Starting phenix.real_space_refine on Tue May 13 10:05:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8jcc_36157/05_2025/8jcc_36157.cif Found real_map, /net/cci-nas-00/data/ceres_data/8jcc_36157/05_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_36157/05_2025/8jcc_36157.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8jcc_36157/05_2025/8jcc_36157.map" model { file = "/net/cci-nas-00/data/ceres_data/8jcc_36157/05_2025/8jcc_36157.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8jcc_36157/05_2025/8jcc_36157.cif" } resolution = 3.42 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.025 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 232 5.49 5 S 16 5.16 5 C 5770 2.51 5 N 1958 2.21 5 O 2382 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10358 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 766 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 3, 'TRANS': 90} Chain: "B" Number of atoms: 633 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 633 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "C" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 710 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 720 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 1, 'TRANS': 90} Chain: "E" Number of atoms: 626 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 626 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 2, 'TRANS': 74} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 766 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 766 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "H" Number of atoms: 733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 733 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 1, 'TRANS': 92} Chain: "I" Number of atoms: 2391 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2391 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Chain: "J" Number of atoms: 2365 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 2365 Classifications: {'DNA': 116} Link IDs: {'rna3p': 115} Time building chain proxies: 6.25, per 1000 atoms: 0.60 Number of scatterers: 10358 At special positions: 0 Unit cell: (83.74, 114.48, 115.54, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 16 16.00 P 232 15.00 O 2382 8.00 N 1958 7.00 C 5770 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.92 Conformation dependent library (CDL) restraints added in 938.4 milliseconds 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1316 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 10 sheets defined 75.7% alpha, 3.1% beta 114 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 4.63 Creating SS restraints... Processing helix chain 'A' and resid 45 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.894A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 3.911A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 31 through 42 removed outlier: 4.044A pdb=" N LEU B 37 " --> pdb=" O ALA B 33 " (cutoff:3.500A) Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.968A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N THR B 71 " --> pdb=" O ARG B 67 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N THR B 73 " --> pdb=" O ALA B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.650A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.343A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.608A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 58 through 68 Processing helix chain 'D' and resid 76 through 105 Processing helix chain 'D' and resid 111 through 123 removed outlier: 3.578A pdb=" N ALA D 118 " --> pdb=" O GLU D 114 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N ARG D 120 " --> pdb=" O ARG D 116 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N LEU D 121 " --> pdb=" O MET D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 124 through 129 removed outlier: 3.801A pdb=" N LYS D 129 " --> pdb=" O GLY D 125 " (cutoff:3.500A) Processing helix chain 'D' and resid 130 through 147 removed outlier: 3.729A pdb=" N ALA D 138 " --> pdb=" O GLU D 134 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N SER D 143 " --> pdb=" O VAL D 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 4.005A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.611A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.843A pdb=" N TYR F 88 " --> pdb=" O MET F 84 " (cutoff:3.500A) Processing helix chain 'G' and resid 26 through 38 removed outlier: 3.683A pdb=" N ASN G 38 " --> pdb=" O LEU G 34 " (cutoff:3.500A) Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.275A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.628A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'H' and resid 58 through 71 Processing helix chain 'H' and resid 76 through 105 removed outlier: 3.523A pdb=" N THR H 105 " --> pdb=" O LEU H 101 " (cutoff:3.500A) Processing helix chain 'H' and resid 111 through 123 removed outlier: 3.598A pdb=" N VAL H 119 " --> pdb=" O THR H 115 " (cutoff:3.500A) Processing helix chain 'H' and resid 125 through 144 Processing helix chain 'H' and resid 145 through 147 No H-bonds generated for 'chain 'H' and resid 145 through 147' Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.641A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.378A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.671A pdb=" N ARG C 42 " --> pdb=" O ILE D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 6.839A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.385A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.443A pdb=" N ARG G 42 " --> pdb=" O ILE H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 379 hydrogen bonds defined for protein. 1125 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 297 hydrogen bonds 594 hydrogen bond angles 0 basepair planarities 114 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 3.90 Time building geometry restraints manager: 3.39 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: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 29.390 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.130 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7761 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 11001 Z= 0.200 Angle : 0.600 9.395 15843 Z= 0.346 Chirality : 0.036 0.204 1815 Planarity : 0.004 0.054 1203 Dihedral : 28.833 178.878 4687 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 11.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 0.34 % Allowed : 31.62 % Favored : 68.