Starting phenix.real_space_refine on Sun Apr 5 18:31:01 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igj_52852/04_2026/9igj_52852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igj_52852/04_2026/9igj_52852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9igj_52852/04_2026/9igj_52852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igj_52852/04_2026/9igj_52852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9igj_52852/04_2026/9igj_52852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igj_52852/04_2026/9igj_52852.map" } resolution = 3.8 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= 0.002 sd= 0.007 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 250 5.49 5 S 22 5.16 5 C 7126 2.51 5 N 2332 2.21 5 O 2799 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 83 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12529 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 791 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 843 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 784 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 3, 'TRANS': 91} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 795 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 5, 'TRANS': 97} Chain: "H" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 90, 699 Classifications: {'peptide': 90} Link IDs: {'PTRANS': 2, 'TRANS': 87} Chain: "L" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 737 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "K" Number of atoms: 737 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 737 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "J" Number of atoms: 2560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2560 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Chain: "I" Number of atoms: 2565 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 2565 Classifications: {'DNA': 125} Link IDs: {'rna3p': 124} Time building chain proxies: 2.97, per 1000 atoms: 0.24 Number of scatterers: 12529 At special positions: 0 Unit cell: (88.672, 138.224, 143.44, 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 22 16.00 P 250 15.00 O 2799 8.00 N 2332 7.00 C 7126 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: 1.13 Conformation dependent library (CDL) restraints added in 416.7 milliseconds 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1724 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 12 sheets defined 70.9% alpha, 5.0% beta 125 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 1.70 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 24 through 29 removed outlier: 3.709A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.772A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 124 removed outlier: 3.653A pdb=" N ALA D 107 " --> pdb=" O PRO D 103 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.753A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 92 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 73 removed outlier: 4.558A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.501A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.575A pdb=" N LYS H 108 " --> pdb=" O GLY H 104 " (cutoff:3.500A) Processing helix chain 'L' and resid 209 through 220 Processing helix chain 'L' and resid 223 through 227 Processing helix chain 'L' and resid 233 through 235 No H-bonds generated for 'chain 'L' and resid 233 through 235' Processing helix chain 'L' and resid 242 through 254 Processing helix chain 'L' and resid 260 through 274 removed outlier: 3.697A pdb=" N GLN L 273 " --> pdb=" O ARG L 269 " (cutoff:3.500A) Processing helix chain 'K' and resid 209 through 220 Processing helix chain 'K' and resid 223 through 227 Processing helix chain 'K' and resid 233 through 235 No H-bonds generated for 'chain 'K' and resid 233 through 235' Processing helix chain 'K' and resid 242 through 254 Processing helix chain 'K' and resid 260 through 274 removed outlier: 3.702A pdb=" N GLN K 273 " --> pdb=" O ARG K 269 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.897A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.945A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.550A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.907A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.095A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'L' and resid 228 through 232 removed outlier: 6.778A pdb=" N ILE L 237 " --> pdb=" O THR L 231 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 228 through 232 removed outlier: 5.671A pdb=" N TRP K 230 " --> pdb=" O LYS K 239 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LYS K 239 " --> pdb=" O TRP K 230 " (cutoff:3.500A) 483 hydrogen bonds defined for protein. 1419 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 322 hydrogen bonds 644 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 2.36 Time building geometry restraints manager: 1.43 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1682 1.32 - 1.44: 4666 1.44 - 1.57: 6381 1.57 - 1.69: 500 1.69 - 1.81: 38 Bond restraints: 13267 Sorted by residual: bond pdb=" C1' DG I 58 " pdb=" N9 DG I 58 " ideal model delta sigma weight residual 1.460 1.388 0.072 2.00e-02 2.50e+03 1.30e+01 bond pdb=" CA ALA C 103 " pdb=" CB ALA C 103 " ideal model delta sigma weight residual 1.529 1.471 0.059 1.69e-02 3.50e+03 1.20e+01 bond pdb=" CZ ARG A 129 " pdb=" NH2 ARG A 129 " ideal model delta sigma weight residual 1.330 1.285 0.045 1.30e-02 5.92e+03 1.18e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.460 1.392 0.068 2.00e-02 2.50e+03 1.17e+01 bond pdb=" CZ ARG A 134 " pdb=" NH2 ARG A 134 " ideal model delta sigma weight residual 1.330 1.287 0.043 1.30e-02 5.92e+03 1.10e+01 ... (remaining 13262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 18673 3.18 - 6.36: 288 6.36 - 9.54: 14 9.54 - 12.72: 0 12.72 - 15.90: 2 Bond angle restraints: 18977 Sorted by residual: angle pdb=" C5' DC J 7 " pdb=" C4' DC J 7 " pdb=" O4' DC J 7 " ideal model delta sigma weight residual 109.40 115.29 -5.89 1.50e+00 4.44e-01 1.54e+01 