Starting phenix.real_space_refine on Wed Aug 5 19:25:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jc6_61358/08_2026/9jc6_61358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jc6_61358/08_2026/9jc6_61358.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.34 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9jc6_61358/08_2026/9jc6_61358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jc6_61358/08_2026/9jc6_61358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jc6_61358/08_2026/9jc6_61358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jc6_61358/08_2026/9jc6_61358.map" } resolution = 3.34 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.024 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 263 5.49 5 S 20 5.16 5 C 6321 2.51 5 N 2139 2.21 5 O 2626 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11369 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 796 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 796 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "D" Number of atoms: 743 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 743 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "E" Number of atoms: 799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 799 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 668 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "G" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 696 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 696 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 3, 'TRANS': 87} Chain: "I" Number of atoms: 2688 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2688 Classifications: {'DNA': 132} Link IDs: {'rna3p': 131} Chain: "J" Number of atoms: 2721 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 2721 Classifications: {'DNA': 132} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 131} Time building chain proxies: 2.39, per 1000 atoms: 0.21 Number of scatterers: 11369 At special positions: 0 Unit cell: (85.86, 116.6, 116.6, 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 20 16.00 P 263 15.00 O 2626 8.00 N 2139 7.00 C 6321 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.68 Conformation dependent library (CDL) restraints added in 249.1 milliseconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1402 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 71.7% alpha, 1.9% beta 133 base pairs and 221 stacking pairs defined. Time for finding SS restraints: 1.11 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 23 through 29 removed outlier: 3.862A pdb=" N ILE B 26 " --> pdb=" O ARG B 23 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 77 Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 38 removed outlier: 3.514A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN C 38 " --> pdb=" O LEU C 34 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 72 Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU C 115 " --> pdb=" O GLN C 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 63 through 68 removed outlier: 3.976A pdb=" N LEU D 67 " --> pdb=" O PHE D 63 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N LYS D 68 " --> pdb=" O PRO D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 68' Processing helix chain 'D' and resid 77 through 106 removed outlier: 4.186A pdb=" N SER D 82 " --> pdb=" O GLN D 78 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLU D 98 " --> pdb=" O ARG D 94 " (cutoff:3.500A) Processing helix chain 'D' and resid 112 through 124 removed outlier: 3.871A pdb=" N ARG D 121 " --> pdb=" O GLN D 117 " (cutoff:3.500A) Processing helix chain 'D' and resid 125 through 146 removed outlier: 3.542A pdb=" N LEU D 131 " --> pdb=" O LYS D 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 53 removed outlier: 3.679A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE E 51 " --> pdb=" O ALA E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.965A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (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: 4.107A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.553A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 98 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 62 through 69 removed outlier: 3.625A pdb=" N GLN H 69 " --> pdb=" O ARG H 65 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 104 Processing helix chain 'H' and resid 112 through 124 Processing helix chain 'H' and resid 125 through 146 removed outlier: 3.651A pdb=" N CYS H 146 " --> pdb=" O ARG H 142 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA2, first strand: chain 'B' and resid 96 through 97 removed outlier: 7.021A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.308A pdb=" N ARG C 42 " --> pdb=" O ILE D 111 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 101 removed outlier: 3.587A pdb=" N THR C 101 " --> pdb=" O THR F 96 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.546A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.721A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 384 hydrogen bonds defined for protein. 1128 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 340 hydrogen bonds 672 hydrogen bond angles 0 basepair planarities 133 basepair parallelities 221 stacking parallelities Total time for adding SS restraints: 1.80 Time building geometry restraints manager: 0.95 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: 2371 1.33 - 1.45: 3697 1.45 - 1.57: 5478 1.57 - 1.69: 525 1.69 - 1.81: 34 Bond restraints: 12105 Sorted by residual: bond pdb=" C3' DA J -38 " pdb=" C2' DA J -38 " ideal model delta sigma weight residual 1.516 1.543 -0.027 8.00e-03 1.56e+04 1.15e+01 bond pdb=" C3' DG I -1 " pdb=" C2' DG I -1 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DC I 4 " pdb=" C2' DC I 4 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.05e+01 bond pdb=" C3' DG J -6 " pdb=" C2' DG J -6 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 1.00e+01 bond pdb=" C3' DC I 21 " pdb=" C2' DC I 21 " ideal model delta sigma weight residual 1.516 1.540 -0.024 8.00e-03 1.56e+04 9.05e+00 ... (remaining 12100 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.16: 15370 1.16 - 2.32: 1750 2.32 - 3.48: 323 3.48 - 4.64: 22 4.64 - 5.81: 16 Bond angle restraints: 17481 Sorted by residual: angle pdb=" O4' DG I 26 " pdb=" C4' DG I 26 " pdb=" C3' DG I 26 " ideal model delta sigma weight residual 106.00 102.81 3.19 6.00e-01 2.78e+00 2.83e+01 angle pdb=" O4' DA I 17 " pdb=" C4' DA I 17 " pdb=" C3' DA I 17 " ideal model delta sigma weight residual 106.00 103.21 2.79 6.00e-01 2.78e+00 2.16e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.62 -2.72 6.00e-01 2.78e+00 2.06e+01 angle pdb=" O4' DC I -20 " pdb=" C4' DC I -20 " pdb=" C3' DC I -20 " ideal model delta sigma weight residual 106.00 103.28 2.72 6.00e-01 2.78e+00 2.05e+01 angle pdb=" O4' DC J -26 " pdb=" C4' DC J -26 " pdb=" C3' DC J -26 " ideal model delta sigma weight residual 106.00 103.33 2.67 6.00e-01 2.78e+00 1.99e+01 ... (remaining 17476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.63: 5279 35.63 - 71.27: 1305 71.27 - 106.90: 21 106.90 - 142.53: 2 142.53 - 178.17: 1 Dihedral angle restraints: 6608 sinusoidal: 4437 harmonic: 2171 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.17 -178.17 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 48 " pdb=" C3' DG J 48 " pdb=" O3' DG J 48 " pdb=" P DC J 49 " ideal model delta sinusoidal sigma weight residual -140.00 -0.47 -139.53 1 3.50e+01 8.16e-04 1.38e+01 dihedral pdb=" CA ASP H 85 " pdb=" CB ASP H 85 " pdb=" CG ASP H 85 " pdb=" OD1 ASP H 85 " ideal model delta sinusoidal sigma weight residual -30.00 -88.37 58.37 1 2.00e+01 2.50e-03 1.14e+01 ... (remaining 6605 