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.32), residues: 691 helix: 1.75 (0.23), residues: 525 sheet: None (None), residues: 0 loop : -1.39 (0.42), residues: 166 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 113 HIS 0.003 0.001 HIS H 70 PHE 0.007 0.001 PHE D 58 TYR 0.011 0.001 TYR D 145 ARG 0.005 0.000 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.11443 ( 676) hydrogen bonds : angle 4.05117 ( 1719) covalent geometry : bond 0.00460 (11001) covalent geometry : angle 0.59995 (15843) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 0.726 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: 0.3118 time to fit residues: 128.7233 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 : 0.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 75 optimal weight: 10.0000 chunk 67 optimal weight: 10.0000 chunk 37 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 45 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 69 optimal weight: 10.0000 chunk 26 optimal weight: 1.9990 chunk 42 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 80 optimal weight: 10.0000 overall best weight: 2.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 94 ASN D 70 HIS ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.049132 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2699 r_free = 0.2699 target = 0.034662 restraints weight = 57044.099| |-----------------------------------------------------------------------------| r_work (start): 0.2640 rms_B_bonded: 3.61 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11001 Z= 0.189 Angle : 0.630 5.988 15843 Z= 0.363 Chirality : 0.036 0.377 1815 Planarity : 0.005 0.053 1203 Dihedral : 30.321 178.452 3304 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.15 % Allowed : 34.70 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.33), residues: 691 helix: 1.93 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.28 (0.43), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.022 0.002 PHE D 62 TYR 0.015 0.002 TYR B 98 ARG 0.012 0.001 ARG C 35 Details of bonding type rmsd hydrogen bonds : bond 0.03934 ( 676) hydrogen bonds : angle 3.33880 ( 1719) covalent geometry : bond 0.00422 (11001) covalent geometry : angle 0.63032 (15843) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 305 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 269 time to evaluate : 0.797 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: 0.9411 (tt0) cc_final: 0.8676 (tp30) REVERT: A 125 GLN cc_start: 0.9375 (OUTLIER) cc_final: 0.9074 (mp10) REVERT: C 25 PHE cc_start: 0.8489 (m-10) cc_final: 0.7912 (m-80) REVERT: C 38 ASN cc_start: 0.9044 (t0) cc_final: 0.8615 (t0) REVERT: C 39 TYR cc_start: 0.8328 (m-80) cc_final: 0.8070 (m-80) REVERT: C 42 ARG cc_start: 0.8103 (mtp180) cc_final: 0.7017 (mmm-85) REVERT: C 57 TYR cc_start: 0.8145 (t80) cc_final: 0.7421 (t80) REVERT: C 61 GLU cc_start: 0.8880 (tt0) cc_final: 0.8487 (tt0) REVERT: C 73 ASN cc_start: 0.9072 (OUTLIER) cc_final: 0.8848 (t0) REVERT: C 77 ARG cc_start: 0.6960 (OUTLIER) cc_final: 0.5934 (mtt180) REVERT: C 88 ARG cc_start: 0.9351 (ttm110) cc_final: 0.8679 (ttm110) REVERT: C 95 LYS cc_start: 0.9464 (tppt) cc_final: 0.9250 (tppt) REVERT: C 99 ARG cc_start: 0.9052 (mmm160) cc_final: 0.8560 (mmp80) REVERT: C 104 GLN cc_start: 0.8474 (mp10) cc_final: 0.7885 (mp10) REVERT: D 89 ASP cc_start: 0.9159 (t0) cc_final: 0.8907 (t0) REVERT: D 108 GLN cc_start: 0.8345 (pm20) cc_final: 0.7880 (pm20) REVERT: D 137 LYS cc_start: 0.9220 (mtmm) cc_final: 0.8918 (mtmm) REVERT: E 105 GLU cc_start: 0.9170 (tp30) cc_final: 0.8565 (tp30) REVERT: E 128 ARG cc_start: 0.9538 (mtp-110) cc_final: 0.8851 (mmm-85) REVERT: G 41 GLU cc_start: 0.9124 (mt-10) cc_final: 0.8855 (mt-10) REVERT: G 56 GLU cc_start: 0.8928 (tt0) cc_final: 0.8322 (tt0) REVERT: G 57 TYR cc_start: 0.8783 (t80) cc_final: 0.8562 (t80) REVERT: G 61 GLU cc_start: 0.9045 (tt0) cc_final: 0.8837 (tt0) REVERT: G 94 ASN cc_start: 0.9445 (t0) cc_final: 0.9133 (t0) REVERT: H 89 ASP cc_start: 0.9166 (t0) cc_final: 0.8738 (t0) REVERT: H 114 GLU cc_start: 0.9175 (mp0) cc_final: 0.8679 (mp0) REVERT: H 129 LYS cc_start: 0.8970 (OUTLIER) cc_final: 0.8670 (mtmm) REVERT: H 141 ARG cc_start: 0.9203 (mmm-85) cc_final: 0.8895 (mmm-85) REVERT: H 142 THR cc_start: 0.9544 (OUTLIER) cc_final: 0.9217 (p) outliers start: 36 outliers final: 12 residues processed: 286 average time/residue: 0.2909 time to fit residues: 106.8365 Evaluate side-chains 259 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 242 time to evaluate : 0.741 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 77 ARG Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 81 SER Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 104 SER Chi-restraints excluded: chain H residue 129 LYS Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 87 optimal weight: 10.0000 chunk 50 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 63 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 chunk 68 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN A 108 ASN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN C 94 ASN F 25 ASN G 112 GLN H 108 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.049191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.034671 restraints weight = 58720.257| |-----------------------------------------------------------------------------| r_work (start): 0.2648 rms_B_bonded: 3.66 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8647 moved from start: 0.2719 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= 0.176 Angle : 0.624 10.177 15843 Z= 0.359 Chirality : 0.036 0.337 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.276 178.385 3304 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 12.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.62 % Allowed : 34.70 % Favored : 60.