 0.019 0.002 TYR H 61 PHE 0.032 0.002 PHE D 62 TRP 0.001 0.000 TRP D 113 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00418 / 0.21 (11001) covalent geometry : angle 0.75443 / 0.42 (15843) hydrogen bonds : bond 0.04341 / 2.83 ( 676) hydrogen bonds : angle 3.54726 / 2.58 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1864.47 seconds wall clock time: 32 minutes 41.17 seconds (1961.17 seconds total)