Starting phenix.real_space_refine on Wed Aug 5 13:03:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcc_36157/08_2026/8jcc_36157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcc_36157/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2026/8jcc_36157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2026/8jcc_36157.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2026/8jcc_36157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2026/8jcc_36157.cif" } 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 2.13, per 1000 atoms: 0.21 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: 0.96 Conformation dependent library (CDL) restraints added in 230.0 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: 1.30 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: 1.69 Time building geometry restraints manager: 1.30 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: 15212 1.88 - 3.76: 598 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: 0.510 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 10.970 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:1.370 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.250 ------------------------------------------------------------------------------- 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 : 0.749 9.395 15843 Z= 0.633 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 0.74900 / 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 : 0.190 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7118 (t0) cc_final: 0.6517 (t0) REVERT: C 57 TYR cc_start: 0.7832 (t80) cc_final: 0.7583 (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: 0.6983 (pt0) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.1273 time to fit residues: 53.4409 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 : 0.194 ------------------------------------------------------------------------------- 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 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.049508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.034694 restraints weight = 56180.701| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.55 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11001 Z= 0.182 Angle : 0.728 8.120 15843 Z= 0.415 Chirality : 0.046 0.407 1815 Planarity : 0.005 0.053 1203 Dihedral : 30.582 178.268 3304 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 15.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.50 % Allowed : 35.21 % Favored : 58.29 % 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: 1.61 (0.32), residues: 691 helix: 1.73 (0.23), residues: 537 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG C 35 TYR 0.018 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 F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.18 (11001) covalent geometry : angle 0.72803 / 0.41 (15843) hydrogen bonds : bond 0.04970 / 3.32 ( 676) hydrogen bonds : angle 3.50398 / 2.58 ( 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 293 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 255 time to evaluate : 0.296 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: A 50 GLU cc_start: 0.9421 (tt0) cc_final: 0.8687 (tp30) REVERT: A 68 GLN cc_start: 0.9405 (tt0) cc_final: 0.9150 (tt0) REVERT: C 25 PHE cc_start: 0.8651 (m-10) cc_final: 0.8137 (m-80) REVERT: C 38 ASN cc_start: 0.9047 (t0) cc_final: 0.8742 (t0) REVERT: C 57 TYR cc_start: 0.8061 (t80) cc_final: 0.7794 (t80) REVERT: C 99 ARG cc_start: 0.8980 (mmm160) cc_final: 0.8626 (mmp80) REVERT: C 104 GLN cc_start: 0.8418 (mp10) cc_final: 0.7841 (mp10) REVERT: E 62 ILE cc_start: 0.9308 (mm) cc_final: 0.9053 (mm) REVERT: E 105 GLU cc_start: 0.9176 (tp30) cc_final: 0.8698 (tp30) REVERT: E 120 MET cc_start: 0.8796 (OUTLIER) cc_final: 0.8578 (mmm) REVERT: E 128 ARG cc_start: 0.9546 (mtp-110) cc_final: 0.8840 (mmm-85) REVERT: G 41 GLU cc_start: 0.9055 (mt-10) cc_final: 0.8760 (mt-10) REVERT: G 56 GLU cc_start: 0.8795 (tt0) cc_final: 0.8499 (tt0) REVERT: G 57 TYR cc_start: 0.8749 (t80) cc_final: 0.8452 (t80) REVERT: G 87 ILE cc_start: 0.9350 (tt) cc_final: 0.9127 (tp) REVERT: G 94 ASN cc_start: 0.9430 (t0) cc_final: 0.9043 (t0) REVERT: H 100 HIS cc_start: 0.9433 (OUTLIER) cc_final: 0.9230 (t-90) REVERT: H 114 GLU cc_start: 0.9097 (mp0) cc_final: 0.8666 (mp0) REVERT: H 129 LYS cc_start: 0.8939 (mtmm) cc_final: 0.8569 (mtmm) REVERT: H 132 GLU cc_start: 0.8838 (tt0) cc_final: 0.8271 (tm-30) outliers start: 38 outliers final: 17 residues processed: 274 average time/residue: 0.1249 time to fit residues: 45.7910 Evaluate side-chains 255 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 236 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 81 ASP Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain A residue 125 GLN 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 C residue 94 ASN 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 66 ILE Chi-restraints excluded: chain H residue 100 HIS 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: 20.0000 chunk 34 optimal weight: 5.9990 chunk 65 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 56 optimal weight: 9.9990 chunk 13 optimal weight: 2.9990 chunk 72 optimal weight: 30.