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.32), residues: 691 helix: 1.84 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.27 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.014 0.001 PHE D 62 TYR 0.010 0.001 TYR D 61 ARG 0.010 0.001 ARG D 103 Details of bonding type rmsd hydrogen bonds : bond 0.03547 ( 676) hydrogen bonds : angle 3.23865 ( 1719) covalent geometry : bond 0.00389 (11001) covalent geometry : angle 0.62434 (15843) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 254 time to evaluate : 0.746 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.9237 (tp30) cc_final: 0.8926 (tp30) REVERT: B 63 GLU cc_start: 0.9008 (mt-10) cc_final: 0.8617 (mt-10) REVERT: B 79 LYS cc_start: 0.8928 (OUTLIER) cc_final: 0.8670 (mtpt) REVERT: B 84 MET cc_start: 0.8819 (tpp) cc_final: 0.8149 (mmm) REVERT: C 25 PHE cc_start: 0.8607 (m-10) cc_final: 0.8103 (m-80) REVERT: C 38 ASN cc_start: 0.9166 (t0) cc_final: 0.8520 (t0) REVERT: C 39 TYR cc_start: 0.8477 (m-80) cc_final: 0.8197 (m-80) REVERT: C 57 TYR cc_start: 0.8316 (t80) cc_final: 0.7445 (t80) REVERT: C 61 GLU cc_start: 0.8968 (tt0) cc_final: 0.8486 (tt0) REVERT: C 75 LYS cc_start: 0.8652 (mmtp) cc_final: 0.8422 (mmmm) REVERT: C 89 ASN cc_start: 0.9424 (m-40) cc_final: 0.9118 (m110) REVERT: C 92 GLU cc_start: 0.9299 (pp20) cc_final: 0.8911 (tt0) REVERT: C 99 ARG cc_start: 0.9078 (mmm160) cc_final: 0.8650 (mmp80) REVERT: C 104 GLN cc_start: 0.8445 (mp10) cc_final: 0.8107 (mp10) REVERT: D 89 ASP cc_start: 0.9111 (t0) cc_final: 0.8783 (t0) REVERT: D 107 ARG cc_start: 0.8934 (mtp85) cc_final: 0.8459 (mtp85) REVERT: D 126 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7398 (tp-100) REVERT: D 136 THR cc_start: 0.9400 (m) cc_final: 0.9188 (p) REVERT: D 137 LYS cc_start: 0.9262 (mtmm) cc_final: 0.8890 (mtmm) REVERT: E 105 GLU cc_start: 0.9106 (tp30) cc_final: 0.8402 (tp30) REVERT: E 128 ARG cc_start: 0.9338 (mtp-110) cc_final: 0.8960 (mmm-85) REVERT: G 56 GLU cc_start: 0.8870 (tt0) cc_final: 0.8358 (tt0) REVERT: G 57 TYR cc_start: 0.8707 (t80) cc_final: 0.8098 (t80) REVERT: G 61 GLU cc_start: 0.9110 (tt0) cc_final: 0.8320 (tt0) REVERT: G 64 GLU cc_start: 0.8954 (tm-30) cc_final: 0.8678 (tm-30) REVERT: G 68 ASN cc_start: 0.9273 (m-40) cc_final: 0.8432 (m-40) REVERT: G 87 ILE cc_start: 0.9339 (tp) cc_final: 0.9090 (tp) REVERT: G 94 ASN cc_start: 0.9455 (t0) cc_final: 0.9166 (t0) REVERT: H 84 ASP cc_start: 0.9121 (OUTLIER) cc_final: 0.8584 (m-30) REVERT: H 89 ASP cc_start: 0.9240 (t0) cc_final: 0.8739 (t0) REVERT: H 108 GLN cc_start: 0.8947 (pt0) cc_final: 0.8214 (pt0) REVERT: H 114 GLU cc_start: 0.9162 (mp0) cc_final: 0.8560 (mp0) REVERT: H 127 MET cc_start: 0.9035 (ttp) cc_final: 0.8681 (tpp) REVERT: H 141 ARG cc_start: 0.9189 (mmm-85) cc_final: 0.8831 (mmm-85) REVERT: H 142 THR cc_start: 0.9556 (OUTLIER) cc_final: 0.9191 (p) outliers start: 27 outliers final: 15 residues processed: 267 average time/residue: 0.2842 time to fit residues: 97.6141 Evaluate side-chains 263 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 245 time to evaluate : 0.752 ------------------------------------------------------------------------------- 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 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain G residue 15 LYS Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 142 THR Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 80 optimal weight: 10.0000 chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 49 optimal weight: 2.9990 chunk 83 optimal weight: 8.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN B 25 ASN C 73 ASN C 94 ASN E 108 ASN E 113 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.035089 restraints weight = 58056.794| |-----------------------------------------------------------------------------| r_work (start): 0.2667 rms_B_bonded: 3.73 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.3070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11001 Z= 0.165 Angle : 0.611 8.123 15843 Z= 0.353 Chirality : 0.035 0.155 1815 Planarity : 0.004 0.052 1203 Dihedral : 30.286 178.321 3302 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 5.64 % Allowed : 35.38 % Favored : 58.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.32), residues: 691 helix: 1.82 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.18 (0.44), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.005 0.001 HIS E 113 PHE 0.010 0.001 PHE D 62 TYR 0.013 0.001 TYR F 98 ARG 0.007 0.001 ARG D 63 Details of bonding type rmsd hydrogen bonds : bond 0.03374 ( 676) hydrogen bonds : angle 3.15218 ( 1719) covalent geometry : bond 0.00363 (11001) covalent geometry : angle 0.61082 (15843) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 256 time to evaluate : 0.727 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: 0.9493 (tt0) cc_final: 0.9114 (pp20) REVERT: B 50 ILE cc_start: 0.9468 (mm) cc_final: 0.9170 (mm) REVERT: B 63 GLU cc_start: 0.9015 (mt-10) cc_final: 0.8537 (mt-10) REVERT: B 79 LYS cc_start: 0.8938 (mtpt) cc_final: 0.8604 (mtmt) REVERT: B 84 MET cc_start: 0.8841 (tpp) cc_final: 0.7973 (mmm) REVERT: C 25 PHE cc_start: 0.8649 (m-10) cc_final: 0.8261 (m-80) REVERT: C 38 ASN cc_start: 0.9224 (t0) cc_final: 0.8550 (t0) REVERT: C 39 TYR cc_start: 0.8671 (m-80) cc_final: 0.8419 (m-80) REVERT: C 57 TYR cc_start: 0.8398 (t80) cc_final: 0.7546 (t80) REVERT: C 61 GLU cc_start: 0.8944 (tt0) cc_final: 0.8506 (tt0) REVERT: C 62 ILE cc_start: 0.9422 (mt) cc_final: 0.9127 (tt) REVERT: C 77 ARG cc_start: 0.7450 (tpp80) cc_final: 0.7230 (tpp80) REVERT: C 92 GLU cc_start: 0.9232 (pp20) cc_final: 0.8927 (tt0) REVERT: C 94 ASN cc_start: 0.9373 (OUTLIER) cc_final: 0.8918 (t0) REVERT: C 99 ARG cc_start: 0.9067 (mmm160) cc_final: 0.8692 (mmp80) REVERT: C 104 GLN cc_start: 0.8487 (mp10) cc_final: 0.8131 (mp10) REVERT: D 62 PHE cc_start: 0.9427 (m-80) cc_final: 0.9129 (m-80) REVERT: D 84 ASP cc_start: 0.8800 (OUTLIER) cc_final: 0.8572 (m-30) REVERT: D 89 ASP cc_start: 0.9183 (t0) cc_final: 0.8879 (t0) REVERT: D 103 ARG cc_start: 0.8856 (mtm110) cc_final: 0.8470 (mtm-85) REVERT: D 107 ARG cc_start: 0.8906 (mtp85) cc_final: 0.8408 (mtp85) REVERT: D 126 GLN cc_start: 0.8333 (tp-100) cc_final: 0.7427 (tp-100) REVERT: D 136 THR cc_start: 0.9389 (m) cc_final: 0.9186 (p) REVERT: D 137 LYS cc_start: 0.9238 (mtmm) cc_final: 0.8769 (mtmm) REVERT: E 105 GLU cc_start: 0.9011 (tp30) cc_final: 0.8290 (tp30) REVERT: E 109 LEU cc_start: 0.9772 (OUTLIER) cc_final: 0.9429 (mm) REVERT: F 24 ASP cc_start: 0.9057 (t0) cc_final: 0.8829 (p0) REVERT: G 56 GLU cc_start: 0.8838 (tt0) cc_final: 0.8314 (tt0) REVERT: G 57 TYR cc_start: 0.8725 (t80) cc_final: 0.8088 (t80) REVERT: G 61 GLU cc_start: 0.9152 (tt0) cc_final: 0.8296 (tt0) REVERT: G 64 GLU cc_start: 0.8908 (tm-30) cc_final: 0.8472 (tm-30) REVERT: G 68 ASN cc_start: 0.9271 (m-40) cc_final: 0.8651 (m-40) REVERT: G 87 ILE cc_start: 0.9388 (tp) cc_final: 0.9165 (tp) REVERT: G 94 ASN cc_start: 0.9455 (t0) cc_final: 0.9202 (t0) REVERT: H 78 GLU cc_start: 0.9401 (mp0) cc_final: 0.9004 (mp0) REVERT: H 84 ASP cc_start: 0.9104 (OUTLIER) cc_final: 0.8524 (m-30) REVERT: H 89 ASP cc_start: 0.9288 (t0) cc_final: 0.8735 (t0) REVERT: H 108 GLN cc_start: 0.8782 (pt0) cc_final: 0.8406 (pt0) REVERT: H 114 GLU cc_start: 0.9160 (mp0) cc_final: 0.8537 (mp0) REVERT: H 127 MET cc_start: 0.9037 (ttp) cc_final: 0.8734 (tpp) REVERT: H 129 LYS cc_start: 0.9008 (mtmm) cc_final: 0.8689 (mtmm) REVERT: H 141 ARG cc_start: 0.9194 (mmm-85) cc_final: 0.8771 (mmm-85) outliers start: 33 outliers final: 17 residues processed: 271 average time/residue: 0.2884 time to fit residues: 100.7327 Evaluate side-chains 263 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.853 ------------------------------------------------------------------------------- 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 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 94 ASN Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 84 ASP Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 29 optimal weight: 10.0000 chunk 48 optimal weight: 7.9990 chunk 63 optimal weight: 0.9980 chunk 75 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.0370 chunk 47 optimal weight: 0.7980 chunk 86 optimal weight: 10.0000 overall best weight: 0.7058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 75 HIS ** C 84 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 = 0.3364 r_free = 0.3364 target = 0.053551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2867 r_free = 0.2867 target = 0.038470 restraints weight = 60552.972| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.64 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.3347 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= 0.153 Angle : 0.613 11.915 15843 Z= 0.351 Chirality : 0.034 0.167 1815 Planarity : 0.005 0.052 1203 Dihedral : 30.189 178.669 3302 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 11.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 4.27 % Allowed : 36.58 % Favored : 59.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.32), residues: 691 helix: 1.87 (0.23), residues: 530 sheet: None (None), residues: 0 loop : -1.16 (0.43), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP D 113 HIS 0.003 0.001 HIS F 75 PHE 0.009 0.001 PHE D 62 TYR 0.019 0.001 TYR F 98 ARG 0.009 0.001 ARG H 77 Details of bonding type rmsd hydrogen bonds : bond 0.03269 ( 676) hydrogen bonds : angle 3.01541 ( 1719) covalent geometry : bond 0.00333 (11001) covalent geometry : angle 0.61345 (15843) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 290 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 265 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9316 (mt) cc_final: 0.9074 (mm) REVERT: A 94 GLU cc_start: 0.9139 (tp30) cc_final: 0.8908 (tp30) REVERT: B 63 GLU cc_start: 0.9002 (mt-10) cc_final: 0.8415 (mt-10) REVERT: B 79 LYS cc_start: 0.8927 (OUTLIER) cc_final: 0.8495 (mtmm) REVERT: B 84 MET cc_start: 0.8785 (tpp) cc_final: 0.7952 (mmm) REVERT: C 25 PHE cc_start: 0.8645 (m-10) cc_final: 0.8282 (m-80) REVERT: C 32 ARG cc_start: 0.8888 (ttp80) cc_final: 0.8579 (ttp80) REVERT: C 35 ARG cc_start: 0.9526 (ttm110) cc_final: 0.8737 (mtt90) REVERT: C 38 ASN cc_start: 0.9229 (t0) cc_final: 0.8490 (t0) REVERT: C 39 TYR cc_start: 0.8804 (m-80) cc_final: 0.8603 (m-80) REVERT: C 42 ARG cc_start: 0.8059 (mtp180) cc_final: 0.7812 (mmm-85) REVERT: C 57 TYR cc_start: 0.8449 (t80) cc_final: 0.7610 (t80) REVERT: C 61 GLU cc_start: 0.8962 (tt0) cc_final: 0.8543 (tt0) REVERT: C 68 ASN cc_start: 0.9372 (m-40) cc_final: 0.9128 (m-40) REVERT: C 72 ASP cc_start: 0.9460 (t0) cc_final: 0.9250 (m-30) REVERT: C 77 ARG cc_start: 0.7155 (tpp80) cc_final: 0.6885 (tpp80) REVERT: C 89 ASN cc_start: 0.9422 (m-40) cc_final: 0.9189 (m110) REVERT: C 92 GLU cc_start: 0.9200 (pp20) cc_final: 0.8937 (tt0) REVERT: C 94 ASN cc_start: 0.9386 (t0) cc_final: 0.9039 (m-40) REVERT: C 99 ARG cc_start: 0.8956 (mmm160) cc_final: 0.8621 (mmp80) REVERT: C 104 GLN cc_start: 0.8552 (mp10) cc_final: 0.8172 (mp10) REVERT: D 62 PHE cc_start: 0.9407 (m-80) cc_final: 0.9148 (m-80) REVERT: D 63 ARG cc_start: 0.9652 (ttm110) cc_final: 0.9377 (ttm110) REVERT: D 77 ARG cc_start: 0.8426 (mmt-90) cc_final: 0.8096 (mmp80) REVERT: D 103 ARG cc_start: 0.8861 (mtm110) cc_final: 0.8428 (mtm-85) REVERT: D 107 ARG cc_start: 0.8829 (mtp85) cc_final: 0.8380 (mtp85) REVERT: D 126 GLN cc_start: 0.8316 (tp-100) cc_final: 0.7473 (tp-100) REVERT: D 136 THR cc_start: 0.9404 (m) cc_final: 0.9191 (p) REVERT: D 137 LYS cc_start: 0.9234 (mtmm) cc_final: 0.8817 (mtmm) REVERT: E 68 GLN cc_start: 0.9226 (tt0) cc_final: 0.8964 (tm-30) REVERT: E 73 GLU cc_start: 0.9480 (tm-30) cc_final: 0.9001 (tt0) REVERT: E 105 GLU cc_start: 0.8949 (tp30) cc_final: 0.8342 (tp30) REVERT: E 133 GLU cc_start: 0.8711 (pm20) cc_final: 0.8413 (pm20) REVERT: F 43 VAL cc_start: 0.9535 (t) cc_final: 0.9335 (p) REVERT: G 39 TYR cc_start: 0.9434 (m-80) cc_final: 0.8846 (m-80) REVERT: G 56 GLU cc_start: 0.8734 (tt0) cc_final: 0.8197 (tt0) REVERT: G 57 TYR cc_start: 0.8741 (t80) cc_final: 0.8077 (t80) REVERT: G 61 GLU cc_start: 0.9123 (tt0) cc_final: 0.8180 (tt0) REVERT: G 64 GLU cc_start: 0.8842 (tm-30) cc_final: 0.8352 (tm-30) REVERT: G 68 ASN cc_start: 0.9269 (m-40) cc_final: 0.8623 (m-40) REVERT: G 87 ILE cc_start: 0.9398 (tp) cc_final: 0.9174 (tp) REVERT: G 91 GLU cc_start: 0.9005 (pm20) cc_final: 0.8749 (pm20) REVERT: H 68 GLN cc_start: 0.9440 (tm-30) cc_final: 0.9232 (tm-30) REVERT: H 77 ARG cc_start: 0.9120 (ttm110) cc_final: 0.8538 (ptp-110) REVERT: H 78 GLU cc_start: 0.9407 (mp0) cc_final: 0.8926 (mp0) REVERT: H 84 ASP cc_start: 0.9094 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: H 89 ASP cc_start: 0.9272 (t0) cc_final: 0.8740 (t0) REVERT: H 108 GLN cc_start: 0.8831 (pt0) cc_final: 0.8588 (pt0) REVERT: H 114 GLU cc_start: 0.9142 (mp0) cc_final: 0.8514 (mp0) REVERT: H 127 MET cc_start: 0.8972 (ttp) cc_final: 0.8692 (tpp) REVERT: H 129 LYS cc_start: 0.8970 (mtmm) cc_final: 0.8653 (mtmm) REVERT: H 132 GLU cc_start: 0.8735 (tt0) cc_final: 0.8418 (tp30) REVERT: H 141 ARG cc_start: 0.9171 (mmm-85) cc_final: 0.8769 (mmm-85) outliers start: 25 outliers final: 16 residues processed: 278 average time/residue: 0.2764 time to fit residues: 99.5126 Evaluate side-chains 271 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 253 time to evaluate : 0.768 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 25 ASN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 25 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 66 optimal weight: 0.7980 chunk 23 optimal weight: 10.0000 chunk 44 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 68 optimal weight: 10.0000 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 113 HIS C 84 GLN D 100 HIS E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.049350 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2728 r_free = 0.2728 target = 0.034909 restraints weight = 58555.717| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.81 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.3523 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= 0.180 Angle : 0.624 8.289 15843 Z= 0.358 Chirality : 0.035 0.167 1815 Planarity : 0.005 0.050 1203 Dihedral : 30.211 178.033 3302 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.47 % Allowed : 36.92 % Favored : 57.