angle pdb=" C2' DT J -57 " pdb=" C1' DT J -57 " pdb=" N1 DT J -57 " ideal model delta sigma weight residual 113.50 119.30 -5.80 1.50e+00 4.44e-01 1.49e+01 angle pdb=" C PRO H 50 " pdb=" N ASP H 51 " pdb=" CA ASP H 51 " ideal model delta sigma weight residual 120.72 127.13 -6.41 1.67e+00 3.59e-01 1.47e+01 angle pdb=" CD ARG G 35 " pdb=" NE ARG G 35 " pdb=" CZ ARG G 35 " ideal model delta sigma weight residual 124.40 129.71 -5.31 1.40e+00 5.10e-01 1.44e+01 angle pdb=" CB HIS H 82 " pdb=" CG HIS H 82 " pdb=" CD2 HIS H 82 " ideal model delta sigma weight residual 131.20 126.28 4.92 1.30e+00 5.92e-01 1.43e+01 ... (remaining 18972 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.66: 5052 17.66 - 35.32: 1001 35.32 - 52.97: 991 52.97 - 70.63: 275 70.63 - 88.29: 20 Dihedral angle restraints: 7339 sinusoidal: 4661 harmonic: 2678 Sorted by residual: dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 151.87 28.13 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" CA LEU F 22 " pdb=" C LEU F 22 " pdb=" N ARG F 23 " pdb=" CA ARG F 23 " ideal model delta harmonic sigma weight residual -180.00 -158.00 -22.00 0 5.00e+00 4.00e-02 1.94e+01 dihedral pdb=" CA PRO D 103 " pdb=" C PRO D 103 " pdb=" N GLY D 104 " pdb=" CA GLY D 104 " ideal model delta harmonic sigma weight residual 180.00 158.43 21.57 0 5.00e+00 4.00e-02 1.86e+01 ... (remaining 7336 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.117: 2038 0.117 - 0.234: 80 0.234 - 0.351: 10 0.351 - 0.468: 0 0.468 - 0.585: 11 Chirality restraints: 2139 Sorted by residual: chirality pdb=" P DG J -71 " pdb=" OP1 DG J -71 " pdb=" OP2 DG J -71 " pdb=" O5' DG J -71 " both_signs ideal model delta sigma weight residual True 2.35 -2.93 -0.59 2.00e-01 2.50e+01 8.57e+00 chirality pdb=" P DA J 29 " pdb=" OP1 DA J 29 " pdb=" OP2 DA J 29 " pdb=" O5' DA J 29 " both_signs ideal model delta sigma weight residual True 2.35 -2.87 -0.52 2.00e-01 2.50e+01 6.81e+00 chirality pdb=" P DT I -29 " pdb=" OP1 DT I -29 " pdb=" OP2 DT I -29 " pdb=" O5' DT I -29 " both_signs ideal model delta sigma weight residual True 2.35 -2.86 -0.51 2.00e-01 2.50e+01 6.59e+00 ... (remaining 2136 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT I -24 " 0.050 2.00e-02 2.50e+03 6.63e-02 1.10e+02 pdb=" N1 DT I -24 " 0.047 2.00e-02 2.50e+03 pdb=" C2 DT I -24 " -0.018 2.00e-02 2.50e+03 pdb=" O2 DT I -24 " -0.117 2.00e-02 2.50e+03 pdb=" N3 DT I -24 " 0.013 2.00e-02 2.50e+03 pdb=" C4 DT I -24 " 0.027 2.00e-02 2.50e+03 pdb=" O4 DT I -24 " 0.080 2.00e-02 2.50e+03 pdb=" C5 DT I -24 " -0.005 2.00e-02 2.50e+03 pdb=" C7 DT I -24 " -0.125 2.00e-02 2.50e+03 pdb=" C6 DT I -24 " 0.048 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 5 " 0.101 2.00e-02 2.50e+03 6.31e-02 8.96e+01 pdb=" N1 DC J 5 " 0.023 2.00e-02 2.50e+03 pdb=" C2 DC J 5 " -0.008 2.00e-02 2.50e+03 pdb=" O2 DC J 5 " -0.067 2.00e-02 2.50e+03 pdb=" N3 DC J 5 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 5 " -0.023 2.00e-02 2.50e+03 pdb=" N4 DC J 5 " 0.107 2.00e-02 2.50e+03 pdb=" C5 DC J 5 " -0.078 2.00e-02 2.50e+03 pdb=" C6 DC J 5 " -0.051 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 7 " 0.111 2.00e-02 2.50e+03 5.98e-02 8.04e+01 pdb=" N1 DC J 7 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DC J 7 " -0.016 2.00e-02 2.50e+03 pdb=" O2 DC J 7 " -0.064 2.00e-02 2.50e+03 pdb=" N3 DC J 7 " 0.004 2.00e-02 2.50e+03 pdb=" C4 DC J 7 " -0.004 2.00e-02 2.50e+03 pdb=" N4 DC J 7 " 0.089 2.00e-02 2.50e+03 pdb=" C5 DC J 7 " -0.067 2.00e-02 2.50e+03 pdb=" C6 DC J 7 " -0.056 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 3041 2.83 - 3.35: 10718 3.35 - 3.86: 24366 3.86 - 4.38: 28734 4.38 - 4.90: 40422 Nonbonded interactions: 107281 Sorted by model distance: nonbonded pdb=" NH2 ARG G 42 " pdb=" OP1 DA I -34 " model vdw 2.308 3.120 nonbonded pdb=" O CYS L 224 " pdb=" O ILE L 228 " model vdw 2.396 3.040 nonbonded pdb=" O CYS K 224 " pdb=" O ILE K 228 " model vdw 2.407 3.040 nonbonded pdb=" O MET L 292 " pdb=" CA PRO L 293 " model vdw 2.431 2.776 nonbonded pdb=" N ASP D 51 " pdb=" OD1 ASP D 51 " model vdw 2.444 3.120 ... (remaining 107276 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 40 through 133) selection = (chain 'E' and resid 40 through 133) } ncs_group { reference = (chain 'B' and resid 22 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 15 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 35 through 124) selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 0.450 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.110 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.180 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 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 : 0.007 0.072 13267 Z= 0.369 Angle : 0.963 15.902 18977 Z= 0.595 Chirality : 0.065 0.585 2139 Planarity : 0.010 0.112 1531 Dihedral : 26.349 88.289 5615 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.44 % Allowed : 1.00 % Favored : 98.56 % Rotamer: Outliers : 0.77 % Allowed : 10.04 % Favored : 89.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.65 (0.27), residues: 900 helix: 1.76 (0.20), residues: 622 sheet: -2.68 (0.81), residues: 32 loop : 0.03 (0.36), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG F 35 TYR 0.036 0.003 TYR G 39 PHE 0.014 0.002 PHE L 289 TRP 0.014 0.002 TRP K 250 HIS 0.007 0.002 HIS G 82 Details of bonding type rmsd covalent geometry : bond 0.00710 (13267) covalent geometry : angle 0.96306 (18977) hydrogen bonds : bond 0.13008 ( 805) hydrogen bonds : angle 4.52164 ( 2063) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 373 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 367 time to evaluate : 0.359 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 94 GLU cc_start: 0.8130 (mm-30) cc_final: 0.7564 (mm-30) REVERT: B 24 ASP cc_start: 0.4875 (m-30) cc_final: 0.3200 (m-30) REVERT: C 92 GLU cc_start: 0.6992 (mm-30) cc_final: 0.6429 (mm-30) REVERT: E 122 LYS cc_start: 0.7790 (ptpt) cc_final: 0.7517 (ptmm) REVERT: F 86 VAL cc_start: 0.7778 (t) cc_final: 0.7523 (t) REVERT: G 49 VAL cc_start: 0.6275 (t) cc_final: 0.6072 (t) outliers start: 6 outliers final: 0 residues processed: 367 average time/residue: 0.1453 time to fit residues: 70.6081 Evaluate side-chains 200 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 200 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 108 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 5 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 30.0000 chunk 106 optimal weight: 7.