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1421 0.043 - 0.085: 442 0.085 - 0.128: 124 0.128 - 0.171: 7 0.171 - 0.213: 1 Chirality restraints: 1995 Sorted by residual: chirality pdb=" CB ILE D 111 " pdb=" CA ILE D 111 " pdb=" CG1 ILE D 111 " pdb=" CG2 ILE D 111 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" P DC J 49 " pdb=" OP1 DC J 49 " pdb=" OP2 DC J 49 " pdb=" O5' DC J 49 " both_signs ideal model delta sigma weight residual True 2.34 -2.49 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.18e-01 ... (remaining 1992 not shown) Planarity restraints: 1303 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC I -50 " 0.005 2.00e-02 2.50e+03 1.98e-02 8.80e+00 pdb=" N1 DC I -50 " -0.014 2.00e-02 2.50e+03 pdb=" C2 DC I -50 " 0.048 2.00e-02 2.50e+03 pdb=" O2 DC I -50 " -0.029 2.00e-02 2.50e+03 pdb=" N3 DC I -50 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC I -50 " 0.008 2.00e-02 2.50e+03 pdb=" N4 DC I -50 " -0.006 2.00e-02 2.50e+03 pdb=" C5 DC I -50 " -0.005 2.00e-02 2.50e+03 pdb=" C6 DC I -50 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 51 " 0.002 2.00e-02 2.50e+03 1.15e-02 4.00e+00 pdb=" N9 DG J 51 " 0.007 2.00e-02 2.50e+03 pdb=" C8 DG J 51 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 51 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG J 51 " -0.001 2.00e-02 2.50e+03 pdb=" C6 DG J 51 " -0.009 2.00e-02 2.50e+03 pdb=" O6 DG J 51 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DG J 51 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG J 51 " -0.031 2.00e-02 2.50e+03 pdb=" N2 DG J 51 " 0.020 2.00e-02 2.50e+03 pdb=" N3 DG J 51 " -0.000 2.00e-02 2.50e+03 pdb=" C4 DG J 51 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 62 " -0.007 2.00e-02 2.50e+03 1.40e-02 1.95e+00 pdb=" C LEU B 62 " 0.024 2.00e-02 2.50e+03 pdb=" O LEU B 62 " -0.009 2.00e-02 2.50e+03 pdb=" N GLU B 63 " -0.008 2.00e-02 2.50e+03 ... (remaining 1300 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.25: 5 2.25 - 2.91: 4313 2.91 - 3.57: 19938 3.57 - 4.24: 30956 4.24 - 4.90: 44296 Nonbonded interactions: 99508 Sorted by model distance: nonbonded pdb=" NE2 GLN D 101 " pdb=" OH TYR D 105 " model vdw 1.585 3.120 nonbonded pdb=" N2 DG I 71 " pdb=" O2 DC J -71 " model vdw 2.104 2.496 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.127 3.040 nonbonded pdb=" OG1 THR G 76 " pdb=" OP1 DG I 58 " model vdw 2.185 3.040 nonbonded pdb=" OG SER C 40 " pdb=" O VAL D 109 " model vdw 2.189 3.040 ... (remaining 99503 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 'A' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } 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 117) } ncs_group { reference = (chain 'D' and resid 56 through 146) selection = chain 'H' } 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: 0.490 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: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 10.480 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8542 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 12105 Z= 0.515 Angle : 0.771 5.805 17481 Z= 0.685 Chirality : 0.044 0.213 1995 Planarity : 0.003 0.034 1303 Dihedral : 28.617 178.165 5206 Min Nonbonded Distance : 1.585 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.20 (0.27), residues: 737 helix: -0.67 (0.20), residues: 504 sheet: None (None), residues: 0 loop : -3.13 (0.36), residues: 233 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 81 TYR 0.009 0.001 TYR F 51 PHE 0.005 0.001 PHE E 104 TRP 0.002 0.001 TRP D 149 HIS 0.004 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00587 / 0.51 (12105) covalent geometry : angle 0.77052 / 0.68 (17481) hydrogen bonds : bond 0.10889 / 7.28 ( 724) hydrogen bonds : angle 4.48238 / 3.15 ( 1800) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 266 time to evaluate : 0.223 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9007 (pm20) cc_final: 0.8747 (pm20) REVERT: A 68 GLN cc_start: 0.8975 (tm-30) cc_final: 0.8258 (tm-30) REVERT: A 79 LYS cc_start: 0.8553 (tttt) cc_final: 0.8341 (ttmm) REVERT: A 93 GLN cc_start: 0.9128 (tp40) cc_final: 0.8558 (tp40) REVERT: A 110 CYS cc_start: 0.8953 (t) cc_final: 0.8506 (t) REVERT: B 44 LYS cc_start: 0.8826 (ttmt) cc_final: 0.8573 (ttmm) REVERT: B 59 LYS cc_start: 0.9182 (ttmt) cc_final: 0.8706 (tttm) REVERT: B 63 GLU cc_start: 0.9212 (mt-10) cc_final: 0.8738 (mt-10) REVERT: B 74 GLU cc_start: 0.9253 (tp30) cc_final: 0.9031 (tp30) REVERT: C 16 THR cc_start: 0.9661 (p) cc_final: 0.9306 (p) REVERT: C 20 ARG cc_start: 0.9189 (ttm170) cc_final: 0.8674 (ttm110) REVERT: C 36 LYS cc_start: 0.9368 (tmtt) cc_final: 0.8725 (tptt) REVERT: C 56 GLU cc_start: 0.8827 (tt0) cc_final: 0.8617 (tt0) REVERT: C 57 TYR cc_start: 0.8823 (t80) cc_final: 0.8447 (t80) REVERT: C 73 ASN cc_start: 0.9642 (t0) cc_final: 0.9125 (t0) REVERT: C 75 LYS cc_start: 0.9001 (mttm) cc_final: 0.8791 (mmmm) REVERT: C 84 GLN cc_start: 0.9593 (tp40) cc_final: 0.8957 (tp40) REVERT: C 102 ILE cc_start: 0.9524 (mp) cc_final: 0.9273 (mp) REVERT: D 65 ARG cc_start: 0.8856 (ptm-80) cc_final: 0.8643 (ptp-170) REVERT: D 78 GLN cc_start: 0.9490 (tp40) cc_final: 0.9109 (tp40) REVERT: D 90 ASP cc_start: 0.9158 (t70) cc_final: 0.8953 (t0) REVERT: D 117 GLN cc_start: 0.8682 (tm-30) cc_final: 0.7887 (tm-30) REVERT: D 118 MET cc_start: 0.9390 (mmt) cc_final: 0.8824 (mmm) REVERT: D 142 ARG cc_start: 0.9409 (mtt90) cc_final: 0.9149 (ptp-110) REVERT: E 59 GLU cc_start: 0.8910 (pm20) cc_final: 0.8690 (pm20) REVERT: E 60 LEU cc_start: 0.9326 (mt) cc_final: 0.8956 (mt) REVERT: E 85 GLN cc_start: 0.9478 (mt0) cc_final: 0.8538 (mt0) REVERT: E 105 GLU cc_start: 0.8501 (pp20) cc_final: 0.8174 (pp20) REVERT: E 106 ASP cc_start: 0.8806 (m-30) cc_final: 0.8126 (m-30) REVERT: E 133 GLU cc_start: 0.9080 (pm20) cc_final: 0.8851 (pm20) REVERT: E 134 ARG cc_start: 0.8557 (mmp-170) cc_final: 0.8260 (tpp-160) REVERT: F 22 LEU cc_start: 0.8412 (tt) cc_final: 0.8183 (tp) REVERT: F 44 LYS cc_start: 0.9261 (mtpt) cc_final: 0.8729 (mtpp) REVERT: F 79 LYS cc_start: 0.9165 (mttp) cc_final: 0.8886 (mtmm) REVERT: F 85 ASP cc_start: 0.9228 (m-30) cc_final: 0.8989 (m-30) REVERT: F 88 TYR cc_start: 0.9449 (m-10) cc_final: 0.9134 (m-80) REVERT: G 36 LYS cc_start: 0.9686 (tttt) cc_final: 0.9441 (ttmm) REVERT: G 56 GLU cc_start: 0.8884 (tt0) cc_final: 0.8528 (tt0) REVERT: G 61 GLU cc_start: 0.9191 (tp30) cc_final: 0.8939 (tp30) REVERT: G 64 GLU cc_start: 0.8710 (tm-30) cc_final: 0.8135 (tm-30) REVERT: H 69 GLN cc_start: 0.9489 (pt0) cc_final: 0.9186 (pp30) REVERT: H 101 GLN cc_start: 0.8527 (pp30) cc_final: 0.6948 (pp30) REVERT: H 105 TYR cc_start: 0.8398 (m-10) cc_final: 0.6444 (m-10) REVERT: H 118 MET cc_start: 0.9143 (mmt) cc_final: 0.8909 (mmm) REVERT: H 138 ASN cc_start: 0.9589 (m-40) cc_final: 0.9367 (m110) REVERT: H 142 ARG cc_start: 0.9510 (ttm-80) cc_final: 0.8738 (ttm110) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1077 time to fit residues: 38.4690 Evaluate side-chains 236 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 0.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.4980 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 8.9990 chunk 65 optimal weight: 0.9990 chunk 62 optimal weight: 0.4980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 6.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 30.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 39 HIS D 104 HIS D 135 GLN D 150 GLN F 27 GLN G 84 GLN H 104 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.073693 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.046053 restraints weight = 48614.974| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 3.73 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.1246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 12105 Z= 0.176 Angle : 0.731 8.334 17481 Z= 0.420 Chirality : 0.046 0.239 1995 Planarity : 0.005 0.046 1303 Dihedral : 31.791 176.532 3719 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 1.92 % Allowed : 17.76 % Favored : 80.