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.91 (0.32), residues: 691 helix: 1.98 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.22 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.001 TRP H 113 HIS 0.005 0.001 HIS D 100 PHE 0.007 0.001 PHE D 62 TYR 0.032 0.002 TYR F 98 ARG 0.005 0.000 ARG C 71 Details of bonding type rmsd hydrogen bonds : bond 0.03557 ( 676) hydrogen bonds : angle 3.09064 ( 1719) covalent geometry : bond 0.00401 (11001) covalent geometry : angle 0.62385 (15843) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 280 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 248 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9260 (pt0) cc_final: 0.9015 (pp20) REVERT: A 94 GLU cc_start: 0.9197 (tp30) cc_final: 0.8985 (tp30) REVERT: B 63 GLU cc_start: 0.8970 (mt-10) cc_final: 0.8343 (mt-10) REVERT: B 79 LYS cc_start: 0.8951 (OUTLIER) cc_final: 0.8505 (mtmm) REVERT: B 84 MET cc_start: 0.8850 (tpp) cc_final: 0.8003 (mmm) REVERT: C 25 PHE cc_start: 0.8709 (m-10) cc_final: 0.8298 (m-80) REVERT: C 32 ARG cc_start: 0.8876 (ttp80) cc_final: 0.8386 (ttp-170) REVERT: C 35 ARG cc_start: 0.9551 (ttm110) cc_final: 0.9272 (ttm110) REVERT: C 38 ASN cc_start: 0.9284 (t0) cc_final: 0.8548 (t0) REVERT: C 39 TYR cc_start: 0.8810 (m-80) cc_final: 0.8587 (m-80) REVERT: C 42 ARG cc_start: 0.8086 (mtp180) cc_final: 0.7846 (mmm-85) REVERT: C 57 TYR cc_start: 0.8446 (t80) cc_final: 0.7818 (t80) REVERT: C 68 ASN cc_start: 0.9430 (m-40) cc_final: 0.9108 (m-40) REVERT: C 72 ASP cc_start: 0.9574 (t0) cc_final: 0.9283 (m-30) REVERT: C 77 ARG cc_start: 0.7122 (tpp80) cc_final: 0.6815 (tpp80) REVERT: C 89 ASN cc_start: 0.9446 (m-40) cc_final: 0.9220 (m110) REVERT: C 94 ASN cc_start: 0.9362 (t0) cc_final: 0.9067 (m-40) REVERT: C 99 ARG cc_start: 0.8916 (mmm160) cc_final: 0.8712 (mmp80) REVERT: C 104 GLN cc_start: 0.8566 (mp10) cc_final: 0.8189 (mp10) REVERT: D 62 PHE cc_start: 0.9423 (m-80) cc_final: 0.9217 (m-80) REVERT: D 77 ARG cc_start: 0.8453 (mmt-90) cc_final: 0.8120 (mmp80) REVERT: D 107 ARG cc_start: 0.8790 (mtp85) cc_final: 0.8312 (mtp85) REVERT: D 137 LYS cc_start: 0.9191 (mtmm) cc_final: 0.8735 (mtmm) REVERT: E 73 GLU cc_start: 0.9488 (tm-30) cc_final: 0.9145 (tt0) REVERT: E 105 GLU cc_start: 0.9007 (tp30) cc_final: 0.8408 (tp30) REVERT: E 120 MET cc_start: 0.8854 (mmm) cc_final: 0.8359 (mmm) REVERT: E 133 GLU cc_start: 0.8795 (pm20) cc_final: 0.8310 (pm20) REVERT: G 39 TYR cc_start: 0.9492 (m-80) cc_final: 0.8985 (m-80) REVERT: G 56 GLU cc_start: 0.8792 (tt0) cc_final: 0.8310 (tt0) REVERT: G 57 TYR cc_start: 0.8725 (t80) cc_final: 0.8518 (t80) REVERT: G 61 GLU cc_start: 0.9140 (tt0) cc_final: 0.8904 (tt0) REVERT: G 64 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8367 (tm-30) REVERT: G 68 ASN cc_start: 0.9267 (m-40) cc_final: 0.8631 (m110) REVERT: G 87 ILE cc_start: 0.9404 (tp) cc_final: 0.9141 (tp) REVERT: G 91 GLU cc_start: 0.9102 (pm20) cc_final: 0.8805 (pm20) REVERT: G 94 ASN cc_start: 0.9374 (t0) cc_final: 0.9154 (t0) REVERT: H 77 ARG cc_start: 0.9101 (ttm110) cc_final: 0.8476 (ptp-110) REVERT: H 78 GLU cc_start: 0.9409 (mp0) cc_final: 0.8946 (mp0) REVERT: H 84 ASP cc_start: 0.9090 (OUTLIER) cc_final: 0.8494 (m-30) REVERT: H 89 ASP cc_start: 0.9306 (t0) cc_final: 0.8763 (t0) REVERT: H 108 GLN cc_start: 0.8832 (pt0) cc_final: 0.8602 (pt0) REVERT: H 114 GLU cc_start: 0.9147 (mp0) cc_final: 0.8649 (mp0) REVERT: H 129 LYS cc_start: 0.9008 (mtmm) cc_final: 0.8704 (mtmm) REVERT: H 141 ARG cc_start: 0.9213 (mmm-85) cc_final: 0.8846 (mmm-85) outliers start: 32 outliers final: 22 residues processed: 263 average time/residue: 0.2787 time to fit residues: 95.4141 Evaluate side-chains 262 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 238 time to evaluate : 0.824 ------------------------------------------------------------------------------- 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 C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain H residue 147 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 62 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 83 optimal weight: 9.9990 chunk 86 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 6 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 chunk 45 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 84 optimal weight: 8.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.049046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.034557 restraints weight = 59782.261| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 3.89 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.3617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11001 Z= 0.189 Angle : 0.644 11.485 15843 Z= 0.366 Chirality : 0.035 0.175 1815 Planarity : 0.005 0.049 1203 Dihedral : 30.266 178.094 3302 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.30 % Allowed : 38.29 % Favored : 56.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.32), residues: 691 helix: 1.95 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.21 (0.42), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE D 62 TYR 0.020 0.002 TYR F 98 ARG 0.006 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03599 ( 676) hydrogen bonds : angle 3.14513 ( 1719) covalent geometry : bond 0.00422 (11001) covalent geometry : angle 0.64365 (15843) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 237 time to evaluate : 0.861 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8689 (m-10) cc_final: 0.8428 (m-80) REVERT: A 94 GLU cc_start: 0.9147 (tp30) cc_final: 0.8939 (tp30) REVERT: B 63 GLU cc_start: 0.8976 (mt-10) cc_final: 0.8305 (mt-10) REVERT: B 79 LYS cc_start: 0.8976 (OUTLIER) cc_final: 0.8765 (mtpt) REVERT: B 84 MET cc_start: 0.8814 (tpp) cc_final: 0.7952 (mmm) REVERT: C 25 PHE cc_start: 0.8738 (m-10) cc_final: 0.8285 (m-80) REVERT: C 32 ARG cc_start: 0.8850 (ttp80) cc_final: 0.8371 (ttp-170) REVERT: C 35 ARG cc_start: 0.9547 (ttm110) cc_final: 