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 30.0000 chunk 52 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 overall best weight: 3.9588 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.047618 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.033596 restraints weight = 56384.980| |-----------------------------------------------------------------------------| r_work (start): 0.2623 rms_B_bonded: 3.48 r_work (final): 0.2623 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.2326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 11001 Z= 0.217 Angle : 0.725 10.049 15843 Z= 0.411 Chirality : 0.045 0.359 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.695 176.426 3302 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 15.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.32 % Allowed : 33.68 % Favored : 60.00 % 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: 1.67 (0.32), residues: 691 helix: 1.83 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.36 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 88 TYR 0.012 0.002 TYR D 61 PHE 0.018 0.002 PHE D 62 TRP 0.006 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00420 / 0.22 (11001) covalent geometry : angle 0.72454 / 0.41 (15843) hydrogen bonds : bond 0.04815 / 3.20 ( 676) hydrogen bonds : angle 3.55154 / 2.64 ( 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 278 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.243 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: A 94 GLU cc_start: 0.9222 (tp30) cc_final: 0.8945 (tp30) REVERT: A 105 GLU cc_start: 0.9213 (tt0) cc_final: 0.8730 (tp30) REVERT: B 63 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8642 (mt-10) REVERT: B 79 LYS cc_start: 0.8841 (OUTLIER) cc_final: 0.8607 (mtpt) REVERT: B 98 TYR cc_start: 0.9168 (m-10) cc_final: 0.8965 (m-10) REVERT: C 25 PHE cc_start: 0.8638 (m-10) cc_final: 0.8048 (m-80) REVERT: C 38 ASN cc_start: 0.9048 (t0) cc_final: 0.8609 (t0) REVERT: C 57 TYR cc_start: 0.8304 (t80) cc_final: 0.7977 (t80) REVERT: C 61 GLU cc_start: 0.8924 (tt0) cc_final: 0.8723 (tt0) REVERT: C 89 ASN cc_start: 0.9385 (m-40) cc_final: 0.9095 (m110) REVERT: C 94 ASN cc_start: 0.9275 (t0) cc_final: 0.9000 (t0) REVERT: C 99 ARG cc_start: 0.9013 (mmm160) cc_final: 0.8503 (mmp80) REVERT: C 104 GLN cc_start: 0.8565 (mp10) cc_final: 0.7877 (mp10) REVERT: D 103 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8640 (mtm-85) REVERT: D 137 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8980 (mtmm) REVERT: E 105 GLU cc_start: 0.9150 (tp30) cc_final: 0.8610 (tp30) REVERT: E 128 ARG cc_start: 0.9352 (mtp-110) cc_final: 0.8762 (mmm-85) REVERT: E 133 GLU cc_start: 0.8117 (pm20) cc_final: 0.7253 (pm20) REVERT: F 30 THR cc_start: 0.9065 (OUTLIER) cc_final: 0.8864 (p) REVERT: G 41 GLU cc_start: 0.8967 (mt-10) cc_final: 0.8745 (mt-10) REVERT: G 56 GLU cc_start: 0.8907 (tt0) cc_final: 0.8302 (tt0) REVERT: G 57 TYR cc_start: 0.8766 (t80) cc_final: 0.8489 (t80) REVERT: G 87 ILE cc_start: 0.9426 (tt) cc_final: 0.9208 (tp) REVERT: G 94 ASN cc_start: 0.9435 (t0) cc_final: 0.9123 (t0) REVERT: H 89 ASP cc_start: 0.9228 (t0) cc_final: 0.8762 (t0) REVERT: H 114 GLU cc_start: 0.9078 (mp0) cc_final: 0.8545 (mp0) REVERT: H 129 LYS cc_start: 0.9004 (OUTLIER) cc_final: 0.8650 (mtmm) REVERT: H 141 ARG cc_start: 0.9411 (mmm-85) cc_final: 0.9125 (mmm-85) REVERT: H 142 THR cc_start: 0.9605 (OUTLIER) cc_final: 0.9261 (p) outliers start: 37 outliers final: 19 residues processed: 259 average time/residue: 0.1201 time to fit residues: 41.9459 Evaluate side-chains 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 234 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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 125 GLN Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL 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 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 87 SER Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 30.0000 chunk 1 optimal weight: 6.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 87 optimal weight: 30.0000 chunk 26 optimal weight: 0.9990 chunk 79 optimal weight: 30.0000 chunk 68 optimal weight: 30.0000 chunk 38 optimal weight: 1.9990 chunk 14 optimal weight: 7.9990 chunk 75 optimal weight: 20.0000 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 113 HIS C 84 GLN C 94 ASN E 108 ASN ** F 25 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 = 0.3190 r_free = 0.3190 target = 0.048257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2672 r_free = 0.2672 target = 0.033868 restraints weight = 57970.724| |-----------------------------------------------------------------------------| r_work (start): 0.2609 rms_B_bonded: 3.62 r_work (final): 0.2609 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11001 Z= 0.189 Angle : 0.693 9.007 15843 Z= 0.398 Chirality : 0.044 0.302 1815 Planarity : 0.006 0.109 1203 Dihedral : 30.762 176.747 3302 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 13.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.64 % Allowed : 36.41 % Favored : 57.95 % 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: 1.81 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.36 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG E 134 TYR 0.019 0.002 TYR F 98 PHE 0.014 0.001 PHE D 62 TRP 0.002 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00357 / 0.19 (11001) covalent geometry : angle 0.69294 / 0.40 (15843) hydrogen bonds : bond 0.04454 / 2.94 ( 676) hydrogen bonds : angle 3.46929 / 2.57 ( 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 271 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9573 (tt0) cc_final: 0.8894 (tp30) REVERT: A 68 GLN cc_start: 0.9435 (tt0) cc_final: 0.9232 (tt0) REVERT: A 105 GLU cc_start: 0.9243 (tt0) cc_final: 0.8715 (tp30) REVERT: B 53 GLU cc_start: 0.8950 (tt0) cc_final: 0.8649 (tt0) REVERT: B 