Starting phenix.real_space_refine on Fri Jul 3 01:32:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jc6_61358/07_2026/9jc6_61358.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jc6_61358/07_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_61358/07_2026/9jc6_61358.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jc6_61358/07_2026/9jc6_61358.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9jc6_61358/07_2026/9jc6_61358.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jc6_61358/07_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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/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: 2.72, per 1000 atoms: 0.24 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: 1.04 Conformation dependent library (CDL) restraints added in 231.3 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: 1.85 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: 2.02 Time building geometry restraints manager: 1.36 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: 15421 1.16 - 2.32: 1703 2.32 - 3.48: 319 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: 0.760 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 13.430 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.030 ------------------------------------------------------------------------------- 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 : 0.764 5.805 17481 Z= 0.679 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 0.76376 / 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 : 0.305 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: 0.8726 (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: 0.8790 (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: 0.9274 (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: 0.8691 (pm20) REVERT: E 60 LEU cc_start: 0.9326 (mt) cc_final: 0.8955 (mt) REVERT: E 85 GLN cc_start: 0.9478 (mt0) cc_final: 0.9273 (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: 0.8182 (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: 0.8870 (mtmm) REVERT: F 85 ASP cc_start: 0.9228 (m-30) cc_final: 0.8991 (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: 0.8908 (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: 0.8742 (ttm110) outliers start: 0 outliers final: 0 residues processed: 266 average time/residue: 0.1348 time to fit residues: 47.8894 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 : 0.303 ------------------------------------------------------------------------------- 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: 0.9980 chunk 51 optimal weight: 1.9990 chunk 38 optimal weight: 4.9990 chunk 61 optimal weight: 9.9990 chunk 45 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 = 0.3547 r_free = 0.3547 target = 0.073815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2879 r_free = 0.2879 target = 0.046179 restraints weight = 48215.991| |-----------------------------------------------------------------------------| r_work (start): 0.2758 rms_B_bonded: 3.70 r_work (final): 0.2758 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 12105 Z= 0.170 Angle : 0.713 8.359 17481 Z= 0.414 Chirality : 0.046 0.225 1995 Planarity : 0.005 0.045 1303 Dihedral : 31.868 175.994 3719 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 2.08 % Allowed : 17.92 % Favored : 80.00 % 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: -0.63 (0.30), residues: 737 helix: 0.50 (0.22), residues: 515 sheet: None (None), residues: 0 loop : -2.58 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 32 TYR 0.023 0.002 TYR B 88 PHE 0.006 0.001 PHE E 78 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 0.00300 / 0.17 (12105) covalent geometry : angle 0.71283 / 0.41 (17481) hydrogen bonds : bond 0.06075 / 4.22 ( 724) hydrogen bonds : angle 3.80614 / 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 275 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 262 time to evaluate : 0.309 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: 0.9181 (pm20) cc_final: 0.8905 (pm20) REVERT: A 73 GLU cc_start: 0.8383 (mm-30) cc_final: 0.7586 (tt0) REVERT: A 93 GLN cc_start: 0.9110 (tp40) cc_final: 0.8855 (tp40) REVERT: A 97 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8678 (mm-30) REVERT: A 110 CYS cc_start: 0.8457 (t) cc_final: 0.8078 (t) REVERT: B 44 LYS cc_start: 0.9093 (ttmt) cc_final: 0.8856 (ttmm) REVERT: B 59 LYS cc_start: 0.9172 (ttmt) cc_final: 0.8661 (tttm) REVERT: B 63 GLU cc_start: 0.9254 (mt-10) cc_final: 0.8715 (mt-10) REVERT: B 74 GLU cc_start: 0.9272 (tp30) cc_final: 0.9071 (tp30) REVERT: C 25 PHE cc_start: 0.8649 (m-80) cc_final: 0.8233 (m-80) REVERT: C 36 LYS cc_start: 0.9367 (tmtt) cc_final: 0.8643 (tptt) REVERT: C 56 GLU cc_start: 0.8855 (tt0) cc_final: 0.8560 (tt0) REVERT: C 84 GLN cc_start: 0.9499 (tp40) cc_final: 0.8851 (tp40) REVERT: C 99 ARG cc_start: 0.8776 (mmm160) cc_final: 0.8365 (mmp80) REVERT: C 102 ILE cc_start: 0.9370 (mp) cc_final: 0.9057 (mp) REVERT: C 104 GLN cc_start: 0.8367 (mp10) cc_final: 0.7645 (mp10) REVERT: D 65 ARG cc_start: 0.8983 (ptm-80) cc_final: 0.8549 (ptt180) REVERT: D 117 GLN cc_start: 0.8705 (tm-30) cc_final: 0.7881 (tm-30) REVERT: D 118 MET cc_start: 0.9379 (mmt) cc_final: 0.8864 (mmm) REVERT: D 127 LYS cc_start: 0.9567 (tppt) cc_final: 0.9205 (tppt) REVERT: D 128 MET cc_start: 0.9434 (mtt) cc_final: 0.9186 (mtt) REVERT: D 130 LYS cc_start: 0.9226 (pttm) cc_final: 0.9016 (pttm) REVERT: E 59 GLU cc_start: 0.8807 (pm20) cc_final: 0.8589 (pm20) REVERT: E 73 GLU cc_start: 0.9182 (tt0) cc_final: 0.8698 (tt0) REVERT: E 79 LYS cc_start: 0.8707 (tttt) cc_final: 0.8348 (ttmt) REVERT: E 105 GLU cc_start: 0.8554 (pp20) cc_final: 0.8122 (pp20) REVERT: E 106 ASP cc_start: 0.9003 (m-30) cc_final: 0.8255 (m-30) REVERT: F 44 LYS cc_start: 0.9220 (mtpt) cc_final: 0.9016 (mtpp) REVERT: F 74 GLU cc_start: 0.9484 (tp30) cc_final: 0.9007 (tp30) REVERT: F 77 LYS cc_start: 0.9550 (mttp) cc_final: 0.9344 (mtpp) REVERT: F 79 LYS cc_start: 0.9183 (mttp) cc_final: 0.8863 (mtmm) REVERT: F 85 ASP cc_start: 0.9317 (m-30) cc_final: 0.9039 (m-30) REVERT: F 88 TYR cc_start: 0.9395 (m-10) cc_final: 0.9123 (m-80) REVERT: G 35 ARG cc_start: 0.9615 (ttp-110) cc_final: 0.9293 (ttm110) REVERT: G 36 LYS cc_start: 0.9710 (tttt) cc_final: 0.9390 (ttmm) REVERT: G 56 GLU cc_start: 0.8916 (tt0) cc_final: 0.8535 (tt0) REVERT: G 61 GLU cc_start: 0.9181 (tp30) cc_final: 0.8822 (tp30) REVERT: G 64 GLU cc_start: 0.8771 (tm-30) cc_final: 0.8147 (tm-30) REVERT: G 87 ILE cc_start: 0.9213 (tp) cc_final: 