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 108 ASN B 25 ASN D 63 ASN F 25 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 73 ASN G 104 GLN K 232 GLN ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.035544 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2878 r_free = 0.2878 target = 0.027939 restraints weight = 134300.883| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.028706 restraints weight = 69441.694| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2925 r_free = 0.2925 target = 0.029232 restraints weight = 44205.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2938 r_free = 0.2938 target = 0.029542 restraints weight = 32103.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.029807 restraints weight = 25917.603| |-----------------------------------------------------------------------------| r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13267 Z= 0.176 Angle : 0.681 10.400 18977 Z= 0.389 Chirality : 0.037 0.163 2139 Planarity : 0.005 0.060 1531 Dihedral : 28.713 94.422 3758 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Rotamer: Outliers : 2.19 % Allowed : 21.11 % Favored : 76.71 % 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: 1.92 (0.27), residues: 900 helix: 1.84 (0.20), residues: 639 sheet: -2.79 (0.99), residues: 20 loop : 0.24 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 67 TYR 0.021 0.002 TYR B 88 PHE 0.026 0.002 PHE H 65 TRP 0.013 0.002 TRP L 211 HIS 0.005 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00376 (13267) covalent geometry : angle 0.68114 (18977) hydrogen bonds : bond 0.04417 ( 805) hydrogen bonds : angle 3.56084 ( 2063) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 261 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 244 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.9014 (mm-30) cc_final: 0.8724 (mm-30) REVERT: A 125 GLN cc_start: 0.9026 (mt0) cc_final: 0.8783 (mt0) REVERT: B 44 LYS cc_start: 0.9427 (tttt) cc_final: 0.9007 (ttpt) REVERT: B 49 LEU cc_start: 0.9752 (mt) cc_final: 0.9423 (mm) REVERT: B 68 ASP cc_start: 0.8787 (m-30) cc_final: 0.8460 (m-30) REVERT: D 68 ASP cc_start: 0.9157 (t0) cc_final: 0.7522 (t0) REVERT: D 71 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8737 (pp20) REVERT: D 93 GLU cc_start: 0.8952 (mp0) cc_final: 0.8330 (mp0) REVERT: D 102 LEU cc_start: 0.9300 (tp) cc_final: 0.9096 (tp) REVERT: F 24 ASP cc_start: 0.8138 (t0) cc_final: 0.7625 (t0) REVERT: F 74 GLU cc_start: 0.8708 (pp20) cc_final: 0.8434 (pp20) REVERT: G 24 GLN cc_start: 0.9018 (mm-40) cc_final: 0.8681 (mp10) REVERT: G 41 GLU cc_start: 0.9084 (mp0) cc_final: 0.8879 (mp0) REVERT: H 42 TYR cc_start: 0.8802 (OUTLIER) cc_final: 0.8478 (m-80) REVERT: H 68 ASP cc_start: 0.8963 (t0) cc_final: 0.8720 (t0) REVERT: H 73 ILE cc_start: 0.9611 (OUTLIER) cc_final: 0.9332 (tp) REVERT: H 95 GLN cc_start: 0.9177 (pt0) cc_final: 0.8367 (pp30) REVERT: H 109 HIS cc_start: 0.9180 (m170) cc_final: 0.8796 (m90) REVERT: H 113 GLU cc_start: 0.9362 (tt0) cc_final: 0.8877 (mt-10) REVERT: L 264 MET cc_start: 0.9047 (ppp) cc_final: 0.8530 (ppp) REVERT: K 232 GLN cc_start: 0.9019 (tp-100) cc_final: 0.8462 (tm-30) REVERT: K 264 MET cc_start: 0.9607 (ttp) cc_final: 0.9165 (mtp) outliers start: 17 outliers final: 4 residues processed: 250 average time/residue: 0.1431 time to fit residues: 47.4967 Evaluate side-chains 203 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 197 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 73 ILE Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 26 optimal weight: 4.9990 chunk 45 optimal weight: 10.0000 chunk 94 optimal weight: 9.9990 chunk 101 optimal weight: 10.0000 chunk 85 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 44 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 102 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 113 HIS ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS H 84 ASN K 288 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.030727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.023292 restraints weight = 148051.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.024007 restraints weight = 75375.179| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024477 restraints weight = 47963.952| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.024781 restraints weight = 34963.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.025000 restraints weight = 28110.786| |-----------------------------------------------------------------------------| r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.5466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13267 Z= 0.296 Angle : 0.707 7.576 18977 Z= 0.407 Chirality : 0.040 0.190 2139 Planarity : 0.006 0.052 1531 Dihedral : 29.513 85.765 3758 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.47 % Allowed : 21.62 % Favored : 74.90 % 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: 1.69 (0.27), residues: 900 helix: 1.63 (0.20), residues: 644 sheet: -2.21 (0.90), residues: 32 loop : 0.35 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 52 TYR 0.029 0.002 TYR B 88 PHE 0.023 0.002 PHE H 65 TRP 0.011 0.003 TRP L 250 HIS 0.010 0.002 HIS K 253 Details of bonding type rmsd covalent geometry : bond 0.00652 (13267) covalent geometry : angle 0.70702 (18977) hydrogen bonds : bond 0.06395 ( 805) hydrogen bonds : angle 3.86839 ( 2063) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 220 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8760 (tp-100) cc_final: 0.8479 (tm-30) REVERT: A 126 LEU cc_start: 0.9245 (OUTLIER) cc_final: 0.8818 (tp) REVERT: B 64 ASN cc_start: 0.9471 (m-40) cc_final: 0.8985 (m-40) REVERT: B 88 TYR cc_start: 0.9471 (m-10) cc_final: 0.8848 (m-10) REVERT: D 83 TYR cc_start: 0.9130 (m-10) cc_final: 0.8914 (m-80) REVERT: D 102 LEU cc_start: 0.9444 (tp) cc_final: 0.9206 (tp) REVERT: D 106 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9166 (mt) REVERT: E 52 ARG cc_start: 0.9478 (OUTLIER) cc_final: 0.9185 (mtm-85) REVERT: E 94 GLU cc_start: 0.8530 (tp30) cc_final: 0.7698 (tp30) REVERT: E 120 MET cc_start: 0.8502 (mtp) cc_final: 0.8090 (mtp) REVERT: F 84 MET cc_start: 0.9351 (mmm) cc_final: 0.8751 (mmm) REVERT: G 56 GLU cc_start: 0.9110 (tt0) cc_final: 0.8592 (mt-10) REVERT: G 89 ASN cc_start: 0.9567 (m-40) cc_final: 0.9284 (m-40) REVERT: H 41 VAL cc_start: 0.9693 (t) cc_final: 0.9478 (p) REVERT: H 42 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8681 (m-80) REVERT: H 68 ASP cc_start: 0.9331 (t0) cc_final: 0.8978 (t0) REVERT: H 76 GLU cc_start: 0.9332 (mm-30) cc_final: 0.8944 (mm-30) REVERT: H 82 HIS cc_start: 0.9426 (t-90) cc_final: 0.9092 (t-90) REVERT: H 93 GLU cc_start: 0.9446 (mp0) cc_final: 0.9198 (mp0) REVERT: H 109 HIS cc_start: 0.9244 (m170) cc_final: 0.8788 (m90) REVERT: L 264 MET cc_start: 0.9422 (ppp) cc_final: 0.9074 (ppp) REVERT: K 227 TYR cc_start: 0.9431 (m-80) cc_final: 0.9134 (m-80) REVERT: K 264 MET cc_start: 0.9395 (ttp) cc_final: 0.8742 (mtm) REVERT: K 292 MET cc_start: 0.3803 (ttp) cc_final: 0.3311 (mtm) outliers start: 27 outliers final: 14 residues processed: 231 average time/residue: 0.1354 time to fit residues: 42.1746 Evaluate side-chains 205 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 187 time to evaluate : 0.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 258 ASP Chi-restraints excluded: chain K residue 262 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 10.0000 chunk 23 optimal weight: 0.0970 chunk 5 optimal weight: 1.9990 chunk 72 optimal weight: 10.0000 chunk 99 optimal weight: 10.0000 chunk 64 optimal weight: 8.9990 chunk 34 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 8.9990 chunk 6 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 288 GLN K 288 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.031874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2739 r_free = 0.2739 target = 0.024151 restraints weight = 141838.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024888 restraints weight = 71877.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2791 r_free = 0.2791 target = 0.025364 restraints weight = 45943.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 46)----------------| | r_work = 0.2805 r_free = 0.2805 target = 0.025675 restraints weight = 33573.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.025875 restraints weight = 27000.981| |-----------------------------------------------------------------------------| r_work (final): 0.2793 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.5797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 13267 Z= 0.190 Angle : 0.645 11.314 18977 Z= 0.372 Chirality : 0.037 0.188 2139 Planarity : 0.004 0.051 1531 Dihedral : 29.195 87.157 3758 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.96 % Allowed : 23.55 % Favored : 73.49 % 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: 1.91 (0.28), residues: 900 helix: 1.83 (0.20), residues: 644 sheet: -2.14 (0.92), residues: 32 loop : 0.31 (0.39), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG H 99 TYR 0.025 0.002 TYR C 39 PHE 0.036 0.002 PHE H 65 TRP 0.014 0.002 TRP L 230 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00420 (13267) covalent geometry : angle 0.64523 (18977) hydrogen bonds : bond 0.04140 ( 805) hydrogen bonds : angle 3.58084 ( 2063) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 208 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9028 (pm20) cc_final: 0.8817 (pm20) REVERT: A 106 ASP cc_start: 0.9174 (m-30) cc_final: 0.8819 (m-30) REVERT: A 126 LEU cc_start: 0.9218 (OUTLIER) cc_final: 0.8865 (tp) REVERT: B 26 ILE cc_start: 0.9158 (tt) cc_final: 0.8930 (tp) REVERT: B 64 ASN cc_start: 0.9237 (m-40) cc_final: 0.8980 (m110) REVERT: B 88 TYR cc_start: 0.9352 (m-10) cc_final: 0.8763 (m-10) REVERT: D 68 ASP cc_start: 0.9093 (t0) cc_final: 0.8196 (t0) REVERT: D 71 GLU cc_start: 0.8993 (tm-30) cc_final: 0.8770 (pp20) REVERT: D 102 LEU cc_start: 0.9450 (tp) cc_final: 0.9202 (tp) REVERT: E 52 ARG cc_start: 0.9483 (OUTLIER) cc_final: 0.9145 (mtm-85) REVERT: E 94 GLU cc_start: 0.8424 (tp30) cc_final: 0.7703 (tp30) REVERT: G 30 VAL cc_start: 0.9447 (t) cc_final: 0.9219 (p) REVERT: G 56 GLU cc_start: 0.9130 (tt0) cc_final: 0.8766 (tt0) REVERT: H 42 TYR cc_start: 0.8916 (OUTLIER) cc_final: 0.8610 (m-80) REVERT: H 68 ASP cc_start: 0.9453 (t0) cc_final: 0.9113 (t0) REVERT: H 93 GLU cc_start: 0.9446 (mp0) cc_final: 0.9219 (mp0) REVERT: H 109 HIS cc_start: 0.9303 (m170) cc_final: 0.8910 (m-70) REVERT: L 242 ASP cc_start: 0.8986 (p0) cc_final: 0.8785 (p0) REVERT: L 264 MET cc_start: 0.9464 (ppp) cc_final: 0.9177 (ppp) REVERT: K 229 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7974 (tppt) REVERT: K 232 GLN cc_start: 0.9200 (tp-100) cc_final: 0.8721 (tm-30) REVERT: K 264 MET cc_start: 0.9394 (ttp) cc_final: 0.8840 (mtm) outliers start: 23 outliers final: 8 residues processed: 220 average time/residue: 0.1317 time to fit residues: 39.0565 Evaluate side-chains 199 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 187 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 256 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 71 optimal weight: 10.0000 chunk 9 optimal weight: 9.9990 chunk 110 optimal weight: 10.0000 chunk 80 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 45 optimal weight: 6.9990 chunk 96 optimal weight: 10.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 253 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.029553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2647 r_free = 0.2647 target = 0.021939 restraints weight = 151703.461| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2678 r_free = 0.2678 target = 0.022611 restraints weight = 77438.