63 GLU cc_start: 0.9027 (mt-10) cc_final: 0.8628 (mt-10) REVERT: B 79 LYS cc_start: 0.8846 (OUTLIER) cc_final: 0.8620 (mtpt) REVERT: C 25 PHE cc_start: 0.8726 (m-10) cc_final: 0.8236 (m-80) REVERT: C 38 ASN cc_start: 0.9100 (t0) cc_final: 0.8620 (t0) REVERT: C 57 TYR cc_start: 0.8372 (t80) cc_final: 0.7861 (t80) REVERT: C 61 GLU cc_start: 0.9135 (OUTLIER) cc_final: 0.8851 (tt0) REVERT: C 94 ASN cc_start: 0.9265 (OUTLIER) cc_final: 0.9035 (t0) REVERT: C 99 ARG cc_start: 0.9046 (mmm160) cc_final: 0.8567 (mmp80) REVERT: C 104 GLN cc_start: 0.8550 (mp10) cc_final: 0.7881 (mp10) REVERT: D 103 ARG cc_start: 0.8894 (mtm110) cc_final: 0.8624 (mtm-85) REVERT: D 137 LYS cc_start: 0.9268 (mtmm) cc_final: 0.8939 (mtmm) REVERT: E 105 GLU cc_start: 0.9130 (tp30) cc_final: 0.8538 (tp30) REVERT: E 128 ARG cc_start: 0.9477 (mtp-110) cc_final: 0.9024 (mmm-85) REVERT: E 133 GLU cc_start: 0.8612 (pm20) cc_final: 0.8039 (pm20) REVERT: F 24 ASP cc_start: 0.9096 (t0) cc_final: 0.8669 (p0) REVERT: G 39 TYR cc_start: 0.9556 (m-80) cc_final: 0.9236 (m-80) REVERT: G 41 GLU cc_start: 0.8973 (mt-10) cc_final: 0.8689 (mt-10) REVERT: G 56 GLU cc_start: 0.8902 (tt0) cc_final: 0.8265 (tt0) REVERT: G 57 TYR cc_start: 0.8739 (t80) cc_final: 0.8433 (t80) REVERT: G 64 GLU cc_start: 0.9061 (tm-30) cc_final: 0.8518 (tm-30) REVERT: G 68 ASN cc_start: 0.9186 (m-40) cc_final: 0.8606 (m-40) REVERT: G 87 ILE cc_start: 0.9455 (tt) cc_final: 0.9219 (tp) REVERT: G 94 ASN cc_start: 0.9417 (t0) cc_final: 0.9115 (t0) REVERT: H 77 ARG cc_start: 0.9157 (ttm110) cc_final: 0.8709 (ptp-110) REVERT: H 78 GLU cc_start: 0.9404 (mp0) cc_final: 0.8986 (mp0) REVERT: H 84 ASP cc_start: 0.9076 (OUTLIER) cc_final: 0.8646 (m-30) REVERT: H 89 ASP cc_start: 0.9271 (t0) cc_final: 0.8790 (t0) REVERT: H 108 GLN cc_start: 0.8936 (pt0) cc_final: 0.8486 (pt0) REVERT: H 114 GLU cc_start: 0.9089 (mp0) cc_final: 0.8524 (mp0) REVERT: H 129 LYS cc_start: 0.8986 (OUTLIER) cc_final: 0.8558 (mtmm) REVERT: H 132 GLU cc_start: 0.8849 (tt0) cc_final: 0.8251 (tm-30) REVERT: H 141 ARG cc_start: 0.9423 (mmm-85) cc_final: 0.9109 (mmm-85) REVERT: H 142 THR cc_start: 0.9573 (OUTLIER) cc_final: 0.9240 (p) outliers start: 33 outliers final: 23 residues processed: 250 average time/residue: 0.1097 time to fit residues: 37.0106 Evaluate side-chains 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 61 GLU 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 87 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 122 LYS Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 15 LYS 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: 8.9990 chunk 16 optimal weight: 4.9990 chunk 49 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN C 94 ASN E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.049321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.034738 restraints weight = 58021.105| |-----------------------------------------------------------------------------| r_work (start): 0.2638 rms_B_bonded: 3.69 r_work (final): 0.2638 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8577 moved from start: 0.2681 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 11001 Z= 0.157 Angle : 0.685 10.893 15843 Z= 0.392 Chirality : 0.043 0.279 1815 Planarity : 0.005 0.051 1203 Dihedral : 30.750 177.618 3302 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 5.47 % Allowed : 36.92 % Favored : 57.61 % 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: 530 sheet: None (None), residues: 0 loop : -1.32 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 134 TYR 0.033 0.002 TYR F 98 PHE 0.013 0.001 PHE D 62 TRP 0.005 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00288 / 0.16 (11001) covalent geometry : angle 0.68497 / 0.39 (15843) hydrogen bonds : bond 0.04087 / 2.69 ( 676) hydrogen bonds : angle 3.35263 / 2.47 ( 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 280 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.299 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9575 (tt0) cc_final: 0.8912 (tp30) REVERT: A 60 LEU cc_start: 0.9240 (OUTLIER) cc_final: 0.8842 (mm) REVERT: A 68 GLN cc_start: 0.9389 (tt0) cc_final: 0.9188 (tt0) REVERT: A 94 GLU cc_start: 0.9239 (tp30) cc_final: 0.8931 (tp30) REVERT: A 105 GLU cc_start: 0.9259 (tt0) cc_final: 0.8719 (tp30) REVERT: B 63 GLU cc_start: 0.9010 (mt-10) cc_final: 0.8498 (mt-10) REVERT: B 79 LYS cc_start: 0.8837 (OUTLIER) cc_final: 0.8618 (mtpt) REVERT: B 84 MET cc_start: 0.8858 (tpp) cc_final: 0.8225 (mmm) REVERT: C 25 PHE cc_start: 0.8756 (m-10) cc_final: 0.8264 (m-80) REVERT: C 38 ASN cc_start: 0.9168 (t0) cc_final: 0.8612 (t0) REVERT: C 57 TYR cc_start: 0.8396 (t80) cc_final: 0.7787 (t80) REVERT: C 61 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8814 (tt0) REVERT: C 89 ASN cc_start: 0.9332 (m-40) cc_final: 0.9069 (m110) REVERT: C 92 GLU cc_start: 0.9439 (OUTLIER) cc_final: 0.9150 (pp20) REVERT: C 99 ARG cc_start: 0.9029 (mmm160) cc_final: 0.8596 (mmp80) REVERT: C 104 GLN cc_start: 0.8599 (mp10) cc_final: 0.7927 (mp10) REVERT: D 83 MET cc_start: 0.9373 (mmm) cc_final: 0.9160 (tpp) REVERT: D 103 ARG cc_start: 0.8905 (mtm180) cc_final: 0.8609 (mtm-85) REVERT: D 114 GLU cc_start: 0.9521 (mp0) cc_final: 0.8784 (mm-30) REVERT: D 137 LYS cc_start: 0.9282 (mtmm) cc_final: 0.8914 (mtmm) REVERT: E 105 GLU cc_start: 0.9078 (tp30) cc_final: 0.8433 (tp30) REVERT: E 128 ARG cc_start: 0.9458 (mtp-110) cc_final: 0.9124 (mmm-85) REVERT: E 133 GLU cc_start: 0.8696 (pm20) cc_final: 0.8484 (pm20) REVERT: F 30 THR cc_start: 0.9016 (OUTLIER) cc_final: 0.8810 (p) REVERT: F 50 ILE cc_start: 0.9466 (mm) cc_final: 0.9077 (mm) REVERT: G 25 PHE cc_start: 0.9217 (m-80) cc_final: 0.8989 (m-80) REVERT: G 39 TYR cc_start: 0.9529 (m-80) cc_final: 0.9237 (m-80) REVERT: G 41 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8723 (mt-10) REVERT: G 56 GLU cc_start: 0.8869 (tt0) cc_final: 0.8206 (tt0) REVERT: G 57 TYR cc_start: 0.8693 (t80) cc_final: 0.8418 (t80) REVERT: G 64 GLU cc_start: 0.9046 (tm-30) cc_final: 0.8411 (tm-30) REVERT: G 68 ASN cc_start: 0.9188 (m-40) cc_final: 0.8569 (m-40) REVERT: G 84 GLN cc_start: 0.9361 (OUTLIER) cc_final: 0.8866 (tp40) REVERT: G 87 ILE cc_start: 0.9469 (tt) cc_final: 0.9227 (tp) REVERT: G 94 ASN cc_start: 0.9403 (t0) cc_final: 0.9108 (t0) REVERT: H 77 ARG cc_start: 0.9148 (ttm110) cc_final: 0.8635 (ptp90) REVERT: H 78 GLU cc_start: 0.9392 (mp0) cc_final: 0.8874 (mp0) REVERT: H 84 ASP cc_start: 0.9097 (OUTLIER) cc_final: 0.8610 (m-30) REVERT: H 89 ASP cc_start: 0.9265 (t0) cc_final: 0.8692 (t0) REVERT: H 108 GLN cc_start: 0.8931 (pt0) cc_final: 0.8448 (pt0) REVERT: H 114 GLU cc_start: 0.9111 (mp0) cc_final: 0.8530 (mp0) REVERT: H 129 LYS cc_start: 0.8966 (OUTLIER) cc_final: 0.8537 (mtmm) REVERT: H 132 GLU cc_start: 0.8821 (tt0) cc_final: 0.8215 (tm-30) REVERT: H 141 ARG cc_start: 0.9406 (mmm-85) cc_final: 0.9061 (mmm-85) REVERT: H 142 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9196 (p) outliers start: 32 outliers final: 13 residues processed: 262 average time/residue: 0.1121 time to fit residues: 39.6385 Evaluate side-chains 267 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 245 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 130 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain G residue 84 GLN 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: 0.6980 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 0.9980 chunk 62 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 86 optimal weight: 30.0000 chunk 23 optimal weight: 5.9990 chunk 21 optimal weight: 10.0000 chunk 51 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN ** F 25 ASN ** 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 = 0.3250 r_free = 0.3250 target = 0.049486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.035163 restraints weight = 57865.354| |-----------------------------------------------------------------------------| r_work (start): 0.2697 rms_B_bonded: 3.65 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 11001 Z= 0.152 Angle : 0.686 8.584 15843 Z= 0.391 Chirality : 0.043 0.282 1815 Planarity : 0.004 0.052 1203 Dihedral : 30.713 178.383 3302 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 6.50 % Allowed : 36.92 % 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: 1.61 (0.32), residues: 691 helix: 1.79 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.50 (0.42), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 103 TYR 0.045 0.002 TYR F 98 PHE 0.011 0.001 PHE D 62 TRP 0.005 0.001 TRP D 113 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00277 / 0.15 (11001) covalent geometry : angle 0.68598 / 0.39 (15843) hydrogen bonds : bond 0.03970 / 2.61 ( 676) hydrogen bonds : angle 3.27484 / 2.42 ( 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 288 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 250 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9575 (tt0) cc_final: 0.8872 (tp30) REVERT: A 105 GLU cc_start: 0.9205 (tt0) cc_final: 0.8706 (tp30) REVERT: B 53 GLU cc_start: 0.8833 (tt0) cc_final: 0.8522 (tt0) REVERT: B 63 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8449 (mt-10) REVERT: B 79 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8654 (mtpt) REVERT: B 84 MET cc_start: 0.8794 (tpp) cc_final: 0.7969 (mmm) REVERT: C 25 PHE cc_start: 0.8702 (m-10) cc_final: 0.8287 (m-80) REVERT: C 35 ARG cc_start: 0.9485 (ttm110) cc_final: 0.9124 (ttm-80) REVERT: C 38 ASN cc_start: 0.9160 (t0) cc_final: 0.8503 (t0) REVERT: C 42 ARG cc_start: 0.8314 (mtp180) cc_final: 0.7986 (mmm-85) REVERT: C 57 TYR cc_start: 0.8526 (t80) cc_final: 0.7984 (t80) REVERT: C 61 GLU cc_start: 0.9148 (OUTLIER) cc_final: 0.8802 (mt-10) REVERT: C 71 ARG cc_start: 0.8447 (mtm-85) cc_final: 0.8234 (mtm-85) REVERT: C 77 ARG cc_start: 0.7471 (tpp80) cc_final: 0.7267 (tpp80) REVERT: C 88 ARG cc_start: 0.9347 (ttm110) cc_final: 0.9112 (tpp80) REVERT: C 89 ASN cc_start: 0.9412 (m-40) cc_final: 0.9130 (m110) REVERT: C 92 GLU cc_start: 0.9422 (OUTLIER) cc_final: 0.9147 (pp20) REVERT: C 94 ASN cc_start: 0.9351 (OUTLIER) cc_final: 0.8857 (m-40) REVERT: C 99 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8524 (mmp80) REVERT: C 104 GLN cc_start: 0.8653 (mp10) cc_final: 0.8018 (mp10) REVERT: D 103 ARG cc_start: 0.8925 (mtm180) cc_final: 0.8578 (mtm-85) REVERT: D 114 GLU cc_start: 0.9481 (mp0) cc_final: 0.8756 (mm-30) REVERT: D 137 LYS cc_start: 0.9324 (mtmm) cc_final: 0.8942 (mtmm) REVERT: E 128 ARG cc_start: 0.9478 (mtp-110) cc_final: 0.9149 (mmm-85) REVERT: F 50 ILE cc_start: 0.9561 (mm) cc_final: 0.9132 (mm) REVERT: G 39 TYR cc_start: 0.9526 (m-80) cc_final: 0.9140 (m-80) REVERT: G 41 GLU cc_start: 0.8953 (mt-10) cc_final: 0.8695 (mt-10) REVERT: G 56 GLU cc_start: 0.8858 (tt0) cc_final: 0.8219 (tt0) REVERT: G 57 TYR cc_start: 0.8705 (t80) cc_final: 0.8451 (t80) REVERT: G 64 GLU cc_start: 0.9003 (tm-30) cc_final: 0.8214 (tm-30) REVERT: G 68 ASN cc_start: 0.9191 (m-40) cc_final: 0.8622 (m-40) REVERT: G 84 GLN cc_start: 0.9409 (OUTLIER) cc_final: 0.8888 (tp40) REVERT: G 87 ILE cc_start: 0.9568 (tt) cc_final: 0.9300 (tp) REVERT: G 93 