Starting phenix.real_space_refine on Sat Aug 23 05:23:03 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcc_36157/08_2025/8jcc_36157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcc_36157/08_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_36157/08_2025/8jcc_36157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2025/8jcc_36157.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2025/8jcc_36157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcc_36157/08_2025/8jcc_36157.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 232 5.49 5 S 16 5.16 5 C 5770 2.51 5 N 1958 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "I" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2391 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "J" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2365 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Time building chain proxies: 2.50, per 1000 atoms: 0.24 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: 1.01 Conformation dependent library (CDL) restraints added in 234.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 75.7% alpha, 3.1% beta 114 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.894A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.911A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 31 through 42 removed outlier: 4.044A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.968A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.650A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.343A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.608A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 76 through 105 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.578A pdb=" N ALA D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.801A pdb=" N LYS D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 removed outlier: 3.729A pdb=" N ALA D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.005A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.611A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.843A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.683A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.628A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 76 through 105 removed outlier: 3.523A pdb=" N THR H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 123 removed outlier: 3.598A pdb=" N VAL H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 144 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.641A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.378A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.671A pdb=" N ARG C 42 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.839A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.443A pdb=" N ARG G 42 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 379 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 297 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 1.91 Time building geometry restraints manager: 1.33 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: 0.730 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.290 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.780 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.53 (0.32), residues: 691 helix: 1.75 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 103 TYR 0.011 0.001 TYR D 145 PHE 0.007 0.001 PHE D 58 TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS H 70 Details of bonding type rmsd covalent geometry : bond 0.00460 (11001) covalent geometry : angle 0.59995 (15843) hydrogen bonds : bond 0.11443 ( 676) hydrogen bonds : angle 4.05117 ( 1719) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.297 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: 0.1575 time to fit residues: 65.3852 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 : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 74 optimal weight: 10.0000 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.049306 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.034794 restraints weight = 57166.961| |-----------------------------------------------------------------------------| r_work (start): 0.2645 rms_B_bonded: 3.61 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.2205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11001 Z= 0.182 Angle : 0.631 5.895 15843 Z= 0.363 Chirality : 0.036 0.369 1815 Planarity : 0.005 0.053 1203 Dihedral : 30.295 178.177 3304 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 13.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 6.32 % Allowed : 34.02 % Favored : 59.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.81 (0.33), residues: 691 helix: 1.92 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG C 35 TYR 0.015 0.002 TYR B 98 PHE 0.022 0.002 PHE D 62 TRP 0.003 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00400 (11001) covalent geometry : angle 0.63105 (15843) hydrogen bonds : bond 0.03811 ( 676) hydrogen bonds : angle 3.31999 ( 1719) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 273 time to evaluate : 0.299 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: 0.9398 (tt0) cc_final: 0.8650 (tp30) REVERT: A 125 GLN cc_start: 0.9396 (OUTLIER) cc_final: 0.9109 (mp10) REVERT: B 84 MET cc_start: 0.8907 (tpp) cc_final: 0.8231 (mmm) REVERT: C 25 PHE cc_start: 0.8484 (m-10) cc_final: 0.7889 (m-80) REVERT: C 35 ARG cc_start: 0.9483 (ttm110) cc_final: 0.9219 (ttm110) REVERT: C 38 ASN cc_start: 0.9046 (t0) cc_final: 0.8628 (t0) REVERT: C 39 TYR cc_start: 0.8342 (m-80) cc_final: 0.8041 (m-80) REVERT: C 42 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7026 (mmm-85) REVERT: C 57 TYR cc_start: 0.8155 (t80) cc_final: 0.7441 (t80) REVERT: C 61 GLU cc_start: 0.8894 (tt0) cc_final: 0.8522 (tt0) REVERT: C 88 ARG cc_start: 0.9355 (ttm110) cc_final: 0.8681 (ttm110) REVERT: C 99 ARG cc_start: 0.9044 (mmm160) cc_final: 0.8772 (mmp80) REVERT: C 104 GLN cc_start: 0.8476 (mp10) cc_final: 0.7885 (mp10) REVERT: D 89 ASP cc_start: 0.9150 (t0) cc_final: 0.8843 (t0) REVERT: D 108 GLN cc_start: 0.8336 (pm20) cc_final: 0.7873 (pm20) REVERT: D 137 LYS cc_start: 0.9230 (mtmm) cc_final: 0.8884 (mtmm) REVERT: E 105 GLU cc_start: 0.9155 (tp30) cc_final: 0.8571 (tp30) REVERT: E 128 ARG cc_start: 0.9536 (mtp-110) cc_final: 0.8850 (mmm-85) REVERT: F 98 TYR cc_start: 0.9233 (m-10) cc_final: 0.8892 (m-10) REVERT: G 41 GLU cc_start: 0.9133 (mt-10) cc_final: 0.8864 (mt-10) REVERT: G 56 GLU cc_start: 0.8887 (tt0) cc_final: 0.8297 (tt0) REVERT: G 57 TYR cc_start: 0.8778 (t80) cc_final: 0.8567 (t80) REVERT: G 61 GLU cc_start: 0.9057 (tt0) cc_final: 0.8846 (tt0) REVERT: G 94 ASN cc_start: 0.9449 (t0) cc_final: 0.9141 (t0) REVERT: H 89 ASP cc_start: 0.9185 (t0) cc_final: 0.8745 (t0) REVERT: H 114 GLU cc_start: 0.9183 (mp0) cc_final: 0.8655 (mp0) REVERT: H 129 LYS cc_start: 0.8984 (OUTLIER) cc_final: 0.8688 (mtmm) REVERT: H 141 ARG cc_start: 0.9196 (mmm-85) cc_final: 0.8876 (mmm-85) REVERT: H 142 THR cc_start: 0.9546 (OUTLIER) cc_final: 0.9217 (p) outliers start: 37 outliers final: 13 residues processed: 289 average time/residue: 0.1469 time to fit residues: 54.8259 Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 244 time to evaluate : 0.337 ------------------------------------------------------------------------------- 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 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 84 ASP Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 72 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 83 optimal weight: 6.9990 chunk 52 optimal weight: 8.9990 chunk 10 optimal weight: 4.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- 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 C 84 GLN C 94 ASN E 108 ASN F 25 ASN H 108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.046626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.032947 restraints weight = 58178.321| |-----------------------------------------------------------------------------| r_work (start): 0.2613 rms_B_bonded: 3.62 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 11001 Z= 0.246 Angle : 0.650 9.310 15843 Z= 0.374 Chirality : 0.037 0.337 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.488 177.191 3304 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.30 % Allowed : 35.38 % Favored : 59.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.65 (0.32), residues: 691 helix: 1.80 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.33 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 77 TYR 0.012 0.002 TYR B 98 PHE 0.015 0.001 PHE D 62 TRP 0.002 0.001 TRP D 113 HIS 0.004 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00548 (11001) covalent geometry : angle 0.65021 (15843) hydrogen bonds : bond 0.04404 ( 676) hydrogen bonds : angle 3.45792 ( 1719) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 246 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8631 (mt-10) REVERT: C 25 PHE cc_start: 0.8689 (m-10) cc_final: 0.8095 (m-80) REVERT: C 35 ARG cc_start: 0.9476 (ttm110) cc_final: 0.9160 (ttm110) REVERT: C 38 ASN cc_start: 0.9283 (t0) cc_final: 0.8254 (t0) REVERT: C 39 TYR cc_start: 0.8478 (m-80) cc_final: 0.8260 (m-80) REVERT: C 42 ARG cc_start: 0.8374 (mtp180) cc_final: 0.7240 (mmm-85) REVERT: C 57 TYR cc_start: 0.8371 (t80) cc_final: 0.7671 (t80) REVERT: C 61 GLU cc_start: 0.8934 (tt0) cc_final: 0.8454 (tt0) REVERT: C 71 ARG cc_start: 0.8524 (mtm-85) cc_final: 0.8195 (mtm-85) REVERT: C 88 ARG cc_start: 0.9414 (ttm110) cc_final: 0.9090 (tpp80) REVERT: C 89 ASN cc_start: 0.9432 (m-40) cc_final: 0.9113 (m110) REVERT: C 94 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.9154 (t0) REVERT: C 99 ARG cc_start: 0.9104 (mmm160) cc_final: 0.8671 (mmp80) REVERT: C 104 GLN cc_start: 0.8523 (mp10) cc_final: 0.8198 (mp10) REVERT: D 89 ASP cc_start: 0.9169 (t0) cc_final: 0.8887 (t0) REVERT: D 107 ARG cc_start: 0.8953 (mtp85) cc_final: 0.8516 (mtp85) REVERT: D 127 MET cc_start: 0.9104 (mtm) cc_final: 0.8589 (mtt) REVERT: D 137 LYS cc_start: 0.9266 (mtmm) cc_final: 0.8938 (mtmm) REVERT: E 73 GLU cc_start: 0.9043 (tt0) cc_final: 0.8466 (tt0) REVERT: E 105 GLU cc_start: 0.9133 (tp30) cc_final: 0.8396 (tp30) REVERT: E 109 LEU cc_start: 0.9803 (OUTLIER) cc_final: 0.9494 (mm) REVERT: E 128 ARG cc_start: 0.9395 (mtp-110) cc_final: 0.8936 (mmm-85) REVERT: E 133 GLU cc_start: 0.8482 (pm20) cc_final: 0.8037 (pm20) REVERT: F 24 ASP cc_start: 0.9188 (t0) cc_final: 0.8984 (t0) REVERT: G 38 ASN cc_start: 0.9234 (t0) cc_final: 0.9030 (t0) REVERT: G 56 GLU cc_start: 0.8947 (tt0) cc_final: 0.8455 (tt0) REVERT: G 57 TYR cc_start: 0.8761 (t80) cc_final: 0.8157 (t80) REVERT: G 61 GLU cc_start: 0.9108 (tt0) cc_final: 0.8319 (tt0) REVERT: G 87 ILE cc_start: 0.9368 (tp) cc_final: 0.9156 (tp) REVERT: G 94 ASN cc_start: 0.9467 (t0) cc_final: 0.9172 (t0) REVERT: H 78 GLU cc_start: 0.9447 (mp0) cc_final: 0.9047 (mp0) REVERT: H 84 ASP cc_start: 0.9118 (m-30) cc_final: 0.8647 (m-30) REVERT: H 89 ASP cc_start: 0.9242 (t0) cc_final: 0.8750 (t0) REVERT: H 114 GLU cc_start: 0.9118 (mp0) cc_final: 0.8563 (mp0) REVERT: H 127 MET cc_start: 0.9054 (ttp) cc_final: 0.8770 (tpp) REVERT: H 129 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8724 (mtmm) REVERT: H 141 ARG cc_start: 0.9208 (mmm-85) cc_final: 0.8861 (mmm-85) REVERT: H 142 THR cc_start: 0.9587 (OUTLIER) cc_final: 0.9243 (p) outliers start: 31 outliers final: 19 residues processed: 259 average time/residue: 0.1406 time to fit residues: 47.0412 Evaluate side-chains 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 240 time to evaluate : 0.289 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain C residue 54 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 