0.8994 (tp) REVERT: H 69 GLN cc_start: 0.9504 (pt0) cc_final: 0.9176 (pp30) REVERT: H 85 ASP cc_start: 0.9332 (t0) cc_final: 0.8817 (t0) REVERT: H 101 GLN cc_start: 0.8560 (pp30) cc_final: 0.7556 (pp30) REVERT: H 104 HIS cc_start: 0.9020 (t70) cc_final: 0.8407 (t-90) REVERT: H 105 TYR cc_start: 0.8496 (m-10) cc_final: 0.6824 (m-10) REVERT: H 118 MET cc_start: 0.9295 (mmt) cc_final: 0.8961 (mmm) REVERT: H 127 LYS cc_start: 0.9608 (mmmm) cc_final: 0.9390 (mmmm) REVERT: H 128 MET cc_start: 0.9477 (mtt) cc_final: 0.9116 (mtt) REVERT: H 142 ARG cc_start: 0.9415 (ttm-80) cc_final: 0.8621 (ttm110) outliers start: 13 outliers final: 8 residues processed: 264 average time/residue: 0.1188 time to fit residues: 42.7084 Evaluate side-chains 248 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 240 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 0.9980 chunk 35 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 3 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 39 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 84 optimal weight: 50.0000 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN D 101 GLN D 135 GLN G 94 ASN H 138 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.073437 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.045889 restraints weight = 48710.395| |-----------------------------------------------------------------------------| r_work (start): 0.2750 rms_B_bonded: 3.75 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 12105 Z= 0.170 Angle : 0.698 8.370 17481 Z= 0.405 Chirality : 0.045 0.221 1995 Planarity : 0.005 0.054 1303 Dihedral : 31.785 175.937 3719 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.00 % Allowed : 22.08 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.31), residues: 737 helix: 0.86 (0.23), residues: 515 sheet: None (None), residues: 0 loop : -2.32 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 134 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 0.004 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00308 / 0.17 (12105) covalent geometry : angle 0.69750 / 0.41 (17481) hydrogen bonds : bond 0.05811 / 4.06 ( 724) hydrogen bonds : angle 3.63886 / 2.53 ( 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 272 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 247 time to evaluate : 0.196 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: 0.9001 (pm20) cc_final: 0.8730 (pm20) REVERT: A 73 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7544 (tt0) REVERT: A 93 GLN cc_start: 0.9049 (tp40) cc_final: 0.8647 (tp40) REVERT: B 44 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8744 (ttmt) REVERT: B 59 LYS cc_start: 0.9201 (ttmt) cc_final: 0.8670 (tttm) REVERT: B 63 GLU cc_start: 0.9280 (mt-10) cc_final: 0.8698 (mt-10) REVERT: C 25 PHE cc_start: 0.8658 (m-80) cc_final: 0.8186 (m-80) REVERT: C 36 LYS cc_start: 0.9208 (tmtt) cc_final: 0.8556 (tptt) REVERT: C 56 GLU cc_start: 0.8860 (tt0) cc_final: 0.8581 (tt0) REVERT: C 57 TYR cc_start: 0.8712 (t80) cc_final: 0.8416 (t80) REVERT: C 72 ASP cc_start: 0.9307 (p0) cc_final: 0.8970 (p0) REVERT: C 73 ASN cc_start: 0.9261 (OUTLIER) cc_final: 0.9028 (t0) REVERT: C 84 GLN cc_start: 0.9498 (tp40) cc_final: 0.8978 (tp40) REVERT: C 99 ARG cc_start: 0.8767 (mmm160) cc_final: 0.8408 (mmp80) REVERT: C 102 ILE cc_start: 0.9416 (mp) cc_final: 0.9123 (mp) REVERT: C 104 GLN cc_start: 0.8410 (mp10) cc_final: 0.7724 (mp10) REVERT: D 65 ARG cc_start: 0.9079 (ptm-80) cc_final: 0.8715 (ptp-170) REVERT: D 78 GLN cc_start: 0.9359 (tp40) cc_final: 0.9021 (mm-40) REVERT: D 117 GLN cc_start: 0.8704 (tm-30) cc_final: 0.7911 (tm-30) REVERT: D 118 MET cc_start: 0.9377 (mmt) cc_final: 0.8747 (mmm) REVERT: D 127 LYS cc_start: 0.9574 (tppt) cc_final: 0.9229 (tppt) REVERT: D 128 MET cc_start: 0.9416 (mtt) cc_final: 0.9131 (mtt) REVERT: D 130 LYS cc_start: 0.9233 (pttm) cc_final: 0.9033 (pttm) REVERT: D 142 ARG cc_start: 0.9498 (mtt90) cc_final: 0.9251 (mtt-85) REVERT: E 58 THR cc_start: 0.7684 (OUTLIER) cc_final: 0.7470 (m) REVERT: E 59 GLU cc_start: 0.8727 (pm20) cc_final: 0.8408 (pm20) REVERT: E 73 GLU cc_start: 0.9163 (tt0) cc_final: 0.8538 (tt0) REVERT: E 79 LYS cc_start: 0.8696 (tttt) cc_final: 0.8355 (ttmt) REVERT: E 105 GLU cc_start: 0.8549 (pp20) cc_final: 0.8176 (pp20) REVERT: E 106 ASP cc_start: 0.8999 (m-30) cc_final: 0.8302 (m-30) REVERT: F 44 LYS cc_start: 0.9233 (mtpt) cc_final: 0.9032 (mtpp) REVERT: F 74 GLU cc_start: 0.9485 (tp30) cc_final: 0.8992 (tp30) REVERT: F 79 LYS cc_start: 0.9135 (mttp) cc_final: 0.8865 (mtmm) REVERT: F 85 ASP cc_start: 0.9303 (m-30) cc_final: 0.9079 (m-30) REVERT: F 88 TYR cc_start: 0.9368 (m-10) cc_final: 0.9123 (m-80) REVERT: F 98 TYR cc_start: 0.8522 (m-80) cc_final: 0.7595 (m-80) REVERT: G 36 LYS cc_start: 0.9692 (tttt) cc_final: 0.9372 (ttmm) REVERT: G 56 GLU cc_start: 0.8865 (tt0) cc_final: 0.8467 (tt0) REVERT: G 61 GLU cc_start: 0.9193 (tp30) cc_final: 0.8829 (tp30) REVERT: G 64 GLU cc_start: 0.8796 (tm-30) cc_final: 0.8186 (tm-30) REVERT: G 87 ILE cc_start: 0.9266 (tp) cc_final: 0.8939 (tp) REVERT: G 90 ASP cc_start: 0.8554 (t0) cc_final: 0.8054 (t0) REVERT: G 92 GLU cc_start: 0.9065 (pm20) cc_final: 0.8842 (pm20) REVERT: H 69 GLN cc_start: 0.9504 (pt0) cc_final: 0.9181 (pp30) REVERT: H 101 GLN cc_start: 0.8735 (pp30) cc_final: 0.7749 (pp30) REVERT: H 104 HIS cc_start: 0.9038 (t70) cc_final: 0.8431 (t-90) REVERT: H 105 TYR cc_start: 0.8557 (m-10) cc_final: 0.6864 (m-10) REVERT: H 118 MET cc_start: 0.9279 (mmt) cc_final: 0.8942 (mmm) REVERT: H 142 ARG cc_start: 0.9432 (ttm-80) cc_final: 0.8630 (ttm110) outliers start: 25 outliers final: 12 residues processed: 259 average time/residue: 0.1104 time to fit residues: 39.4206 Evaluate side-chains 252 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 238 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU 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 73 ASN Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain G residue 85 LEU Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 21 optimal weight: 6.9990 chunk 69 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 74 optimal weight: 30.0000 chunk 3 optimal weight: 1.9990 chunk 94 optimal weight: 30.0000 chunk 24 optimal weight: 4.9990 chunk 64 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 37 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 = 0.3537 r_free = 0.3537 target = 0.073274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2855 r_free = 0.2855 target = 0.045562 restraints weight = 47619.169| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.67 r_work (final): 0.2738 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 12105 Z= 0.180 Angle : 0.694 8.102 17481 Z= 0.402 Chirality : 0.045 0.246 1995 Planarity : 0.005 0.059 1303 Dihedral : 31.750 175.717 3719 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.80 % Allowed : 23.52 % Favored : 71.