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9292 (mm) REVERT: G 94 ASN cc_start: 0.9422 (t0) cc_final: 0.9133 (t0) REVERT: H 77 ARG cc_start: 0.9105 (ttm110) cc_final: 0.8610 (ptp90) REVERT: H 78 GLU cc_start: 0.9336 (mp0) cc_final: 0.8864 (mp0) REVERT: H 84 ASP cc_start: 0.9109 (OUTLIER) cc_final: 0.8580 (m-30) REVERT: H 89 ASP cc_start: 0.9252 (t0) cc_final: 0.8736 (t0) REVERT: H 108 GLN cc_start: 0.8995 (pt0) cc_final: 0.8397 (pt0) REVERT: H 114 GLU cc_start: 0.9051 (mp0) cc_final: 0.8497 (mp0) REVERT: H 129 LYS cc_start: 0.8989 (OUTLIER) cc_final: 0.8589 (mtmm) REVERT: H 141 ARG cc_start: 0.9407 (mmm-85) cc_final: 0.9069 (mmm-85) REVERT: H 142 THR cc_start: 0.9570 (OUTLIER) cc_final: 0.9198 (p) outliers start: 38 outliers final: 20 residues processed: 268 average time/residue: 0.1354 time to fit residues: 47.5073 Evaluate side-chains 274 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 245 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 92 GLU 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 115 THR Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 122 LYS 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 15 LYS 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 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: 8.9990 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 58 optimal weight: 1.9990 chunk 25 optimal weight: 9.9990 chunk 27 optimal weight: 5.9990 chunk 65 optimal weight: 7.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN ** F 25 ASN ** 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 = 0.3220 r_free = 0.3220 target = 0.049265 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.034810 restraints weight = 57574.143| |-----------------------------------------------------------------------------| r_work (start): 0.2643 rms_B_bonded: 3.68 r_work (final): 0.2643 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 11001 Z= 0.165 Angle : 0.717 11.096 15843 Z= 0.402 Chirality : 0.044 0.297 1815 Planarity : 0.005 0.064 1203 Dihedral : 30.716 178.720 3302 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.50 % Allowed : 38.46 % 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: 1.54 (0.32), residues: 691 helix: 1.72 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.46 (0.41), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG D 63 TYR 0.042 0.002 TYR F 98 PHE 0.012 0.001 PHE G 25 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 0.00317 / 0.16 (11001) covalent geometry : angle 0.71719 / 0.40 (15843) hydrogen bonds : bond 0.04043 / 2.65 ( 676) hydrogen bonds : angle 3.35903 / 2.48 ( 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 286 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 248 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9570 (tt0) cc_final: 0.8880 (tp30) REVERT: A 105 GLU cc_start: 0.9287 (tt0) cc_final: 0.8730 (tp30) REVERT: B 63 GLU cc_start: 0.9041 (mt-10) cc_final: 0.8451 (mt-10) REVERT: B 84 MET cc_start: 0.8847 (tpp) cc_final: 0.8109 (mmm) REVERT: C 25 PHE cc_start: 0.8730 (m-10) cc_final: 0.8256 (m-80) REVERT: C 32 ARG cc_start: 0.8911 (tmm-80) cc_final: 0.8264 (ttp-170) REVERT: C 38 ASN cc_start: 0.9215 (t0) cc_final: 0.8591 (t0) REVERT: C 42 ARG cc_start: 0.8228 (mtp180) cc_final: 0.7898 (mmm-85) REVERT: C 57 TYR cc_start: 0.8477 (t80) cc_final: 0.7629 (t80) REVERT: C 61 GLU cc_start: 0.9176 (tt0) cc_final: 0.8771 (mt-10) REVERT: C 71 ARG cc_start: 0.8477 (mtm-85) cc_final: 0.8137 (mtm-85) REVERT: C 72 ASP cc_start: 0.9634 (t0) cc_final: 0.9211 (m-30) REVERT: C 88 ARG cc_start: 0.9372 (ttm110) cc_final: 0.9152 (tpp80) REVERT: C 89 ASN cc_start: 0.9382 (m-40) cc_final: 0.9073 (m110) REVERT: C 94 ASN cc_start: 0.9236 (OUTLIER) cc_final: 0.8928 (t0) REVERT: C 99 ARG cc_start: 0.8934 (mmm160) cc_final: 0.8505 (mmp80) REVERT: C 104 GLN cc_start: 0.8589 (mp10) cc_final: 0.7957 (mp10) REVERT: D 103 ARG cc_start: 0.8958 (mtm180) cc_final: 0.8572 (mtm-85) REVERT: D 107 ARG cc_start: 0.8911 (mtm-85) cc_final: 0.8307 (mtp85) REVERT: D 114 GLU cc_start: 0.9460 (OUTLIER) cc_final: 0.8594 (mm-30) REVERT: D 137 LYS cc_start: 0.9311 (mtmm) cc_final: 0.9006 (mtmm) REVERT: F 50 ILE cc_start: 0.9481 (mm) cc_final: 0.9027 (mm) REVERT: G 39 TYR cc_start: 0.9524 (m-80) cc_final: 0.9180 (m-80) REVERT: G 41 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8661 (mt-10) REVERT: G 56 GLU cc_start: 0.8864 (tt0) cc_final: 0.8245 (tt0) REVERT: G 57 TYR cc_start: 0.8684 (t80) cc_final: 0.8403 (t80) REVERT: G 64 GLU cc_start: 0.9120 (tm-30) cc_final: 0.8330 (tm-30) REVERT: G 68 ASN cc_start: 0.9233 (m-40) cc_final: 0.8666 (m-40) REVERT: G 84 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8857 (tp40) REVERT: G 87 ILE cc_start: 0.9496 (tt) cc_final: 0.9247 (tp) REVERT: G 93 LEU cc_start: 0.9512 (OUTLIER) cc_final: 0.9259 (mm) REVERT: H 77 ARG cc_start: 0.9160 (ttm110) cc_final: 0.8679 (ptp90) REVERT: H 78 GLU cc_start: 0.9398 (mp0) cc_final: 0.8939 (mp0) REVERT: H 84 ASP cc_start: 0.9095 (OUTLIER) cc_final: 0.8551 (m-30) REVERT: H 89 ASP cc_start: 0.9299 (t0) cc_final: 0.8727 (t0) REVERT: H 108 GLN cc_start: 0.8904 (pt0) cc_final: 0.8376 (pt0) REVERT: H 114 GLU cc_start: 0.9095 (mp0) cc_final: 0.8514 (mp0) REVERT: H 129 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8586 (mtmm) REVERT: H 141 ARG cc_start: 0.9427 (mmm-85) cc_final: 0.9078 (mmm-85) REVERT: H 142 THR cc_start: 0.9543 (OUTLIER) cc_final: 0.9180 (p) outliers start: 38 outliers final: 23 residues processed: 263 average time/residue: 0.1344 time to fit residues: 46.3152 Evaluate