Starting phenix.real_space_refine on Wed Apr 30 22:45:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcc_36157/04_2025/8jcc_36157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcc_36157/04_2025/8jcc_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_36157/04_2025/8jcc_36157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcc_36157/04_2025/8jcc_36157.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcc_36157/04_2025/8jcc_36157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcc_36157/04_2025/8jcc_36157.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5669/modules/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: 6.52, per 1000 atoms: 0.63 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: 2.91 Conformation dependent library (CDL) restraints added in 749.8 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 75.7% alpha, 3.1% beta 114 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 4.99 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: 3.96 Time building geometry restraints manager: 3.42 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' DT I -17 " pdb=" O3' DT I -17 " ideal model delta sigma weight residual 1.422 1.458 -0.036 3.00e-02 1.11e+03 1.44e+00 bond pdb=" C3' DA I -38 " pdb=" O3' DA I -38 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 9.96e-01 bond pdb=" CB ILE A 74 " pdb=" CG2 ILE A 74 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.35e-01 bond pdb=" C3' DC J 4 " pdb=" O3' DC J 4 " ideal model delta sigma weight residual 1.422 1.450 -0.028 3.00e-02 1.11e+03 8.67e-01 bond pdb=" C4' DG I -35 " pdb=" C3' DG I -35 " ideal model delta sigma weight residual 1.523 1.504 0.019 2.00e-02 2.50e+03 8.61e-01 ... (remaining 10996 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 15524 1.88 - 3.76: 287 3.76 - 5.64: 24 5.64 - 7.52: 5 7.52 - 9.40: 3 Bond angle restraints: 15843 Sorted by residual: angle pdb=" O3' DG I 4 " pdb=" C3' DG I 4 " pdb=" C2' DG I 4 " ideal model delta sigma weight residual 111.50 105.19 6.31 1.50e+00 4.44e-01 1.77e+01 angle pdb=" O3' DA J -25 " pdb=" C3' DA J -25 " pdb=" C2' DA J -25 " ideal model delta sigma weight residual 111.50 106.11 5.39 1.50e+00 4.44e-01 1.29e+01 angle pdb=" O3' DA J 16 " pdb=" C3' DA J 16 " pdb=" C2' DA J 16 " ideal model delta sigma weight residual 111.50 106.50 5.00 1.50e+00 4.44e-01 1.11e+01 angle pdb=" CB MET H 117 " pdb=" CG MET H 117 " pdb=" SD MET H 117 " ideal model delta sigma weight residual 112.70 122.10 -9.40 3.00e+00 1.11e-01 9.81e+00 angle pdb=" O3' DC I -27 " pdb=" C3' DC I -27 " pdb=" C2' DC I -27 " ideal model delta sigma weight residual 111.50 106.87 4.63 1.50e+00 4.44e-01 9.54e+00 ... (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: 1426 0.041 - 0.082: 322 0.082 - 0.122: 56 0.122 - 0.163: 8 0.163 - 0.204: 3 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' DA J -25 " pdb=" C4' DA J -25 " pdb=" O3' DA J -25 " pdb=" C2' DA J -25 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" C3' DG I 4 " pdb=" C4' DG I 4 " pdb=" O3' DG I 4 " pdb=" C2' DG I 4 " both_signs ideal model delta sigma weight residual False -2.66 -2.83 0.17 2.00e-01 2.50e+01 7.03e-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: 0.500 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: 0.400 Check model and map are aligned: 0.080 Set scattering table: 0.110 Process input model: 30.710 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.050 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 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 : 0.005 0.037 11001 Z= 0.200 Angle : 0.600 9.395 15843 Z= 0.346 Chirality : 0.036 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS H 70 PHE 0.007 0.001 PHE D 58 TYR 0.011 0.001 TYR D 145 ARG 0.005 0.000 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.11443 ( 676) hydrogen bonds : angle 4.05117 ( 1719) covalent geometry : bond 0.00460 (11001) covalent geometry : angle 0.59995 (15843) *********************** 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 : 0.845 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 38 ASN cc_start: 0.7118 (t0) cc_final: 0.6514 (t0) REVERT: C 57 TYR cc_start: 0.7832 (t80) cc_final: 0.7582 (t80) REVERT: G 61 GLU cc_start: 0.6135 (tt0) cc_final: 0.5169 (tt0) REVERT: H 108 GLN cc_start: 0.7506 (pt0) cc_final: 0.6928 (pt0) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.3301 time to fit residues: 137.4310 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 : 0.797 ------------------------------------------------------------------------------- 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 75 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 70 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.3204 r_free = 0.3204 target = 0.048593 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.034787 restraints weight = 55917.031| |-----------------------------------------------------------------------------| r_work (start): 0.2655 rms_B_bonded: 3.51 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11001 Z= 0.189 Angle : 0.630 5.988 15843 Z= 0.363 Chirality : 0.036 0.377 1815 Planarity : 0.005 0.053 1203 Dihedral : 30.321 178.452 3304 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.15 % Allowed : 34.70 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.33), residues: 691 helix: 1.93 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.022 0.002 PHE D 62 TYR 0.015 0.002 TYR B 98 ARG 0.012 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 676) hydrogen bonds : angle 3.33880 ( 1719) covalent geometry : bond 0.00422 (11001) covalent geometry : angle 0.63032 (15843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.777 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: 0.9416 (tt0) cc_final: 0.8678 (tp30) REVERT: A 125 GLN cc_start: 0.9368 (OUTLIER) cc_final: 0.9071 (mp10) REVERT: C 25 PHE cc_start: 0.8489 (m-10) cc_final: 0.7915 (m-80) REVERT: C 38 ASN cc_start: 0.9040 (t0) cc_final: 0.8607 (t0) REVERT: C 39 TYR cc_start: 0.8347 (m-80) cc_final: 0.8086 (m-80) REVERT: C 42 ARG cc_start: 0.8169 (mtp180) cc_final: 0.7055 (mmm-85) REVERT: C 57 TYR cc_start: 0.8169 (t80) cc_final: 0.7434 (t80) REVERT: C 61 GLU cc_start: 0.8879 (tt0) cc_final: 0.8480 (tt0) REVERT: C 73 ASN cc_start: 0.9098 (OUTLIER) cc_final: 0.8866 (t0) REVERT: C 77 ARG cc_start: 0.6974 (OUTLIER) cc_final: 0.5926 (mtt180) REVERT: C 88 ARG cc_start: 0.9341 (ttm110) cc_final: 0.8661 (ttm110) REVERT: C 95 LYS cc_start: 0.9468 (tppt) cc_final: 0.9260 (tppt) REVERT: C 99 ARG cc_start: 0.9033 (mmm160) cc_final: 0.8545 (mmp80) REVERT: C 104 GLN cc_start: 0.8489 (mp10) cc_final: 0.7896 (mp10) REVERT: D 89 ASP cc_start: 0.9167 (t0) cc_final: 0.8914 (t0) REVERT: D 108 GLN cc_start: 0.8381 (pm20) cc_final: 0.7912 (pm20) REVERT: D 137 LYS cc_start: 0.9213 (mtmm) cc_final: 0.8910 (mtmm) REVERT: E 105 GLU cc_start: 0.9164 (tp30) cc_final: 0.8558 (tp30) REVERT: E 128 ARG cc_start: 0.9541 (mtp-110) cc_final: 0.8851 (mmm-85) REVERT: G 41 GLU cc_start: 0.9108 (mt-10) cc_final: 0.8836 (mt-10) REVERT: G 55 LEU cc_start: 0.9777 (mt) cc_final: 0.9577 (mt) REVERT: G 56 GLU cc_start: 0.8932 (tt0) cc_final: 0.8329 (tt0) REVERT: G 57 TYR cc_start: 0.8783 (t80) cc_final: 0.8561 (t80) REVERT: G 61 GLU cc_start: 0.9040 (tt0) cc_final: 0.8833 (tt0) REVERT: G 94 ASN cc_start: 0.9454 (t0) cc_final: 0.9145 (t0) REVERT: H 89 ASP cc_start: 0.9163 (t0) cc_final: 0.8733 (t0) REVERT: H 114 GLU cc_start: 0.9169 (mp0) cc_final: 0.8676 (mp0) REVERT: H 129 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8668 (mtmm) REVERT: H 141 ARG cc_start: 0.9200 (mmm-85) cc_final: 0.8890 (mmm-85) REVERT: H 142 THR cc_start: 0.9550 (OUTLIER) cc_final: 0.9221 (p) outliers start: 36 outliers final: 12 residues processed: 286 average time/residue: 0.2975 time to fit residues: 109.4634 Evaluate side-chains 259 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.831 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 77 ARG 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 F residue 22 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 108 LEU 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=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 10.0000 chunk 50 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 53 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 68 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 1.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN F 25 ASN G 112 GLN H 108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049361 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.034836 restraints weight = 58682.914| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.67 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.2708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 11001 Z= 0.172 Angle : 0.624 10.066 15843 Z= 0.359 Chirality : 0.036 0.339 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.261 178.541 3304 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.62 % Allowed : 34.53 % Favored : 60.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.32), residues: 691 helix: 1.85 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.014 0.001 PHE D 62 TYR 0.010 0.001 TYR D 61 ARG 0.011 0.001 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.03510 ( 676) hydrogen bonds : angle 3.22424 ( 1719) covalent geometry : bond 0.00380 (11001) covalent geometry : angle 0.62427 (15843) *********************** 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 282 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 255 time to evaluate : 0.823 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: A 94 GLU cc_start: 0.9231 (tp30) cc_final: 0.8905 (tp30) REVERT: B 63 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8612 (mt-10) REVERT: B 79 LYS cc_start: 0.8924 (OUTLIER) cc_final: 0.8665 (mtpt) REVERT: B 84 MET cc_start: 0.8816 (tpp) cc_final: 0.8147 (mmm) REVERT: C 25 PHE cc_start: 0.8599 (m-10) cc_final: 0.8101 (m-80) REVERT: C 38 ASN cc_start: 0.9179 (t0) cc_final: 0.8552 (t0) REVERT: C 39 TYR cc_start: 0.8470 (m-80) cc_final: 0.8194 (m-80) REVERT: C 57 TYR cc_start: 0.8313 (t80) cc_final: 0.7435 (t80) REVERT: C 61 GLU cc_start: 0.8969 (tt0) cc_final: 0.8478 (tt0) REVERT: C 89 ASN cc_start: 0.9421 (m-40) cc_final: 0.9116 (m110) REVERT: C 92 GLU cc_start: 0.9300 (pp20) cc_final: 0.8903 (tt0) REVERT: C 99 ARG cc_start: 0.9070 (mmm160) cc_final: 0.8641 (mmp80) REVERT: C 104 GLN cc_start: 0.8427 (mp10) cc_final: 0.7854 (mp10) REVERT: D 89 ASP cc_start: 0.9148 (t0) cc_final: 0.8906 (t0) REVERT: D 103 ARG cc_start: 0.8731 (mtm-85) cc_final: 0.8295 (mtm-85) REVERT: D 107 ARG cc_start: 0.8930 (mtp85) cc_final: 0.8455 (mtp85) REVERT: D 126 GLN cc_start: 0.8321 (tp-100) cc_final: 0.7380 (tp-100) REVERT: D 137 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8924 (mtmm) REVERT: E 105 GLU cc_start: 0.9100 (tp30) cc_final: 0.8385 (tp30) REVERT: E 108 ASN cc_start: 0.9495 (t0) cc_final: 0.9285 (t0) REVERT: E 128 ARG cc_start: 0.9337 (mtp-110) cc_final: 0.8957 (mmm-85) REVERT: E 133 GLU cc_start: 0.8296 (pm20) cc_final: 0.8089 (pm20) REVERT: G 56 GLU cc_start: 0.8891 (tt0) cc_final: 0.8394 (tt0) REVERT: G 57 TYR cc_start: 0.8702 (t80) cc_final: 0.8084 (t80) REVERT: G 61 GLU cc_start: 0.9112 (tt0) cc_final: 0.8328 (tt0) REVERT: G 64 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8670 (tm-30) REVERT: G 68 ASN cc_start: 0.9273 (m-40) cc_final: 0.8427 (m-40) REVERT: G 87 ILE cc_start: 0.9333 (tp) cc_final: 0.9083 (tp) REVERT: G 94 ASN cc_start: 0.9454 (t0) cc_final: 0.9165 (t0) REVERT: H 84 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8587 (m-30) REVERT: H 89 ASP cc_start: 0.9239 (t0) cc_final: 0.8734 (t0) REVERT: H 108 GLN cc_start: 0.8948 (pt0) cc_final: 0.8210 (pt0) REVERT: H 114 GLU cc_start: 0.9161 (mp0) cc_final: 0.8560 (mp0) REVERT: H 127 MET cc_start: 0.9037 (ttp) cc_final: 0.8688 (tpp) REVERT: H 141 ARG cc_start: 0.9181 (mmm-85) cc_final: 