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.59 (0.31), residues: 737 helix: 0.51 (0.22), residues: 513 sheet: None (None), residues: 0 loop : -2.50 (0.41), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 32 TYR 0.024 0.002 TYR B 88 PHE 0.006 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.18 (12105) covalent geometry : angle 0.73078 / 0.42 (17481) hydrogen bonds : bond 0.06116 / 4.25 ( 724) hydrogen bonds : angle 3.81388 / 2.66 ( 1800) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 273 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 261 time to evaluate : 0.200 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 59 GLU cc_start: 0.9155 (pm20) cc_final: 0.8877 (pm20) REVERT: A 73 GLU cc_start: 0.8372 (mm-30) cc_final: 0.7584 (tt0) REVERT: A 93 GLN cc_start: 0.9097 (tp40) cc_final: 0.8857 (tp40) REVERT: A 97 GLU cc_start: 0.8863 (mm-30) cc_final: 0.8633 (mm-30) REVERT: A 110 CYS cc_start: 0.8484 (t) cc_final: 0.8078 (t) REVERT: B 44 LYS cc_start: 0.9080 (ttmt) cc_final: 0.8847 (ttmm) REVERT: B 59 LYS cc_start: 0.9152 (ttmt) cc_final: 0.8639 (tttm) REVERT: B 63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8713 (mt-10) REVERT: C 25 PHE cc_start: 0.8621 (m-80) cc_final: 0.8218 (m-80) REVERT: C 36 LYS cc_start: 0.9345 (tmtt) cc_final: 0.8622 (tptt) REVERT: C 56 GLU cc_start: 0.8834 (tt0) cc_final: 0.8546 (tt0) REVERT: C 73 ASN cc_start: 0.9525 (t0) cc_final: 0.9306 (t0) REVERT: C 84 GLN cc_start: 0.9477 (tp40) cc_final: 0.8847 (tp40) REVERT: C 99 ARG cc_start: 0.8766 (mmm160) cc_final: 0.8356 (mmp80) REVERT: C 102 ILE cc_start: 0.9371 (mp) cc_final: 0.9044 (mp) REVERT: C 104 GLN cc_start: 0.8344 (mp10) cc_final: 0.8019 (mp10) REVERT: D 65 ARG cc_start: 0.8961 (ptm-80) cc_final: 0.8556 (ptt180) REVERT: D 117 GLN cc_start: 0.8672 (tm-30) cc_final: 0.7868 (tm-30) REVERT: D 118 MET cc_start: 0.9364 (mmt) cc_final: 0.8854 (mmm) REVERT: D 127 LYS cc_start: 0.9555 (tppt) cc_final: 0.9223 (tppt) REVERT: D 128 MET cc_start: 0.9446 (mtt) cc_final: 0.9189 (mtt) REVERT: E 59 GLU cc_start: 0.8766 (pm20) cc_final: 0.8549 (pm20) REVERT: E 73 GLU cc_start: 0.9159 (tt0) cc_final: 0.8678 (tt0) REVERT: E 79 LYS cc_start: 0.8723 (tttt) cc_final: 0.8361 (ttmt) REVERT: E 105 GLU cc_start: 0.8562 (pp20) cc_final: 0.8152 (pp20) REVERT: E 106 ASP cc_start: 0.8993 (m-30) cc_final: 0.8265 (m-30) REVERT: F 44 LYS cc_start: 0.9217 (mtpt) cc_final: 0.9007 (mtpp) REVERT: F 74 GLU cc_start: 0.9489 (tp30) cc_final: 0.9003 (tp30) REVERT: F 77 LYS cc_start: 0.9556 (mttp) cc_final: 0.9349 (mtpp) REVERT: F 79 LYS cc_start: 0.9180 (mttp) cc_final: 0.8850 (mtmm) REVERT: F 85 ASP cc_start: 0.9317 (m-30) cc_final: 0.9048 (m-30) REVERT: F 88 TYR cc_start: 0.9397 (m-10) cc_final: 0.9074 (m-80) REVERT: G 36 LYS cc_start: 0.9713 (tttt) cc_final: 0.9402 (ttmm) REVERT: G 56 GLU cc_start: 0.8914 (tt0) cc_final: 0.8528 (tt0) REVERT: G 61 GLU cc_start: 0.9181 (tp30) cc_final: 0.8819 (tp30) REVERT: G 64 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8155 (tm-30) REVERT: G 87 ILE cc_start: 0.9168 (tp) cc_final: 0.8953 (tp) REVERT: H 69 GLN cc_start: 0.9515 (pt0) cc_final: 0.9185 (pp30) REVERT: H 85 ASP cc_start: 0.9306 (t0) cc_final: 0.8797 (t0) REVERT: H 101 GLN cc_start: 0.8524 (pp30) cc_final: 0.7612 (pp30) REVERT: H 104 HIS cc_start: 0.9040 (t70) cc_final: 0.8464 (t-90) REVERT: H 105 TYR cc_start: 0.8481 (m-10) cc_final: 0.6815 (m-10) REVERT: H 118 MET cc_start: 0.9282 (mmt) cc_final: 0.8952 (mmm) REVERT: H 127 LYS cc_start: 0.9616 (mmmm) cc_final: 0.9390 (mmmm) REVERT: H 128 MET cc_start: 0.9476 (mtt) cc_final: 0.9117 (mtt) REVERT: H 142 ARG cc_start: 0.9411 (ttm-80) cc_final: 0.8625 (ttm110) outliers start: 12 outliers final: 8 residues processed: 263 average time/residue: 0.1002 time to fit residues: 35.9847 Evaluate side-chains 246 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 238 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 86 optimal weight: 40.0000 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 5 optimal weight: 1.9990 chunk 35 optimal weight: 10.0000 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 8.9990 chunk 84 optimal weight: 50.0000 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 104 HIS G 94 ASN H 138 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.073538 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.046050 restraints weight = 48774.117| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.71 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 12105 Z= 0.168 Angle : 0.714 8.345 17481 Z= 0.410 Chirality : 0.046 0.241 1995 Planarity : 0.005 0.057 1303 Dihedral : 31.717 176.227 3719 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 13.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 3.20 % Allowed : 22.08 % Favored : 74.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.31), residues: 737 helix: 0.86 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -2.34 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 129 TYR 0.023 0.002 TYR C 39 PHE 0.006 0.001 PHE E 67 TRP 0.001 0.000 TRP D 149 HIS 0.007 0.002 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.17 (12105) covalent geometry : angle 0.71399 / 0.41 (17481) hydrogen bonds : bond 0.05787 / 4.05 ( 724) hydrogen bonds : angle 3.63712 / 2.54 ( 1800) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 269 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 249 time to evaluate : 0.292 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9017 (pm20) cc_final: 0.8746 (pm20) REVERT: A 73 GLU cc_start: 0.8324 (mm-30) cc_final: 0.7537 (tt0) REVERT: A 79 LYS cc_start: 0.8860 (ttmm) cc_final: 0.8411 (tttp) REVERT: A 93 GLN cc_start: 0.9036 (tp40) cc_final: 0.8645 (tp40) REVERT: B 44 LYS cc_start: 0.9120 (ttmt) cc_final: 0.8752 (ttmt) REVERT: B 59 LYS cc_start: 0.9196 (ttmt) cc_final: 0.8665 (tttm) REVERT: B 63 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8695 (mt-10) REVERT: B 74 GLU cc_start: 0.9470 (tp30) cc_final: 0.9241 (tp30) REVERT: C 25 PHE cc_start: 0.8660 (m-80) cc_final: 0.8192 (m-80) REVERT: C 36 LYS cc_start: 0.9223 (tmtt) cc_final: 0.8569 (tptt) REVERT: C 56 GLU cc_start: 0.8868 (tt0) cc_final: 0.8589 (tt0) REVERT: C 57 TYR cc_start: 0.8731 (t80) cc_final: 0.8443 (t80) REVERT: C 72 ASP cc_start: 0.9248 (p0) cc_final: 0.8956 (p0) REVERT: C 73 ASN cc_start: 0.9541 (t0) cc_final: 0.9198 (t0) REVERT: C 84 GLN cc_start: 0.9522 (tp40) cc_final: 0.8966 (tp40) REVERT: C 99 ARG cc_start: 0.8769 (mmm160) cc_final: 0.8413 (mmp80) REVERT: C 102 ILE cc_start: 0.9451 (mp) cc_final: 0.9158 (mp) REVERT: C 104 GLN cc_start: 0.8434 (mp10) cc_final: 0.7747 (mp10) REVERT: D 65 ARG cc_start: 0.9092 (ptm-80) cc_final: 0.8733 (ptp-170) REVERT: D 78 GLN cc_start: 0.9363 (tp40) cc_final: 0.9037 (mm-40) REVERT: D 87 MET cc_start: 0.9051 (ttp) cc_final: 0.8796 (ttp) REVERT: D 117 GLN cc_start: 0.8730 (tm-30) cc_final: 0.7863 (tm-30) REVERT: D 118 MET cc_start: 0.9352 (mmt) cc_final: 0.8767 (mmm) REVERT: D 127 LYS cc_start: 0.9566 (tppt) cc_final: 0.9209 (tppt) REVERT: D 128 MET cc_start: 0.9408 (mtt) cc_final: 0.9105 (mtt) REVERT: D 142 ARG cc_start: 0.9499 (mtt90) cc_final: 0.9246 (mtt-85) REVERT: E 59 GLU cc_start: 0.8730 (pm20) cc_final: 0.8529 (pm20) REVERT: E 73 GLU cc_start: 0.9159 (tt0) cc_final: 0.8535 (tt0) REVERT: E 79 LYS cc_start: 0.8656 (tttt) cc_final: 0.8318 (ttmt) REVERT: E 105 GLU cc_start: 0.8531 (pp20) cc_final: 0.8156 (pp20) REVERT: E 