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.2698 r_free = 0.2698 target = 0.023032 restraints weight = 49814.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.023308 restraints weight = 36976.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023504 restraints weight = 30021.097| |-----------------------------------------------------------------------------| r_work (final): 0.2703 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.6719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.046 13267 Z= 0.328 Angle : 0.714 9.568 18977 Z= 0.411 Chirality : 0.040 0.202 2139 Planarity : 0.005 0.040 1531 Dihedral : 29.823 84.436 3758 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 17.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.35 % Allowed : 24.84 % Favored : 71.81 % 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: 1.72 (0.28), residues: 900 helix: 1.70 (0.20), residues: 645 sheet: -2.22 (0.91), residues: 32 loop : 0.15 (0.39), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 116 TYR 0.020 0.002 TYR B 88 PHE 0.022 0.002 PHE A 67 TRP 0.012 0.002 TRP K 250 HIS 0.007 0.002 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00722 (13267) covalent geometry : angle 0.71407 (18977) hydrogen bonds : bond 0.07111 ( 805) hydrogen bonds : angle 3.93628 ( 2063) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 192 time to evaluate : 0.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9125 (pm20) cc_final: 0.8903 (pm20) REVERT: A 68 GLN cc_start: 0.9397 (OUTLIER) cc_final: 0.9108 (pm20) REVERT: A 90 MET cc_start: 0.9075 (mmp) cc_final: 0.8806 (mmp) REVERT: A 105 GLU cc_start: 0.8944 (mm-30) cc_final: 0.8575 (mm-30) REVERT: A 126 LEU cc_start: 0.9300 (OUTLIER) cc_final: 0.8883 (tp) REVERT: B 59 LYS cc_start: 0.9385 (ttpp) cc_final: 0.8892 (tmmt) REVERT: B 64 ASN cc_start: 0.9286 (m-40) cc_final: 0.8975 (m-40) REVERT: B 88 TYR cc_start: 0.9369 (m-10) cc_final: 0.9098 (m-10) REVERT: B 91 LYS cc_start: 0.9336 (pptt) cc_final: 0.9097 (pptt) REVERT: C 64 GLU cc_start: 0.8605 (tp30) cc_final: 0.8329 (tp30) REVERT: D 83 TYR cc_start: 0.9261 (m-80) cc_final: 0.8901 (m-80) REVERT: E 94 GLU cc_start: 0.8520 (tp30) cc_final: 0.7442 (tp30) REVERT: E 120 MET cc_start: 0.8501 (mpp) cc_final: 0.8270 (mpp) REVERT: F 91 LYS cc_start: 0.9547 (tppp) cc_final: 0.9338 (tppt) REVERT: G 41 GLU cc_start: 0.9203 (mp0) cc_final: 0.8999 (mp0) REVERT: H 42 TYR cc_start: 0.8970 (OUTLIER) cc_final: 0.8635 (m-80) REVERT: H 68 ASP cc_start: 0.9520 (t0) cc_final: 0.9179 (t0) REVERT: H 76 GLU cc_start: 0.9233 (mm-30) cc_final: 0.9029 (mm-30) REVERT: H 79 ARG cc_start: 0.9119 (ttm110) cc_final: 0.8214 (ttm110) REVERT: H 83 TYR cc_start: 0.9437 (m-10) cc_final: 0.8823 (m-80) REVERT: H 93 GLU cc_start: 0.9429 (mp0) cc_final: 0.9212 (mp0) REVERT: H 105 GLU cc_start: 0.9223 (tp30) cc_final: 0.8997 (tp30) REVERT: L 264 MET cc_start: 0.9492 (ppp) cc_final: 0.9217 (ppp) REVERT: K 229 LYS cc_start: 0.8866 (OUTLIER) cc_final: 0.7996 (mmmt) REVERT: K 264 MET cc_start: 0.9353 (ttp) cc_final: 0.8820 (mtm) REVERT: K 281 GLU cc_start: 0.9442 (mm-30) cc_final: 0.9122 (mp0) REVERT: K 292 MET cc_start: 0.3186 (ttp) cc_final: 0.2078 (mtm) outliers start: 26 outliers final: 16 residues processed: 206 average time/residue: 0.1393 time to fit residues: 38.6592 Evaluate side-chains 193 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 108 ASN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 256 LYS Chi-restraints excluded: chain K residue 262 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 8.9990 chunk 81 optimal weight: 0.4980 chunk 95 optimal weight: 7.9990 chunk 58 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 107 optimal weight: 7.9990 chunk 79 optimal weight: 8.9990 overall best weight: 3.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 253 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.030572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.022897 restraints weight = 146789.381| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.023600 restraints weight = 73746.889| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.024064 restraints weight = 46940.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2755 r_free = 0.2755 target = 0.024357 restraints weight = 34285.493| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.024555 restraints weight = 27633.357| |-----------------------------------------------------------------------------| r_work (final): 0.2747 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.6923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13267 Z= 0.206 Angle : 0.665 10.796 18977 Z= 0.379 Chirality : 0.037 0.238 2139 Planarity : 0.004 0.034 1531 Dihedral : 29.527 82.558 3758 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 13.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.22 % Allowed : 26.77 % Favored : 70.01 % 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: 1.75 (0.28), residues: 900 helix: 1.75 (0.20), residues: 637 sheet: -1.94 (0.96), residues: 32 loop : 0.12 (0.39), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.019 0.001 TYR G 39 PHE 0.020 0.002 PHE H 65 TRP 0.010 0.002 TRP L 211 HIS 0.006 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00454 (13267) covalent geometry : angle 0.66482 (18977) hydrogen bonds : bond 0.04507 ( 805) hydrogen bonds : angle 3.75830 ( 2063) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 204 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.9079 (pm20) cc_final: 0.8829 (pm20) REVERT: A 90 MET cc_start: 0.9082 (mmp) cc_final: 0.8865 (mmp) REVERT: A 105 GLU cc_start: 0.8829 (mm-30) cc_final: 0.8332 (mm-30) REVERT: A 106 ASP cc_start: 0.9182 (m-30) cc_final: 0.8960 (m-30) REVERT: A 126 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8928 (tp) REVERT: B 46 ILE cc_start: 0.9679 (tp) cc_final: 0.9317 (pt) REVERT: B 59 LYS cc_start: 0.9357 (ttpp) cc_final: 0.9066 (tmmt) REVERT: B 63 GLU cc_start: 