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 D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 81 optimal weight: 8.9990 chunk 1 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 87 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 chunk 14 optimal weight: 0.0270 chunk 75 optimal weight: 8.9990 overall best weight: 2.8044 ------------------------------------------------------------------------------- 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 ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN E 108 ASN H 108 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.047177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2689 r_free = 0.2689 target = 0.033510 restraints weight = 57703.054| |-----------------------------------------------------------------------------| r_work (start): 0.2626 rms_B_bonded: 3.67 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3101 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= 0.200 Angle : 0.627 8.411 15843 Z= 0.361 Chirality : 0.035 0.152 1815 Planarity : 0.004 0.052 1203 Dihedral : 30.529 178.299 3302 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 12.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.30 % Allowed : 34.70 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.64 (0.32), residues: 691 helix: 1.78 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.30 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 77 TYR 0.011 0.001 TYR D 61 PHE 0.012 0.001 PHE D 62 TRP 0.002 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00443 (11001) covalent geometry : angle 0.62660 (15843) hydrogen bonds : bond 0.03708 ( 676) hydrogen bonds : angle 3.30749 ( 1719) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 252 time to evaluate : 0.299 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: 0.9525 (tt0) cc_final: 0.9139 (pp20) REVERT: B 63 GLU cc_start: 0.9018 (mt-10) cc_final: 0.8554 (mt-10) REVERT: B 79 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8538 (mtmm) REVERT: B 84 MET cc_start: 0.8840 (tpp) cc_final: 0.8162 (mmm) REVERT: C 25 PHE cc_start: 0.8705 (m-10) cc_final: 0.8174 (m-80) REVERT: C 35 ARG cc_start: 0.9458 (ttm110) cc_final: 0.9154 (ttm110) REVERT: C 38 ASN cc_start: 0.9047 (t0) cc_final: 0.8566 (t0) REVERT: C 39 TYR cc_start: 0.8692 (m-80) cc_final: 0.8480 (m-80) REVERT: C 57 TYR cc_start: 0.8424 (t80) cc_final: 0.7615 (t80) REVERT: C 61 GLU cc_start: 0.9005 (tt0) cc_final: 0.8565 (tt0) REVERT: C 62 ILE cc_start: 0.9393 (mt) cc_final: 0.9155 (tt) REVERT: C 71 ARG cc_start: 0.8395 (mtm-85) cc_final: 0.8057 (mtm-85) REVERT: C 89 ASN cc_start: 0.9439 (m-40) cc_final: 0.9109 (m110) REVERT: C 94 ASN cc_start: 0.9393 (OUTLIER) cc_final: 0.9150 (t0) REVERT: C 99 ARG cc_start: 0.9063 (mmm160) cc_final: 0.8619 (mmp80) REVERT: C 104 GLN cc_start: 0.8588 (mp10) cc_final: 0.7873 (mp10) REVERT: D 89 ASP cc_start: 0.9205 (t0) cc_final: 0.8958 (t0) REVERT: D 103 ARG cc_start: 0.8742 (mtm110) cc_final: 0.8312 (mtm-85) REVERT: D 107 ARG cc_start: 0.8928 (mtp85) cc_final: 0.8373 (mtp85) REVERT: D 108 GLN cc_start: 0.8174 (pm20) cc_final: 0.7966 (pm20) REVERT: D 137 LYS cc_start: 0.9258 (mtmm) cc_final: 0.8845 (mtmm) REVERT: E 73 GLU cc_start: 0.9127 (tt0) cc_final: 0.8657 (tt0) REVERT: E 105 GLU cc_start: 0.9050 (tp30) cc_final: 0.8349 (tp30) REVERT: E 109 LEU cc_start: 0.9802 (OUTLIER) cc_final: 0.9506 (mm) REVERT: E 128 ARG cc_start: 0.9367 (mtp-110) cc_final: 0.9025 (mmm-85) REVERT: E 133 GLU cc_start: 0.8688 (pm20) cc_final: 0.8481 (pm20) REVERT: E 134 ARG cc_start: 0.7343 (mmm160) cc_final: 0.7101 (mmm160) REVERT: G 38 ASN cc_start: 0.9203 (t0) cc_final: 0.8900 (t0) REVERT: G 56 GLU cc_start: 0.8863 (tt0) cc_final: 0.8349 (tt0) REVERT: G 57 TYR cc_start: 0.8737 (t80) cc_final: 0.8146 (t80) REVERT: G 61 GLU cc_start: 0.9146 (tt0) cc_final: 0.8345 (tt0) REVERT: G 64 GLU cc_start: 0.9066 (tm-30) cc_final: 0.8475 (tm-30) REVERT: G 68 ASN cc_start: 0.9122 (m-40) cc_final: 0.8472 (m-40) REVERT: G 87 ILE cc_start: 0.9399 (tp) cc_final: 0.9151 (tp) REVERT: G 91 GLU cc_start: 0.9069 (pm20) cc_final: 0.8783 (pm20) REVERT: G 94 ASN cc_start: 0.9451 (t0) cc_final: 0.9168 (t0) REVERT: G 100 VAL cc_start: 0.9650 (t) cc_final: 0.9247 (p) REVERT: H 78 GLU cc_start: 0.9442 (mp0) cc_final: 0.9075 (mp0) REVERT: H 84 ASP cc_start: 0.9123 (OUTLIER) cc_final: 0.8585 (m-30) REVERT: H 89 ASP cc_start: 0.9299 (t0) cc_final: 0.8781 (t0) REVERT: H 108 GLN cc_start: 0.8752 (pt0) cc_final: 0.7685 (pm20) REVERT: H 114 GLU cc_start: 0.9124 (mp0) cc_final: 0.8500 (mp0) REVERT: H 127 MET cc_start: 0.9069 (ttp) cc_final: 0.8829 (tpp) REVERT: H 129 LYS cc_start: 0.9032 (OUTLIER) cc_final: 0.8768 (mtmm) REVERT: H 141 ARG cc_start: 0.9275 (mmm-85) cc_final: 0.8925 (mmm-85) REVERT: H 142 THR cc_start: 0.9557 (OUTLIER) cc_final: 0.9197 (p) outliers start: 31 outliers final: 22 residues processed: 265 average time/residue: 0.1465 time to fit residues: 50.0475 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 : 0.299 ------------------------------------------------------------------------------- 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 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU 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 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 71 optimal weight: 8.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 chunk 49 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 14 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 66 optimal weight: 7.9990 chunk 12 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 B 25 ASN B 75 HIS C 94 ASN E 108 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 = 0.3232 r_free = 0.3232 target = 0.049321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.034963 restraints weight = 58335.731| |-----------------------------------------------------------------------------| r_work (start): 0.2671 rms_B_bonded: 3.81 r_work (final): 0.2671 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8663 moved from start: 0.3361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11001 Z= 0.157 Angle : 0.618 11.759 15843 Z= 0.354 Chirality : 0.034 0.148 1815 Planarity : 0.004 0.051 1203 Dihedral : 30.311 179.303 3302 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.96 % Allowed : 37.09 % Favored : 57.