side-chains 278 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 248 time to evaluate : 0.287 ------------------------------------------------------------------------------- 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 85 ASP Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 79 ILE 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 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 109 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS 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: 2.9990 chunk 17 optimal weight: 4.9990 chunk 43 optimal weight: 0.0370 chunk 21 optimal weight: 10.0000 chunk 68 optimal weight: 30.0000 chunk 4 optimal weight: 0.9980 chunk 75 optimal weight: 30.0000 chunk 72 optimal weight: 30.0000 chunk 5 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 overall best weight: 2.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 94 ASN E 108 ASN ** F 25 ASN ** 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 = 0.3231 r_free = 0.3231 target = 0.048351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.034640 restraints weight = 57269.833| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 3.60 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.3020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11001 Z= 0.179 Angle : 0.717 9.495 15843 Z= 0.406 Chirality : 0.044 0.284 1815 Planarity : 0.005 0.050 1203 Dihedral : 30.739 178.934 3302 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 6.32 % Allowed : 38.63 % 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: 534 sheet: None (None), residues: 0 loop : -1.39 (0.41), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 63 TYR 0.050 0.002 TYR F 98 PHE 0.010 0.001 PHE D 62 TRP 0.003 0.001 TRP D 113 HIS 0.010 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00347 / 0.18 (11001) covalent geometry : angle 0.71723 / 0.41 (15843) hydrogen bonds : bond 0.04122 / 2.70 ( 676) hydrogen bonds : angle 3.39317 / 2.50 ( 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 278 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 241 time to evaluate : 0.296 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: A 50 GLU cc_start: 0.9581 (tt0) cc_final: 0.8865 (tp30) REVERT: A 64 LYS cc_start: 0.9228 (mttp) cc_final: 0.8966 (mmtm) REVERT: A 105 GLU cc_start: 0.9229 (tt0) cc_final: 0.8719 (tp30) REVERT: B 63 GLU cc_start: 0.9028 (mt-10) cc_final: 0.8441 (mt-10) REVERT: B 84 MET cc_start: 0.8829 (tpp) cc_final: 0.8136 (mmm) REVERT: C 25 PHE cc_start: 0.8731 (m-10) cc_final: 0.8281 (m-80) REVERT: C 38 ASN cc_start: 0.9253 (t0) cc_final: 0.8616 (t0) REVERT: C 42 ARG cc_start: 0.8364 (mtp180) cc_final: 0.7994 (mmm-85) REVERT: C 57 TYR cc_start: 0.8556 (t80) cc_final: 0.7665 (t80) REVERT: C 61 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8764 (mt-10) REVERT: C 72 ASP cc_start: 0.9621 (t0) cc_final: 0.9204 (m-30) REVERT: C 89 ASN cc_start: 0.9410 (m-40) cc_final: 0.9127 (m110) REVERT: C 94 ASN cc_start: 0.9177 (OUTLIER) cc_final: 0.8663 (m-40) REVERT: C 99 ARG cc_start: 0.8868 (mmm160) cc_final: 0.8428 (mmp80) REVERT: C 104 GLN cc_start: 0.8591 (mp10) cc_final: 0.7966 (mp10) REVERT: D 67 LYS cc_start: 0.9520 (tttt) cc_final: 0.9292 (tttt) REVERT: D 103 ARG cc_start: 0.8936 (mtm180) cc_final: 0.8432 (mtm-85) REVERT: D 107 ARG cc_start: 0.8973 (mtm-85) cc_final: 0.8386 (mtp85) REVERT: D 114 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.8604 (mm-30) REVERT: D 137 LYS cc_start: 0.9317 (mtmm) cc_final: 0.8999 (mtmm) REVERT: E 73 GLU cc_start: 0.8997 (tt0) cc_final: 0.8156 (tt0) REVERT: F 50 ILE cc_start: 0.9549 (mm) cc_final: 0.9086 (mm) REVERT: G 41 GLU cc_start: 0.8923 (mt-10) cc_final: 0.8608 (mt-10) REVERT: G 56 GLU cc_start: 0.8883 (tt0) cc_final: 0.8286 (tt0) REVERT: G 57 TYR cc_start: 0.8739 (t80) cc_final: 0.8486 (t80) REVERT: G 64 GLU cc_start: 0.9087 (tm-30) cc_final: 0.8291 (tm-30) REVERT: G 68 ASN cc_start: 0.9220 (m-40) cc_final: 0.8632 (m-40) REVERT: G 84 GLN cc_start: 0.9414 (OUTLIER) cc_final: 0.8898 (tp40) REVERT: G 87 ILE cc_start: 0.9565 (tt) cc_final: 0.9300 (tp) REVERT: G 93 LEU cc_start: 0.9550 (OUTLIER) cc_final: 0.9293 (mm) REVERT: G 94 ASN cc_start: 0.9376 (t0) cc_final: 0.9117 (t0) REVERT: H 77 ARG cc_start: 0.9096 (ttm110) cc_final: 0.8612 (ptp90) REVERT: H 78 GLU cc_start: 0.9386 (mp0) cc_final: 0.8958 (mp0) REVERT: H 84 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8554 (m-30) REVERT: H 89 ASP cc_start: 0.9306 (t0) cc_final: 0.8746 (t0) REVERT: H 108 GLN cc_start: 0.8975 (pt0) cc_final: 0.8357 (pt0) REVERT: H 114 GLU cc_start: 0.9042 (mp0) cc_final: 0.8500 (mp0) REVERT: H 129 LYS cc_start: 0.9012 (OUTLIER) cc_final: 0.8619 (mtmm) REVERT: H 141 ARG cc_start: 0.9418 (mmm-85) cc_final: 0.9079 (mmm-85) REVERT: H 142 THR cc_start: 0.9586 (OUTLIER) cc_final: 0.9217 (p) outliers start: 37 outliers final: 25 residues processed: 256 average time/residue: 0.1279 time to fit residues: 43.3295 Evaluate side-chains 271 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 238 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 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 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 109 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 6.9990 chunk 59 optimal weight: 9.9990 chunk 34 optimal weight: 0.0980 chunk 65 optimal weight: 7.9990 chunk 84 optimal weight: 30.0000 chunk 69 optimal weight: 30.0000 chunk 76 optimal weight: 30.0000 chunk 53 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 8.9990 overall best weight: 3.