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.19 (0.31), residues: 737 helix: 1.09 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.33 (0.39), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 88 TYR 0.024 0.002 TYR F 98 PHE 0.007 0.001 PHE E 104 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 0.00346 / 0.18 (12105) covalent geometry : angle 0.69362 / 0.40 (17481) hydrogen bonds : bond 0.05716 / 4.01 ( 724) hydrogen bonds : angle 3.56969 / 2.51 ( 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 285 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 255 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: A 59 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8635 (pm20) REVERT: A 93 GLN cc_start: 0.9053 (tp40) cc_final: 0.8446 (tp40) REVERT: A 105 GLU cc_start: 0.8879 (OUTLIER) cc_final: 0.8653 (pp20) REVERT: B 37 LEU cc_start: 0.9561 (OUTLIER) cc_final: 0.9281 (mp) REVERT: B 44 LYS cc_start: 0.9145 (ttmt) cc_final: 0.8722 (ttmt) REVERT: B 59 LYS cc_start: 0.9202 (ttmt) cc_final: 0.8722 (tttm) REVERT: B 63 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8808 (mt-10) REVERT: C 17 ARG cc_start: 0.8922 (mtm180) cc_final: 0.8570 (mtp180) REVERT: C 20 ARG cc_start: 0.9044 (ttm170) cc_final: 0.8557 (ttm110) REVERT: C 25 PHE cc_start: 0.8704 (m-80) cc_final: 0.8176 (m-80) REVERT: C 35 ARG cc_start: 0.9545 (ttp-110) cc_final: 0.9044 (ttm110) REVERT: C 36 LYS cc_start: 0.9192 (tmtt) cc_final: 0.8528 (tptt) REVERT: C 56 GLU cc_start: 0.8889 (tt0) cc_final: 0.8462 (tt0) REVERT: C 57 TYR cc_start: 0.8733 (t80) cc_final: 0.8439 (t80) REVERT: C 72 ASP cc_start: 0.9273 (p0) cc_final: 0.8974 (p0) REVERT: C 73 ASN cc_start: 0.9237 (t0) cc_final: 0.8650 (t0) REVERT: C 75 LYS cc_start: 0.8857 (mttm) cc_final: 0.8580 (mmtp) REVERT: C 84 GLN cc_start: 0.9521 (tp40) cc_final: 0.8906 (tp40) REVERT: C 99 ARG cc_start: 0.8737 (mmm160) cc_final: 0.8287 (mmp80) REVERT: C 102 ILE cc_start: 0.9307 (mp) cc_final: 0.8988 (mp) REVERT: C 104 GLN cc_start: 0.8600 (mp10) cc_final: 0.7957 (mp10) REVERT: D 65 ARG cc_start: 0.9113 (ptm-80) cc_final: 0.8769 (ptp-170) REVERT: D 78 GLN cc_start: 0.9356 (tp40) cc_final: 0.9050 (mm-40) REVERT: D 87 MET cc_start: 0.9047 (ttp) cc_final: 0.8754 (ttp) REVERT: D 117 GLN cc_start: 0.8735 (tm-30) cc_final: 0.8129 (tm-30) REVERT: D 118 MET cc_start: 0.9361 (mmt) cc_final: 0.8861 (mmm) REVERT: D 127 LYS cc_start: 0.9572 (tppt) cc_final: 0.9239 (tppt) REVERT: D 128 MET cc_start: 0.9459 (mtt) cc_final: 0.9213 (mtt) REVERT: D 130 LYS cc_start: 0.9235 (pttm) cc_final: 0.9032 (pttm) REVERT: E 59 GLU cc_start: 0.8742 (pm20) cc_final: 0.8387 (pm20) REVERT: E 73 GLU cc_start: 0.9088 (tt0) cc_final: 0.8545 (tt0) REVERT: E 79 LYS cc_start: 0.8644 (tttt) cc_final: 0.8266 (ttmt) REVERT: E 105 GLU cc_start: 0.8529 (pp20) cc_final: 0.8176 (pp20) REVERT: E 106 ASP cc_start: 0.9021 (m-30) cc_final: 0.8307 (m-30) REVERT: F 74 GLU cc_start: 0.9491 (tp30) cc_final: 0.8993 (tp30) REVERT: F 79 LYS cc_start: 0.9124 (mttp) cc_final: 0.8884 (mtmm) REVERT: F 85 ASP cc_start: 0.9310 (m-30) cc_final: 0.9078 (m-30) REVERT: F 88 TYR cc_start: 0.9377 (m-10) cc_final: 0.9092 (m-80) REVERT: F 98 TYR cc_start: 0.8313 (m-80) cc_final: 0.7401 (m-80) REVERT: G 36 LYS cc_start: 0.9666 (tttt) cc_final: 0.9377 (ttmm) REVERT: G 56 GLU cc_start: 0.8855 (tt0) cc_final: 0.8576 (tt0) REVERT: G 61 GLU cc_start: 0.9171 (tp30) cc_final: 0.8795 (tp30) REVERT: G 64 GLU cc_start: 0.8806 (tm-30) cc_final: 0.8183 (tm-30) REVERT: G 87 ILE cc_start: 0.9272 (tp) cc_final: 0.9036 (tp) REVERT: G 90 ASP cc_start: 0.8583 (t0) cc_final: 0.8153 (t0) REVERT: H 69 GLN cc_start: 0.9514 (pt0) cc_final: 0.9155 (pp30) REVERT: H 101 GLN cc_start: 0.8749 (pp30) cc_final: 0.7813 (pp30) REVERT: H 104 HIS cc_start: 0.9002 (t70) cc_final: 0.8388 (t-90) REVERT: H 105 TYR cc_start: 0.8570 (m-10) cc_final: 0.6813 (m-10) REVERT: H 118 MET cc_start: 0.9276 (mmt) cc_final: 0.8949 (mmm) REVERT: H 142 ARG cc_start: 0.9448 (ttm-80) cc_final: 0.8606 (ttm110) outliers start: 30 outliers final: 14 residues processed: 271 average time/residue: 0.1323 time to fit residues: 47.9768 Evaluate side-chains 258 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 241 time to evaluate : 0.301 ------------------------------------------------------------------------------- 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 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 16 THR Chi-restraints excluded: chain C residue 40 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: 9.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 23 optimal weight: 9.9990 chunk 80 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 73 ASN D 104 HIS E 68 GLN H 89 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.071002 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.043556 restraints weight = 48587.178| |-----------------------------------------------------------------------------| r_work (start): 0.2670 rms_B_bonded: 3.69 r_work (final): 0.2670 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.105 12105 Z= 0.324 Angle : 0.794 8.147 17481 Z= 0.445 Chirality : 0.047 0.215 1995 Planarity : 0.005 0.063 1303 Dihedral : 31.873 174.872 3719 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 17.