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.74 (0.32), residues: 691 helix: 1.84 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.22 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 77 TYR 0.017 0.001 TYR H 61 PHE 0.010 0.001 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00342 (11001) covalent geometry : angle 0.61756 (15843) hydrogen bonds : bond 0.03310 ( 676) hydrogen bonds : angle 3.08605 ( 1719) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 263 time to evaluate : 0.270 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: 0.9494 (tt0) cc_final: 0.9103 (pp20) REVERT: B 63 GLU cc_start: 0.8988 (mt-10) cc_final: 0.8448 (mt-10) REVERT: B 79 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8746 (mtpt) REVERT: B 84 MET cc_start: 0.8806 (tpp) cc_final: 0.7956 (mmm) REVERT: C 25 PHE cc_start: 0.8623 (m-10) cc_final: 0.8279 (m-80) REVERT: C 32 ARG cc_start: 0.8870 (ttp80) cc_final: 0.8564 (ttp80) REVERT: C 35 ARG cc_start: 0.9451 (ttm110) cc_final: 0.9166 (ttm110) REVERT: C 38 ASN cc_start: 0.9200 (t0) cc_final: 0.8406 (t0) REVERT: C 39 TYR cc_start: 0.8859 (m-80) cc_final: 0.8621 (m-80) REVERT: C 57 TYR cc_start: 0.8417 (t80) cc_final: 0.7736 (t80) REVERT: C 61 GLU cc_start: 0.9017 (tt0) cc_final: 0.8756 (tt0) REVERT: C 71 ARG cc_start: 0.8484 (mtm-85) cc_final: 0.8184 (mtm-85) REVERT: C 72 ASP cc_start: 0.9665 (t0) cc_final: 0.9234 (m-30) REVERT: C 94 ASN cc_start: 0.9390 (OUTLIER) cc_final: 0.8927 (t0) REVERT: C 99 ARG cc_start: 0.9047 (mmm160) cc_final: 0.8651 (mmp80) REVERT: C 104 GLN cc_start: 0.8564 (mp10) cc_final: 0.7817 (mp10) REVERT: D 89 ASP cc_start: 0.9214 (t0) cc_final: 0.8949 (t0) REVERT: D 107 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8411 (mtp85) REVERT: E 68 GLN cc_start: 0.9299 (tt0) cc_final: 0.9010 (tm-30) REVERT: E 105 GLU cc_start: 0.9016 (tp30) cc_final: 0.8383 (tp30) REVERT: E 109 LEU cc_start: 0.9779 (mm) cc_final: 0.9493 (mm) REVERT: E 120 MET cc_start: 0.8838 (mmm) cc_final: 0.8624 (mmt) REVERT: E 128 ARG cc_start: 0.9347 (mtp-110) cc_final: 0.8991 (mmm-85) REVERT: E 133 GLU cc_start: 0.8665 (pm20) cc_final: 0.8419 (pm20) REVERT: E 134 ARG cc_start: 0.7461 (mmm160) cc_final: 0.7204 (mmm160) REVERT: F 24 ASP cc_start: 0.9084 (t0) cc_final: 0.8608 (p0) REVERT: F 93 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8390 (tm-30) REVERT: G 38 ASN cc_start: 0.9256 (t0) cc_final: 0.8892 (t0) REVERT: G 39 TYR cc_start: 0.9419 (m-80) cc_final: 0.8831 (m-80) REVERT: G 55 LEU cc_start: 0.9678 (mp) cc_final: 0.9462 (mt) REVERT: G 56 GLU cc_start: 0.8787 (tt0) cc_final: 0.8239 (tt0) REVERT: G 57 TYR cc_start: 0.8728 (t80) cc_final: 0.8159 (t80) REVERT: G 61 GLU cc_start: 0.9163 (tt0) cc_final: 0.8322 (tt0) REVERT: G 64 GLU cc_start: 0.9051 (tm-30) cc_final: 0.8364 (tm-30) REVERT: G 68 ASN cc_start: 0.9131 (m-40) cc_final: 0.8444 (m110) REVERT: G 87 ILE cc_start: 0.9400 (tp) cc_final: 0.9139 (tp) REVERT: G 94 ASN cc_start: 0.9430 (t0) cc_final: 0.9152 (t0) REVERT: G 100 VAL cc_start: 0.9544 (t) cc_final: 0.9207 (p) REVERT: H 77 ARG cc_start: 0.9095 (ttm110) cc_final: 0.8351 (ptp-110) REVERT: H 78 GLU cc_start: 0.9421 (mp0) cc_final: 0.8968 (mp0) REVERT: H 84 ASP cc_start: 0.9101 (OUTLIER) cc_final: 0.8503 (m-30) REVERT: H 89 ASP cc_start: 0.9315 (t0) cc_final: 0.8795 (t0) REVERT: H 107 ARG cc_start: 0.9186 (mmm-85) cc_final: 0.8782 (mmm-85) REVERT: H 114 GLU cc_start: 0.9152 (mp0) cc_final: 0.8520 (mp0) REVERT: H 127 MET cc_start: 0.9113 (ttp) cc_final: 0.8732 (tpp) REVERT: H 129 LYS cc_start: 0.9007 (OUTLIER) cc_final: 0.8694 (mtmm) REVERT: H 132 GLU cc_start: 0.8758 (tt0) cc_final: 0.8458 (tp30) REVERT: H 141 ARG cc_start: 0.9233 (mmm-85) cc_final: 0.8870 (mmm-85) outliers start: 29 outliers final: 17 residues processed: 277 average time/residue: 0.1249 time to fit residues: 45.0492 Evaluate side-chains 275 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 254 time to evaluate : 0.179 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR 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 108 ASN Chi-restraints excluded: chain E residue 122 LYS Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 129 LYS 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 37 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 62 optimal weight: 3.9990 chunk 58 optimal weight: 0.8980 chunk 86 optimal weight: 10.0000 chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- 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 C 84 GLN D 100 HIS E 93 GLN E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.049733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.035411 restraints weight = 59079.176| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 3.90 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8661 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11001 Z= 0.157 Angle : 0.620 8.485 15843 Z= 0.354 Chirality : 0.035 0.188 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.246 179.026 3302 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 12.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.98 % Allowed : 37.09 % Favored : 56.