0.8824 (mmm-85) REVERT: H 142 THR cc_start: 0.9554 (OUTLIER) cc_final: 0.9189 (p) outliers start: 27 outliers final: 14 residues processed: 267 average time/residue: 0.3189 time to fit residues: 109.9322 Evaluate side-chains 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 245 time to evaluate : 0.892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP 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 80 optimal weight: 10.0000 chunk 35 optimal weight: 0.8980 chunk 22 optimal weight: 8.9990 chunk 8 optimal weight: 0.9990 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 83 optimal weight: 10.0000 chunk 52 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 53 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN B 25 ASN C 73 ASN C 94 ASN E 113 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.049112 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.034848 restraints weight = 57429.344| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.68 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.3057 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11001 Z= 0.170 Angle : 0.613 8.600 15843 Z= 0.354 Chirality : 0.035 0.155 1815 Planarity : 0.004 0.052 1203 Dihedral : 30.300 178.149 3302 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.96 % Allowed : 35.38 % Favored : 59.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.32), residues: 691 helix: 1.88 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.19 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.011 0.001 PHE D 62 TYR 0.010 0.001 TYR D 61 ARG 0.004 0.000 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03415 ( 676) hydrogen bonds : angle 3.16418 ( 1719) covalent geometry : bond 0.00378 (11001) covalent geometry : angle 0.61306 (15843) *********************** 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 280 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 251 time to evaluate : 0.877 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: B 50 ILE cc_start: 0.9487 (mm) cc_final: 0.9178 (mm) REVERT: B 63 GLU cc_start: 0.9014 (mt-10) cc_final: 0.8542 (mt-10) REVERT: B 84 MET cc_start: 0.8840 (tpp) cc_final: 0.7975 (mmm) REVERT: C 25 PHE cc_start: 0.8666 (m-10) cc_final: 0.8248 (m-80) REVERT: C 38 ASN cc_start: 0.9229 (t0) cc_final: 0.8561 (t0) REVERT: C 39 TYR cc_start: 0.8696 (m-80) cc_final: 0.8436 (m-80) REVERT: C 57 TYR cc_start: 0.8399 (t80) cc_final: 0.7544 (t80) REVERT: C 61 GLU cc_start: 0.8938 (tt0) cc_final: 0.8504 (tt0) REVERT: C 62 ILE cc_start: 0.9416 (mt) cc_final: 0.9170 (tt) REVERT: C 64 GLU cc_start: 0.8954 (tp30) cc_final: 0.8712 (mm-30) REVERT: C 77 ARG cc_start: 0.7376 (tpp80) cc_final: 0.7153 (tpp80) REVERT: C 92 GLU cc_start: 0.9274 (pp20) cc_final: 0.8950 (tt0) REVERT: C 94 ASN cc_start: 0.9367 (OUTLIER) cc_final: 0.8915 (t0) REVERT: C 99 ARG cc_start: 0.9077 (mmm160) cc_final: 0.8688 (mmp80) REVERT: C 104 GLN cc_start: 0.8477 (mp10) cc_final: 0.8114 (mp10) REVERT: D 89 ASP cc_start: 0.9163 (t0) cc_final: 0.8915 (t0) REVERT: D 103 ARG cc_start: 0.8753 (mtm-85) cc_final: 0.8442 (mtm-85) REVERT: D 107 ARG cc_start: 0.8895 (mtp85) cc_final: 0.8405 (mtp85) REVERT: D 126 GLN cc_start: 0.8346 (tp-100) cc_final: 0.7432 (tp-100) REVERT: D 136 THR cc_start: 0.9384 (m) cc_final: 0.9183 (p) REVERT: D 137 LYS cc_start: 0.9237 (mtmm) cc_final: 0.8770 (mtmm) REVERT: E 105 GLU cc_start: 0.9069 (tp30) cc_final: 0.8479 (tp30) REVERT: E 128 ARG cc_start: 0.9417 (mtp-110) cc_final: 0.9134 (mmm-85) REVERT: G 56 GLU cc_start: 0.8853 (tt0) cc_final: 0.8401 (tt0) REVERT: G 57 TYR cc_start: 0.8711 (t80) cc_final: 0.8086 (t80) REVERT: G 61 GLU cc_start: 0.9137 (tt0) cc_final: 0.8308 (tt0) REVERT: G 64 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8471 (tm-30) REVERT: G 68 ASN cc_start: 0.9266 (m-40) cc_final: 0.8640 (m-40) REVERT: G 87 ILE cc_start: 0.9387 (tp) cc_final: 0.9171 (tp) REVERT: G 91 GLU cc_start: 0.9049 (pm20) cc_final: 0.8778 (pm20) REVERT: G 94 ASN cc_start: 0.9463 (t0) cc_final: 0.9208 (t0) REVERT: G 100 VAL cc_start: 0.9691 (t) cc_final: 0.9320 (p) REVERT: H 77 ARG cc_start: 0.9107 (ttm110) cc_final: 0.8591 (ptp-110) REVERT: H 78 GLU cc_start: 0.9406 (mp0) cc_final: 0.8984 (mp0) REVERT: H 84 ASP cc_start: 0.9105 (OUTLIER) cc_final: 0.8548 (m-30) REVERT: H 89 ASP cc_start: 0.9296 (t0) cc_final: 0.8744 (t0) REVERT: H 108 GLN cc_start: 0.8792 (pt0) cc_final: 0.8420 (pt0) REVERT: H 114 GLU cc_start: 0.9132 (mp0) cc_final: 0.8509 (mp0) REVERT: H 127 MET cc_start: 0.9048 (ttp) cc_final: 0.8753 (tpp) REVERT: H 129 LYS cc_start: 0.9021 (mtmm) cc_final: 0.8709 (mtmm) REVERT: H 141 ARG cc_start: 0.9206 (mmm-85) cc_final: 0.8788 (mmm-85) outliers start: 29 outliers final: 17 residues processed: 263 average time/residue: 0.3329 time to fit residues: 112.9901 Evaluate side-chains 257 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 238 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 76 THR 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 80 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain H residue 147 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 7.9990 chunk 48 optimal weight: 6.9990 chunk 63 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 2.9990 chunk 34 optimal weight: 0.0030 chunk 47 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 overall best weight: 2.1796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.049017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2713 r_free = 0.2713 target = 0.034540 restraints weight = 58061.816| |-----------------------------------------------------------------------------| r_work (start): 0.2656 rms_B_bonded: 3.73 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8669 moved from start: 0.3222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11001 Z= 0.180 Angle : 0.613 11.426 15843 Z= 0.353 Chirality : 0.035 0.160 1815 Planarity : 0.005 0.051 1203 Dihedral : 30.318 178.197 3302 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.44 % Allowed : 36.41 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.32), residues: 691 helix: 1.90 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.20 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP D 113 HIS 0.004 0.001 HIS D 100 PHE 0.009 0.001 PHE D 62 TYR 0.018 0.001 TYR H 61 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 676) hydrogen bonds : angle 3.14472 ( 1719) covalent geometry : bond 0.00399 (11001) covalent geometry : angle 0.61259 (15843) *********************** 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 277 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 251 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8993 (mt-10) cc_final: 0.8454 (mt-10) REVERT: B 79 LYS cc_start: 0.8953 (OUTLIER) cc_final: 0.8525 (mtmm) REVERT: B 84 MET cc_start: 0.8813 (tpp) cc_final: 0.7949 (mmm) REVERT: C 25 PHE cc_start: 0.8694 (m-10) cc_final: 0.8299 (m-80) REVERT: C 32 ARG cc_start: 0.8884 (ttp80) cc_final: 0.8569 (ttp80) REVERT: C 35 ARG cc_start: 0.9538 (ttm110) cc_final: 0.9278 (ttm110) REVERT: C 38 ASN cc_start: 0.9258 (t0) cc_final: 0.8553 (t0) REVERT: C 39 TYR cc_start: 0.8859 (m-80) cc_final: 0.8641 (m-80) REVERT: C 57 TYR cc_start: 0.8414 (t80) cc_final: 0.7696 (t80) REVERT: C 61 GLU cc_start: 0.8951 (tt0) cc_final: 0.8669 (tt0) REVERT: C 68 ASN cc_start: 0.9395 (m-40) cc_final: 0.9167 (m-40) REVERT: C 72 ASP cc_start: 0.9526 (t0) cc_final: 0.9259 (m-30) REVERT: C 73 ASN cc_start: 0.9245 (t0) cc_final: 0.8927 (t0) REVERT: C 77 ARG cc_start: 0.7183 (tpp80) cc_final: 0.6972 (tpp80) REVERT: C 89 ASN cc_start: 0.9419 (m-40) cc_final: 0.9191 (m110) REVERT: C 94 ASN cc_start: 0.9411 (t0) cc_final: 0.9034 (m-40) REVERT: C 99 ARG cc_start: 0.9042 (mmm160) cc_final: 0.8678 (mmp80) REVERT: C 104 GLN cc_start: 0.8559 (mp10) cc_final: 0.7836 (mp10) REVERT: D 62 PHE cc_start: 0.9422 (m-80) cc_final: 0.9145 (m-80) REVERT: D 89 ASP cc_start: 0.9205 (t0) cc_final: 0.8986 (t0) REVERT: D 103 ARG cc_start: 0.8773 (mtm-85) cc_final: 0.8297 (mtm-85) REVERT: D 107 ARG cc_start: 0.8836 (mtp85) cc_final: 0.8378 (mtp85) REVERT: D 136 THR cc_start: 0.9404 (m) cc_final: 0.9202 (p) REVERT: D 137 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8803 (mtmm) REVERT: E 73 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9132 (tt0) REVERT: E 105 GLU cc_start: 0.8980 (tp30) cc_final: 0.8397 (tp30) REVERT: E 120 MET cc_start: 0.8808 (mmm) cc_final: 0.8542 (mmt) REVERT: F 24 ASP cc_start: 0.8933 (t0) cc_final: 0.8692 (p0) REVERT: G 39 TYR cc_start: 0.9503 (m-80) cc_final: 0.9010 (m-80) REVERT: G 56 GLU cc_start: 0.8826 (tt0) cc_final: 0.8357 (tt0) REVERT: G 61 GLU cc_start: 0.9108 (tt0) cc_final: 0.8876 (tt0) REVERT: G 64 GLU cc_start: 0.8926 (tm-30) cc_final: 0.8459 (tm-30) REVERT: G 68 ASN cc_start: 0.9278 (m-40) cc_final: 0.8643 (m-40) REVERT: G 87 ILE cc_start: 0.9393 (tp) cc_final: 0.9129 (tp) REVERT: G 91 GLU cc_start: 0.9092 (pm20) cc_final: 0.8777 (pm20) REVERT: G 94 ASN cc_start: 0.9454 (t0) cc_final: 0.9193 (t0) REVERT: G 100 VAL cc_start: 0.9663 (t) cc_final: 0.9253 (p) REVERT: H 68 GLN cc_start: 0.9437 (tm-30) cc_final: 0.9229 (tm-30) REVERT: H 77 ARG cc_start: 0.9095 (ttm110) cc_final: 0.8234 (ptp-170) REVERT: H 78 GLU cc_start: 0.9435 (mp0) cc_final: 0.8892 (mp0) REVERT: H 84 ASP cc_start: 0.9102 (OUTLIER) cc_final: 0.8535 (m-30) REVERT: H 89 ASP cc_start: 0.9307 (t0) cc_final: 0.8753 (t0) REVERT: H 108 GLN cc_start: 0.8770 (pt0) cc_final: 0.8548 (pt0) REVERT: H 114 GLU cc_start: 0.9142 (mp0) cc_final: 0.8519 (mp0) REVERT: H 129 LYS cc_start: 0.8973 (mtmm) cc_final: 0.8700 (mtmm) REVERT: H 132 GLU cc_start: 0.8767 (tt0) cc_final: 0.8433 (tp30) REVERT: H 141 ARG cc_start: 0.9229 (mmm-85) cc_final: 0.8833 (mmm-85) outliers start: 26 outliers final: 16 residues processed: 263 average time/residue: 0.3441 time to fit residues: 117.6084 Evaluate side-chains 266 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 248 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 25 ASN 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 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU 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 25 optimal weight: 0.9990 chunk 61 optimal weight: 7.9990 chunk 65 optimal weight: 10.0000 chunk 66 optimal weight: 6.9990 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 9 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 113 HIS C 73 ASN C 84 GLN C 94 ASN E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.046993 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.032654 restraints weight = 59316.690| |-----------------------------------------------------------------------------| r_work (start): 0.2600 rms_B_bonded: 3.79 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 11001 Z= 0.239 Angle : 0.640 8.269 15843 Z= 0.370 Chirality : 0.036 0.178 1815 Planarity : 0.005 0.056 1203 Dihedral : 30.478 177.774 3302 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 13.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 6.50 % Allowed : 35.90 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.32), residues: 691 helix: 1.90 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.25 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE D 62 TYR 0.014 0.002 TYR G 57 ARG 0.004 0.000 ARG H 103 Details of bonding type rmsd hydrogen bonds : bond 0.04309 ( 676) hydrogen bonds : angle 3.31499 ( 1719) covalent geometry : bond 0.00533 (11001) covalent geometry : angle 0.64032 (15843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 237 time to evaluate : 0.817 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8969 (mt-10) cc_final: 0.8411 (mt-10) REVERT: B 79 LYS cc_start: 0.8969 (mtpt) cc_final: 0.8759 (mtpt) REVERT: B 84 MET cc_start: 0.8886 (tpp) cc_final: 0.8232 (mmm) REVERT: C 25 PHE cc_start: 0.8746 (m-10) cc_final: 0.8207 (m-80) REVERT: C 38 ASN cc_start: 0.9331 (t0) cc_final: 0.8718 (t0) REVERT: C 57 TYR cc_start: 0.8390 (t80) cc_final: 