106 ASP cc_start: 0.8996 (m-30) cc_final: 0.8280 (m-30) REVERT: F 44 LYS cc_start: 0.9238 (mtpt) cc_final: 0.9035 (mtpp) REVERT: F 74 GLU cc_start: 0.9475 (tp30) cc_final: 0.8977 (tp30) REVERT: F 79 LYS cc_start: 0.9137 (mttp) cc_final: 0.8821 (mtmm) REVERT: F 85 ASP cc_start: 0.9334 (m-30) cc_final: 0.9100 (m-30) REVERT: F 88 TYR cc_start: 0.9371 (m-10) cc_final: 0.9092 (m-80) REVERT: F 98 TYR cc_start: 0.8563 (m-80) cc_final: 0.7626 (m-80) REVERT: G 35 ARG cc_start: 0.9563 (ttp-110) cc_final: 0.9098 (ttm110) REVERT: G 36 LYS cc_start: 0.9710 (tttt) cc_final: 0.9385 (ttmm) REVERT: G 56 GLU cc_start: 0.8870 (tt0) cc_final: 0.8479 (tt0) REVERT: G 61 GLU cc_start: 0.9194 (tp30) cc_final: 0.8838 (tp30) REVERT: G 64 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8175 (tm-30) REVERT: G 87 ILE cc_start: 0.9249 (tp) cc_final: 0.8918 (tp) REVERT: G 90 ASP cc_start: 0.8528 (t0) cc_final: 0.8017 (t0) REVERT: G 92 GLU cc_start: 0.9055 (pm20) cc_final: 0.8834 (pm20) REVERT: H 69 GLN cc_start: 0.9484 (pt0) cc_final: 0.9157 (pp30) REVERT: H 101 GLN cc_start: 0.8709 (pp30) cc_final: 0.7752 (pp30) REVERT: H 104 HIS cc_start: 0.9009 (t70) cc_final: 0.8380 (t-90) REVERT: H 105 TYR cc_start: 0.8578 (m-10) cc_final: 0.6981 (m-10) REVERT: H 118 MET cc_start: 0.9280 (mmt) cc_final: 0.8946 (mmm) REVERT: H 142 ARG cc_start: 0.9423 (ttm-80) cc_final: 0.8629 (ttm110) outliers start: 20 outliers final: 10 residues processed: 259 average time/residue: 0.0964 time to fit residues: 34.7252 Evaluate side-chains 249 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 239 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 4.9990 chunk 69 optimal weight: 0.8980 chunk 25 optimal weight: 9.9990 chunk 74 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 24 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 37 optimal weight: 5.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN G 94 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.073863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.046164 restraints weight = 47282.429| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 3.74 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8543 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 12105 Z= 0.162 Angle : 0.695 7.350 17481 Z= 0.401 Chirality : 0.045 0.242 1995 Planarity : 0.005 0.058 1303 Dihedral : 31.636 176.023 3719 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.80 % Allowed : 22.72 % Favored : 72.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.20 (0.31), residues: 737 helix: 1.09 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.29 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 88 TYR 0.026 0.002 TYR F 98 PHE 0.007 0.001 PHE E 67 TRP 0.001 0.000 TRP D 149 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.16 (12105) covalent geometry : angle 0.69461 / 0.40 (17481) hydrogen bonds : bond 0.05525 / 3.89 ( 724) hydrogen bonds : angle 3.53703 / 2.47 ( 1800) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 266 time to evaluate : 0.233 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 59 GLU cc_start: 0.8865 (OUTLIER) cc_final: 0.8586 (pm20) REVERT: A 79 LYS cc_start: 0.8943 (ttmm) cc_final: 0.8499 (tttp) REVERT: A 93 GLN cc_start: 0.8958 (tp40) cc_final: 0.8384 (tp40) REVERT: B 37 LEU cc_start: 0.9540 (OUTLIER) cc_final: 0.9253 (mp) REVERT: B 59 LYS cc_start: 0.9171 (ttmt) cc_final: 0.8715 (tttm) REVERT: B 63 GLU cc_start: 0.9290 (mt-10) cc_final: 0.8824 (mt-10) REVERT: B 88 TYR cc_start: 0.9267 (m-10) cc_final: 0.8878 (m-80) REVERT: C 17 ARG cc_start: 0.8879 (mtm180) cc_final: 0.8525 (mtm180) REVERT: C 20 ARG cc_start: 0.9008 (ttm170) cc_final: 0.8529 (ttm110) REVERT: C 25 PHE cc_start: 0.8652 (m-80) cc_final: 0.8113 (m-80) REVERT: C 35 ARG cc_start: 0.9536 (ttp-110) cc_final: 0.9036 (ttm110) REVERT: C 36 LYS cc_start: 0.9162 (tmtt) cc_final: 0.8854 (tptp) REVERT: C 56 GLU cc_start: 0.8833 (tt0) cc_final: 0.8421 (tt0) REVERT: C 57 TYR cc_start: 0.8701 (t80) cc_final: 0.8386 (t80) REVERT: C 72 ASP cc_start: 0.9291 (p0) cc_final: 0.9010 (p0) REVERT: C 73 ASN cc_start: 0.9537 (t0) cc_final: 0.9186 (t0) REVERT: C 77 ARG cc_start: 0.8682 (tpp80) cc_final: 0.8064 (mmm-85) REVERT: C 84 GLN cc_start: 0.9491 (tp40) cc_final: 0.8944 (tp40) REVERT: C 99 ARG cc_start: 0.8757 (mmm160) cc_final: 0.8317 (mmp80) REVERT: C 102 ILE cc_start: 0.9319 (mp) cc_final: 0.9023 (mp) REVERT: D 65 ARG cc_start: 0.9095 (ptm-80) cc_final: 0.8743 (ptp-170) REVERT: D 75 SER cc_start: 0.8245 (m) cc_final: 0.6968 (t) REVERT: D 78 GLN cc_start: 0.9345 (tp40) cc_final: 0.9025 (mm-40) REVERT: D 87 MET cc_start: 0.8979 (ttp) cc_final: 0.8727 (ttp) REVERT: D 117 GLN cc_start: 0.8661 (tm-30) cc_final: 0.7850 (tm-30) REVERT: D 118 MET cc_start: 0.9322 (mmt) cc_final: 0.8768 (mmm) REVERT: D 127 LYS cc_start: 0.9563 (tppt) cc_final: 0.9251 (tppt) REVERT: E 59 GLU cc_start: 0.8647 (pm20) cc_final: 0.8342 (pm20) REVERT: E 73 GLU cc_start: 0.9101 (tt0) cc_final: 0.8548 (tt0) REVERT: E 79 LYS cc_start: 0.8618 (tttt) cc_final: 0.8247 (ttmt) REVERT: E 105 GLU cc_start: 0.8534 (pp20) cc_final: 0.8172 (pp20) REVERT: E 106 ASP cc_start: 0.9092 (m-30) cc_final: 0.8368 (m-30) REVERT: E 120 MET cc_start: 0.8780 (mmm) cc_final: 0.8407 (mmm) REVERT: F 74 GLU cc_start: 0.9507 (tp30) cc_final: 0.9003 (tp30) REVERT: F 79 LYS cc_start: 0.9103 (mttp) cc_final: 0.8863 (mtmm) REVERT: F 85 ASP cc_start: 0.9313 (m-30) cc_final: 0.9087 (m-30) REVERT: F 88 TYR cc_start: 0.9353 (m-10) cc_final: 0.9050 (m-80) REVERT: F 98 TYR cc_start: 0.8283 (m-80) cc_final: 0.7342 (m-80) REVERT: G 36 LYS cc_start: 0.9670 (tttt) cc_final: 0.9351 (ttmm) REVERT: G 56 GLU cc_start: 0.8881 (tt0) cc_final: 0.8587 (tt0) REVERT: G 61 GLU cc_start: 0.9173 (tp30) cc_final: 0.8651 (tp30) REVERT: G 64 GLU cc_start: 0.8773 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 87 ILE cc_start: 0.9253 (tp) cc_final: 0.9025 (tp) REVERT: G 90 ASP cc_start: 0.8503 (t0) cc_final: 0.8283 (t0) REVERT: H 62 TYR cc_start: 0.9404 (m-80) cc_final: 0.8889 (m-80) REVERT: H 69 GLN cc_start: 0.9517 (pt0) cc_final: 0.9146 (pp30) REVERT: H 85 ASP cc_start: 0.9332 (t0) cc_final: 0.8795 (t0) REVERT: H 101 GLN cc_start: 0.8642 (pp30) cc_final: 0.7733 (pp30) REVERT: H 105 TYR cc_start: 0.8549 (m-10) cc_final: 0.6804 (m-10) REVERT: H 118 MET cc_start: 0.9270 (mmt) cc_final: 0.8944 (mmm) REVERT: H 142 ARG cc_start: 0.9416 (ttm-80) cc_final: 0.8585 (ttm110) outliers start: 30 outliers final: 16 residues processed: 281 average time/residue: 0.1047 time to fit residues: 39.5668 Evaluate side-chains 268 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 250 time to evaluate : 0.261 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 76 optimal weight: 20.0000 chunk 25 optimal weight: 20.0000 chunk 32 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 40.0000 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 5.9990 chunk 23 optimal weight: 6.9990 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 104 HIS E 68 GLN H 89 HIS H 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.074207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.046051 restraints weight = 47749.669| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 3.68 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8605 moved from start: 0.1932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 12105 Z= 0.283 Angle : 0.776 7.703 17481 Z= 0.435 Chirality : 0.047 0.236 1995 Planarity : 0.005 0.063 1303 Dihedral : 31.693 175.070 3719 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 16.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.02 % Favored : 94.98 % Rotamer: Outliers : 6.40 % Allowed : 22.72 % Favored : 70.