0.9324 (mt-10) cc_final: 0.8815 (mt-10) REVERT: B 64 ASN cc_start: 0.9311 (m-40) cc_final: 0.9007 (m-40) REVERT: B 74 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8278 (mt-10) REVERT: B 88 TYR cc_start: 0.9327 (m-10) cc_final: 0.8914 (m-10) REVERT: B 91 LYS cc_start: 0.9285 (pptt) cc_final: 0.9061 (pptt) REVERT: B 92 ARG cc_start: 0.9261 (OUTLIER) cc_final: 0.8775 (ptm-80) REVERT: B 93 GLN cc_start: 0.9176 (mm110) cc_final: 0.8903 (mm110) REVERT: C 104 GLN cc_start: 0.9133 (pp30) cc_final: 0.8695 (pp30) REVERT: D 68 ASP cc_start: 0.9051 (t0) cc_final: 0.8779 (t0) REVERT: D 71 GLU cc_start: 0.9102 (tm-30) cc_final: 0.8836 (pp20) REVERT: D 83 TYR cc_start: 0.9244 (m-80) cc_final: 0.8852 (m-80) REVERT: E 52 ARG cc_start: 0.9473 (OUTLIER) cc_final: 0.9088 (mtm-85) REVERT: E 120 MET cc_start: 0.8609 (mpp) cc_final: 0.8074 (mpp) REVERT: G 56 GLU cc_start: 0.9157 (OUTLIER) cc_final: 0.8730 (mt-10) REVERT: G 95 LYS cc_start: 0.9675 (tmtt) cc_final: 0.9435 (ptmm) REVERT: H 42 TYR cc_start: 0.9008 (OUTLIER) cc_final: 0.8643 (m-80) REVERT: H 68 ASP cc_start: 0.9465 (t0) cc_final: 0.9151 (t0) REVERT: H 83 TYR cc_start: 0.9412 (m-10) cc_final: 0.8929 (m-80) REVERT: H 93 GLU cc_start: 0.9455 (mp0) cc_final: 0.9247 (mp0) REVERT: L 264 MET cc_start: 0.9473 (ppp) cc_final: 0.9269 (ppp) REVERT: K 229 LYS cc_start: 0.8802 (OUTLIER) cc_final: 0.8148 (tppt) REVERT: K 238 PHE cc_start: 0.8864 (p90) cc_final: 0.8171 (p90) REVERT: K 281 GLU cc_start: 0.9398 (mm-30) cc_final: 0.9124 (mp0) REVERT: K 292 MET cc_start: 0.3487 (ttp) cc_final: 0.2400 (mtm) outliers start: 25 outliers final: 12 residues processed: 216 average time/residue: 0.1440 time to fit residues: 41.5853 Evaluate side-chains 200 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 229 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 8.9990 chunk 74 optimal weight: 40.0000 chunk 50 optimal weight: 10.0000 chunk 45 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 8.9990 chunk 85 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 62 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.029380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2654 r_free = 0.2654 target = 0.022001 restraints weight = 151641.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.022675 restraints weight = 77645.216| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.2707 r_free = 0.2707 target = 0.023109 restraints weight = 49741.600| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2721 r_free = 0.2721 target = 0.023410 restraints weight = 36584.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.023590 restraints weight = 29388.210| |-----------------------------------------------------------------------------| r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8416 moved from start: 0.7328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 13267 Z= 0.297 Angle : 0.734 10.581 18977 Z= 0.414 Chirality : 0.040 0.236 2139 Planarity : 0.004 0.035 1531 Dihedral : 29.865 88.931 3758 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 16.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.47 % Allowed : 26.51 % Favored : 70.01 % 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: 1.65 (0.28), residues: 900 helix: 1.68 (0.21), residues: 634 sheet: -1.85 (0.98), residues: 32 loop : 0.07 (0.38), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 99 TYR 0.017 0.002 TYR G 39 PHE 0.036 0.002 PHE H 65 TRP 0.023 0.002 TRP K 250 HIS 0.007 0.002 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00655 (13267) covalent geometry : angle 0.73416 (18977) hydrogen bonds : bond 0.06310 ( 805) hydrogen bonds : angle 4.00346 ( 2063) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 188 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.9087 (pm20) cc_final: 0.8817 (pm20) REVERT: A 90 MET cc_start: 0.9086 (mmp) cc_final: 0.8805 (mmp) REVERT: A 105 GLU cc_start: 0.8916 (mm-30) cc_final: 0.8519 (mm-30) REVERT: A 126 LEU cc_start: 0.9274 (OUTLIER) cc_final: 0.8875 (tp) REVERT: B 64 ASN cc_start: 0.9334 (m-40) cc_final: 0.9056 (m-40) REVERT: B 74 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8386 (mt-10) REVERT: B 88 TYR cc_start: 0.9391 (m-10) cc_final: 0.9003 (m-10) REVERT: B 91 LYS cc_start: 0.9287 (pptt) cc_final: 0.9043 (pptt) REVERT: B 92 ARG cc_start: 0.9344 (OUTLIER) cc_final: 0.8900 (ptm-80) REVERT: B 93 GLN cc_start: 0.9187 (mm110) cc_final: 0.8913 (mm110) REVERT: C 104 GLN cc_start: 0.9190 (pp30) cc_final: 0.8630 (pm20) REVERT: D 68 ASP cc_start: 0.9070 (t0) cc_final: 0.8583 (t0) REVERT: D 71 GLU cc_start: 0.9180 (tm-30) cc_final: 0.8862 (pp20) REVERT: D 83 TYR cc_start: 0.9259 (m-80) cc_final: 0.8912 (m-80) REVERT: E 52 ARG cc_start: 0.9462 (OUTLIER) cc_final: 0.9045 (mtm-85) REVERT: E 94 GLU cc_start: 0.8743 (mm-30) cc_final: 0.8512 (mm-30) REVERT: E 120 MET cc_start: 0.8614 (mpp) cc_final: 0.8014 (mpp) REVERT: G 56 GLU cc_start: 0.9079 (OUTLIER) cc_final: 0.8760 (mt-10) REVERT: H 42 TYR cc_start: 0.8994 (OUTLIER) cc_final: 0.8601 (m-80) REVERT: H 68 ASP cc_start: 0.9471 (t0) cc_final: 0.9183 (t0) REVERT: H 76 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8779 (tp30) REVERT: H 80 LEU cc_start: 0.9743 (mp) cc_final: 0.9448 (mt) REVERT: H 83 TYR cc_start: 0.9439 (m-10) cc_final: 0.8910 (m-80) REVERT: H 105 GLU cc_start: 0.9456 (tp30) cc_final: 0.8612 (tp30) REVERT: H 109 HIS cc_start: 0.9408 (m170) cc_final: 0.8967 (m170) REVERT: H 113 GLU cc_start: 0.9574 (tt0) cc_final: 0.9343 (mm-30) REVERT: H 116 LYS cc_start: 0.9383 (ptpp) cc_final: 0.8908 (ptpp) REVERT: L 264 MET cc_start: 0.9517 (ppp) cc_final: 0.9292 (ppp) REVERT: K 229 LYS cc_start: 0.8877 (OUTLIER) cc_final: 0.8236 (tppt) REVERT: K 238 PHE cc_start: 0.8859 (p90) cc_final: 0.8176 (p90) REVERT: K 264 MET cc_start: 0.8646 (mmm) cc_final: 0.8054 (mmm) REVERT: K 268 LEU cc_start: 0.9848 (mt) cc_final: 0.9565 (pp) REVERT: K 281 GLU cc_start: 0.9455 (mm-30) cc_final: 0.9120 (mp0) REVERT: K 292 MET cc_start: 0.3676 (ttp) cc_final: 0.2396 (mtm) outliers start: 27 outliers final: 15 residues processed: 203 average time/residue: 0.1387 time to fit residues: 38.0139 Evaluate side-chains 199 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 178 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 262 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 8.9990 chunk 39 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 60 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 83 optimal weight: 20.0000 chunk 3 optimal weight: 5.9990 chunk 27 optimal weight: 2.