0.9257 (ttm110) REVERT: C 38 ASN cc_start: 0.9278 (t0) cc_final: 0.8558 (t0) REVERT: C 57 TYR cc_start: 0.8442 (t80) cc_final: 0.7773 (t80) REVERT: C 68 ASN cc_start: 0.9427 (m-40) cc_final: 0.9071 (m-40) REVERT: C 72 ASP cc_start: 0.9601 (t0) cc_final: 0.9288 (m-30) REVERT: C 77 ARG cc_start: 0.7115 (tpp80) cc_final: 0.6797 (tpp80) REVERT: C 89 ASN cc_start: 0.9445 (m-40) cc_final: 0.9163 (m110) REVERT: C 94 ASN cc_start: 0.9369 (t0) cc_final: 0.9060 (m-40) REVERT: C 104 GLN cc_start: 0.8621 (mp10) cc_final: 0.8240 (mp10) REVERT: D 77 ARG cc_start: 0.8490 (mmt-90) cc_final: 0.8138 (mmp80) REVERT: D 107 ARG cc_start: 0.8712 (mtp85) cc_final: 0.8314 (mtp85) REVERT: D 134 GLU cc_start: 0.9379 (tp30) cc_final: 0.9165 (tp30) REVERT: E 73 GLU cc_start: 0.9509 (tm-30) cc_final: 0.9122 (tt0) REVERT: E 105 GLU cc_start: 0.9034 (tp30) cc_final: 0.8435 (tp30) REVERT: E 128 ARG cc_start: 0.9479 (mmm-85) cc_final: 0.9127 (mmm-85) REVERT: E 133 GLU cc_start: 0.8844 (pm20) cc_final: 0.8258 (pm20) REVERT: F 30 THR cc_start: 0.9004 (OUTLIER) cc_final: 0.8795 (p) REVERT: F 44 LYS cc_start: 0.9585 (mtpt) cc_final: 0.9360 (mtpp) REVERT: F 53 GLU cc_start: 0.9328 (tp30) cc_final: 0.9106 (tp30) REVERT: G 56 GLU cc_start: 0.8802 (tt0) cc_final: 0.8315 (tt0) REVERT: G 57 TYR cc_start: 0.8740 (t80) cc_final: 0.8064 (t80) REVERT: G 61 GLU cc_start: 0.9080 (tt0) cc_final: 0.8256 (tt0) REVERT: G 64 GLU cc_start: 0.8916 (tm-30) cc_final: 0.8388 (tm-30) REVERT: G 68 ASN cc_start: 0.9272 (m-40) cc_final: 0.8636 (m110) REVERT: G 87 ILE cc_start: 0.9410 (tp) cc_final: 0.9172 (tp) REVERT: G 93 LEU cc_start: 0.9545 (OUTLIER) cc_final: 0.9323 (mm) REVERT: G 94 ASN cc_start: 0.9403 (t0) cc_final: 0.9191 (t0) REVERT: H 77 ARG cc_start: 0.9089 (ttm110) cc_final: 0.8375 (ptp90) REVERT: H 78 GLU cc_start: 0.9416 (mp0) cc_final: 0.8930 (mp0) REVERT: H 84 ASP cc_start: 0.9100 (OUTLIER) cc_final: 0.8502 (m-30) REVERT: H 89 ASP cc_start: 0.9312 (t0) cc_final: 0.8756 (t0) REVERT: H 108 GLN cc_start: 0.8780 (pt0) cc_final: 0.8525 (pt0) REVERT: H 114 GLU cc_start: 0.9149 (mp0) cc_final: 0.8647 (mp0) REVERT: H 127 MET cc_start: 0.9106 (ttp) cc_final: 0.8727 (tpp) REVERT: H 129 LYS cc_start: 0.9049 (mtmm) cc_final: 0.8746 (mtmm) REVERT: H 132 GLU cc_start: 0.8746 (tt0) cc_final: 0.8417 (tp30) REVERT: H 141 ARG cc_start: 0.9233 (mmm-85) cc_final: 0.8875 (mmm-85) outliers start: 31 outliers final: 22 residues processed: 252 average time/residue: 0.2814 time to fit residues: 91.9237 Evaluate side-chains 255 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 229 time to evaluate : 0.738 ------------------------------------------------------------------------------- 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 C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU 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 93 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 123 LEU Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 7 optimal weight: 4.9990 chunk 16 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 15 optimal weight: 5.9990 chunk 76 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.9980 chunk 56 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 9 optimal weight: 0.8980 overall best weight: 2.7784 ------------------------------------------------------------------------------- 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 E 108 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.048348 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.033972 restraints weight = 58943.266| |-----------------------------------------------------------------------------| r_work (start): 0.2646 rms_B_bonded: 3.84 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3722 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11001 Z= 0.202 Angle : 0.655 8.795 15843 Z= 0.373 Chirality : 0.036 0.179 1815 Planarity : 0.005 0.044 1203 Dihedral : 30.363 177.998 3302 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 5.64 % Allowed : 39.32 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.32), residues: 691 helix: 1.92 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.23 (0.42), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE D 58 TYR 0.016 0.002 TYR G 39 ARG 0.009 0.001 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03790 ( 676) hydrogen bonds : angle 3.27880 ( 1719) covalent geometry : bond 0.00451 (11001) covalent geometry : angle 0.65531 (15843) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 227 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 GLU cc_start: 0.8975 (mt-10) cc_final: 0.8266 (mt-10) REVERT: B 79 LYS cc_start: 0.8986 (mtpt) cc_final: 0.8635 (mtmt) REVERT: C 25 PHE cc_start: 0.8747 (m-10) cc_final: 0.8192 (m-80) REVERT: C 38 ASN cc_start: 0.9351 (t0) cc_final: 0.8702 (t0) REVERT: C 57 TYR cc_start: 0.8414 (t80) cc_final: 0.7819 (t80) REVERT: C 61 GLU cc_start: 0.8938 (tt0) cc_final: 0.8600 (tt0) REVERT: C 68 ASN cc_start: 0.9445 (m-40) cc_final: 0.9133 (m-40) REVERT: C 72 ASP cc_start: 0.9598 (t0) cc_final: 0.9314 (m-30) REVERT: C 89 ASN cc_start: 0.9456 (m-40) cc_final: 0.9197 (m110) REVERT: C 94 ASN cc_start: 0.9341 (t0) cc_final: 0.9023 (m-40) REVERT: C 104 GLN cc_start: 0.8617 (mp10) cc_final: 0.8247 (mp10) REVERT: D 103 ARG cc_start: 0.8820 (mtm110) cc_final: 0.8429 (mtm-85) REVERT: D 107 ARG cc_start: 0.8713 (mtp85) cc_final: 0.8368 (mtp85) REVERT: D 129 LYS cc_start: 0.8853 (mtmm) cc_final: 0.8613 (mttm) REVERT: E 105 GLU cc_start: 0.9032 (tp30) cc_final: 0.8387 (tp30) REVERT: E 128 ARG cc_start: 0.9428 (mmm-85) cc_final: 0.9044 (mmm-85) REVERT: E 133 GLU cc_start: 0.8804 (pm20) cc_final: 0.8212 (pm20) REVERT: F 30 THR cc_start: 0.9033 (OUTLIER) cc_final: 0.8828 (p) REVERT: F 44 LYS cc_start: 0.9609 (mtpt) cc_final: 0.9403 (mtpp) REVERT: F 79 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8093 (mmmm) REVERT: G 56 GLU cc_start: 0.8878 (tt0) cc_final: 0.8390 (tt0) REVERT: G 57 TYR cc_start: 0.8736 (t80) cc_final: 0.7586 (t80) REVERT: G 61 GLU cc_start: 0.9123 (tt0) cc_final: 0.8477 (tt0) REVERT: G 64 GLU cc_start: 0.8922 (tm-30) cc_final: 0.8385 (tm-30) REVERT: G 68 ASN cc_start: 0.9282 (m-40) cc_final: 0.8646 (m110) REVERT: G 87 ILE cc_start: 0.9404 (tp) cc_final: 0.9183 (tp) REVERT: G 93 LEU cc_start: 0.9538 (OUTLIER) cc_final: 0.9328 (mm) REVERT: H 77 ARG cc_start: 0.9074 (ttm110) cc_final: 0.8470 (ptp90) REVERT: H 78 GLU cc_start: 0.9429 (mp0) cc_final: 0.8998 (mp0) REVERT: H 84 ASP cc_start: 0.9096 (OUTLIER) cc_final: 0.8508 (m-30) REVERT: H 89 ASP cc_start: 0.9319 (t0) cc_final: 0.8772 (t0) REVERT: H 114 GLU cc_start: 0.9147 (mp0) cc_final: 0.8617 (mp0) REVERT: H 127 MET cc_start: 0.9116 (ttp) cc_final: 0.8591 (mmm) REVERT: H 129 LYS cc_start: 0.9035 (mtmm) cc_final: 0.8729 (mtmm) REVERT: H 132 GLU cc_start: 0.8763 (tt0) cc_final: 0.8411 (tp30) REVERT: H 141 ARG cc_start: 0.9270 (mmm-85) cc_final: 0.8912 (mmm-85) outliers start: 33 outliers final: 24 residues processed: 241 average time/residue: 0.2588 time to fit residues: 82.5667 Evaluate side-chains 253 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 225 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU 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 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 104 SER Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 108 ASN Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain F residue 30 THR 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 F residue 98 TYR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Chi-restraints excluded: chain H residue 147 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 58 optimal weight: 0.1980 chunk 70 optimal weight: 10.0000 chunk 19 optimal weight: 0.9980 chunk 87 optimal weight: 10.0000 chunk 34 optimal weight: 3.9990 chunk 26 optimal weight: 7.9990 chunk 73 optimal weight: 10.0000 chunk 51 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 32 optimal weight: 10.0000 overall best weight: 2.2386 ------------------------------------------------------------------------------- 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 ** 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 = 0.3220 r_free = 0.3220 target = 0.048600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.034291 restraints weight = 59774.331| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 3.86 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.3841 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11001 Z= 0.188 Angle : 0.676 11.651 15843 Z= 0.379 Chirality : 0.036 0.197 1815 Planarity : 0.005 0.046 1203 Dihedral : 30.363 178.228 3302 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 14.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 4.96 % Allowed : 41.03 % Favored : 54.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.32), residues: 691 helix: 1.89 (0.23), residues: 531 sheet: None (None), residues: 0 loop : -1.10 (0.44), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE D 58 TYR 0.018 0.002 TYR H 61 ARG 0.008 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03647 ( 676) hydrogen bonds : angle 3.26366 ( 1719) covalent geometry : bond 0.00421 (11001) covalent geometry : angle 0.67585 (15843) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 260 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 231 time to evaluate : 0.751 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: 0.9053 (m-30) cc_final: 0.8532 (m-30) REVERT: B 63 GLU cc_start: 0.8925 (mt-10) cc_final: 0.8149 (mp0) REVERT: B 79 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8649 (mtmt) REVERT: B 84 MET cc_start: 0.8805 (tpp) cc_final: 0.7913 (mmm) REVERT: C 25 PHE cc_start: 0.8752 (m-10) cc_final: 0.8256 (m-80) REVERT: C 38 ASN cc_start: 0.9375 (t0) cc_final: 0.8774 (t0) REVERT: C 57 TYR cc_start: 0.8464 (t80) cc_final: 0.7799 (t80) REVERT: C 61 GLU cc_start: 0.8986 (tt0) cc_final: 0.8594 (tt0) REVERT: C 68 ASN cc_start: 0.9431 (m-40) cc_final: 0.8952 (m-40) REVERT: C 72 ASP cc_start: 0.9614 (t0) cc_final: 0.9289 (m-30) REVERT: C 89 ASN cc_start: 0.9452 (m-40) cc_final: 0.9167 (m110) REVERT: C 94 ASN cc_start: 0.9317 (t0) cc_final: 0.9023 (m-40) REVERT: C 104 GLN cc_start: 0.8631 (mp10) cc_final: 0.8261 (mp10) REVERT: D 77 ARG cc_start: 0.8538 (mmt180) cc_final: 0.8222 (mmp80) REVERT: D 103 ARG cc_start: 0.8844 (mtm110) cc_final: 0.8446 (mtm-85) REVERT: D 129 LYS cc_start: 0.8804 (mtmm) cc_final: 0.8573 (mttm) REVERT: E 68 GLN cc_start: 0.9248 (tt0) cc_final: 0.8987 (tm-30) REVERT: E 73 GLU cc_start: 0.9572 (tm-30) cc_final: 0.8919 (tt0) REVERT: E 105 GLU cc_start: 0.9055 (tp30) cc_final: 0.8284 (tp30) REVERT: E 128 ARG cc_start: 0.9404 (mmm-85) cc_final: 0.9018 (mmm-85) REVERT: E 133 GLU cc_start: 0.8779 (pm20) cc_final: 0.8170 (pm20) REVERT: F 30 THR cc_start: 0.9015 (OUTLIER) cc_final: 0.8806 (p) REVERT: F 44 LYS cc_start: 0.9601 (mtpt) cc_final: 0.9399 (mtpp) REVERT: F 79 LYS cc_start: 0.8542 (OUTLIER) cc_final: 0.8104 (mmmm) REVERT: G 55 LEU cc_start: 0.9680 (mp) cc_final: 0.9417 (mt) REVERT: G 56 GLU cc_start: 0.8887 (tt0) cc_final: 0.8347 (tt0) REVERT: G 57 TYR cc_start: 0.8768 (t80) cc_final: 0.7586 (t80) REVERT: G 61 GLU cc_start: 0.9109 (tt0) cc_final: 0.8456 (tt0) REVERT: G 64 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8366 (tm-30) REVERT: G 68 ASN cc_start: 0.9260 (m-40) cc_final: 0.8617 (m110) REVERT: G 87 ILE cc_start: 0.9404 (tp) cc_final: 0.9182 (tp) REVERT: H 77 ARG cc_start: 0.9057 (ttm110) cc_final: 0.8493 (ptp90) REVERT: H 78 GLU cc_start: 0.9445 (mp0) cc_final: 0.8971 (mp0) REVERT: H 84 ASP cc_start: 0.9128 (OUTLIER) cc_final: 0.8559 (m-30) REVERT: H 89 ASP cc_start: 0.9346 (t0) cc_final: 0.8854 (t0) REVERT: H 127 MET cc_start: 0.9156 (ttp) cc_final: 0.8607 (mmm) REVERT: H 129 LYS cc_start: 0.9039 (mtmm) cc_final: 0.8716 (mtmm) REVERT: H 132 GLU cc_start: 0.8784 (tt0) cc_final: 0.8398 (tp30) REVERT: H 141 ARG cc_start: 0.9269 (mmm-85) cc_final: 0.8989 (mmm-85) outliers start: 29 outliers final: 20 residues processed: 244 average time/residue: 0.2548 time to fit residues: 81.9469 Evaluate side-chains 248 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 224 time to evaluate : 0.750 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER 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 79 LYS Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 98 TYR Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 144 LEU Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 23 optimal weight: 0.0060 chunk 64 optimal weight: 5.9990 chunk 65 optimal weight: 2.9990 chunk 61 optimal weight: 0.8980 chunk 29 optimal weight: 8.9990 chunk 69 optimal weight: 10.0000 chunk 30 optimal weight: 5.9990 chunk 59 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 78 optimal weight: 10.0000 overall best weight: 1.9802 ------------------------------------------------------------------------------- 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 ** 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 = 0.3225 r_free = 0.3225 target = 0.048781 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.034367 restraints weight = 58938.817| |-----------------------------------------------------------------------------| r_work (start): 0.2660 rms_B_bonded: 3.87 r_work (final): 0.2660 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8686 moved from start: 0.3964 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 : 0.691 11.889 15843 Z= 0.384 Chirality : 0.036 0.176 1815 Planarity : 0.005 0.048 1203 Dihedral : 30.344 178.300 3302 Min Nonbonded Distance : 2.416 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.44 % Allowed : 41.37 % Favored : 54.