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.31 (0.31), residues: 737 helix: 1.11 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.07 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 92 TYR 0.024 0.002 TYR C 39 PHE 0.012 0.001 PHE E 104 TRP 0.001 0.001 TRP D 149 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00586 / 0.28 (12105) covalent geometry : angle 0.77590 / 0.43 (17481) hydrogen bonds : bond 0.06687 / 4.63 ( 724) hydrogen bonds : angle 3.80330 / 2.64 ( 1800) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 232 time to evaluate : 0.181 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8617 (pm20) REVERT: A 73 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7403 (tt0) REVERT: A 93 GLN cc_start: 0.9079 (tp40) cc_final: 0.8423 (tp40) REVERT: A 105 GLU cc_start: 0.8915 (OUTLIER) cc_final: 0.8681 (pp20) REVERT: B 59 LYS cc_start: 0.9222 (ttmt) cc_final: 0.8849 (ttpp) REVERT: B 63 GLU cc_start: 0.9271 (mt-10) cc_final: 0.8835 (mt-10) REVERT: B 88 TYR cc_start: 0.9294 (m-10) cc_final: 0.8562 (m-10) REVERT: C 17 ARG cc_start: 0.8979 (mtm180) cc_final: 0.8576 (mtm180) REVERT: C 20 ARG cc_start: 0.9120 (ttm170) cc_final: 0.8621 (ttm110) REVERT: C 25 PHE cc_start: 0.8715 (m-80) cc_final: 0.8161 (m-80) REVERT: C 36 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8593 (tptt) REVERT: C 42 ARG cc_start: 0.7828 (ptp-170) cc_final: 0.7533 (ptm160) REVERT: C 56 GLU cc_start: 0.8916 (tt0) cc_final: 0.8633 (tt0) REVERT: C 57 TYR cc_start: 0.8795 (t80) cc_final: 0.8544 (t80) REVERT: C 72 ASP cc_start: 0.9321 (p0) cc_final: 0.9044 (p0) REVERT: C 73 ASN cc_start: 0.9499 (t0) cc_final: 0.9157 (t0) REVERT: C 84 GLN cc_start: 0.9513 (tp40) cc_final: 0.8954 (tp40) REVERT: C 99 ARG cc_start: 0.8786 (mmm160) cc_final: 0.8333 (mmp80) REVERT: C 102 ILE cc_start: 0.9362 (mp) cc_final: 0.9063 (mp) REVERT: D 57 ASP cc_start: 0.7326 (t0) cc_final: 0.6979 (t0) REVERT: D 65 ARG cc_start: 0.9206 (ptm-80) cc_final: 0.8819 (ptp-170) REVERT: D 68 LYS cc_start: 0.9443 (mppt) cc_final: 0.9048 (mmtm) REVERT: D 87 MET cc_start: 0.9001 (ttp) cc_final: 0.8733 (ttp) REVERT: D 117 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8272 (tm-30) REVERT: D 118 MET cc_start: 0.9372 (mmt) cc_final: 0.8880 (mmm) REVERT: D 127 LYS cc_start: 0.9608 (tppt) cc_final: 0.9381 (tppt) REVERT: E 59 GLU cc_start: 0.8741 (pm20) cc_final: 0.8416 (pm20) REVERT: E 73 GLU cc_start: 0.9178 (tt0) cc_final: 0.8516 (tt0) REVERT: E 105 GLU cc_start: 0.8526 (pp20) cc_final: 0.8173 (pp20) REVERT: E 106 ASP cc_start: 0.9034 (m-30) cc_final: 0.8406 (m-30) REVERT: E 120 MET cc_start: 0.8762 (mmm) cc_final: 0.8380 (mmm) REVERT: F 74 GLU cc_start: 0.9490 (tp30) cc_final: 0.9127 (tp30) REVERT: F 79 LYS cc_start: 0.9143 (mttp) cc_final: 0.8849 (mtmm) REVERT: F 85 ASP cc_start: 0.9342 (m-30) cc_final: 0.9116 (m-30) REVERT: F 88 TYR cc_start: 0.9415 (m-10) cc_final: 0.9072 (m-80) REVERT: F 98 TYR cc_start: 0.8540 (m-80) cc_final: 0.7716 (m-80) REVERT: G 36 LYS cc_start: 0.9717 (tttt) cc_final: 0.9349 (ttmm) REVERT: G 56 GLU cc_start: 0.8861 (tt0) cc_final: 0.8647 (tt0) REVERT: G 61 GLU cc_start: 0.9214 (tp30) cc_final: 0.8868 (tp30) REVERT: G 64 GLU cc_start: 0.8833 (tm-30) cc_final: 0.8241 (tm-30) REVERT: G 87 ILE cc_start: 0.9318 (tp) cc_final: 0.9106 (tp) REVERT: H 69 GLN cc_start: 0.9556 (pt0) cc_final: 0.9200 (pp30) REVERT: H 104 HIS cc_start: 0.9038 (t70) cc_final: 0.8485 (t-90) REVERT: H 105 TYR cc_start: 0.8532 (m-10) cc_final: 0.7455 (m-10) REVERT: H 118 MET cc_start: 0.9242 (mmt) cc_final: 0.8989 (mmm) REVERT: H 142 ARG cc_start: 0.9501 (ttm-80) cc_final: 0.8699 (ttm110) outliers start: 40 outliers final: 28 residues processed: 251 average time/residue: 0.1074 time to fit residues: 36.2983 Evaluate side-chains 257 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 0.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 116 ILE Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 55 optimal weight: 3.9990 chunk 28 optimal weight: 8.9990 chunk 59 optimal weight: 4.9990 chunk 27 optimal weight: 2.9990 chunk 82 optimal weight: 50.0000 chunk 71 optimal weight: 50.0000 chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 4 optimal weight: 5.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 7.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.075483 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.046985 restraints weight = 47260.011| |-----------------------------------------------------------------------------| r_work (start): 0.2730 rms_B_bonded: 3.74 r_work (final): 0.2730 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2036 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 12105 Z= 0.188 Angle : 0.726 8.561 17481 Z= 0.411 Chirality : 0.046 0.235 1995 Planarity : 0.005 0.064 1303 Dihedral : 31.683 175.943 3719 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 5.12 % Allowed : 24.64 % Favored : 70.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.31), residues: 737 helix: 1.20 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.92 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 35 TYR 0.024 0.002 TYR C 39 PHE 0.008 0.001 PHE E 104 TRP 0.001 0.000 TRP D 149 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00368 / 0.19 (12105) covalent geometry : angle 0.72597 / 0.41 (17481) hydrogen bonds : bond 0.05666 / 3.97 ( 724) hydrogen bonds : angle 3.59817 / 2.51 ( 1800) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 281 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 249 time to evaluate : 0.176 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8916 (OUTLIER) cc_final: 0.8575 (pm20) REVERT: A 73 GLU cc_start: 0.8285 (mm-30) cc_final: 0.7459 (tt0) REVERT: A 93 GLN cc_start: 0.9072 (tp40) cc_final: 0.8337 (tp40) REVERT: B 59 LYS cc_start: 0.9161 (ttmt) cc_final: 0.8739 (tttm) REVERT: B 63 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8724 (mt-10) REVERT: C 25 PHE cc_start: 0.8638 (m-80) cc_final: 0.7998 (m-80) REVERT: C 35 ARG cc_start: 0.9492 (ttm110) cc_final: 0.9133 (ttp-110) REVERT: C 36 LYS cc_start: 0.9129 (tmtt) cc_final: 0.8845 (tptp) REVERT: C 42 ARG cc_start: 0.7781 (ptp-170) cc_final: 0.7301 (ptm160) REVERT: C 56 GLU cc_start: 0.8882 (tt0) cc_final: 0.8341 (tt0) REVERT: C 57 TYR cc_start: 0.8796 (t80) cc_final: 0.8486 (t80) REVERT: C 72 ASP cc_start: 0.9327 (p0) cc_final: 0.9070 (p0) REVERT: C 73 ASN cc_start: 0.9472 (t0) cc_final: 0.9130 (t0) REVERT: C 84 GLN cc_start: 0.9491 (tp40) cc_final: 0.8937 (tp40) REVERT: C 99 ARG cc_start: 0.8801 (mmm160) cc_final: 0.8378 (mmp80) REVERT: C 102 ILE cc_start: 0.9282 (mp) cc_final: 0.8994 (mp) REVERT: C 104 GLN cc_start: 0.8501 (mp10) cc_final: 0.8153 (mp10) REVERT: D 65 ARG cc_start: 0.9182 (ptm-80) cc_final: 0.8827 (ptp-170) REVERT: D 78 GLN cc_start: 0.9381 (tp40) cc_final: 0.9061 (mm-40) REVERT: D 87 MET cc_start: 0.8951 (ttp) cc_final: 0.8704 (ttp) REVERT: D 117 GLN cc_start: 0.8811 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 118 MET cc_start: 0.9321 (mmt) cc_final: 0.8844 (mmm) REVERT: D 127 LYS cc_start: 0.9569 (tppt) cc_final: 0.9303 (tppt) REVERT: E 59 GLU cc_start: 0.8677 (pm20) cc_final: 0.8367 (pm20) REVERT: E 73 GLU cc_start: 0.9114 (tt0) cc_final: 0.8302 (tt0) REVERT: E 79 LYS cc_start: 0.8615 (ttmt) cc_final: 0.8404 (ttmt) REVERT: E 105 GLU cc_start: 0.8581 (pp20) cc_final: 0.8185 (pp20) REVERT: E 106 ASP cc_start: 0.9060 (m-30) cc_final: 0.8354 (m-30) REVERT: E 120 MET cc_start: 0.8810 (mmm) cc_final: 0.8439 (mmm) REVERT: F 74 GLU cc_start: 0.9561 (tp30) cc_final: 0.9031 (tp30) REVERT: F 79 LYS cc_start: 0.9148 (mttp) cc_final: 0.8919 (mtmm) REVERT: F 85 ASP cc_start: 0.9331 (m-30) cc_final: 0.9095 (m-30) REVERT: F 88 TYR cc_start: 0.9382 (m-10) cc_final: 