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.030289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.022940 restraints weight = 147528.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2723 r_free = 0.2723 target = 0.023655 restraints weight = 74297.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.024127 restraints weight = 46802.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024440 restraints weight = 33667.347| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024649 restraints weight = 26681.612| |-----------------------------------------------------------------------------| r_work (final): 0.2752 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.7484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13267 Z= 0.199 Angle : 0.712 11.108 18977 Z= 0.398 Chirality : 0.038 0.208 2139 Planarity : 0.004 0.074 1531 Dihedral : 29.483 88.283 3758 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 13.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.96 % Allowed : 26.64 % Favored : 70.40 % 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: 1.72 (0.28), residues: 900 helix: 1.70 (0.21), residues: 634 sheet: -2.32 (1.29), residues: 20 loop : 0.12 (0.37), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.001 ARG L 226 TYR 0.041 0.002 TYR K 261 PHE 0.014 0.001 PHE A 67 TRP 0.014 0.002 TRP K 250 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00439 (13267) covalent geometry : angle 0.71242 (18977) hydrogen bonds : bond 0.04468 ( 805) hydrogen bonds : angle 3.80992 ( 2063) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: 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: 0.8711 (pm20) REVERT: A 90 MET cc_start: 0.9124 (mmp) cc_final: 0.8901 (mmp) REVERT: A 105 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8453 (mm-30) REVERT: B 44 LYS cc_start: 0.9478 (tttt) cc_final: 0.9138 (ttpt) REVERT: B 46 ILE cc_start: 0.9659 (tp) cc_final: 0.9368 (pt) REVERT: B 59 LYS cc_start: 0.9535 (ttpp) cc_final: 0.9079 (tmmt) REVERT: B 63 GLU cc_start: 0.9315 (mt-10) cc_final: 0.8843 (mt-10) REVERT: B 64 ASN cc_start: 0.9354 (m-40) cc_final: 0.9081 (m-40) REVERT: B 74 GLU cc_start: 0.8677 (mt-10) cc_final: 0.8207 (mt-10) REVERT: B 88 TYR cc_start: 0.9355 (m-10) cc_final: 0.8873 (m-10) REVERT: B 91 LYS cc_start: 0.9231 (pptt) cc_final: 0.9025 (pptt) REVERT: B 92 ARG cc_start: 0.9313 (OUTLIER) cc_final: 0.9003 (ptm-80) REVERT: C 104 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8692 (pm20) REVERT: D 68 ASP cc_start: 0.8989 (t0) cc_final: 0.8468 (t0) REVERT: D 71 GLU cc_start: 0.9122 (tm-30) cc_final: 0.8815 (pp20) REVERT: D 83 TYR cc_start: 0.9258 (m-80) cc_final: 0.8867 (m-80) REVERT: E 52 ARG cc_start: 0.9479 (OUTLIER) cc_final: 0.9092 (mtm-85) REVERT: E 94 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8442 (mm-30) REVERT: E 120 MET cc_start: 0.8608 (mpp) cc_final: 0.8048 (mpp) REVERT: F 84 MET cc_start: 0.9379 (mmm) cc_final: 0.8819 (mmm) REVERT: G 56 GLU cc_start: 0.9086 (OUTLIER) cc_final: 0.8828 (mt-10) REVERT: G 95 LYS cc_start: 0.9672 (ptmm) cc_final: 0.9315 (pttt) REVERT: H 42 TYR cc_start: 0.8943 (OUTLIER) cc_final: 0.8575 (m-80) REVERT: H 68 ASP cc_start: 0.9475 (t0) cc_final: 0.9172 (t0) REVERT: H 76 GLU cc_start: 0.9204 (mm-30) cc_final: 0.8639 (tp30) REVERT: H 80 LEU cc_start: 0.9691 (mp) cc_final: 0.9304 (mt) REVERT: H 83 TYR cc_start: 0.9415 (m-10) cc_final: 0.8928 (m-80) REVERT: H 105 GLU cc_start: 0.9242 (tp30) cc_final: 0.8337 (tp30) REVERT: H 109 HIS cc_start: 0.9377 (m170) cc_final: 0.8874 (m170) REVERT: L 264 MET cc_start: 0.9489 (ppp) cc_final: 0.9284 (ppp) REVERT: K 229 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8328 (tppt) REVERT: K 238 PHE cc_start: 0.8824 (p90) cc_final: 0.8087 (p90) REVERT: K 264 MET cc_start: 0.8612 (mmm) cc_final: 0.8233 (mmm) REVERT: K 268 LEU cc_start: 0.9874 (mt) cc_final: 0.9581 (pp) REVERT: K 281 GLU cc_start: 0.9462 (mm-30) cc_final: 0.9090 (mp0) REVERT: K 292 MET cc_start: 0.3713 (ttp) cc_final: 0.1960 (mtm) outliers start: 23 outliers final: 14 residues processed: 205 average time/residue: 0.1339 time to fit residues: 37.3482 Evaluate side-chains 205 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 185 time to evaluate : 0.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 262 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 4.9990 chunk 66 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 3 optimal weight: 5.9990 chunk 108 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.6980 chunk 75 optimal weight: 30.0000 chunk 41 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 283 GLN K 288 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.029681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2670 r_free = 0.2670 target = 0.022366 restraints weight = 150153.163| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.2700 r_free = 0.2700 target = 0.023005 restraints weight = 76049.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.023461 restraints weight = 48159.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2736 r_free = 0.2736 target = 0.023747 restraints weight = 34918.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2747 r_free = 0.2747 target = 0.023958 restraints weight = 28016.762| |-----------------------------------------------------------------------------| r_work (final): 0.2728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.7696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 13267 Z= 0.238 Angle : 0.727 10.664 18977 Z= 0.406 Chirality : 0.039 0.223 2139 Planarity : 0.004 0.063 1531 Dihedral : 29.645 89.671 3758 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 13.