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.72 % Allowed : 22.56 % Favored : 70.72 % 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: 0.20 (0.31), residues: 737 helix: 1.04 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -2.15 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 92 TYR 0.027 0.002 TYR B 88 PHE 0.015 0.002 PHE E 104 TRP 0.002 0.001 TRP D 149 HIS 0.006 0.002 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00669 / 0.32 (12105) covalent geometry : angle 0.79446 / 0.45 (17481) hydrogen bonds : bond 0.07382 / 5.08 ( 724) hydrogen bonds : angle 3.92879 / 2.75 ( 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 273 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 231 time to evaluate : 0.295 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8920 (OUTLIER) cc_final: 0.8630 (pm20) REVERT: A 73 GLU cc_start: 0.8304 (mm-30) cc_final: 0.7447 (tt0) REVERT: A 93 GLN cc_start: 0.9133 (tp40) cc_final: 0.8627 (tp40) REVERT: A 105 GLU cc_start: 0.8927 (pp20) cc_final: 0.8682 (pp20) REVERT: B 44 LYS cc_start: 0.9215 (ttmt) cc_final: 0.8796 (ttmt) REVERT: B 59 LYS cc_start: 0.9253 (ttmt) cc_final: 0.8849 (ttpp) REVERT: B 63 GLU cc_start: 0.9292 (mt-10) cc_final: 0.8843 (mt-10) REVERT: B 88 TYR cc_start: 0.9285 (m-10) cc_final: 0.8509 (m-10) REVERT: C 17 ARG cc_start: 0.9021 (mtm180) cc_final: 0.8575 (mtp180) REVERT: C 20 ARG cc_start: 0.9096 (ttm170) cc_final: 0.8570 (ttm110) REVERT: C 25 PHE cc_start: 0.8719 (m-80) cc_final: 0.8186 (m-80) REVERT: C 36 LYS cc_start: 0.9216 (tmtt) cc_final: 0.8652 (tptt) REVERT: C 42 ARG cc_start: 0.7914 (ptp-170) cc_final: 0.7570 (ptm160) REVERT: C 56 GLU cc_start: 0.8964 (tt0) cc_final: 0.8673 (tt0) REVERT: C 57 TYR cc_start: 0.8769 (t80) cc_final: 0.8446 (t80) REVERT: C 72 ASP cc_start: 0.9372 (p0) cc_final: 0.9128 (p0) REVERT: C 73 ASN cc_start: 0.9321 (OUTLIER) cc_final: 0.8465 (t0) REVERT: C 75 LYS cc_start: 0.8966 (mttm) cc_final: 0.8623 (mmtp) REVERT: C 84 GLN cc_start: 0.9596 (tp40) cc_final: 0.9044 (tp40) REVERT: C 99 ARG cc_start: 0.8801 (mmm160) cc_final: 0.8327 (mmp80) REVERT: C 102 ILE cc_start: 0.9395 (mp) cc_final: 0.9137 (mp) REVERT: D 57 ASP cc_start: 0.7563 (t0) cc_final: 0.7174 (t0) REVERT: D 65 ARG cc_start: 0.9214 (ptm-80) cc_final: 0.8821 (ptt180) REVERT: D 68 LYS cc_start: 0.9436 (mppt) cc_final: 0.9026 (mmtm) REVERT: D 87 MET cc_start: 0.9040 (ttp) cc_final: 0.8803 (ttp) REVERT: D 117 GLN cc_start: 0.8929 (tm-30) cc_final: 0.8316 (tm-30) REVERT: D 118 MET cc_start: 0.9358 (mmt) cc_final: 0.8873 (mmm) REVERT: D 127 LYS cc_start: 0.9595 (tppt) cc_final: 0.9257 (tppt) REVERT: D 128 MET cc_start: 0.9464 (mtt) cc_final: 0.9170 (mtp) REVERT: E 59 GLU cc_start: 0.8721 (pm20) cc_final: 0.8429 (pm20) REVERT: E 73 GLU cc_start: 0.9147 (tt0) cc_final: 0.8425 (tt0) REVERT: E 79 LYS cc_start: 0.8643 (tttt) cc_final: 0.8404 (ttmt) REVERT: E 105 GLU cc_start: 0.8574 (pp20) cc_final: 0.8257 (pp20) REVERT: E 106 ASP cc_start: 0.8972 (m-30) cc_final: 0.8394 (m-30) REVERT: F 74 GLU cc_start: 0.9475 (tp30) cc_final: 0.9103 (tp30) REVERT: F 79 LYS cc_start: 0.9161 (mttp) cc_final: 0.8832 (mtmm) REVERT: F 85 ASP cc_start: 0.9339 (m-30) cc_final: 0.9128 (m-30) REVERT: F 88 TYR cc_start: 0.9432 (m-10) cc_final: 0.9073 (m-80) REVERT: F 98 TYR cc_start: 0.8654 (m-80) cc_final: 0.7942 (m-80) REVERT: G 36 LYS cc_start: 0.9729 (tttt) cc_final: 0.9356 (ttmm) REVERT: G 56 GLU cc_start: 0.8846 (tt0) cc_final: 0.8606 (tt0) REVERT: G 61 GLU cc_start: 0.9215 (tp30) cc_final: 0.8911 (tp30) REVERT: G 64 GLU cc_start: 0.8871 (tm-30) cc_final: 0.8288 (tm-30) REVERT: G 87 ILE cc_start: 0.9303 (tp) cc_final: 0.9070 (tp) REVERT: H 69 GLN cc_start: 0.9549 (pt0) cc_final: 0.9205 (pp30) REVERT: H 85 ASP cc_start: 0.9320 (t0) cc_final: 0.8898 (t0) REVERT: H 104 HIS cc_start: 0.9031 (t70) cc_final: 0.8551 (t-90) REVERT: H 105 TYR cc_start: 0.8567 (m-10) cc_final: 0.7336 (m-10) REVERT: H 118 MET cc_start: 0.9262 (mmt) cc_final: 0.8993 (mmm) REVERT: H 130 LYS cc_start: 0.9507 (mmtp) cc_final: 0.9107 (mmmt) REVERT: H 142 ARG cc_start: 0.9513 (ttm-80) cc_final: 0.8720 (ttm110) outliers start: 42 outliers final: 27 residues processed: 254 average time/residue: 0.1125 time to fit residues: 38.3847 Evaluate side-chains 257 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 228 time to evaluate : 0.298 ------------------------------------------------------------------------------- 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 100 LEU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 60 VAL 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 73 ASN Chi-restraints excluded: chain C residue 92 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 60 THR 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 124 ILE 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 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: 2.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 82 optimal weight: 50.0000 chunk 71 optimal weight: 50.0000 chunk 7 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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 = 0.3530 r_free = 0.3530 target = 0.072872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.044997 restraints weight = 48019.521| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.76 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.1990 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= 0.178 Angle : 0.718 8.746 17481 Z= 0.409 Chirality : 0.045 0.217 1995 Planarity : 0.005 0.066 1303 Dihedral : 31.847 175.816 3719 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 14.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 4.80 % Allowed : 24.64 % Favored : 70.56 % 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: 0.45 (0.31), residues: 737 helix: 1.20 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.98 (0.42), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG C 35 TYR 0.026 0.002 TYR D 105 PHE 0.009 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00341 / 0.18 (12105) covalent geometry : angle 0.71826 / 0.41 (17481) hydrogen bonds : bond 0.05835 / 4.07 ( 724) hydrogen bonds : angle 3.60358 / 2.53 ( 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 279 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 249 time to evaluate : 0.303 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: 0.8873 (OUTLIER) cc_final: 0.8568 (pm20) REVERT: A 73 GLU cc_start: 0.8315 (mm-30) cc_final: 0.7488 (tt0) REVERT: A 93 GLN cc_start: 0.9059 (tp40) cc_final: 0.8467 (tp40) REVERT: B 44 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8749 (ttmt) REVERT: B 59 LYS cc_start: 0.9210 (ttmt) cc_final: 0.8784 (ttpp) REVERT: B 63 GLU cc_start: 0.9284 (mt-10) cc_final: 0.8837 (mt-10) REVERT: C 17 ARG cc_start: 0.8975 (mtm180) cc_final: 0.8588 (mtp180) REVERT: C 20 ARG cc_start: 0.9019 (ttm170) cc_final: 0.8538 (ttm110) REVERT: C 25 PHE cc_start: 0.8667 (m-80) cc_final: 0.8095 (m-80) REVERT: C 36 LYS cc_start: 0.9166 (tmtt) cc_final: 0.8530 (tptt) REVERT: C 42 ARG cc_start: 0.7833 (ptp-170) cc_final: 0.7094 (mtm110) REVERT: C 56 GLU cc_start: 0.8918 (tt0) cc_final: 0.8482 (tt0) REVERT: C 57 TYR cc_start: 0.8759 (t80) cc_final: 0.8459 (t80) REVERT: C 72 ASP cc_start: 0.9263 (p0) cc_final: 0.9010 (p0) REVERT: C 73 ASN cc_start: 0.9222 (t0) cc_final: 0.8530 (t0) REVERT: C 75 LYS cc_start: 0.8839 (mttm) cc_final: 0.8544 (mmtp) REVERT: C 84 GLN cc_start: 0.9516 (tp40) cc_final: 0.8959 (tp40) REVERT: C 99 ARG cc_start: 