0.7663 (t80) REVERT: C 68 ASN cc_start: 0.9456 (m-40) cc_final: 0.9127 (m-40) REVERT: C 72 ASP cc_start: 0.9554 (t0) cc_final: 0.9298 (m-30) REVERT: C 73 ASN cc_start: 0.9313 (OUTLIER) cc_final: 0.9060 (t0) REVERT: C 89 ASN cc_start: 0.9435 (m-40) cc_final: 0.9147 (m110) REVERT: C 99 ARG cc_start: 0.9123 (mmm160) cc_final: 0.8903 (mmm160) REVERT: C 104 GLN cc_start: 0.8598 (mp10) cc_final: 0.7854 (mp10) REVERT: D 62 PHE cc_start: 0.9448 (m-80) cc_final: 0.9194 (m-80) REVERT: D 84 ASP cc_start: 0.8907 (OUTLIER) cc_final: 0.8576 (m-30) REVERT: D 89 ASP cc_start: 0.9253 (t0) cc_final: 0.9005 (t0) REVERT: D 103 ARG cc_start: 0.8770 (mtm-85) cc_final: 0.8136 (mtm-85) REVERT: D 108 GLN cc_start: 0.8025 (pm20) cc_final: 0.7697 (pm20) REVERT: D 127 MET cc_start: 0.9131 (mtm) cc_final: 0.8728 (mtm) REVERT: D 136 THR cc_start: 0.9403 (m) cc_final: 0.9191 (p) REVERT: D 137 LYS cc_start: 0.9214 (mtmm) cc_final: 0.8717 (mtmm) REVERT: E 73 GLU cc_start: 0.9507 (tm-30) cc_final: 0.9128 (tt0) REVERT: E 105 GLU cc_start: 0.9061 (tp30) cc_final: 0.8441 (tp30) REVERT: E 133 GLU cc_start: 0.8873 (pm20) cc_final: 0.8083 (pm20) REVERT: F 35 ARG cc_start: 0.9357 (mtp85) cc_final: 0.9141 (mtp-110) REVERT: F 53 GLU cc_start: 0.9305 (tp30) cc_final: 0.8819 (tp30) REVERT: G 38 ASN cc_start: 0.9189 (t0) cc_final: 0.8914 (t0) REVERT: G 56 GLU cc_start: 0.8916 (tt0) cc_final: 0.8429 (tt0) REVERT: G 57 TYR cc_start: 0.8724 (t80) cc_final: 0.8179 (t80) REVERT: G 61 GLU cc_start: 0.9099 (tt0) cc_final: 0.8386 (tt0) REVERT: G 64 GLU cc_start: 0.8979 (tm-30) cc_final: 0.8485 (tm-30) REVERT: G 68 ASN cc_start: 0.9290 (m-40) cc_final: 0.8670 (m-40) REVERT: G 87 ILE cc_start: 0.9434 (tp) cc_final: 0.9227 (tp) REVERT: G 100 VAL cc_start: 0.9729 (t) cc_final: 0.9367 (p) REVERT: H 77 ARG cc_start: 0.9098 (ttm110) cc_final: 0.8633 (ptp-110) REVERT: H 78 GLU cc_start: 0.9431 (mp0) cc_final: 0.8955 (mp0) REVERT: H 84 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8579 (m-30) REVERT: H 89 ASP cc_start: 0.9314 (t0) cc_final: 0.8755 (t0) REVERT: H 108 GLN cc_start: 0.8754 (pt0) cc_final: 0.8485 (pt0) REVERT: H 114 GLU cc_start: 0.9124 (mp0) cc_final: 0.8498 (mp0) REVERT: H 127 MET cc_start: 0.9072 (ttp) cc_final: 0.8756 (tpp) REVERT: H 129 LYS cc_start: 0.9066 (mtmm) cc_final: 0.8777 (mtmm) REVERT: H 141 ARG cc_start: 0.9282 (mmm-85) cc_final: 0.8956 (mmm-85) REVERT: H 142 THR cc_start: 0.9581 (OUTLIER) cc_final: 0.9212 (p) outliers start: 38 outliers final: 26 residues processed: 254 average time/residue: 0.2684 time to fit residues: 89.6406 Evaluate side-chains 261 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 231 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL 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 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 73 ASN 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 80 VAL 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 E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN 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 H residue 84 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain H residue 147 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 0.9980 chunk 53 optimal weight: 0.5980 chunk 83 optimal weight: 8.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 27 optimal weight: 0.6980 chunk 54 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 73 ASN D 100 HIS E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.050411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.035608 restraints weight = 56852.580| |-----------------------------------------------------------------------------| r_work (start): 0.2769 rms_B_bonded: 3.56 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.3612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11001 Z= 0.160 Angle : 0.625 7.874 15843 Z= 0.359 Chirality : 0.035 0.167 1815 Planarity : 0.004 0.048 1203 Dihedral : 30.360 178.927 3302 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.13 % Allowed : 37.26 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.32), residues: 691 helix: 2.02 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.17 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.004 0.001 HIS D 100 PHE 0.007 0.001 PHE E 84 TYR 0.021 0.002 TYR G 39 ARG 0.005 0.000 ARG H 103 Details of bonding type rmsd hydrogen bonds : bond 0.03328 ( 676) hydrogen bonds : angle 3.04156 ( 1719) covalent geometry : bond 0.00353 (11001) covalent geometry : angle 0.62520 (15843) *********************** 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 280 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 250 time to evaluate : 0.800 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: B 63 GLU cc_start: 0.8951 (mt-10) cc_final: 0.8320 (mt-10) REVERT: B 79 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8648 (mtmt) REVERT: B 84 MET cc_start: 0.8774 (tpp) cc_final: 0.7920 (mmm) REVERT: C 25 PHE cc_start: 0.8693 (m-10) cc_final: 0.8308 (m-80) REVERT: C 38 ASN cc_start: 0.9282 (t0) cc_final: 0.8551 (t0) REVERT: C 57 TYR cc_start: 0.8391 (t80) cc_final: 0.7724 (t80) REVERT: C 68 ASN cc_start: 0.9451 (m-40) cc_final: 0.9090 (m-40) REVERT: C 73 ASN cc_start: 0.9365 (OUTLIER) cc_final: 0.9020 (t0) REVERT: C 89 ASN cc_start: 0.9443 (m-40) cc_final: 0.9139 (m110) REVERT: C 94 ASN cc_start: 0.9389 (t0) cc_final: 0.9100 (m-40) REVERT: C 99 ARG cc_start: 0.8998 (mmm160) cc_final: 0.8777 (mmm160) REVERT: C 104 GLN cc_start: 0.8658 (mp10) cc_final: 0.7902 (mp10) REVERT: D 62 PHE cc_start: 0.9445 (m-80) cc_final: 0.9217 (m-80) REVERT: D 89 ASP cc_start: 0.9249 (t0) cc_final: 0.8989 (t0) REVERT: D 103 ARG cc_start: 0.8754 (mtm-85) cc_final: 0.8142 (mtm-85) REVERT: D 107 ARG cc_start: 0.8819 (mtp85) cc_final: 0.8403 (mtp85) REVERT: D 108 GLN cc_start: 0.8070 (pm20) cc_final: 0.7794 (pm20) REVERT: D 136 THR cc_start: 0.9399 (m) cc_final: 0.9191 (p) REVERT: D 137 LYS cc_start: 0.9243 (mtmm) cc_final: 0.8772 (mtmm) REVERT: E 68 