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.89 (0.32), residues: 691 helix: 1.96 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.23 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 63 TYR 0.026 0.001 TYR F 98 PHE 0.032 0.001 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00344 (11001) covalent geometry : angle 0.62001 (15843) hydrogen bonds : bond 0.03360 ( 676) hydrogen bonds : angle 3.05889 ( 1719) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 255 time to evaluate : 0.298 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 123 ASP cc_start: 0.8935 (m-30) cc_final: 0.8340 (m-30) REVERT: B 63 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8393 (mt-10) REVERT: B 79 LYS cc_start: 0.8972 (OUTLIER) cc_final: 0.8753 (mtpt) REVERT: B 84 MET cc_start: 0.8803 (tpp) cc_final: 0.7960 (mmm) REVERT: C 25 PHE cc_start: 0.8593 (m-10) cc_final: 0.8245 (m-80) REVERT: C 32 ARG cc_start: 0.8860 (ttp80) cc_final: 0.8399 (ttp-170) REVERT: C 35 ARG cc_start: 0.9464 (ttm110) cc_final: 0.9179 (ttm110) REVERT: C 38 ASN cc_start: 0.9187 (t0) cc_final: 0.8521 (t0) REVERT: C 39 TYR cc_start: 0.8809 (m-80) cc_final: 0.8598 (m-80) REVERT: C 42 ARG cc_start: 0.8096 (mtp180) cc_final: 0.7704 (mmm-85) REVERT: C 57 TYR cc_start: 0.8495 (t80) cc_final: 0.7963 (t80) REVERT: C 71 ARG cc_start: 0.8431 (mtm-85) cc_final: 0.8173 (mtm-85) REVERT: C 72 ASP cc_start: 0.9639 (t0) cc_final: 0.9194 (m-30) REVERT: C 94 ASN cc_start: 0.9429 (t0) cc_final: 0.9107 (m-40) REVERT: C 99 ARG cc_start: 0.8994 (mmm160) cc_final: 0.8675 (mmp80) REVERT: C 104 GLN cc_start: 0.8678 (mp10) cc_final: 0.7919 (mp10) REVERT: D 107 ARG cc_start: 0.8895 (mtp85) cc_final: 0.8361 (mtp85) REVERT: D 108 GLN cc_start: 0.7963 (pm20) cc_final: 0.7553 (pm20) REVERT: E 68 GLN cc_start: 0.9321 (tt0) cc_final: 0.9023 (tm-30) REVERT: E 73 GLU cc_start: 0.9494 (tm-30) cc_final: 0.9042 (tt0) REVERT: E 105 GLU cc_start: 0.9008 (tp30) cc_final: 0.8398 (tp30) REVERT: E 128 ARG cc_start: 0.9390 (mtp-110) cc_final: 0.9182 (mmm-85) REVERT: G 38 ASN cc_start: 0.9290 (t0) cc_final: 0.8958 (t0) REVERT: G 39 TYR cc_start: 0.9393 (m-80) cc_final: 0.8831 (m-80) REVERT: G 56 GLU cc_start: 0.8818 (tt0) cc_final: 0.8309 (tt0) REVERT: G 57 TYR cc_start: 0.8771 (t80) cc_final: 0.8110 (t80) REVERT: G 61 GLU cc_start: 0.9175 (tt0) cc_final: 0.8302 (tt0) REVERT: G 64 GLU cc_start: 0.9059 (tm-30) cc_final: 0.8172 (tm-30) REVERT: G 68 ASN cc_start: 0.9116 (m-40) cc_final: 0.8451 (m110) REVERT: G 87 ILE cc_start: 0.9422 (tp) cc_final: 0.9189 (tp) REVERT: G 94 ASN cc_start: 0.9458 (t0) cc_final: 0.9209 (t0) REVERT: G 100 VAL cc_start: 0.9561 (t) cc_final: 0.9144 (p) REVERT: H 77 ARG cc_start: 0.9118 (ttm110) cc_final: 0.8517 (ptp-110) REVERT: H 78 GLU cc_start: 0.9404 (mp0) cc_final: 0.8926 (mp0) REVERT: H 84 ASP cc_start: 0.9093 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: H 89 ASP cc_start: 0.9303 (t0) cc_final: 0.8775 (t0) REVERT: H 108 GLN cc_start: 0.8685 (pt0) cc_final: 0.8201 (pm20) REVERT: H 114 GLU cc_start: 0.9144 (mp0) cc_final: 0.8644 (mp0) REVERT: H 127 MET cc_start: 0.9091 (ttp) cc_final: 0.8787 (tpp) REVERT: H 129 LYS cc_start: 0.9028 (OUTLIER) cc_final: 0.8741 (mtmm) REVERT: H 132 GLU cc_start: 0.8745 (tt0) cc_final: 0.8420 (tp30) REVERT: H 141 ARG cc_start: 0.9223 (mmm-85) cc_final: 0.8866 (mmm-85) outliers start: 35 outliers final: 21 residues processed: 272 average time/residue: 0.1384 time to fit residues: 48.8140 Evaluate side-chains 270 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 246 time to evaluate : 0.215 ------------------------------------------------------------------------------- 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 B residue 97 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR 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 129 LYS Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 6.9990 chunk 55 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 65 optimal weight: 0.0670 overall best weight: 0.6720 ------------------------------------------------------------------------------- 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 89 ASN C 94 ASN E 93 GLN E 108 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.053743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.038749 restraints weight = 60831.580| |-----------------------------------------------------------------------------| r_work (start): 0.2789 rms_B_bonded: 3.75 r_work (final): 0.2789 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.3860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11001 Z= 0.158 Angle : 0.652 12.971 15843 Z= 0.364 Chirality : 0.035 0.165 1815 Planarity : 0.004 0.052 1203 Dihedral : 30.166 178.843 3302 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 5.30 % Allowed : 38.97 % Favored : 55.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.79 (0.32), residues: 691 helix: 1.89 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 141 TYR 0.036 0.002 TYR F 98 PHE 0.042 0.002 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (11001) covalent geometry : angle 0.65167 (15843) hydrogen bonds : bond 0.03385 ( 676) hydrogen bonds : angle 3.08948 ( 1719) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 259 time to evaluate : 0.297 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 123 ASP cc_start: 0.8769 (m-30) cc_final: 0.8079 (m-30) REVERT: B 63 GLU cc_start: 0.8950 (mt-10) cc_final: 0.8336 (mt-10) REVERT: B 79 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8598 (mtmm) REVERT: B 84 MET cc_start: 0.8747 (tpp) cc_final: 0.7958 (mmm) REVERT: C 25 PHE cc_start: 0.8589 (m-10) cc_final: 0.8188 (m-80) REVERT: C 32 ARG cc_start: 0.8831 (ttp80) cc_final: 0.8407 (ttp-170) REVERT: C 35 ARG cc_start: 0.9465 (ttm110) cc_final: 0.9196 (ttm110) REVERT: C 38 ASN cc_start: 0.9238 (t0) cc_final: 0.8463 (t0) REVERT: C 39 TYR cc_start: 0.8833 (m-80) cc_final: 0.8623 (m-80) REVERT: C 57 TYR cc_start: 0.8526 (t80) cc_final: 0.7830 (t80) REVERT: C 61 GLU cc_start: 0.8957 (tt0) cc_final: 0.8518 (mt-10) REVERT: C 71 ARG cc_start: 0.8442 (mtm-85) cc_final: 0.8191 (mtm-85) REVERT: C 72 ASP cc_start: 0.9607 (t0) cc_final: 0.9179 (m-30) REVERT: C 94 ASN cc_start: 0.9383 (OUTLIER) cc_final: 0.9017 (m-40) REVERT: C 99 ARG cc_start: 0.8877 (mmm160) cc_final: 0.8676 (mmp80) REVERT: C 104 GLN cc_start: 0.8671 (mp10) cc_final: 0.7928 (mp10) REVERT: D 83 MET cc_start: 0.9631 (tpp) cc_final: 0.9428 (tpp) REVERT: D 107 ARG cc_start: 0.8894 (mtp85) cc_final: 0.8389 (mtp85) REVERT: D 108 GLN cc_start: 0.8045 (pm20) cc_final: 0.7648 (pm20) REVERT: D 126 GLN cc_start: 0.8255 (tp-100) cc_final: 0.8048 (tp-100) REVERT: D 129 LYS cc_start: 0.8658 (mtmt) cc_final: 0.8342 (mttm) REVERT: E 68 GLN cc_start: 0.9309 (tt0) cc_final: 0.9035 (tm-30) REVERT: E 73 GLU cc_start: 0.9482 (tm-30) cc_final: 0.9115 (tt0) REVERT: E 97 GLU cc_start: 0.9136 (mm-30) cc_final: 0.8914 (mt-10) REVERT: E 105 GLU cc_start: 0.8928 (tp30) cc_final: 0.8169 (tp30) REVERT: E 120 MET cc_start: 0.8858 (mmm) cc_final: 0.8654 (mmt) REVERT: G 38 ASN cc_start: 0.9319 (t0) cc_final: 0.9003 (t0) REVERT: G 39 TYR cc_start: 0.9339 (m-80) cc_final: 0.8795 (m-80) REVERT: G 56 GLU cc_start: 0.8794 (tt0) cc_final: 0.8243 (tt0) REVERT: G 57 TYR cc_start: 0.8839 (t80) cc_final: 0.8207 (t80) REVERT: G 61 GLU cc_start: 0.9110 (tt0) cc_final: 0.8144 (tt0) REVERT: G 64 GLU cc_start: 0.8966 (tm-30) cc_final: 0.8068 (tm-30) REVERT: G 68 ASN cc_start: 0.9107 (m-40) cc_final: 0.8401 (m110) REVERT: G 87 ILE cc_start: 0.9449 (tp) cc_final: 0.9234 (tp) REVERT: G 100 VAL cc_start: 0.9547 (t) cc_final: 0.9129 (p) REVERT: H 77 ARG cc_start: 0.9112 (ttm110) cc_final: 0.8550 (ptp-110) REVERT: H 78 GLU cc_start: 0.9349 (mp0) cc_final: 0.8901 (mp0) REVERT: H 84 ASP cc_start: 0.9130 (OUTLIER) cc_final: 0.8505 (m-30) REVERT: H 89 ASP cc_start: 0.9286 (t0) cc_final: 0.8853 (t0) REVERT: H 107 ARG cc_start: 0.9142 (mmm-85) cc_final: 0.8932 (mmm-85) REVERT: H 108 GLN cc_start: 0.8725 (pt0) cc_final: 0.8271 (pm20) REVERT: H 114 GLU cc_start: 0.9051 (mp0) cc_final: 0.8562 (mp0) REVERT: H 127 MET cc_start: 0.9057 (ttp) cc_final: 0.8790 (tpp) REVERT: H 129 LYS cc_start: 0.9049 (OUTLIER) cc_final: 0.8737 (mtmm) REVERT: H 132 GLU cc_start: 0.8694 (tt0) cc_final: 0.8395 (tp30) REVERT: H 141 ARG cc_start: 0.9185 (mmm-85) cc_final: 0.8873 (mmm-85) outliers start: 31 outliers final: 21 residues processed: 272 average time/residue: 0.1366 time to fit residues: 48.0747 Evaluate side-chains 263 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 238 time to evaluate : 0.294 ------------------------------------------------------------------------------- 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 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 67 optimal weight: 20.0000 chunk 3 optimal weight: 2.9990 chunk 17 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 chunk 4 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 72 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 29 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- 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 94 ASN D 100 HIS E 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.047115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.033581 restraints weight = 58466.923| |-----------------------------------------------------------------------------| r_work (start): 0.2653 rms_B_bonded: 3.75 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.3864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 11001 Z= 0.248 Angle : 0.682 7.663 15843 Z= 0.387 Chirality : 0.037 0.175 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.403 178.129 3302 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 5.81 % Allowed : 39.15 % Favored : 55.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.85 (0.32), residues: 691 helix: 1.93 (0.23), residues: 533 sheet: None (None), residues: 0 loop : -1.23 (0.44), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 141 TYR 0.030 0.002 TYR F 98 PHE 0.050 0.002 PHE D 62 TRP 0.003 0.001 TRP D 113 HIS 0.004 0.001 HIS D 100 Details of bonding type rmsd covalent geometry : bond 0.00557 (11001) covalent geometry : angle 0.68194 (15843) hydrogen bonds : bond 0.04259 ( 676) hydrogen bonds : angle 3.40740 ( 1719) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 234 time to evaluate : 0.176 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: 0.9145 (mmtm) cc_final: 0.8894 (mmtm) REVERT: B 63 GLU cc_start: 0.9003 (mt-10) cc_final: 0.8392 (mt-10) REVERT: B 79 LYS cc_start: 0.8994 (mtpt) cc_final: 0.8777 (mtpt) REVERT: B 84 MET cc_start: 0.8873 (tpp) cc_final: 0.8218 (mmm) REVERT: C 25 PHE cc_start: 0.8665 (m-10) cc_final: 0.8014 (m-10) REVERT: C 29 ARG cc_start: 0.9384 (ttm-80) cc_final: 0.9041 (ttm-80) REVERT: C 38 ASN cc_start: 0.9343 (t0) cc_final: 0.9001 (t0) REVERT: C 39 TYR cc_start: 0.8865 (m-80) cc_final: 0.8621 (m-80) REVERT: C 42 ARG cc_start: 0.7884 (OUTLIER) cc_final: 0.7127 (mmm-85) REVERT: C 57 TYR cc_start: 0.8446 (t80) cc_final: 0.7777 (t80) REVERT: C 72 ASP cc_start: 0.9666 (t0) cc_final: 0.9252 (m-30) REVERT: C 94 ASN cc_start: 0.9438 (OUTLIER) cc_final: 0.8930 (m110) REVERT: C 104 GLN cc_start: 0.8686 (mp10) cc_final: 0.7939 (mp10) REVERT: D 68 GLN cc_start: 0.9530 (pp30) cc_final: 0.9265 (pp30) REVERT: D 103 ARG cc_start: 0.8742 (mtm110) cc_final: 0.8303 (mtm110) REVERT: D 126 GLN cc_start: 0.8581 (tp-100) cc_final: 0.8362 (tp-100) REVERT: D 129 LYS cc_start: 0.8946 (mtmt) cc_final: 0.8659 (mttm) REVERT: E 73 GLU cc_start: 0.9560 (tm-30) cc_final: 0.9042 (tt0) REVERT: E 105 GLU cc_start: 0.9050 (tp30) cc_final: 0.8408 (tp30) REVERT: E 120 MET cc_start: 0.8903 (mmm) cc_final: 0.8650 (mmt) REVERT: F 44 LYS cc_start: 0.9562 (mtpt) cc_final: 0.9318 (mtpp) REVERT: F 79 LYS cc_start: 0.8743 (OUTLIER) cc_final: 0.8530 (mmmm) REVERT: G 38 ASN cc_start: 0.9399 (t0) cc_final: 0.8903 (p0) REVERT: G 56 GLU cc_start: 0.8943 (tt0) cc_final: 0.8421 (tt0) REVERT: G 57 TYR cc_start: 0.8868 (t80) cc_final: 