0.9052 (m-80) REVERT: F 98 TYR cc_start: 0.8637 (m-10) cc_final: 0.7910 (m-80) REVERT: G 36 LYS cc_start: 0.9617 (tttt) cc_final: 0.9383 (ttmm) REVERT: G 56 GLU cc_start: 0.8854 (tt0) cc_final: 0.8648 (tt0) REVERT: G 61 GLU cc_start: 0.9160 (tp30) cc_final: 0.8655 (tp30) REVERT: G 64 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8152 (tm-30) REVERT: G 87 ILE cc_start: 0.9367 (tp) cc_final: 0.9158 (tp) REVERT: G 88 ARG cc_start: 0.9519 (mmt-90) cc_final: 0.9252 (tpp80) REVERT: G 90 ASP cc_start: 0.8763 (t0) cc_final: 0.8315 (t0) REVERT: H 69 GLN cc_start: 0.9557 (pt0) cc_final: 0.9191 (pp30) REVERT: H 85 ASP cc_start: 0.9307 (t0) cc_final: 0.8976 (t0) REVERT: H 105 TYR cc_start: 0.8687 (m-10) cc_final: 0.7428 (m-10) REVERT: H 118 MET cc_start: 0.9255 (mmt) cc_final: 0.8921 (mmm) REVERT: H 127 LYS cc_start: 0.9405 (mmmm) cc_final: 0.9180 (mmmm) REVERT: H 142 ARG cc_start: 0.9483 (ttm-80) cc_final: 0.8664 (ttm110) outliers start: 32 outliers final: 22 residues processed: 264 average time/residue: 0.1047 time to fit residues: 37.2215 Evaluate side-chains 262 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 239 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 60 THR Chi-restraints excluded: chain D residue 82 SER Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 30.0000 chunk 29 optimal weight: 0.8980 chunk 80 optimal weight: 20.0000 chunk 22 optimal weight: 2.9990 chunk 58 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 88 optimal weight: 20.0000 chunk 92 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 0.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 104 HIS H 89 HIS H 101 GLN H 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.074838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2908 r_free = 0.2908 target = 0.046374 restraints weight = 46786.364| |-----------------------------------------------------------------------------| r_work (start): 0.2774 rms_B_bonded: 3.49 r_work (final): 0.2774 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 12105 Z= 0.166 Angle : 0.719 7.417 17481 Z= 0.409 Chirality : 0.045 0.240 1995 Planarity : 0.005 0.064 1303 Dihedral : 31.611 175.593 3719 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 5.44 % Allowed : 25.44 % Favored : 69.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.62 (0.32), residues: 737 helix: 1.31 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.85 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG G 35 TYR 0.030 0.002 TYR D 105 PHE 0.006 0.001 PHE E 104 TRP 0.000 0.000 TRP D 149 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.17 (12105) covalent geometry : angle 0.71946 / 0.41 (17481) hydrogen bonds : bond 0.05463 / 3.86 ( 724) hydrogen bonds : angle 3.48506 / 2.44 ( 1800) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 288 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 254 time to evaluate : 0.193 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8843 (OUTLIER) cc_final: 0.8564 (pm20) REVERT: A 73 GLU cc_start: 0.8303 (mm-30) cc_final: 0.7492 (tt0) REVERT: A 93 GLN cc_start: 0.8974 (tp40) cc_final: 0.8244 (tp40) REVERT: B 59 LYS cc_start: 0.9133 (ttmt) cc_final: 0.8707 (tttm) REVERT: B 63 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8735 (mt-10) REVERT: B 74 GLU cc_start: 0.9472 (tp30) cc_final: 0.9094 (mm-30) REVERT: B 88 TYR cc_start: 0.9247 (m-10) cc_final: 0.8928 (m-80) REVERT: C 36 LYS cc_start: 0.9154 (tmtt) cc_final: 0.8864 (tptp) REVERT: C 42 ARG cc_start: 0.7741 (ptp-170) cc_final: 0.7333 (ptm160) REVERT: C 56 GLU cc_start: 0.8901 (tt0) cc_final: 0.8547 (tt0) REVERT: C 57 TYR cc_start: 0.8818 (t80) cc_final: 0.8497 (t80) REVERT: C 72 ASP cc_start: 0.9319 (p0) cc_final: 0.9067 (p0) REVERT: C 73 ASN cc_start: 0.9486 (t0) cc_final: 0.9143 (t0) REVERT: C 84 GLN cc_start: 0.9510 (tp40) cc_final: 0.8940 (tp40) REVERT: C 102 ILE cc_start: 0.9268 (mp) cc_final: 0.8980 (mp) REVERT: C 104 GLN cc_start: 0.8540 (mp10) cc_final: 0.8206 (mp10) REVERT: D 75 SER cc_start: 0.8163 (m) cc_final: 0.7484 (p) REVERT: D 78 GLN cc_start: 0.9411 (tp40) cc_final: 0.9143 (mm-40) REVERT: D 87 MET cc_start: 0.9029 (ttp) cc_final: 0.8780 (ttp) REVERT: D 117 GLN cc_start: 0.8805 (tm-30) cc_final: 0.8128 (tm-30) REVERT: D 118 MET cc_start: 0.9341 (mmt) cc_final: 0.8891 (mmm) REVERT: D 127 LYS cc_start: 0.9564 (tppt) cc_final: 0.9297 (tppt) REVERT: E 59 GLU cc_start: 0.8679 (pm20) cc_final: 0.8461 (pm20) REVERT: E 73 GLU cc_start: 0.9089 (tt0) cc_final: 0.8261 (tt0) REVERT: E 79 LYS cc_start: 0.8660 (ttmt) cc_final: 0.8439 (ttmt) REVERT: E 105 GLU cc_start: 0.8597 (pp20) cc_final: 0.8224 (pp20) REVERT: E 106 ASP cc_start: 0.9107 (m-30) cc_final: 0.8390 (m-30) REVERT: E 120 MET cc_start: 0.8766 (mmm) cc_final: 0.8396 (mmm) REVERT: F 74 GLU cc_start: 0.9565 (tp30) cc_final: 0.9015 (tp30) REVERT: F 79 LYS cc_start: 0.9143 (mttp) cc_final: 0.8924 (mtmm) REVERT: F 85 ASP cc_start: 0.9311 (m-30) cc_final: 0.9089 (m-30) REVERT: F 88 TYR cc_start: 0.9371 (m-10) cc_final: 0.8980 (m-10) REVERT: F 98 TYR cc_start: 0.8630 (m-10) cc_final: 0.7944 (m-80) REVERT: G 36 LYS cc_start: 0.9662 (tttt) cc_final: 0.9280 (ttmm) REVERT: G 39 TYR cc_start: 0.8844 (m-80) cc_final: 0.8639 (m-80) REVERT: G 56 GLU cc_start: 0.8824 (tt0) cc_final: 0.8539 (tt0) REVERT: G 61 GLU cc_start: 0.9157 (tp30) cc_final: 0.8620 (tp30) REVERT: G 64 GLU cc_start: 0.8786 (tm-30) cc_final: 0.8171 (tm-30) REVERT: G 87 ILE cc_start: 0.9341 (tp) cc_final: 0.9122 (tp) REVERT: G 88 ARG cc_start: 0.9481 (mmt-90) cc_final: 0.9159 (tpp80) REVERT: G 90 ASP cc_start: 0.8443 (t0) cc_final: 0.8025 (t0) REVERT: H 69 GLN cc_start: 0.9532 (pt0) cc_final: 0.9158 (pp30) REVERT: H 85 ASP cc_start: 0.9316 (t0) cc_final: 0.8961 (t0) REVERT: H 105 TYR cc_start: 0.8636 (m-10) cc_final: 0.7528 (m-10) REVERT: H 118 MET cc_start: 0.9264 (mmt) cc_final: 0.8934 (mmm) REVERT: H 142 ARG cc_start: 0.9461 (ttm-80) cc_final: 0.8614 (ttm110) outliers start: 34 outliers final: 22 residues processed: 269 average time/residue: 0.1005 time to fit residues: 36.6076 Evaluate side-chains 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 249 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 50.0000 chunk 27 optimal weight: 10.0000 chunk 33 optimal weight: 4.9990 chunk 82 optimal weight: 50.0000 chunk 7 optimal weight: 7.9990 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 chunk 94 optimal weight: 30.0000 overall best weight: 1.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 89 HIS H 104 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.075111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.046392 restraints weight = 46836.005| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 3.56 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12105 Z= 0.166 Angle : 0.733 9.630 17481 Z= 0.412 Chirality : 0.046 0.305 1995 Planarity : 0.005 0.064 1303 Dihedral : 31.565 175.380 3719 Min Nonbonded Distance : 2.054 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 4.32 % Allowed : 27.68 % Favored : 68.