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.047969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.034394 restraints weight = 57709.517| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.60 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.3073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11001 Z= 0.194 Angle : 0.730 11.277 15843 Z= 0.411 Chirality : 0.044 0.285 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.780 179.141 3302 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.98 % Allowed : 39.32 % Favored : 54.70 % 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: 1.71 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.36 (0.41), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 63 TYR 0.040 0.002 TYR F 98 PHE 0.010 0.001 PHE D 62 TRP 0.002 0.001 TRP D 113 HIS 0.006 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00381 / 0.19 (11001) covalent geometry : angle 0.73035 / 0.41 (15843) hydrogen bonds : bond 0.04236 / 2.78 ( 676) hydrogen bonds : angle 3.42728 / 2.52 ( 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 277 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 242 time to evaluate : 0.287 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9596 (tt0) cc_final: 0.8873 (tp30) REVERT: A 64 LYS cc_start: 0.9229 (mttp) cc_final: 0.8974 (mmtm) REVERT: A 105 GLU cc_start: 0.9238 (tt0) cc_final: 0.8722 (tp30) REVERT: B 63 GLU cc_start: 0.9022 (mt-10) cc_final: 0.8419 (mt-10) REVERT: B 84 MET cc_start: 0.8846 (tpp) cc_final: 0.8113 (mmm) REVERT: C 25 PHE cc_start: 0.8749 (m-10) cc_final: 0.8298 (m-80) REVERT: C 38 ASN cc_start: 0.9328 (t0) cc_final: 0.8705 (t0) REVERT: C 42 ARG cc_start: 0.8371 (mtp180) cc_final: 0.8006 (mmm-85) REVERT: C 57 TYR cc_start: 0.8548 (t80) cc_final: 0.7649 (t80) REVERT: C 61 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8810 (mt-10) REVERT: C 68 ASN cc_start: 0.9489 (m-40) cc_final: 0.9182 (m-40) REVERT: C 72 ASP cc_start: 0.9626 (t0) cc_final: 0.9209 (m-30) REVERT: C 88 ARG cc_start: 0.9315 (ttm110) cc_final: 0.8886 (mmt90) REVERT: C 89 ASN cc_start: 0.9420 (m-40) cc_final: 0.9124 (m110) REVERT: C 92 GLU cc_start: 0.9448 (OUTLIER) cc_final: 0.9185 (pp20) REVERT: C 94 ASN cc_start: 0.9124 (t0) cc_final: 0.8511 (m-40) REVERT: C 99 ARG cc_start: 0.8890 (mmm160) cc_final: 0.8427 (mmp80) REVERT: C 104 GLN cc_start: 0.8527 (mp10) cc_final: 0.8126 (mp10) REVERT: D 103 ARG cc_start: 0.8960 (mtm180) cc_final: 0.8428 (mtm-85) REVERT: D 107 ARG cc_start: 0.8979 (mtm-85) cc_final: 0.8371 (mtp85) REVERT: D 114 GLU cc_start: 0.9416 (OUTLIER) cc_final: 0.8630 (mm-30) REVERT: D 137 LYS cc_start: 0.9322 (mtmm) cc_final: 0.9000 (mtmm) REVERT: F 50 ILE cc_start: 0.9547 (mm) cc_final: 0.9090 (mm) REVERT: G 41 GLU cc_start: 0.8938 (mt-10) cc_final: 0.8635 (mt-10) REVERT: G 56 GLU cc_start: 0.8931 (tt0) cc_final: 0.8370 (tt0) REVERT: G 57 TYR cc_start: 0.8733 (t80) cc_final: 0.8492 (t80) REVERT: G 64 GLU cc_start: 0.9090 (tm-30) cc_final: 0.8283 (tm-30) REVERT: G 68 ASN cc_start: 0.9220 (m-40) cc_final: 0.8620 (m-40) REVERT: G 84 GLN cc_start: 0.9408 (OUTLIER) cc_final: 0.8872 (tp40) REVERT: G 94 ASN cc_start: 0.9391 (t0) cc_final: 0.9134 (t0) REVERT: H 77 ARG cc_start: 0.9114 (ttm110) cc_final: 0.8622 (ptp90) REVERT: H 78 GLU cc_start: 0.9386 (mp0) cc_final: 0.8970 (mp0) REVERT: H 84 ASP cc_start: 0.9133 (OUTLIER) cc_final: 0.8582 (m-30) REVERT: H 89 ASP cc_start: 0.9327 (t0) cc_final: 0.8767 (t0) REVERT: H 108 GLN cc_start: 0.8976 (pt0) cc_final: 0.8362 (pt0) REVERT: H 114 GLU cc_start: 0.9061 (mp0) cc_final: 0.8528 (mp0) REVERT: H 129 LYS cc_start: 0.9024 (OUTLIER) cc_final: 0.8660 (mtmm) REVERT: H 141 ARG cc_start: 0.9443 (mmm-85) cc_final: 0.9110 (mmm-85) REVERT: H 142 THR cc_start: 0.9582 (OUTLIER) cc_final: 0.9227 (p) outliers start: 35 outliers final: 22 residues processed: 257 average time/residue: 0.1227 time to fit residues: 41.6028 Evaluate side-chains 266 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 237 time to evaluate : 0.297 ------------------------------------------------------------------------------- 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 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU 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 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 F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS 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 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 chunk 4 optimal weight: 9.9990 chunk 54 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 1.9990 chunk 60 optimal weight: 10.0000 chunk 20 optimal weight: 4.9990 chunk 43 optimal weight: 10.0000 chunk 73 optimal weight: 30.0000 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 25 ASN ** 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 = 0.3232 r_free = 0.3232 target = 0.048385 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.034128 restraints weight = 57738.715| |-----------------------------------------------------------------------------| r_work (start): 0.2682 rms_B_bonded: 3.62 r_work (final): 0.2682 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8662 moved from start: 0.3188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 11001 Z= 0.178 Angle : 0.748 14.161 15843 Z= 0.413 Chirality : 0.044 0.285 1815 Planarity : 0.005 0.050 1203 Dihedral : 30.805 179.348 3302 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.81 % Allowed : 39.66 % Favored : 54.53 % 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: 1.76 (0.23), residues: 