0.7964 (t80) REVERT: G 61 GLU cc_start: 0.9139 (tt0) cc_final: 0.8066 (tt0) REVERT: G 64 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8158 (tm-30) REVERT: G 68 ASN cc_start: 0.9163 (m-40) cc_final: 0.8489 (m110) REVERT: G 100 VAL cc_start: 0.9681 (t) cc_final: 0.9317 (p) REVERT: H 77 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8609 (ptp-110) REVERT: H 78 GLU cc_start: 0.9417 (mp0) cc_final: 0.8955 (mp0) REVERT: H 89 ASP cc_start: 0.9368 (t0) cc_final: 0.8873 (t0) REVERT: H 107 ARG cc_start: 0.9093 (mmm-85) cc_final: 0.8826 (mmm-85) REVERT: H 127 MET cc_start: 0.9139 (ttp) cc_final: 0.8829 (tpp) REVERT: H 129 LYS cc_start: 0.9040 (OUTLIER) cc_final: 0.8724 (mtmm) REVERT: H 141 ARG cc_start: 0.9300 (mmm-85) cc_final: 0.8995 (mmm-85) outliers start: 34 outliers final: 22 residues processed: 249 average time/residue: 0.1442 time to fit residues: 46.3702 Evaluate side-chains 248 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 222 time to evaluate : 0.318 ------------------------------------------------------------------------------- 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 42 ARG Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 126 LEU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 34 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 32 optimal weight: 0.7980 chunk 59 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 69 optimal weight: 10.0000 chunk 76 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 89 ASN C 94 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** H 108 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3248 r_free = 0.3248 target = 0.049687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.035373 restraints weight = 59125.492| |-----------------------------------------------------------------------------| r_work (start): 0.2691 rms_B_bonded: 3.88 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8670 moved from start: 0.4042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11001 Z= 0.167 Angle : 0.703 13.539 15843 Z= 0.387 Chirality : 0.036 0.169 1815 Planarity : 0.005 0.046 1203 Dihedral : 30.307 178.990 3302 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.76 % Allowed : 42.56 % Favored : 53.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.71 (0.32), residues: 691 helix: 1.85 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.34 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 141 TYR 0.021 0.002 TYR G 39 PHE 0.045 0.001 PHE D 62 TRP 0.005 0.001 TRP D 113 HIS 0.003 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (11001) covalent geometry : angle 0.70256 (15843) hydrogen bonds : bond 0.03473 ( 676) hydrogen bonds : angle 3.26336 ( 1719) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 259 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 237 time to evaluate : 0.297 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: 0.9180 (mmtm) cc_final: 0.8913 (mmtm) REVERT: A 123 ASP cc_start: 0.8928 (m-30) cc_final: 0.8267 (m-30) REVERT: B 63 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 79 LYS cc_start: 0.9035 (mtpt) cc_final: 0.8692 (mtmt) REVERT: B 84 MET cc_start: 0.8795 (tpp) cc_final: 0.7949 (mmm) REVERT: C 25 PHE cc_start: 0.8590 (m-10) cc_final: 0.8190 (m-80) REVERT: C 38 ASN cc_start: 0.9310 (t0) cc_final: 0.8545 (t0) REVERT: C 57 TYR cc_start: 0.8449 (t80) cc_final: 0.7756 (t80) REVERT: C 68 ASN cc_start: 0.9481 (m-40) cc_final: 0.9130 (m-40) REVERT: C 72 ASP cc_start: 0.9676 (t0) cc_final: 0.9301 (m-30) REVERT: C 94 ASN cc_start: 0.9314 (OUTLIER) cc_final: 0.8823 (m-40) REVERT: C 99 ARG cc_start: 0.8853 (mmm160) cc_final: 0.8525 (mmp80) REVERT: C 104 GLN cc_start: 0.8657 (mp10) cc_final: 0.7927 (mp10) REVERT: D 103 ARG cc_start: 0.8767 (mtm110) cc_final: 0.8409 (mtm-85) REVERT: D 107 ARG cc_start: 0.8759 (mtp85) cc_final: 0.8327 (mtp85) REVERT: D 108 GLN cc_start: 0.8003 (pm20) cc_final: 0.7720 (pm20) REVERT: D 129 LYS cc_start: 0.8785 (mtmt) cc_final: 0.8522 (mttm) REVERT: E 68 GLN cc_start: 0.9325 (tt0) cc_final: 0.9028 (tm-30) REVERT: E 73 GLU cc_start: 0.9561 (tm-30) cc_final: 0.9073 (tt0) REVERT: E 120 MET cc_start: 0.8887 (mmm) cc_final: 0.8663 (mmt) REVERT: F 44 LYS cc_start: 0.9540 (mtpt) cc_final: 0.9295 (mtpp) REVERT: G 38 ASN cc_start: 0.9394 (t0) cc_final: 0.9112 (t0) REVERT: G 56 GLU cc_start: 0.8807 (tt0) cc_final: 0.8241 (tt0) REVERT: G 61 GLU cc_start: 0.9181 (tt0) cc_final: 0.8948 (tt0) REVERT: G 64 GLU cc_start: 0.9064 (tm-30) cc_final: 0.8168 (tm-30) REVERT: G 68 ASN cc_start: 0.9123 (m-40) cc_final: 0.8430 (m110) REVERT: G 100 VAL cc_start: 0.9559 (t) cc_final: 0.9164 (p) REVERT: H 77 ARG cc_start: 0.9098 (ttm110) cc_final: 0.8556 (ptp-110) REVERT: H 78 GLU cc_start: 0.9418 (mp0) cc_final: 0.8976 (mp0) REVERT: H 84 ASP cc_start: 0.9107 (OUTLIER) cc_final: 0.8534 (m-30) REVERT: H 89 ASP cc_start: 0.9367 (t0) cc_final: 0.8889 (t0) REVERT: H 107 ARG cc_start: 0.9108 (mmm-85) cc_final: 0.8806 (mmm-85) REVERT: H 129 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8715 (mtmm) REVERT: H 132 GLU cc_start: 0.8773 (tt0) cc_final: 0.8518 (tp30) REVERT: H 141 ARG cc_start: 0.9284 (mmm-85) cc_final: 0.8971 (mmm-85) outliers start: 22 outliers final: 15 residues processed: 246 average time/residue: 0.1392 time to fit residues: 45.1856 Evaluate side-chains 249 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 231 time to evaluate : 0.327 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 59 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 12 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 chunk 60 optimal weight: 9.9990 chunk 20 optimal weight: 0.9980 chunk 43 optimal weight: 8.9990 chunk 73 optimal weight: 9.