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.32), residues: 737 helix: 1.31 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.72 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.019 0.001 ARG C 99 TYR 0.035 0.002 TYR B 88 PHE 0.006 0.001 PHE E 104 TRP 0.000 0.000 TRP D 149 HIS 0.006 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.17 (12105) covalent geometry : angle 0.73294 / 0.41 (17481) hydrogen bonds : bond 0.05416 / 3.83 ( 724) hydrogen bonds : angle 3.47431 / 2.44 ( 1800) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 251 time to evaluate : 0.206 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8786 (OUTLIER) cc_final: 0.8555 (pm20) REVERT: A 73 GLU cc_start: 0.8296 (mm-30) cc_final: 0.7472 (tt0) REVERT: A 93 GLN cc_start: 0.8910 (tp40) cc_final: 0.8237 (tp40) REVERT: B 59 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8705 (tttm) REVERT: B 63 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8745 (mt-10) REVERT: B 88 TYR cc_start: 0.9210 (m-10) cc_final: 0.8972 (m-80) REVERT: C 20 ARG cc_start: 0.9072 (ttm170) cc_final: 0.8465 (tpp80) REVERT: C 25 PHE cc_start: 0.8684 (m-80) cc_final: 0.8043 (m-80) REVERT: C 36 LYS cc_start: 0.9125 (tmtt) cc_final: 0.8847 (tptp) REVERT: C 42 ARG cc_start: 0.7837 (ptp-170) cc_final: 0.7387 (ptm160) REVERT: C 56 GLU cc_start: 0.8933 (tt0) cc_final: 0.8425 (tt0) REVERT: C 72 ASP cc_start: 0.9329 (p0) cc_final: 0.9066 (p0) REVERT: C 73 ASN cc_start: 0.9465 (t0) cc_final: 0.9123 (t0) REVERT: C 84 GLN cc_start: 0.9505 (tp40) cc_final: 0.8937 (tp40) REVERT: C 92 GLU cc_start: 0.9437 (OUTLIER) cc_final: 0.9084 (pt0) REVERT: C 99 ARG cc_start: 0.8840 (mmm160) cc_final: 0.8387 (mmp80) REVERT: C 102 ILE cc_start: 0.9218 (mp) cc_final: 0.8951 (mp) REVERT: C 104 GLN cc_start: 0.8682 (mp10) cc_final: 0.7900 (mp10) REVERT: D 75 SER cc_start: 0.8143 (m) cc_final: 0.7490 (p) REVERT: D 78 GLN cc_start: 0.9419 (tp40) cc_final: 0.9169 (mm-40) REVERT: D 87 MET cc_start: 0.9027 (ttp) cc_final: 0.8776 (ttp) REVERT: D 117 GLN cc_start: 0.8768 (tm-30) cc_final: 0.8092 (tm-30) REVERT: D 118 MET cc_start: 0.9328 (mmt) cc_final: 0.8896 (mmm) REVERT: D 127 LYS cc_start: 0.9551 (tppt) cc_final: 0.9305 (tppt) REVERT: E 59 GLU cc_start: 0.8658 (pm20) cc_final: 0.8421 (pm20) REVERT: E 73 GLU cc_start: 0.9078 (tt0) cc_final: 0.8348 (tt0) REVERT: E 79 LYS cc_start: 0.8659 (ttmt) cc_final: 0.8437 (ttmt) REVERT: E 105 GLU cc_start: 0.8579 (pp20) cc_final: 0.8223 (pp20) REVERT: E 106 ASP cc_start: 0.9103 (m-30) cc_final: 0.8423 (m-30) REVERT: E 120 MET cc_start: 0.8776 (mmm) cc_final: 0.8392 (mmm) REVERT: F 74 GLU cc_start: 0.9573 (tp30) cc_final: 0.9004 (tp30) REVERT: F 79 LYS cc_start: 0.9126 (mttp) cc_final: 0.8902 (mtmm) REVERT: F 85 ASP cc_start: 0.9319 (m-30) cc_final: 0.9101 (m-30) REVERT: F 98 TYR cc_start: 0.8639 (m-10) cc_final: 0.7962 (m-80) REVERT: G 36 LYS cc_start: 0.9589 (tttt) cc_final: 0.9343 (ttmm) REVERT: G 39 TYR cc_start: 0.8931 (m-80) cc_final: 0.8716 (m-80) REVERT: G 56 GLU cc_start: 0.8776 (tt0) cc_final: 0.8474 (tt0) REVERT: G 61 GLU cc_start: 0.9174 (tp30) cc_final: 0.8655 (tp30) REVERT: G 64 GLU cc_start: 0.8796 (tm-30) cc_final: 0.7993 (tm-30) REVERT: G 68 ASN cc_start: 0.9016 (m-40) cc_final: 0.8317 (m-40) REVERT: G 87 ILE cc_start: 0.9344 (tp) cc_final: 0.9113 (tp) REVERT: G 88 ARG cc_start: 0.9473 (mmt-90) cc_final: 0.9136 (tpp80) REVERT: G 90 ASP cc_start: 0.8236 (t0) cc_final: 0.7873 (t0) REVERT: H 62 TYR cc_start: 0.9434 (m-80) cc_final: 0.9013 (m-80) REVERT: H 69 GLN cc_start: 0.9548 (pt0) cc_final: 0.9175 (pp30) REVERT: H 85 ASP cc_start: 0.9289 (t0) cc_final: 0.8935 (t0) REVERT: H 118 MET cc_start: 0.9249 (mmt) cc_final: 0.8920 (mmm) REVERT: H 142 ARG cc_start: 0.9457 (ttm-80) cc_final: 0.8646 (ttm110) outliers start: 27 outliers final: 21 residues processed: 260 average time/residue: 0.1018 time to fit residues: 35.5654 Evaluate side-chains 271 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 248 time to evaluate : 0.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 3 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 7.9990 chunk 32 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 36 optimal weight: 6.9990 chunk 56 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 11 optimal weight: 0.9980 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 104 HIS H 89 HIS H 101 GLN H 104 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.075370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2920 r_free = 0.2920 target = 0.046537 restraints weight = 45856.814| |-----------------------------------------------------------------------------| r_work (start): 0.2784 rms_B_bonded: 3.65 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 12105 Z= 0.166 Angle : 0.738 9.823 17481 Z= 0.414 Chirality : 0.045 0.242 1995 Planarity : 0.005 0.066 1303 Dihedral : 31.506 175.342 3719 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 5.12 % Allowed : 27.68 % Favored : 67.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.32), residues: 737 helix: 1.34 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.54 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 99 TYR 0.030 0.002 TYR B 88 PHE 0.007 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.009 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.17 (12105) covalent geometry : angle 0.73757 / 0.41 (17481) hydrogen bonds : bond 0.05305 / 3.75 ( 724) hydrogen bonds : angle 3.45773 / 2.44 ( 1800) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 255 time to evaluate : 0.178 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: A 59 GLU cc_start: 0.8749 (OUTLIER) cc_final: 0.8530 (pm20) REVERT: A 73 GLU cc_start: 0.8305 (mm-30) cc_final: 0.7484 (tt0) REVERT: A 93 GLN cc_start: 0.8870 (tp40) cc_final: 0.8256 (tp40) REVERT: B 59 LYS cc_start: 0.9106 (ttmt) cc_final: 0.8669 (tttm) REVERT: B 63 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8803 (mt-10) REVERT: B 88 TYR cc_start: 0.9161 (m-10) cc_final: 0.8926 (m-80) REVERT: C 25 PHE cc_start: 0.8749 (m-80) cc_final: 0.8130 (m-80) REVERT: C 36 LYS cc_start: 0.9110 (tmtt) cc_final: 0.8818 (tptp) REVERT: C 39 TYR cc_start: 0.8619 (m-80) cc_final: 0.8182 (m-80) REVERT: C 42 ARG cc_start: 0.7816 (ptp-170) cc_final: 0.7373 (ptm160) REVERT: C 56 GLU cc_start: 0.8895 (tt0) cc_final: 0.8407 (tt0) REVERT: C 57 TYR cc_start: 0.8761 (t80) cc_final: 0.8540 (t80) REVERT: C 64 GLU cc_start: 0.8963 (tp30) cc_final: 0.8751 (mm-30) REVERT: C 72 ASP cc_start: 0.9322 (p0) cc_final: 0.9064 (p0) REVERT: C 73 ASN cc_start: 0.9438 (t0) cc_final: 0.9089 (t0) REVERT: C 84 GLN cc_start: 0.9514 (tp40) cc_final: 0.8953 (tp40) REVERT: C 92 GLU cc_start: 0.9379 (OUTLIER) cc_final: 0.9076 (pt0) REVERT: C 99 ARG cc_start: 0.8854 (mmm160) cc_final: 0.8455 (mmp80) REVERT: C 102 ILE cc_start: 0.9165 (mp) cc_final: 0.8898 (mp) REVERT: C 104 GLN cc_start: 0.8693 (mp10) cc_final: 0.7908 (mp10) REVERT: D 75 SER cc_start: 0.8162 (m) cc_final: 0.7466 (p) REVERT: D 78 GLN cc_start: 0.9421 (tp40) cc_final: 0.9213 (mm-40) REVERT: D 87 MET cc_start: 0.9011 (ttp) cc_final: 0.8769 (ttp) REVERT: D 93 ASP cc_start: 0.9007 (t0) cc_final: 0.8770 (t0) REVERT: D 117 GLN cc_start: 0.8758 (tm-30) cc_final: 0.8169 (tm-30) REVERT: D 118 MET cc_start: 0.9316 (mmt) cc_final: 0.8895 (mmm) REVERT: D 127 LYS cc_start: 0.9543 (tppt) cc_final: 0.9322 (tppt) REVERT: E 59 GLU cc_start: 0.8594 (pm20) cc_final: 0.8375 (pm20) REVERT: E 73 GLU cc_start: 0.9095 (tt0) cc_final: 0.8325 (tt0) REVERT: E 79 LYS cc_start: 0.8679 (ttmt) cc_final: 0.8472 (ttmt) REVERT: E 105 GLU cc_start: 0.8599 (pp20) cc_final: 0.8275 (pp20) REVERT: E 106 ASP cc_start: 0.9102 (m-30) cc_final: 0.8463 (m-30) REVERT: E 120 MET cc_start: 0.8794 (mmm) cc_final: 0.8445 (mmm) REVERT: F 74 GLU cc_start: 0.9585 (tp30) cc_final: 0.9035 (tp30) REVERT: F 85 ASP cc_start: 0.9346 (m-30) cc_final: 0.9142 (m-30) REVERT: F 98 TYR cc_start: 0.8645 (m-10) cc_final: 0.7935 (m-80) REVERT: G 36 LYS cc_start: 0.9645 (tttt) cc_final: 0.9280 (ttmm) REVERT: G 39 TYR cc_start: 0.8920 (m-80) cc_final: 0.8660 (m-80) REVERT: G 56 GLU cc_start: 0.8784 (tt0) cc_final: 0.8495 (tt0) REVERT: G 61 GLU cc_start: 0.9182 (tp30) cc_final: 0.8661 (tp30) REVERT: G 64 GLU cc_start: 0.8797 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 68 ASN cc_start: 0.9002 (m-40) cc_final: 0.8265 (m-40) REVERT: G 87 ILE cc_start: 0.9331 (tp) cc_final: 0.9098 (tp) REVERT: G 88 ARG cc_start: 0.9476 (mmt-90) cc_final: 0.9124 (tpp80) REVERT: G 90 ASP cc_start: 0.8318 (t0) cc_final: 0.8077 (t0) REVERT: H 62 TYR cc_start: 0.9430 (m-80) cc_final: 0.9015 (m-80) REVERT: H 69 GLN cc_start: 0.9553 (pt0) cc_final: 0.9181 (pp30) REVERT: H 85 ASP cc_start: 0.9284 (t0) cc_final: 0.8935 (t0) REVERT: H 101 GLN cc_start: 0.9007 (OUTLIER) cc_final: 0.8718 (tm-30) REVERT: H 118 MET cc_start: 0.9260 (mmt) cc_final: 0.8935 (mmm) REVERT: H 142 ARG cc_start: 0.9453 (ttm-80) cc_final: 0.8636 (ttm110) outliers start: 32 outliers final: 22 residues processed: 267 average time/residue: 0.1024 time to fit residues: 36.8965 Evaluate side-chains 278 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 253 time to evaluate : 0.