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.80 (0.32), residues: 691 helix: 1.85 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.09 (0.44), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP H 113 HIS 0.003 0.001 HIS F 75 PHE 0.007 0.001 PHE D 58 TYR 0.017 0.002 TYR G 39 ARG 0.008 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03628 ( 676) hydrogen bonds : angle 3.23594 ( 1719) covalent geometry : bond 0.00412 (11001) covalent geometry : angle 0.69129 (15843) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1382 Ramachandran restraints generated. 691 Oldfield, 0 Emsley, 691 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 252 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 226 time to evaluate : 0.793 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9499 (OUTLIER) cc_final: 0.9020 (pp20) REVERT: A 123 ASP cc_start: 0.9040 (m-30) cc_final: 0.8514 (m-30) REVERT: B 63 GLU cc_start: 0.8909 (mt-10) cc_final: 0.8125 (mp0) REVERT: B 79 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8637 (mtmt) REVERT: B 84 MET cc_start: 0.8758 (tpp) cc_final: 0.7820 (mmm) REVERT: C 25 PHE cc_start: 0.8740 (m-10) cc_final: 0.8253 (m-80) REVERT: C 38 ASN cc_start: 0.9387 (t0) cc_final: 0.8801 (t0) REVERT: C 57 TYR cc_start: 0.8477 (t80) cc_final: 0.7797 (t80) REVERT: C 61 GLU cc_start: 0.9027 (tt0) cc_final: 0.8610 (tt0) REVERT: C 68 ASN cc_start: 0.9440 (m-40) cc_final: 0.9085 (m-40) REVERT: C 72 ASP cc_start: 0.9622 (t0) cc_final: 0.9332 (m-30) REVERT: C 89 ASN cc_start: 0.9442 (m-40) cc_final: 0.9168 (m110) REVERT: C 94 ASN cc_start: 0.9315 (t0) cc_final: 0.9028 (m-40) REVERT: C 104 GLN cc_start: 0.8648 (mp10) cc_final: 0.8271 (mp10) REVERT: D 77 ARG cc_start: 0.8535 (mmt180) cc_final: 0.8262 (mmp80) REVERT: D 103 ARG cc_start: 0.8841 (mtm110) cc_final: 0.8436 (mtm-85) REVERT: D 107 ARG cc_start: 0.8686 (mtp85) cc_final: 0.8380 (mtp85) REVERT: D 127 MET cc_start: 0.9212 (mtm) cc_final: 0.8813 (mpp) REVERT: D 129 LYS cc_start: 0.8846 (mtmm) cc_final: 0.8631 (mttp) REVERT: E 68 GLN cc_start: 0.9241 (tt0) cc_final: 0.8978 (tm-30) REVERT: E 73 GLU cc_start: 0.9580 (tm-30) cc_final: 0.8931 (tt0) REVERT: E 105 GLU cc_start: 0.9056 (tp30) cc_final: 0.8418 (tp30) REVERT: E 128 ARG cc_start: 0.9365 (mmm-85) cc_final: 0.8962 (mmm-85) REVERT: E 133 GLU cc_start: 0.8736 (pm20) cc_final: 0.8104 (pm20) REVERT: F 30 THR cc_start: 0.8991 (OUTLIER) cc_final: 0.8784 (p) REVERT: F 44 LYS cc_start: 0.9591 (mtpt) cc_final: 0.9389 (mtpp) REVERT: G 56 GLU cc_start: 0.8865 (tt0) cc_final: 0.8343 (tt0) REVERT: G 57 TYR cc_start: 0.8778 (t80) cc_final: 0.7601 (t80) REVERT: G 61 GLU cc_start: 0.9130 (tt0) cc_final: 0.8440 (tt0) REVERT: G 64 GLU cc_start: 0.8918 (tm-30) cc_final: 0.8371 (tm-30) REVERT: G 68 ASN cc_start: 0.9276 (m-40) cc_final: 0.8641 (m110) REVERT: G 87 ILE cc_start: 0.9379 (tp) cc_final: 0.9142 (tp) REVERT: G 93 LEU cc_start: 0.9525 (OUTLIER) cc_final: 0.9301 (mm) REVERT: H 77 ARG cc_start: 0.9069 (ttm110) cc_final: 0.8493 (ptp90) REVERT: H 78 GLU cc_start: 0.9406 (mp0) cc_final: 0.8936 (mp0) REVERT: H 84 ASP cc_start: 0.9119 (OUTLIER) cc_final: 0.8567 (m-30) REVERT: H 89 ASP cc_start: 0.9325 (t0) cc_final: 0.8846 (t0) REVERT: H 127 MET cc_start: 0.9147 (ttp) cc_final: 0.8604 (mmm) REVERT: H 129 LYS cc_start: 0.9025 (mtmm) cc_final: 0.8739 (mtmm) REVERT: H 141 ARG cc_start: 0.9324 (mmm-85) cc_final: 0.8976 (mmm-85) outliers start: 26 outliers final: 19 residues processed: 237 average time/residue: 0.2638 time to fit residues: 82.4083 Evaluate side-chains 253 residues out of total 585 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 229 time to evaluate : 0.805 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 GLU Chi-restraints excluded: chain A residue 101 VAL Chi-restraints excluded: chain A residue 113 HIS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 80 VAL Chi-restraints excluded: chain D residue 87 VAL Chi-restraints excluded: chain D residue 114 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 87 SER 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 F residue 98 TYR Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain H residue 84 ASP Chi-restraints excluded: chain H residue 145 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 89 random chunks: chunk 5 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 85 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 81 optimal weight: 8.9990 chunk 40 optimal weight: 0.8980 chunk 12 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 14 optimal weight: 2.9990 chunk 30 optimal weight: 3.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN C 84 GLN D 100 HIS E 108 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.049070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.034856 restraints weight = 58523.910| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 3.86 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8683 moved from start: 0.4043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 11001 Z= 0.174 Angle : 0.687 11.845 15843 Z= 0.384 Chirality : 0.036 0.229 1815 Planarity : 0.005 0.048 1203 Dihedral : 30.316 178.392 3302 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 4.79 % Allowed : 41.88 % Favored : 53.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.73 (0.32), residues: 691 helix: 1.81 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -1.17 (0.43), residues: 159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 113 HIS 0.004 0.001 HIS D 100 PHE 0.005 0.001 PHE D 58 TYR 0.018 0.002 TYR H 61 ARG 0.007 0.000 ARG D 141 Details of bonding type rmsd hydrogen bonds : bond 0.03520 ( 676) hydrogen bonds : angle 3.21457 ( 1719) covalent geometry : bond 0.00392 (11001) covalent geometry : angle 0.68685 (15843) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3738.60 seconds wall clock time: 65 minutes 37.40 seconds (3937.40 seconds total)