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 94 ASN D 100 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.049809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.035658 restraints weight = 58790.253| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 3.86 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 11001 Z= 0.170 Angle : 0.697 11.196 15843 Z= 0.386 Chirality : 0.037 0.279 1815 Planarity : 0.005 0.048 1203 Dihedral : 30.245 178.582 3302 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 14.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 3.76 % Allowed : 41.54 % Favored : 54.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.32), residues: 691 helix: 1.69 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.32 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 141 TYR 0.022 0.002 TYR F 98 PHE 0.045 0.002 PHE D 62 TRP 0.004 0.001 TRP D 113 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00387 (11001) covalent geometry : angle 0.69652 (15843) hydrogen bonds : bond 0.03570 ( 676) hydrogen bonds : angle 3.32451 ( 1719) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 230 time to evaluate : 0.308 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 64 LYS cc_start: 0.9179 (mmtm) cc_final: 0.8924 (mmtm) REVERT: A 123 ASP cc_start: 0.8922 (m-30) cc_final: 0.8271 (m-30) REVERT: B 79 LYS cc_start: 0.9054 (mtpt) cc_final: 0.8705 (mtmt) REVERT: B 84 MET cc_start: 0.8826 (tpp) cc_final: 0.7991 (mmm) REVERT: C 25 PHE cc_start: 0.8552 (m-10) cc_final: 0.8104 (m-80) REVERT: C 38 ASN cc_start: 0.9389 (t0) cc_final: 0.8672 (t0) REVERT: C 57 TYR cc_start: 0.8415 (t80) cc_final: 0.7725 (t80) REVERT: C 72 ASP cc_start: 0.9667 (t0) cc_final: 0.9289 (m-30) REVERT: C 94 ASN cc_start: 0.9276 (OUTLIER) cc_final: 0.8749 (m-40) REVERT: C 99 ARG cc_start: 0.8865 (mmm160) cc_final: 0.8535 (mmp80) REVERT: C 104 GLN cc_start: 0.8687 (mp10) cc_final: 0.7962 (mp10) REVERT: D 68 GLN cc_start: 0.9484 (pp30) cc_final: 0.9198 (pp30) REVERT: D 107 ARG cc_start: 0.8760 (mtp85) cc_final: 0.8379 (mtp85) REVERT: D 108 GLN cc_start: 0.8039 (pm20) cc_final: 0.7770 (pm20) REVERT: D 129 LYS cc_start: 0.8778 (mtmt) cc_final: 0.8540 (mttp) REVERT: E 68 GLN cc_start: 0.9345 (tt0) cc_final: 0.9035 (tm-30) REVERT: E 73 GLU cc_start: 0.9556 (tm-30) cc_final: 0.9060 (tt0) REVERT: E 120 MET cc_start: 0.8874 (mmm) cc_final: 0.8665 (mmt) REVERT: F 44 LYS cc_start: 0.9519 (mtpt) cc_final: 0.9286 (mtpp) REVERT: F 79 LYS cc_start: 0.8556 (OUTLIER) cc_final: 0.8115 (mmmm) REVERT: F 92 ARG cc_start: 0.9600 (OUTLIER) cc_final: 0.9355 (mmm160) REVERT: G 38 ASN cc_start: 0.9407 (t0) cc_final: 0.9157 (t0) REVERT: G 56 GLU cc_start: 0.8787 (tt0) cc_final: 0.8218 (tt0) REVERT: G 57 TYR cc_start: 0.8654 (t80) cc_final: 0.8124 (t80) REVERT: G 61 GLU cc_start: 0.9075 (tt0) cc_final: 0.8391 (tt0) REVERT: G 64 GLU cc_start: 0.9057 (tm-30) cc_final: 0.8164 (tm-30) REVERT: G 68 ASN cc_start: 0.9121 (m-40) cc_final: 0.8426 (m110) REVERT: G 100 VAL cc_start: 0.9559 (t) cc_final: 0.9144 (p) REVERT: H 77 ARG cc_start: 0.9108 (ttm110) cc_final: 0.8565 (ptp-110) REVERT: H 78 GLU cc_start: 0.9422 (mp0) cc_final: 0.8961 (mp0) REVERT: H 84 ASP cc_start: 0.9092 (OUTLIER) cc_final: 0.8506 (m-30) REVERT: H 89 ASP cc_start: 0.9355 (t0) cc_final: 0.8885 (t0) REVERT: H 100 HIS cc_start: 0.9333 (t-90) cc_final: 0.8794 (t-90) REVERT: H 107 ARG cc_start: 0.9085 (mmm-85) cc_final: 0.8818 (mmm-85) REVERT: H 127 MET cc_start: 0.9044 (ttp) cc_final: 0.8639 (tpp) REVERT: H 129 LYS cc_start: 0.9003 (OUTLIER) cc_final: 0.8686 (mtmm) REVERT: H 132 GLU cc_start: 0.8713 (tt0) cc_final: 0.8505 (tp30) REVERT: H 141 ARG cc_start: 0.9319 (mmm-85) cc_final: 0.9046 (mmm-85) outliers start: 22 outliers final: 13 residues processed: 237 average time/residue: 0.1399 time to fit residues: 43.3936 Evaluate side-chains 244 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 226 time to evaluate : 0.256 ------------------------------------------------------------------------------- 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 43 VAL Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 79 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 15 optimal weight: 7.9990 chunk 83 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 chunk 69 optimal weight: 10.0000 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 27 optimal weight: 9.9990 chunk 5 optimal weight: 0.8980 chunk 16 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 overall best weight: 4.1788 ------------------------------------------------------------------------------- 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 89 ASN C 94 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** F 75 HIS ** 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 = 0.3179 r_free = 0.3179 target = 0.046875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.033363 restraints weight = 59208.306| |-----------------------------------------------------------------------------| r_work (start): 0.2644 rms_B_bonded: 3.78 r_work (final): 0.2644 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.4098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.087 11001 Z= 0.261 Angle : 0.730 9.493 15843 Z= 0.408 Chirality : 0.038 0.252 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.495 177.997 3302 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.10 % Allowed : 42.39 % Favored : 53.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.32), residues: 691 helix: 1.68 (0.22), residues: 531 sheet: None (None), residues: 0 loop : -1.41 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 141 TYR 0.019 0.002 TYR H 61 PHE 0.046 0.002 PHE D 62 TRP 0.005 0.001 TRP D 113 HIS 0.010 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00588 (11001) covalent geometry : angle 0.73037 (15843) hydrogen bonds : bond 0.04631 ( 676) hydrogen bonds : angle 3.63440 ( 1719) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2001.84 seconds wall clock time: 35 minutes 9.89 seconds (2109.89 seconds total)