0.8787 (mmm160) cc_final: 0.8354 (mmp80) REVERT: C 102 ILE cc_start: 0.9313 (mp) cc_final: 0.9077 (mp) REVERT: C 104 GLN cc_start: 0.8514 (mp10) cc_final: 0.8215 (mp10) REVERT: D 63 PHE cc_start: 0.9386 (m-80) cc_final: 0.9067 (m-80) REVERT: D 75 SER cc_start: 0.8269 (m) cc_final: 0.7665 (p) REVERT: D 78 GLN cc_start: 0.9380 (tp40) cc_final: 0.9124 (mm-40) REVERT: D 87 MET cc_start: 0.9025 (ttp) cc_final: 0.8796 (ttp) REVERT: D 117 GLN cc_start: 0.8864 (tm-30) cc_final: 0.8161 (tm-30) REVERT: D 118 MET cc_start: 0.9364 (mmt) cc_final: 0.8870 (mmm) REVERT: D 127 LYS cc_start: 0.9570 (tppt) cc_final: 0.9264 (tppt) REVERT: D 128 MET cc_start: 0.9415 (mtt) cc_final: 0.9202 (mtt) REVERT: E 59 GLU cc_start: 0.8694 (pm20) cc_final: 0.8395 (pm20) REVERT: E 73 GLU cc_start: 0.9098 (tt0) cc_final: 0.8259 (tt0) REVERT: E 79 LYS cc_start: 0.8642 (tttt) cc_final: 0.8330 (ttmt) REVERT: E 105 GLU cc_start: 0.8606 (pp20) cc_final: 0.8233 (pp20) REVERT: E 106 ASP cc_start: 0.9031 (m-30) cc_final: 0.8353 (m-30) REVERT: F 74 GLU cc_start: 0.9477 (tp30) cc_final: 0.9054 (tp30) REVERT: F 79 LYS cc_start: 0.9185 (mttp) cc_final: 0.8867 (mtmm) REVERT: F 85 ASP cc_start: 0.9308 (m-30) cc_final: 0.9062 (m-30) REVERT: F 88 TYR cc_start: 0.9378 (m-10) cc_final: 0.8952 (m-10) REVERT: F 98 TYR cc_start: 0.8605 (m-10) cc_final: 0.7995 (m-80) REVERT: G 36 LYS cc_start: 0.9618 (tttt) cc_final: 0.9374 (ttmm) REVERT: G 39 TYR cc_start: 0.8950 (m-80) cc_final: 0.8719 (m-80) REVERT: G 56 GLU cc_start: 0.8824 (tt0) cc_final: 0.8609 (tt0) REVERT: G 61 GLU cc_start: 0.9196 (tp30) cc_final: 0.8851 (tp30) REVERT: G 64 GLU cc_start: 0.8810 (tm-30) cc_final: 0.8214 (tm-30) REVERT: G 87 ILE cc_start: 0.9332 (tp) cc_final: 0.9126 (tp) REVERT: G 88 ARG cc_start: 0.9503 (mmt-90) cc_final: 0.9212 (tpp80) REVERT: H 69 GLN cc_start: 0.9550 (pt0) cc_final: 0.9192 (pp30) REVERT: H 85 ASP cc_start: 0.9304 (t0) cc_final: 0.8954 (t0) REVERT: H 104 HIS cc_start: 0.9019 (t70) cc_final: 0.8421 (t-90) REVERT: H 105 TYR cc_start: 0.8506 (m-10) cc_final: 0.7602 (m-10) REVERT: H 118 MET cc_start: 0.9251 (mmt) cc_final: 0.9001 (mmm) REVERT: H 142 ARG cc_start: 0.9470 (ttm-80) cc_final: 0.8636 (ttm110) outliers start: 30 outliers final: 19 residues processed: 264 average time/residue: 0.1250 time to fit residues: 44.0793 Evaluate side-chains 262 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 242 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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 110 CYS Chi-restraints excluded: chain A residue 122 LYS Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 37 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 60 THR Chi-restraints excluded: chain D residue 88 ILE Chi-restraints excluded: chain D residue 120 VAL Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 49 LEU 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 81 optimal weight: 30.0000 chunk 29 optimal weight: 0.9980 chunk 80 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 58 optimal weight: 0.1980 chunk 9 optimal weight: 4.9990 chunk 88 optimal weight: 30.0000 chunk 92 optimal weight: 20.0000 chunk 50 optimal weight: 2.9990 chunk 79 optimal weight: 20.0000 chunk 40 optimal weight: 1.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 104 HIS H 89 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3539 r_free = 0.3539 target = 0.073394 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2852 r_free = 0.2852 target = 0.045214 restraints weight = 48144.159| |-----------------------------------------------------------------------------| r_work (start): 0.2731 rms_B_bonded: 3.77 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.2090 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= 0.175 Angle : 0.714 8.242 17481 Z= 0.408 Chirality : 0.045 0.219 1995 Planarity : 0.005 0.068 1303 Dihedral : 31.774 175.310 3719 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 5.44 % Allowed : 24.48 % Favored : 70.08 % 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: 1.27 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.82 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 108 TYR 0.028 0.002 TYR C 39 PHE 0.010 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.007 0.001 HIS A 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 (12105) covalent geometry : angle 0.71401 / 0.41 (17481) hydrogen bonds : bond 0.05600 / 3.94 ( 724) hydrogen bonds : angle 3.53166 / 2.48 ( 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 280 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 246 time to evaluate : 0.308 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: 0.8839 (OUTLIER) cc_final: 0.8511 (pm20) REVERT: A 73 GLU cc_start: 0.8333 (mm-30) cc_final: 0.7503 (tt0) REVERT: A 93 GLN cc_start: 0.9046 (tp40) cc_final: 0.8453 (tp40) REVERT: B 44 LYS cc_start: 0.9190 (ttmt) cc_final: 0.8784 (ttmt) REVERT: B 59 LYS cc_start: 0.9173 (ttmt) cc_final: 0.8743 (tttm) REVERT: B 63 GLU cc_start: 0.9288 (mt-10) cc_final: 0.8747 (mt-10) REVERT: B 88 TYR cc_start: 0.9236 (m-10) cc_final: 0.8926 (m-80) REVERT: C 25 PHE cc_start: 0.8684 (m-80) cc_final: 0.8018 (m-80) REVERT: C 35 ARG cc_start: 0.9537 (ttm110) cc_final: 0.9157 (ttm110) REVERT: C 36 LYS cc_start: 0.9133 (tmtt) cc_final: 0.8853 (tptp) REVERT: C 42 ARG cc_start: 0.7827 (ptp-170) cc_final: 0.7081 (mtm110) REVERT: C 56 GLU cc_start: 0.8919 (tt0) cc_final: 0.8370 (tt0) REVERT: C 57 TYR cc_start: 0.8785 (t80) cc_final: 0.8460 (t80) REVERT: C 72 ASP cc_start: 0.9311 (p0) cc_final: 0.8963 (p0) REVERT: C 73 ASN cc_start: 0.9219 (t0) cc_final: 0.8523 (t0) REVERT: C 75 LYS cc_start: 0.8871 (mttm) cc_final: 0.8544 (mmtp) REVERT: C 77 ARG cc_start: 0.8734 (tpp80) cc_final: 0.8229 (mmm-85) REVERT: C 84 GLN cc_start: 0.9486 (tp40) cc_final: 0.8953 (tp40) REVERT: C 99 ARG cc_start: 0.8788 (mmm160) cc_final: 0.8353 (mmp80) REVERT: C 102 ILE cc_start: 0.9246 (mp) cc_final: 0.8989 (mp) REVERT: C 104 GLN cc_start: 0.8578 (mp10) cc_final: 0.8216 (mp10) REVERT: D 75 SER cc_start: 0.8156 (m) cc_final: 0.7676 (p) REVERT: D 78 GLN cc_start: 0.9400 (tp40) cc_final: 0.9146 (mm-40) REVERT: D 87 MET cc_start: 0.9054 (ttp) cc_final: 0.8817 (ttp) REVERT: D 117 GLN cc_start: 0.8827 (tm-30) cc_final: 0.8111 (tm-30) REVERT: D 118 MET cc_start: 0.9390 (mmt) cc_final: 0.8933 (mmm) REVERT: D 127 LYS cc_start: 0.9578 (tppt) cc_final: 0.9264 (tppt) REVERT: D 128 MET cc_start: 0.9427 (mtt) cc_final: 0.9223 (mtt) REVERT: E 59 GLU cc_start: 0.8660 (pm20) cc_final: 0.8424 (pm20) REVERT: E 73 GLU cc_start: 0.9050 (tt0) cc_final: 0.8334 (tt0) REVERT: E 79 LYS cc_start: 0.8635 (tttt) cc_final: 0.8337 (ttmt) REVERT: E 105 GLU cc_start: 0.8594 (pp20) cc_final: 0.8200 (pp20) REVERT: E 106 ASP cc_start: 0.9039 (m-30) cc_final: 0.8342 (m-30) REVERT: E 120 MET cc_start: 0.8766 (mmm) cc_final: 0.8376 (mmm) REVERT: F 74 GLU cc_start: 0.9485 (tp30) cc_final: 0.9064 (tp30) REVERT: F 79 LYS cc_start: 0.9168 (mttp) cc_final: 0.8928 (mtmm) REVERT: F 85 ASP cc_start: 0.9286 (m-30) cc_final: 0.9072 (m-30) REVERT: F 88 TYR cc_start: 0.9382 (m-10) cc_final: 0.8968 (m-10) REVERT: F 98 TYR cc_start: 0.8682 (m-10) cc_final: 0.7980 (m-80) REVERT: G 36 LYS cc_start: 0.9678 (tttt) cc_final: 0.9295 (ttmm) REVERT: G 39 TYR cc_start: 0.8960 (m-80) cc_final: 0.8707 (m-80) REVERT: G 56 GLU cc_start: 0.8816 (tt0) cc_final: 0.8550 (tt0) REVERT: G 61 GLU cc_start: 0.9199 (tp30) cc_final: 0.8885 (tp30) REVERT: G 64 GLU cc_start: 0.8825 (tm-30) cc_final: 0.8231 (tm-30) REVERT: G 87 ILE cc_start: 0.9364 (tp) cc_final: 0.9143 (tp) REVERT: G 88 ARG cc_start: 0.9507 (mmt-90) cc_final: 0.9183 (tpp80) REVERT: H 69 GLN cc_start: 0.9536 (pt0) cc_final: 0.9164 (pp30) REVERT: H 85 ASP cc_start: 0.9338 (t0) cc_final: 0.8963 (t0) REVERT: H 101 GLN cc_start: 0.9212 (pt0) cc_final: 0.9012 (pt0) REVERT: H 105 TYR cc_start: 0.8691 (m-10) cc_final: 0.7445 (m-10) REVERT: H 118 MET cc_start: 0.9244 (mmt) cc_final: 0.8986 (mmm) REVERT: H 142 ARG cc_start: 0.9468 (ttm-80) cc_final: 0.8665 (ttm110) outliers start: 34 outliers final: 22 residues processed: 263 average time/residue: 0.1338 time to fit residues: 46.9231 Evaluate side-chains 265 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 242 time to evaluate : 0.303 ------------------------------------------------------------------------------- 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 125 GLN 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 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 93 LEU 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 41 optimal weight: 5.9990 chunk 50 optimal weight: 0.9990 chunk 15 optimal weight: 0.8980 chunk 72 optimal weight: 50.0000 chunk 27 optimal weight: 5.9990 chunk 33 optimal weight: 7.9990 chunk 82 optimal weight: 50.0000 chunk 7 optimal weight: 5.9990 chunk 12 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 chunk 94 optimal weight: 30.0000 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.3593 r_free = 0.3593 target = 0.074861 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.045852 restraints weight = 46600.276| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 3.72 r_work (final): 0.2764 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.2257 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= 0.170 Angle : 0.717 10.063 17481 Z= 0.408 Chirality : 0.045 0.220 1995 Planarity : 0.005 0.067 1303 Dihedral : 31.726 175.237 3719 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 14.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.16 % Allowed : 26.56 % Favored : 69.28 % 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: 0.63 (0.32), residues: 737 helix: 1.27 (0.23), residues: 522 sheet: None (None), residues: 0 loop : -1.74 (0.43), residues: 215 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 71 TYR 0.024 0.002 TYR C 39 PHE 0.009 0.001 PHE D 63 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 0.00327 / 0.17 (12105) covalent geometry : angle 0.71723 / 0.41 (17481) hydrogen bonds : bond 0.05500 / 3.87 ( 724) hydrogen bonds : angle 3.51521 / 2.47 ( 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 274 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 248 time to evaluate : 0.267 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 73 GLU cc_start: 0.8321 (mm-30) cc_final: 0.7482 (tt0) REVERT: A 93 GLN cc_start: 0.8984 (tp40) cc_final: 0.8435 (tp40) REVERT: B 44 LYS cc_start: 0.9174 (ttmt) cc_final: 0.8754 (ttmt) REVERT: B 59 LYS cc_start: 0.9104 (ttmt) cc_final: 0.8656 (tttm) REVERT: B 63 GLU cc_start: 0.9266 (mt-10) cc_final: 0.8806 (mt-10) REVERT: B 88 TYR cc_start: 0.9184 (m-10) cc_final: 0.8927 (m-80) REVERT: C 35 ARG cc_start: 0.9529 (ttm110) cc_final: 0.9143 (ttm110) REVERT: C 36 LYS cc_start: 0.9151 (tmtt) cc_final: 0.8862 (tptp) REVERT: C 42 ARG cc_start: 0.7751 (ptp-170) cc_final: 0.7019 (mtm110) REVERT: C 56 GLU cc_start: 0.8928 (tt0) cc_final: 0.8578 (tt0) REVERT: C 57 TYR cc_start: 0.8757 (t80) cc_final: 0.8430 (t80) REVERT: C 72 ASP cc_start: 0.9315 (p0) cc_final: 0.8964 (p0) REVERT: C 73 ASN cc_start: 0.9255 (t0) cc_final: 0.8596 (t0) REVERT: C 75 LYS cc_start: 0.8861 (mttm) cc_final: 0.8518 (mmtp) REVERT: C 77 ARG cc_start: 0.8756 (tpp80) cc_final: 0.8217 (mmm-85) REVERT: C 84 GLN cc_start: 0.9475 (tp40) cc_final: 0.8916 (tp40) REVERT: C 102 ILE cc_start: 0.9170 (mp) cc_final: 0.8925 (mp) REVERT: C 104 GLN cc_start: 0.8672 (mp10) cc_final: 0.8309 (mp10) REVERT: D 75 SER cc_start: 0.8174 (m) cc_final: 0.7679 (p) REVERT: D 78 GLN cc_start: 0.9415 (tp40) cc_final: 0.9185 (mm-40) REVERT: D 87 MET cc_start: 0.9033 (ttp) cc_final: 0.8784 (ttp) REVERT: D 117 GLN cc_start: 0.8772 (tm-30) cc_final: 0.8085 (tm-30) REVERT: D 118 MET cc_start: 0.9326 (mmt) cc_final: 0.8894 (mmm) REVERT: E 59 GLU cc_start: 0.8652 (pm20) cc_final: 0.8418 (pm20) REVERT: E 73 GLU cc_start: 0.9049 (tt0) cc_final: 0.8276 (tt0) REVERT: E 79 LYS cc_start: 0.8586 (tttt) cc_final: 0.8230 (ttmt) REVERT: E 105 GLU cc_start: 0.8604 (pp20) cc_final: 0.8220 (pp20) REVERT: E 106 ASP cc_start: 0.9048 (m-30) cc_final: 0.8371 (m-30) REVERT: E 120 MET cc_start: 0.8770 (mmm) cc_final: 0.8385 (mmm) REVERT: F 74 GLU cc_start: 0.9507 (tp30) cc_final: 0.9120 (tp30) REVERT: F 79 LYS cc_start: 0.9162 (mttp) cc_final: 0.8892 (mtmm) REVERT: F 85 ASP cc_start: 0.9325 (m-30) cc_final: 0.9107 (m-30) REVERT: F 88 TYR cc_start: 0.9395 (m-10) cc_final: 0.8950 (m-10) REVERT: F 98 TYR cc_start: 0.8704 (m-10) cc_final: 0.7961 (m-80) REVERT: G 36 LYS cc_start: 0.9598 (tttt) cc_final: 0.9358 (ttmm) REVERT: G 39 TYR cc_start: 0.8950 (m-80) cc_final: 0.8676 (m-80) REVERT: G 56 GLU cc_start: 0.8773 (tt0) cc_final: 0.8486 (tt0) REVERT: G 61 GLU cc_start: 0.9178 (tp30) cc_final: 0.8846 (tp30) REVERT: G 64 GLU cc_start: 0.8803 (tm-30) cc_final: 0.8227 (tm-30) REVERT: G 87 ILE cc_start: 0.9357 (tp) cc_final: 0.9138 (tp) REVERT: G 88 ARG cc_start: 0.9477 (mmt-90) cc_final: 0.9148 (tpp80) REVERT: H 62 TYR cc_start: 0.9434 (m-80) cc_final: 0.8979 (m-80) REVERT: H 69 GLN cc_start: 0.9572 (pt0) cc_final: 0.9199 (pp30) REVERT: H 85 ASP cc_start: 0.9306 (t0) cc_final: 0.8890 (t0) REVERT: H 105 TYR cc_start: 0.8673 (m-10) cc_final: 0.7481 (m-10) REVERT: H 118 MET cc_start: 0.9232 (mmt) cc_final: 0.8974 (mmm) REVERT: H 142 ARG cc_start: 0.9454 (ttm-80) cc_final: 0.8648 (ttm110) outliers start: 26 outliers final: 19 residues processed: 259 average time/residue: 0.1263 time to fit residues: 43.6767 Evaluate side-chains 262 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 243 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU 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 92 GLU 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 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: 0.9980 chunk 4 optimal weight: 5.9990 chunk 24 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 2 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 36 optimal weight: 20.0000 chunk 56 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 94 optimal weight: 30.0000 chunk 11 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- 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 = 0.3611 r_free = 0.3611 target = 0.075760 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2922 r_free = 0.2922 target = 0.046686 restraints weight = 46149.554| |-----------------------------------------------------------------------------| r_work (start): 0.2790 rms_B_bonded: 3.66 r_work (final): 0.2790 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 12105 Z= 0.161 Angle : 0.732 9.179 17481 Z= 0.415 Chirality : 0.045 0.221 1995 Planarity : 0.005 0.067 1303 Dihedral : 31.663 175.307 3719 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 14.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.16 % Allowed : 27.36 % Favored : 68.48 % 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: 0.64 (0.31), residues: 737 helix: 1.25 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.62 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG C 99 TYR 0.022 0.002 TYR C 39 PHE 0.013 0.001 PHE D 63 TRP 0.001 0.000 TRP D 149 HIS 0.005 0.001 HIS D 104 Details of bonding type rmsd/Z covalent geometry : bond 0.00305 / 0.16 (12105) covalent geometry : angle 0.73173 / 0.41 (17481) hydrogen bonds : bond 0.05324 / 3.77 ( 724) hydrogen bonds : angle 3.48479 / 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 279 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 253 time to evaluate : 0.379 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: 0.8734 (pm20) cc_final: 0.8534 (pm20) REVERT: A 73 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7484 (tt0) REVERT: A 93 GLN cc_start: 0.8857 (tp40) cc_final: 0.8346 (tp40) REVERT: B 44 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8712 (ttmt) REVERT: B 59 LYS cc_start: 0.9087 (ttmt) cc_final: 0.8680 (tttm) REVERT: B 63 GLU cc_start: 0.9260 (mt-10) cc_final: 0.8789 (mt-10) REVERT: B 88 TYR cc_start: 0.9174 (m-10) cc_final: 0.8953 (m-80) REVERT: C 17 ARG cc_start: 0.8494 (mtm180) cc_final: 0.7926 (mtm180) REVERT: C 20 ARG cc_start: 0.9039 (ttm170) cc_final: 0.8529 (ttm110) REVERT: C 25 PHE cc_start: 0.8750 (m-80) cc_final: 0.8202 (m-80) REVERT: C 36 LYS cc_start: 0.9137 (tmtt) cc_final: 0.8850 (tptp) REVERT: C 42 ARG cc_start: 0.7734 (ptp-170) cc_final: 0.6987 (mtm110) REVERT: C 56 GLU cc_start: 0.8947 (tt0) cc_final: 0.8458 (tt0) REVERT: C 57 TYR cc_start: 0.8815 (t80) cc_final: 0.8563 (t80) REVERT: C 72 ASP cc_start: 0.9306 (p0) cc_final: 0.8938 (p0) REVERT: C 73 ASN cc_start: 0.9246 (t0) cc_final: 0.8551 (t0) REVERT: C 75 LYS cc_start: 0.8802 (mttm) cc_final: 0.8559 (mmtm) REVERT: C 84 GLN cc_start: 0.9469 (tp40) cc_final: 0.8958 (tp40) REVERT: C 92 GLU cc_start: 0.9408 (OUTLIER) cc_final: 0.9018 (pt0) REVERT: C 99 ARG cc_start: 0.8816 (mmm160) cc_final: 0.8407 (mmp80) REVERT: C 102 ILE cc_start: 0.9139 (mp) cc_final: 0.8894 (mp) REVERT: C 104 GLN cc_start: 0.8686 (mp10) cc_final: 0.8352 (mp10) REVERT: D 87 MET cc_start: 0.9078 (ttp) cc_final: 0.8822 (ttp) REVERT: D 108 ARG cc_start: 0.8760 (mtm110) cc_final: 0.8554 (mtm110) REVERT: D 118 MET cc_start: 0.9315 (mmt) cc_final: 0.9025 (mmp) REVERT: D 127 LYS cc_start: 0.9551 (tppt) cc_final: 0.9312 (tppt) REVERT: E 59 GLU cc_start: 0.8603 (pm20) cc_final: 0.8396 (pm20) REVERT: E 73 GLU cc_start: 0.9030 (tt0) cc_final: 0.8295 (tt0) REVERT: E 79 LYS cc_start: 0.8528 (tttt) cc_final: 0.8164 (ttmt) REVERT: E 105 GLU cc_start: 0.8595 (pp20) cc_final: 0.8247 (pp20) REVERT: E 106 ASP cc_start: 0.9075 (m-30) cc_final: 0.8415 (m-30) REVERT: E 120 MET cc_start: 0.8794 (mmm) cc_final: 0.8411 (mmm) REVERT: F 74 GLU cc_start: 0.9506 (tp30) cc_final: 0.9105 (tp30) REVERT: F 79 LYS cc_start: 0.9155 (mttp) cc_final: 0.8893 (mtmm) REVERT: F 88 TYR cc_start: 0.9381 (m-10) cc_final: 0.8995 (m-10) REVERT: F 98 TYR cc_start: 0.8593 (m-10) cc_final: 0.7808 (m-80) REVERT: G 36 LYS cc_start: 0.9660 (tttt) cc_final: 0.9299 (ttmm) REVERT: G 39 TYR cc_start: 0.8917 (m-80) cc_final: 0.8603 (m-80) REVERT: G 56 GLU cc_start: 0.8771 (tt0) cc_final: 0.8496 (tt0) REVERT: G 61 GLU cc_start: 0.9149 (tp30) cc_final: 0.8804 (tp30) REVERT: G 64 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8008 (tm-30) REVERT: G 68 ASN cc_start: 0.8948 (m-40) cc_final: 0.8115 (m-40) REVERT: G 87 ILE cc_start: 0.9363 (tp) cc_final: 0.9136 (tp) REVERT: G 88 ARG cc_start: 0.9483 (mmt-90) cc_final: 0.9127 (tpp80) REVERT: H 62 TYR cc_start: 0.9399 (m-80) cc_final: 0.9009 (m-80) REVERT: H 69 GLN cc_start: 0.9531 (pt0) cc_final: 0.9162 (pp30) REVERT: H 85 ASP cc_start: 0.9306 (t0) cc_final: 0.8867 (t0) REVERT: H 105 TYR cc_start: 0.8619 (m-10) cc_final: 0.7372 (m-10) REVERT: H 118 MET cc_start: 0.9241 (mmt) cc_final: 0.8906 (mmm) REVERT: H 142 ARG cc_start: 0.9437 (ttm-80) cc_final: 0.8619 (ttm110) outliers start: 26 outliers final: 18 residues processed: 264 average time/residue: 0.1312 time to fit residues: 46.0659 Evaluate side-chains 263 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 244 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU 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 92 GLU 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 43 VAL 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 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 97 random chunks: chunk 93 optimal weight: 20.0000 chunk 52 optimal weight: 5.9990 chunk 41 optimal weight: 5.9990 chunk 71 optimal weight: 50.0000 chunk 94 optimal weight: 30.0000 chunk 75 optimal weight: 20.0000 chunk 58 optimal weight: 0.3980 chunk 57 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 0.7980 overall best weight: 3.2386 ------------------------------------------------------------------------------- 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 = 0.3587 r_free = 0.3587 target = 0.074650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.045771 restraints weight = 47017.717| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.73 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.2463 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 12105 Z= 0.205 Angle : 0.756 8.877 17481 Z= 0.424 Chirality : 0.046 0.221 1995 Planarity : 0.005 0.068 1303 Dihedral : 31.671 174.928 3719 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 15.