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 30.0000 chunk 52 optimal weight: 10.0000 chunk 41 optimal weight: 4.9990 chunk 71 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 0.5980 chunk 57 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 overall best weight: 1.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 89 HIS H 101 GLN H 104 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.075571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2924 r_free = 0.2924 target = 0.046563 restraints weight = 46413.996| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.75 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12105 Z= 0.166 Angle : 0.745 9.684 17481 Z= 0.417 Chirality : 0.046 0.242 1995 Planarity : 0.005 0.066 1303 Dihedral : 31.481 175.292 3719 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 4.32 % Allowed : 28.80 % Favored : 66.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.77 (0.32), residues: 737 helix: 1.32 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.48 (0.44), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 81 TYR 0.041 0.003 TYR H 105 PHE 0.006 0.001 PHE E 104 TRP 0.001 0.000 TRP D 149 HIS 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00326 / 0.17 (12105) covalent geometry : angle 0.74484 / 0.42 (17481) hydrogen bonds : bond 0.05320 / 3.77 ( 724) hydrogen bonds : angle 3.45133 / 2.44 ( 1800) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 283 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 256 time to evaluate : 0.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8520 (pm20) REVERT: A 73 GLU cc_start: 0.8263 (mm-30) cc_final: 0.7458 (tt0) REVERT: A 93 GLN cc_start: 0.8851 (tp40) cc_final: 0.8257 (tp40) REVERT: B 59 LYS cc_start: 0.9091 (ttmt) cc_final: 0.8693 (tttm) REVERT: B 63 GLU cc_start: 0.9259 (mt-10) cc_final: 0.8761 (mt-10) REVERT: B 88 TYR cc_start: 0.9139 (m-10) cc_final: 0.8897 (m-80) REVERT: C 17 ARG cc_start: 0.8593 (mtm180) cc_final: 0.7810 (mtm180) REVERT: C 20 ARG cc_start: 0.9106 (ttm170) cc_final: 0.8614 (ttm110) REVERT: C 25 PHE cc_start: 0.8807 (m-80) cc_final: 0.8200 (m-80) REVERT: C 39 TYR cc_start: 0.8656 (m-80) cc_final: 0.8261 (m-80) REVERT: C 42 ARG cc_start: 0.7826 (ptp-170) cc_final: 0.7451 (ptm160) REVERT: C 56 GLU cc_start: 0.8914 (tt0) cc_final: 0.8422 (tt0) REVERT: C 57 TYR cc_start: 0.8794 (t80) cc_final: 0.8572 (t80) REVERT: C 64 GLU cc_start: 0.8941 (tp30) cc_final: 0.8735 (mm-30) REVERT: C 72 ASP cc_start: 0.9321 (p0) cc_final: 0.9067 (p0) REVERT: C 73 ASN cc_start: 0.9439 (t0) cc_final: 0.8623 (t0) REVERT: C 75 LYS cc_start: 0.8710 (mttm) cc_final: 0.8325 (mmtp) REVERT: C 84 GLN cc_start: 0.9520 (tp40) cc_final: 0.8962 (tp40) REVERT: C 92 GLU cc_start: 0.9358 (OUTLIER) cc_final: 0.9069 (pt0) REVERT: C 99 ARG cc_start: 0.8852 (mmm160) cc_final: 0.8460 (mmp80) REVERT: C 102 ILE cc_start: 0.9154 (mp) cc_final: 0.8888 (mp) REVERT: C 104 GLN cc_start: 0.8708 (mp10) cc_final: 0.7919 (mp10) REVERT: D 75 SER cc_start: 0.8259 (m) cc_final: 0.7634 (p) REVERT: D 87 MET cc_start: 0.9051 (ttp) cc_final: 0.8836 (ttp) REVERT: D 93 ASP cc_start: 0.8998 (t0) cc_final: 0.8787 (t0) REVERT: D 118 MET cc_start: 0.9385 (mmt) cc_final: 0.9033 (mmp) REVERT: D 127 LYS cc_start: 0.9547 (tppt) cc_final: 0.9333 (tppt) REVERT: E 59 GLU cc_start: 0.8589 (pm20) cc_final: 0.8323 (pm20) REVERT: E 73 GLU cc_start: 0.9096 (tt0) cc_final: 0.8327 (tt0) REVERT: E 105 GLU cc_start: 0.8586 (pp20) cc_final: 0.8269 (pp20) REVERT: E 106 ASP cc_start: 0.9088 (m-30) cc_final: 0.8469 (m-30) REVERT: E 120 MET cc_start: 0.8852 (mmm) cc_final: 0.8479 (mmm) REVERT: F 74 GLU cc_start: 0.9570 (tp30) cc_final: 0.9105 (tp30) REVERT: F 98 TYR cc_start: 0.8643 (m-10) cc_final: 0.7911 (m-80) REVERT: G 36 LYS cc_start: 0.9586 (tttt) cc_final: 0.9349 (ttmm) REVERT: G 39 TYR cc_start: 0.8905 (m-80) cc_final: 0.8627 (m-80) REVERT: G 56 GLU cc_start: 0.8783 (tt0) cc_final: 0.8524 (tt0) REVERT: G 61 GLU cc_start: 0.9189 (tp30) cc_final: 0.8688 (tp30) REVERT: G 64 GLU cc_start: 0.8799 (tm-30) cc_final: 0.8016 (tm-30) REVERT: G 68 ASN cc_start: 0.8925 (m-40) cc_final: 0.8096 (m-40) REVERT: G 87 ILE cc_start: 0.9356 (tp) cc_final: 0.9123 (tp) REVERT: G 88 ARG cc_start: 0.9485 (mmt-90) cc_final: 0.9127 (tpp80) REVERT: G 90 ASP cc_start: 0.8301 (t0) cc_final: 0.7985 (t0) REVERT: H 62 TYR cc_start: 0.9418 (m-80) cc_final: 0.9028 (m-80) REVERT: H 69 GLN cc_start: 0.9542 (pt0) cc_final: 0.9174 (pp30) REVERT: H 85 ASP cc_start: 0.9285 (t0) cc_final: 0.8935 (t0) REVERT: H 101 GLN cc_start: 0.8934 (OUTLIER) cc_final: 0.8298 (tm-30) REVERT: H 104 HIS cc_start: 0.8975 (t70) cc_final: 0.8762 (t-90) REVERT: H 118 MET cc_start: 0.9253 (mmt) cc_final: 0.8927 (mmm) REVERT: H 142 ARG cc_start: 0.9450 (ttm-80) cc_final: 0.8640 (ttm110) outliers start: 27 outliers final: 21 residues processed: 264 average time/residue: 0.1366 time to fit residues: 48.5033 Evaluate side-chains 274 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 250 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 40 SER Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 83 VAL Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 128 MET Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain G residue 40 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 101 GLN Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 25 optimal weight: 10.0000 chunk 89 optimal weight: 30.0000 chunk 71 optimal weight: 50.0000 chunk 4 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 chunk 69 optimal weight: 6.9990 chunk 44 optimal weight: 4.9990 chunk 93 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 104 HIS H 89 HIS H 101 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.075326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.046412 restraints weight = 46674.291| |-----------------------------------------------------------------------------| r_work (start): 0.2786 rms_B_bonded: 3.74 r_work (final): 0.2786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8551 moved from start: 0.2625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 12105 Z= 0.176 Angle : 0.747 9.886 17481 Z= 0.419 Chirality : 0.046 0.242 1995 Planarity : 0.005 0.067 1303 Dihedral : 31.471 175.212 3719 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.96 % Allowed : 28.48 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.75 (0.32), residues: 737 helix: 1.30 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.47 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG G 81 TYR 0.045 0.003 TYR H 105 PHE 0.006 0.001 PHE E 104 TRP 0.001 0.000 TRP D 149 HIS 0.008 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00348 / 0.18 (12105) covalent geometry : angle 0.74677 / 0.42 (17481) hydrogen bonds : bond 0.05344 / 3.78 ( 724) hydrogen bonds : angle 3.47292 / 2.46 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1872.84 seconds wall clock time: 32 minutes 53.19 seconds (1973.19 seconds total)