534 sheet: None (None), residues: 0 loop : -1.40 (0.42), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG D 63 TYR 0.036 0.002 TYR F 98 PHE 0.007 0.001 PHE G 25 TRP 0.001 0.000 TRP H 113 HIS 0.004 0.001 HIS C 31 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.18 (11001) covalent geometry : angle 0.74787 / 0.41 (15843) hydrogen bonds : bond 0.04079 / 2.66 ( 676) hydrogen bonds : angle 3.37415 / 2.47 ( 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 276 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 242 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9580 (tt0) cc_final: 0.8858 (tp30) REVERT: A 64 LYS cc_start: 0.9256 (mttp) cc_final: 0.8986 (mmmm) REVERT: A 105 GLU cc_start: 0.9229 (tt0) cc_final: 0.8720 (tp30) REVERT: B 63 GLU cc_start: 0.9019 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 84 MET cc_start: 0.8857 (tpp) cc_final: 0.8043 (mmm) REVERT: C 25 PHE cc_start: 0.8739 (m-10) cc_final: 0.8331 (m-80) REVERT: C 32 ARG cc_start: 0.8812 (ttp80) cc_final: 0.8271 (ttp-170) REVERT: C 38 ASN cc_start: 0.9326 (t0) cc_final: 0.8716 (t0) REVERT: C 42 ARG cc_start: 0.8369 (mtp180) cc_final: 0.7992 (mmm-85) REVERT: C 57 TYR cc_start: 0.8498 (t80) cc_final: 0.7562 (t80) REVERT: C 61 GLU cc_start: 0.9118 (OUTLIER) cc_final: 0.8744 (tt0) REVERT: C 68 ASN cc_start: 0.9489 (m-40) cc_final: 0.9179 (m-40) REVERT: C 72 ASP cc_start: 0.9626 (t0) cc_final: 0.9209 (m-30) REVERT: C 84 GLN cc_start: 0.9584 (tt0) cc_final: 0.8923 (tt0) REVERT: C 88 ARG cc_start: 0.9321 (ttm110) cc_final: 0.8575 (ttm110) REVERT: C 89 ASN cc_start: 0.9441 (m-40) cc_final: 0.9117 (m110) REVERT: C 92 GLU cc_start: 0.9418 (OUTLIER) cc_final: 0.9214 (pp20) REVERT: C 94 ASN cc_start: 0.9222 (OUTLIER) cc_final: 0.8807 (t0) REVERT: C 99 ARG cc_start: 0.8900 (mmm160) cc_final: 0.8502 (mmp80) REVERT: C 104 GLN cc_start: 0.8556 (mp10) cc_final: 0.8163 (mp10) REVERT: D 62 PHE cc_start: 0.9430 (m-80) cc_final: 0.9209 (m-80) REVERT: D 84 ASP cc_start: 0.8878 (OUTLIER) cc_final: 0.8605 (m-30) REVERT: D 103 ARG cc_start: 0.8932 (mtm180) cc_final: 0.8283 (mtm-85) REVERT: D 107 ARG cc_start: 0.8952 (mtm-85) cc_final: 0.8326 (mtp85) REVERT: D 114 GLU cc_start: 0.9382 (OUTLIER) cc_final: 0.8612 (mm-30) REVERT: D 137 LYS cc_start: 0.9347 (mtmm) cc_final: 0.8981 (mtmm) REVERT: E 90 MET cc_start: 0.9300 (mmp) cc_final: 0.9093 (mmp) REVERT: F 50 ILE cc_start: 0.9550 (mm) cc_final: 0.9081 (mm) REVERT: G 41 GLU cc_start: 0.8930 (mt-10) cc_final: 0.8620 (mt-10) REVERT: G 56 GLU cc_start: 0.8907 (tt0) cc_final: 0.8334 (tt0) REVERT: G 57 TYR cc_start: 0.8724 (t80) cc_final: 0.8493 (t80) REVERT: G 64 GLU cc_start: 0.9043 (tm-30) cc_final: 0.8215 (tm-30) REVERT: G 68 ASN cc_start: 0.9199 (m-40) cc_final: 0.8582 (m-40) REVERT: G 94 ASN cc_start: 0.9419 (t0) cc_final: 0.9160 (t0) REVERT: H 77 ARG cc_start: 0.9111 (ttm110) cc_final: 0.8619 (ptp90) REVERT: H 78 GLU cc_start: 0.9375 (mp0) cc_final: 0.8995 (mp0) REVERT: H 84 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8556 (m-30) REVERT: H 89 ASP cc_start: 0.9304 (t0) cc_final: 0.8724 (t0) REVERT: H 108 GLN cc_start: 0.8982 (pt0) cc_final: 0.8396 (pt0) REVERT: H 114 GLU cc_start: 0.9078 (mp0) cc_final: 0.8521 (mp0) REVERT: H 129 LYS cc_start: 0.9036 (OUTLIER) cc_final: 0.8767 (mtmm) REVERT: H 132 GLU cc_start: 0.8763 (tt0) cc_final: 0.8448 (tp30) REVERT: H 141 ARG cc_start: 0.9443 (mmm-85) cc_final: 0.9078 (mmm-85) REVERT: H 142 THR cc_start: 0.9607 (OUTLIER) cc_final: 0.9240 (p) outliers start: 34 outliers final: 22 residues processed: 255 average time/residue: 0.1220 time to fit residues: 41.1776 Evaluate side-chains 270 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 240 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 92 GLU 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 84 ASP 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 108 ASN Chi-restraints excluded: chain E residue 109 LEU 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 15 LYS 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 0.7980 chunk 83 optimal weight: 30.0000 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 30.0000 chunk 14 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 7.9990 chunk 27 optimal weight: 3.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 25 ASN C 94 ASN ** D 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3239 r_free = 0.3239 target = 0.048668 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.034240 restraints weight = 58490.869| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 3.66 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8659 moved from start: 0.3233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 11001 Z= 0.164 Angle : 0.744 12.490 15843 Z= 0.411 Chirality : 0.044 0.285 1815 Planarity : 0.005 0.050 1203 Dihedral : 30.792 179.256 3302 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.30 % Allowed : 40.51 % Favored : 54.19 % 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: 1.61 (0.32), residues: 691 helix: 1.75 (0.23), residues: 536 sheet: None (None), residues: 0 loop : -1.35 (0.42), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 63 TYR 0.035 0.002 TYR F 98 PHE 0.009 0.001 PHE D 62 TRP 0.002 0.000 TRP D 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.16 (11001) covalent geometry : angle 0.74443 / 0.41 (15843) hydrogen bonds : bond 0.04027 / 2.63 ( 676) hydrogen bonds : angle 3.32286 / 2.44 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1842.57 seconds wall clock time: 32 minutes 20.15 seconds (1940.15 seconds total)