GLN cc_start: 0.9246 (tt0) cc_final: 0.8996 (tm-30) REVERT: E 73 GLU cc_start: 0.9508 (tm-30) cc_final: 0.9089 (tt0) REVERT: E 118 THR cc_start: 0.8640 (p) cc_final: 0.8358 (p) REVERT: E 133 GLU cc_start: 0.8816 (pm20) cc_final: 0.8577 (pm20) REVERT: F 44 LYS cc_start: 0.9544 (mtpt) cc_final: 0.9298 (mtpp) REVERT: F 53 GLU cc_start: 0.9205 (tp30) cc_final: 0.8748 (tp30) REVERT: G 38 ASN cc_start: 0.9180 (t0) cc_final: 0.8897 (t0) REVERT: G 56 GLU cc_start: 0.8830 (tt0) cc_final: 0.8365 (tt0) REVERT: G 57 TYR cc_start: 0.8692 (t80) cc_final: 0.7568 (t80) REVERT: G 61 GLU cc_start: 0.9125 (tt0) cc_final: 0.8497 (tt0) REVERT: G 64 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8392 (tm-30) REVERT: G 68 ASN cc_start: 0.9273 (m-40) cc_final: 0.8638 (m110) REVERT: G 87 ILE cc_start: 0.9417 (tp) cc_final: 0.9183 (tp) REVERT: G 93 LEU cc_start: 0.9557 (OUTLIER) cc_final: 0.9333 (mm) REVERT: G 94 ASN cc_start: 0.9386 (t0) cc_final: 0.9136 (t0) REVERT: G 100 VAL cc_start: 0.9629 (t) cc_final: 0.9200 (p) REVERT: H 68 GLN cc_start: 0.9397 (tm-30) cc_final: 0.9188 (tm-30) REVERT: H 77 ARG cc_start: 0.9075 (ttm110) cc_final: 0.8653 (ptp-110) REVERT: H 78 GLU cc_start: 0.9432 (mp0) cc_final: 0.8977 (mp0) REVERT: H 84 ASP cc_start: 0.9114 (OUTLIER) cc_final: 0.8500 (m-30) REVERT: H 89 ASP cc_start: 0.9296 (t0) cc_final: 0.8766 (t0) REVERT: H 114 GLU cc_start: 0.9115 (mp0) cc_final: 0.8498 (mp0) REVERT: H 127 MET cc_start: 0.9094 (ttp) cc_final: 0.8578 (mmm) REVERT: H 129 LYS cc_start: 0.9042 (mtmm) cc_final: 0.8734 (mtmm) REVERT: H 132 GLU cc_start: 0.8833 (tt0) cc_final: 0.8450 (tp30) REVERT: H 141 ARG cc_start: 0.9224 (mmm-85) cc_final: 0.8863 (mmm-85) outliers start: 30 outliers final: 19 residues processed: 263 average time/residue: 0.2685 time to fit residues: 93.2540 Evaluate side-chains 267 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 244 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL 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 73 ASN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN 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 93 LEU Chi-restraints excluded: chain H residue 84 ASP 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 7 optimal weight: 0.0170 chunk 16 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 7.9990 chunk 56 optimal weight: 0.0970 chunk 27 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 overall best weight: 2.2222 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 94 ASN E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.048184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.034067 restraints weight = 58817.634| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.83 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.3741 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= 0.187 Angle : 0.648 9.146 15843 Z= 0.367 Chirality : 0.035 0.164 1815 Planarity : 0.005 0.048 1203 Dihedral : 30.346 178.571 3302 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.79 % Allowed : 38.80 % Favored : 56.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.32), residues: 691 helix: 1.91 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.11 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE E 84 TYR 0.030 0.002 TYR F 98 ARG 0.008 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03681 ( 676) hydrogen bonds : angle 3.12462 ( 1719) covalent geometry : bond 0.00420 (11001) covalent geometry : angle 0.64762 (15843) *********************** 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 267 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 239 time to evaluate : 0.816 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8298 (mt-10) REVERT: B 79 LYS cc_start: 0.9011 (mtpt) cc_final: 0.8647 (mtmt) REVERT: B 84 MET cc_start: 0.8793 (tpp) cc_final: 0.8127 (mmm) REVERT: C 25 PHE cc_start: 0.8723 (m-10) cc_final: 0.8259 (m-80) REVERT: C 38 ASN cc_start: 0.9328 (t0) cc_final: 0.8680 (t0) REVERT: C 57 TYR cc_start: 0.8367 (t80) cc_final: 0.7665 (t80) REVERT: C 89 ASN cc_start: 0.9459 (m-40) cc_final: 0.9168 (m110) REVERT: C 94 ASN cc_start: 0.9421 (OUTLIER) cc_final: 0.9031 (m-40) REVERT: C 99 ARG cc_start: 0.8984 (mmm160) cc_final: 0.8771 (mmm160) REVERT: C 104 GLN cc_start: 0.8694 (mp10) cc_final: 0.7938 (mp10) REVERT: D 62 PHE cc_start: 0.9459 (m-80) cc_final: 0.9253 (m-80) REVERT: D 77 ARG cc_start: 0.8535 (mmt180) cc_final: 0.8244 (mmp80) REVERT: D 103 ARG cc_start: 0.8778 (mtm-85) cc_final: 0.8119 (mtm-85) REVERT: D 107 ARG cc_start: 0.8796 (mtp85) cc_final: 0.8401 (mtp85) REVERT: D 108 GLN cc_start: 0.8111 (pm20) cc_final: 0.7872 (pm20) REVERT: D 129 LYS cc_start: 0.8912 (mtmt) cc_final: 0.8626 (mttp) REVERT: E 118 THR cc_start: 0.8680 (p) cc_final: 0.8055 (p) REVERT: E 120 MET cc_start: 0.8852 (mmm) cc_final: 0.8270 (mmm) REVERT: E 133 GLU cc_start: 0.8797 (pm20) cc_final: 0.8242 (pm20) REVERT: F 35 ARG cc_start: 0.9384 (mtp85) cc_final: 0.9100 (mtp-110) REVERT: F 44 LYS cc_start: 0.9532 (mtpt) cc_final: 0.9300 (mtpp) REVERT: F 53 GLU cc_start: 0.9220 (tp30) cc_final: 0.8791 (tp30) REVERT: G 38 ASN cc_start: 0.9248 (t0) cc_final: 0.9025 (t0) REVERT: G 56 GLU cc_start: 0.8837 (tt0) cc_final: 0.8355 (tt0) REVERT: G 57 TYR cc_start: 0.8705 (t80) cc_final: 0.7598 (t80) REVERT: G 61 GLU cc_start: 0.9094 (tt0) cc_final: 0.8459 (tt0) REVERT: G 64 GLU cc_start: 0.8947 (tm-30) cc_final: 0.8376 (tm-30) REVERT: G 68 ASN cc_start: 0.9259 (m-40) cc_final: 0.8629 (m110) REVERT: G 87 ILE cc_start: 0.9419 (tp) cc_final: 0.9183 (tp) REVERT: G 93 LEU cc_start: 0.9574 (OUTLIER) cc_final: 0.9359 (mm) REVERT: G 94 ASN cc_start: 0.9410 (t0) cc_final: 0.9172 (t0) REVERT: G 100 VAL cc_start: 0.9667 (t) cc_final: 0.9286 (p) REVERT: H 77 ARG cc_start: 0.9093 (ttm110) cc_final: 0.8239 (ptp-170) REVERT: H 78 GLU cc_start: 0.9444 (mp0) cc_final: 0.8923 (mp0) REVERT: H 84 ASP cc_start: 0.9091 (OUTLIER) cc_final: 0.8465 (m-30) REVERT: H 89 ASP cc_start: 0.9316 (t0) cc_final: 0.8765 (t0) REVERT: H 114 GLU cc_start: 0.9123 (mp0) cc_final: 0.8610 (mp0) REVERT: H 127 MET cc_start: 0.9144 (ttp) cc_final: 0.8629 (mmm) REVERT: H 129 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8758 (mtmm) REVERT: H 132 GLU cc_start: 0.8777 (tt0) cc_final: 0.8439 (tp30) REVERT: H 141 ARG cc_start: 0.9267 (mmm-85) cc_final: 0.8965 (mmm-85) outliers start: 28 outliers final: 21 residues processed: 251 average time/residue: 0.2669 time to fit residues: 88.2594 Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 236 time to evaluate : 0.