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.68 % Allowed : 28.32 % 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: 0.65 (0.31), residues: 737 helix: 1.23 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.53 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG C 99 TYR 0.024 0.002 TYR C 50 PHE 0.012 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 0.00419 / 0.20 (12105) covalent geometry : angle 0.75584 / 0.42 (17481) hydrogen bonds : bond 0.05703 / 4.00 ( 724) hydrogen bonds : angle 3.56685 / 2.49 ( 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 266 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 243 time to evaluate : 0.338 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 73 GLU cc_start: 0.8310 (mm-30) cc_final: 0.7454 (tt0) REVERT: A 93 GLN cc_start: 0.8952 (tp40) cc_final: 0.8433 (tp40) REVERT: B 44 LYS cc_start: 0.9180 (ttmt) cc_final: 0.8794 (ttmt) REVERT: B 59 LYS cc_start: 0.9082 (ttmt) cc_final: 0.8685 (tttm) REVERT: B 63 GLU cc_start: 0.9233 (mt-10) cc_final: 0.8773 (mt-10) REVERT: B 88 TYR cc_start: 0.9202 (m-10) cc_final: 0.8972 (m-80) REVERT: C 17 ARG cc_start: 0.8534 (mtm180) cc_final: 0.7963 (mtm180) REVERT: C 20 ARG cc_start: 0.9083 (ttm170) cc_final: 0.8608 (ttm110) REVERT: C 25 PHE cc_start: 0.8705 (m-80) cc_final: 0.8101 (m-80) REVERT: C 35 ARG cc_start: 0.9556 (ttm110) cc_final: 0.9154 (ttm110) REVERT: C 36 LYS cc_start: 0.9136 (tmtt) cc_final: 0.8917 (tptp) REVERT: C 42 ARG cc_start: 0.7838 (ptp-170) cc_final: 0.7084 (mtm110) REVERT: C 56 GLU cc_start: 0.8905 (tt0) cc_final: 0.8412 (tt0) REVERT: C 71 ARG cc_start: 0.9533 (ttm-80) cc_final: 0.8762 (mmt90) REVERT: C 72 ASP cc_start: 0.9335 (p0) cc_final: 0.8963 (p0) REVERT: C 73 ASN cc_start: 0.9267 (t0) cc_final: 0.8597 (t0) REVERT: C 75 LYS cc_start: 0.8837 (mttm) cc_final: 0.8514 (mmtm) REVERT: C 84 GLN cc_start: 0.9471 (tp40) cc_final: 0.8949 (tp40) REVERT: C 92 GLU cc_start: 0.9451 (OUTLIER) cc_final: 0.9039 (pt0) REVERT: C 93 LEU cc_start: 0.9191 (OUTLIER) cc_final: 0.8937 (mm) REVERT: C 99 ARG cc_start: 0.8849 (mmm160) cc_final: 0.8384 (mmp80) REVERT: C 102 ILE cc_start: 0.9150 (mp) cc_final: 0.8918 (mp) REVERT: C 104 GLN cc_start: 0.8706 (mp10) cc_final: 0.7888 (mp10) REVERT: D 87 MET cc_start: 0.9068 (ttp) cc_final: 0.8861 (ttp) REVERT: D 127 LYS cc_start: 0.9564 (tppt) cc_final: 0.9348 (tppt) REVERT: E 59 GLU cc_start: 0.8582 (pm20) cc_final: 0.8346 (pm20) REVERT: E 73 GLU cc_start: 0.9054 (tt0) cc_final: 0.8292 (tt0) REVERT: E 79 LYS cc_start: 0.8497 (tttt) cc_final: 0.8170 (ttmt) REVERT: E 105 GLU cc_start: 0.8569 (pp20) cc_final: 0.8234 (pp20) REVERT: E 106 ASP cc_start: 0.9071 (m-30) cc_final: 0.8437 (m-30) REVERT: E 120 MET cc_start: 0.8831 (mmm) cc_final: 0.8445 (mmm) REVERT: F 74 GLU cc_start: 0.9521 (tp30) cc_final: 0.9141 (tp30) REVERT: F 79 LYS cc_start: 0.9147 (mttp) cc_final: 0.8873 (mtmm) REVERT: F 88 TYR cc_start: 0.9400 (m-10) cc_final: 0.9011 (m-80) REVERT: F 98 TYR cc_start: 0.8683 (m-10) cc_final: 0.8004 (m-80) REVERT: G 36 LYS cc_start: 0.9623 (tttt) cc_final: 0.9385 (ttmm) REVERT: G 39 TYR cc_start: 0.8937 (m-80) cc_final: 0.8623 (m-80) REVERT: G 56 GLU cc_start: 0.8761 (tt0) cc_final: 0.8481 (tt0) REVERT: G 61 GLU cc_start: 0.9195 (tp30) cc_final: 0.8909 (tp30) REVERT: G 64 GLU cc_start: 0.8835 (tm-30) cc_final: 0.8251 (tm-30) REVERT: G 87 ILE cc_start: 0.9342 (tp) cc_final: 0.9117 (tp) REVERT: H 69 GLN cc_start: 0.9558 (pt0) cc_final: 0.9202 (pp30) REVERT: H 85 ASP cc_start: 0.9272 (t0) cc_final: 0.8856 (t0) REVERT: H 101 GLN cc_start: 0.9144 (tt0) cc_final: 0.8610 (tm-30) REVERT: H 105 TYR cc_start: 0.8627 (m-10) cc_final: 0.6892 (m-10) REVERT: H 118 MET cc_start: 0.9245 (mmt) cc_final: 0.8982 (mmm) REVERT: H 142 ARG cc_start: 0.9460 (ttm-80) cc_final: 0.8637 (ttm110) outliers start: 23 outliers final: 19 residues processed: 253 average time/residue: 0.1323 time to fit residues: 44.8672 Evaluate side-chains 263 residues out of total 625 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 242 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 94 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 92 GLU Chi-restraints excluded: chain C residue 93 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 43 VAL 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 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: 8.9990 chunk 89 optimal weight: 30.0000 chunk 71 optimal weight: 50.0000 chunk 4 optimal weight: 0.9980 chunk 43 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 93 optimal weight: 30.0000 chunk 78 optimal weight: 30.0000 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 38 ASN C 110 ASN D 104 HIS H 89 HIS H 104 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.075949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.046696 restraints weight = 46681.971| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.72 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.2586 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 12105 Z= 0.167 Angle : 0.746 8.731 17481 Z= 0.420 Chirality : 0.046 0.286 1995 Planarity : 0.005 0.068 1303 Dihedral : 31.618 175.397 3719 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 14.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 3.84 % Allowed : 28.48 % Favored : 67.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.65 (0.31), residues: 737 helix: 1.22 (0.23), residues: 521 sheet: None (None), residues: 0 loop : -1.49 (0.43), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 99 TYR 0.022 0.002 TYR C 39 PHE 0.011 0.001 PHE D 63 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 0.00328 / 0.17 (12105) covalent geometry : angle 0.74622 / 0.42 (17481) hydrogen bonds : bond 0.05294 / 3.75 ( 724) hydrogen bonds : angle 3.47400 / 2.43 ( 1800) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2224.12 seconds wall clock time: 38 minutes 53.87 seconds (2333.87 seconds total)