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL 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 E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN 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 93 LEU Chi-restraints excluded: chain H residue 84 ASP 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 58 optimal weight: 0.9980 chunk 70 optimal weight: 10.0000 chunk 19 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 0.0770 chunk 26 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 0.7980 chunk 74 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.9742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 100 HIS E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.049645 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2752 r_free = 0.2752 target = 0.035250 restraints weight = 58872.678| |-----------------------------------------------------------------------------| r_work (start): 0.2695 rms_B_bonded: 3.92 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 11001 Z= 0.164 Angle : 0.669 8.711 15843 Z= 0.375 Chirality : 0.035 0.167 1815 Planarity : 0.005 0.048 1203 Dihedral : 30.263 178.911 3302 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.44 % Allowed : 39.49 % Favored : 56.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.32), residues: 691 helix: 1.88 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.04 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 113 HIS 0.004 0.001 HIS D 100 PHE 0.006 0.001 PHE E 84 TYR 0.040 0.002 TYR F 98 ARG 0.009 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03437 ( 676) hydrogen bonds : angle 3.03908 ( 1719) covalent geometry : bond 0.00367 (11001) covalent geometry : angle 0.66865 (15843) *********************** 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 280 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 254 time to evaluate : 0.864 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 64 LYS cc_start: 0.9093 (mmtm) cc_final: 0.8858 (mmtm) REVERT: A 123 ASP cc_start: 0.8908 (m-30) cc_final: 0.8176 (m-30) REVERT: B 63 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8159 (mp0) REVERT: B 74 GLU cc_start: 0.9472 (mm-30) cc_final: 0.9230 (mm-30) REVERT: B 79 LYS cc_start: 0.9040 (mtpt) cc_final: 0.8677 (mtmt) REVERT: B 84 MET cc_start: 0.8826 (tpp) cc_final: 0.7991 (mmm) REVERT: C 25 PHE cc_start: 0.8711 (m-10) cc_final: 0.8288 (m-80) REVERT: C 32 ARG cc_start: 0.8794 (ttp80) cc_final: 0.8542 (ttp80) REVERT: C 38 ASN cc_start: 0.9330 (t0) cc_final: 0.8683 (t0) REVERT: C 42 ARG cc_start: 0.8213 (mtp180) cc_final: 0.7499 (mmm-85) REVERT: C 57 TYR cc_start: 0.8392 (t80) cc_final: 0.7782 (t80) REVERT: C 89 ASN cc_start: 0.9431 (m-40) cc_final: 0.9124 (m110) REVERT: C 94 ASN cc_start: 0.9396 (t0) cc_final: 0.8930 (m-40) REVERT: C 99 ARG cc_start: 0.8887 (mmm160) cc_final: 0.8647 (mmp80) REVERT: C 104 GLN cc_start: 0.8666 (mp10) cc_final: 0.7933 (mp10) REVERT: D 62 PHE cc_start: 0.9440 (m-80) cc_final: 0.9230 (m-80) REVERT: D 77 ARG cc_start: 0.8524 (mmt180) cc_final: 0.8277 (mmp80) REVERT: D 83 MET cc_start: 0.9483 (mmm) cc_final: 0.9055 (mpp) REVERT: D 103 ARG cc_start: 0.8802 (mtm-85) cc_final: 0.8236 (mtm-85) REVERT: D 107 ARG cc_start: 0.8805 (mtp85) cc_final: 0.8359 (mtp85) REVERT: D 129 LYS cc_start: 0.8819 (mtmt) cc_final: 0.8530 (mttm) REVERT: E 68 GLN cc_start: 0.9228 (tt0) cc_final: 0.8968 (tm-30) REVERT: E 73 GLU cc_start: 0.9567 (tm-30) cc_final: 0.8934 (tt0) REVERT: E 85 GLN cc_start: 0.8655 (pt0) cc_final: 0.8216 (pt0) REVERT: E 118 THR cc_start: 0.8729 (p) cc_final: 0.8119 (p) REVERT: E 120 MET cc_start: 0.8811 (mmm) cc_final: 0.8237 (mmm) REVERT: E 133 GLU cc_start: 0.8825 (pm20) cc_final: 0.8170 (pm20) REVERT: F 44 LYS cc_start: 0.9552 (mtpt) cc_final: 0.9329 (mtpp) REVERT: F 53 GLU cc_start: 0.9228 (tp30) cc_final: 0.8787 (tp30) REVERT: G 38 ASN cc_start: 0.9234 (t0) cc_final: 0.9000 (t0) REVERT: G 56 GLU cc_start: 0.8784 (tt0) cc_final: 0.8318 (tt0) REVERT: G 57 TYR cc_start: 0.8649 (t80) cc_final: 0.7537 (t80) REVERT: G 61 GLU cc_start: 0.9134 (tt0) cc_final: 0.8499 (tt0) REVERT: G 64 GLU cc_start: 0.8902 (tm-30) cc_final: 0.8357 (tm-30) REVERT: G 68 ASN cc_start: 0.9265 (m-40) cc_final: 0.8631 (m110) REVERT: G 87 ILE cc_start: 0.9394 (tp) cc_final: 0.9151 (tp) REVERT: G 93 LEU cc_start: 0.9555 (OUTLIER) cc_final: 0.9329 (mm) REVERT: G 94 ASN cc_start: 0.9392 (t0) cc_final: 0.9161 (t0) REVERT: H 77 ARG cc_start: 0.9107 (ttm110) cc_final: 0.8575 (ptp-110) REVERT: H 78 GLU cc_start: 0.9417 (mp0) cc_final: 0.8947 (mp0) REVERT: H 84 ASP cc_start: 0.9079 (OUTLIER) cc_final: 0.8439 (m-30) REVERT: H 89 ASP cc_start: 0.9296 (t0) cc_final: 0.8782 (t0) REVERT: H 114 GLU cc_start: 0.9130 (mp0) cc_final: 0.8604 (mp0) REVERT: H 127 MET cc_start: 0.9163 (ttp) cc_final: 0.8596 (mmm) REVERT: H 129 LYS cc_start: 0.8990 (mtmm) cc_final: 0.8672 (mtmm) REVERT: H 132 GLU cc_start: 0.8790 (tt0) cc_final: 0.8431 (tp30) REVERT: H 141 ARG cc_start: 0.9277 (mmm-85) cc_final: 0.8975 (mmm-85) outliers start: 26 outliers final: 18 residues processed: 267 average time/residue: 0.3302 time to fit residues: 113.3932 Evaluate side-chains 261 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 241 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 60 THR 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 E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN 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 93 LEU Chi-restraints excluded: chain H residue 84 ASP 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 23 optimal weight: 4.9990 chunk 64 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 29 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 59 optimal weight: 8.9990 chunk 18 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 78 optimal weight: 10.0000 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.046838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2702 r_free = 0.2702 target = 0.033290 restraints weight = 58613.308| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.79 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8727 moved from start: 0.3946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.050 11001 Z= 0.246 Angle : 0.706 12.171 15843 Z= 0.395 Chirality : 0.037 0.162 1815 Planarity : 0.005 0.058 1203 Dihedral : 30.475 177.820 3302 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 16.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 4.44 % Allowed : 40.00 % Favored : 55.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.32), residues: 691 helix: 1.78 (0.22), residues: 533 sheet: None (None), residues: 0 loop : -1.20 (0.43), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP D 113 HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE E 78 TYR 0.022 0.002 TYR F 98 ARG 0.015 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.04488 ( 676) hydrogen bonds : angle 3.36467 ( 1719) covalent geometry : bond 0.00554 (11001) covalent geometry : angle 0.70627 (15843) ********************** 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 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 236 time to evaluate : 0.984 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9116 (mmtm) cc_final: 0.8891 (mmtm) REVERT: B 79 LYS cc_start: 0.9004 (mtpt) cc_final: 0.8555 (mtmm) REVERT: B 84 MET cc_start: 0.8855 (tpp) cc_final: 0.8189 (mmm) REVERT: C 25 PHE cc_start: 0.8769 (m-10) cc_final: 0.8183 (m-10) REVERT: C 38 ASN cc_start: 0.9424 (t0) cc_final: 0.8796 (t0) REVERT: C 57 TYR cc_start: 0.8362 (t80) cc_final: 0.7659 (t80) REVERT: C 89 ASN cc_start: 0.9451 (m-40) cc_final: 0.9140 (m110) REVERT: C 94 ASN cc_start: 0.9411 (OUTLIER) cc_final: 0.9049 (m-40) REVERT: C 99 ARG cc_start: 0.8845 (mmm160) cc_final: 0.8576 (mmp80) REVERT: C 104 GLN cc_start: 0.8705 (mp10) cc_final: 0.7965 (mp10) REVERT: D 103 ARG cc_start: 0.8785 (mtm-85) cc_final: 0.8253 (mtm-85) REVERT: D 129 LYS cc_start: 0.8966 (mtmt) cc_final: 0.8682 (mttm) REVERT: E 73 GLU cc_start: 0.9590 (tm-30) cc_final: 0.9085 (tt0) REVERT: E 120 MET cc_start: 0.8868 (mmm) cc_final: 0.8616 (mmt) REVERT: E 133 GLU cc_start: 0.8812 (pm20) cc_final: 0.8168 (pm20) REVERT: F 44 LYS cc_start: 0.9589 (mtpt) cc_final: 0.9384 (mtpp) REVERT: F 53 GLU cc_start: 0.9289 (tp30) cc_final: 0.8794 (tp30) REVERT: F 88 TYR cc_start: 0.9756 (m-10) cc_final: 0.9529 (m-10) REVERT: G 56 GLU cc_start: 0.8864 (tt0) cc_final: 0.8402 (tt0) REVERT: G 57 TYR cc_start: 0.8768 (t80) cc_final: 0.8157 (t80) REVERT: G 61 GLU cc_start: 0.9106 (tt0) cc_final: 0.8331 (tt0) REVERT: G 64 GLU cc_start: 0.8972 (tm-30) cc_final: 0.8403 (tm-30) REVERT: G 68 ASN cc_start: 0.9265 (m-40) cc_final: 0.8629 (m110) REVERT: G 87 ILE cc_start: 0.9440 (tp) cc_final: 0.9227 (tp) REVERT: G 94 ASN cc_start: 0.9448 (t0) cc_final: 0.9172 (t0) REVERT: H 77 ARG cc_start: 0.9078 (ttm110) cc_final: 0.8653 (ptp-110) REVERT: H 78 GLU cc_start: 0.9455 (mp0) cc_final: 0.8915 (mp0) REVERT: H 89 ASP cc_start: 0.9321 (t0) cc_final: 0.8872 (t0) REVERT: H 108 GLN cc_start: 0.8740 (pt0) cc_final: 0.8374 (pt0) REVERT: H 114 GLU cc_start: 0.9108 (mp0) cc_final: 0.8605 (mp0) REVERT: H 127 MET cc_start: 0.9154 (ttp) cc_final: 0.8790 (tpp) REVERT: H 129 LYS cc_start: 0.9059 (mtmm) cc_final: 0.8760 (mtmm) REVERT: H 141 ARG cc_start: 0.9393 (mmm-85) cc_final: 0.9079 (mmm-85) outliers start: 26 outliers final: 19 residues processed: 246 average time/residue: 0.3339 time to fit residues: 105.7336 Evaluate side-chains 249 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 229 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 93 GLN 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 84 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER 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 F residue 58 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP 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 5 optimal weight: 4.9990 chunk 13 optimal weight: 4.9990 chunk 28 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 chunk 30 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN D 100 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3161 r_free = 0.3161 target = 0.046306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2686 r_free = 0.2686 target = 0.032823 restraints weight = 58405.331| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.76 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8734 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 11001 Z= 0.258 Angle : 0.719 10.251 15843 Z= 0.405 Chirality : 0.038 0.166 1815 Planarity : 0.005 0.048 1203 Dihedral : 30.609 178.429 3302 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 16.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 4.44 % Allowed : 40.17 % Favored : 55.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.31), residues: 691 helix: 1.62 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.21 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP D 113 HIS 0.007 0.001 HIS B 75 PHE 0.009 0.001 PHE D 58 TYR 0.022 0.003 TYR H 61 ARG 0.009 0.001 ARG F 35 Details of bonding type rmsd hydrogen bonds : bond 0.04360 ( 676) hydrogen bonds : angle 3.48425 ( 1719) covalent geometry : bond 0.00580 (11001) covalent geometry : angle 0.71887 (15843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4704.83 seconds wall clock time: 83 minutes 30.05 seconds (5010.05 seconds total)