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.09 % Allowed : 27.93 % Favored : 68.98 % 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: 1.75 (0.28), residues: 900 helix: 1.66 (0.21), residues: 635 sheet: None (None), residues: 0 loop : 0.05 (0.36), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 226 TYR 0.062 0.002 TYR K 261 PHE 0.022 0.002 PHE H 65 TRP 0.014 0.002 TRP K 250 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00529 (13267) covalent geometry : angle 0.72686 (18977) hydrogen bonds : bond 0.05383 ( 805) hydrogen bonds : angle 3.87104 ( 2063) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 185 time to evaluate : 0.385 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8977 (pm20) cc_final: 0.8662 (pm20) REVERT: A 90 MET cc_start: 0.9136 (mmp) cc_final: 0.8919 (mmp) REVERT: A 105 GLU cc_start: 0.8939 (mm-30) cc_final: 0.8487 (mm-30) REVERT: A 126 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8938 (tp) REVERT: B 46 ILE cc_start: 0.9699 (tp) cc_final: 0.9358 (pt) REVERT: B 59 LYS cc_start: 0.9559 (ttpp) cc_final: 0.9068 (tmmt) REVERT: B 63 GLU cc_start: 0.9319 (mt-10) cc_final: 0.8808 (mt-10) REVERT: B 64 ASN cc_start: 0.9335 (m-40) cc_final: 0.9062 (m-40) REVERT: B 74 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8220 (mt-10) REVERT: B 88 TYR cc_start: 0.9380 (m-10) cc_final: 0.8889 (m-10) REVERT: B 92 ARG cc_start: 0.9352 (OUTLIER) cc_final: 0.9075 (ptm-80) REVERT: C 104 GLN cc_start: 0.9188 (OUTLIER) cc_final: 0.8823 (pp30) REVERT: D 68 ASP cc_start: 0.8974 (t0) cc_final: 0.8014 (t0) REVERT: D 71 GLU cc_start: 0.9164 (tm-30) cc_final: 0.8770 (pp20) REVERT: D 72 ARG cc_start: 0.9364 (OUTLIER) cc_final: 0.8897 (mmm-85) REVERT: D 83 TYR cc_start: 0.9234 (m-80) cc_final: 0.8814 (m-80) REVERT: E 52 ARG cc_start: 0.9469 (OUTLIER) cc_final: 0.9095 (mtm-85) REVERT: E 94 GLU cc_start: 0.8833 (mm-30) cc_final: 0.8579 (mm-30) REVERT: E 120 MET cc_start: 0.8623 (mpp) cc_final: 0.8038 (mpp) REVERT: G 56 GLU cc_start: 0.9083 (OUTLIER) cc_final: 0.8562 (mt-10) REVERT: H 42 TYR cc_start: 0.8925 (OUTLIER) cc_final: 0.8567 (m-80) REVERT: H 68 ASP cc_start: 0.9470 (t0) cc_final: 0.9165 (t0) REVERT: H 76 GLU cc_start: 0.9199 (mm-30) cc_final: 0.8655 (tp30) REVERT: H 80 LEU cc_start: 0.9689 (mp) cc_final: 0.9309 (mt) REVERT: H 83 TYR cc_start: 0.9394 (m-10) cc_final: 0.8892 (m-80) REVERT: H 105 GLU cc_start: 0.9156 (tp30) cc_final: 0.8380 (tp30) REVERT: H 109 HIS cc_start: 0.9378 (m170) cc_final: 0.9044 (m170) REVERT: H 113 GLU cc_start: 0.9569 (tt0) cc_final: 0.8932 (mt-10) REVERT: L 264 MET cc_start: 0.9516 (ppp) cc_final: 0.9308 (ppp) REVERT: K 238 PHE cc_start: 0.8771 (p90) cc_final: 0.8098 (p90) REVERT: K 264 MET cc_start: 0.8695 (mmm) cc_final: 0.8448 (mmm) REVERT: K 281 GLU cc_start: 0.9414 (mm-30) cc_final: 0.9117 (mp0) outliers start: 24 outliers final: 17 residues processed: 200 average time/residue: 0.1412 time to fit residues: 37.9357 Evaluate side-chains 204 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 180 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 287 TYR Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 262 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.0970 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 109 optimal weight: 10.0000 chunk 65 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 68 optimal weight: 4.9990 overall best weight: 3.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS H 84 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.030080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.022475 restraints weight = 147805.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.023174 restraints weight = 75009.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.023628 restraints weight = 47895.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.2743 r_free = 0.2743 target = 0.023912 restraints weight = 35006.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.2753 r_free = 0.2753 target = 0.024124 restraints weight = 28245.046| |-----------------------------------------------------------------------------| r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.7813 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13267 Z= 0.211 Angle : 0.733 10.956 18977 Z= 0.408 Chirality : 0.038 0.208 2139 Planarity : 0.005 0.068 1531 Dihedral : 29.513 89.895 3758 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 13.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.09 % Allowed : 28.06 % Favored : 68.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 1.63 (0.28), residues: 900 helix: 1.61 (0.20), residues: 635 sheet: -2.38 (1.21), residues: 20 loop : 0.13 (0.37), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG L 226 TYR 0.026 0.002 TYR K 261 PHE 0.016 0.001 PHE A 67 TRP 0.014 0.002 TRP K 250 HIS 0.005 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00471 (13267) covalent geometry : angle 0.73323 (18977) hydrogen bonds : bond 0.04770 ( 805) hydrogen bonds : angle 3.86713 ( 2063) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1800 Ramachandran restraints generated. 900 Oldfield, 0 Emsley, 900 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 187 time to evaluate : 0.429 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8969 (pm20) cc_final: 0.8641 (pm20) REVERT: A 90 MET cc_start: 0.9109 (mmp) cc_final: 0.8898 (mmp) REVERT: A 105 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8539 (mm-30) REVERT: A 126 LEU cc_start: 0.9261 (OUTLIER) cc_final: 0.8952 (tp) REVERT: B 46 ILE cc_start: 0.9711 (tp) cc_final: 0.9362 (pt) REVERT: B 59 LYS cc_start: 0.9567 (ttpp) cc_final: 0.9084 (tmmt) REVERT: B 63 GLU cc_start: 0.9343 (mt-10) cc_final: 0.8830 (mt-10) REVERT: B 64 ASN cc_start: 0.9341 (m-40) cc_final: 0.9077 (m-40) REVERT: B 88 TYR cc_start: 0.9334 (m-10) cc_final: 0.8886 (m-10) REVERT: C 104 GLN cc_start: 0.9180 (OUTLIER) cc_final: 0.8811 (pp30) REVERT: D 68 ASP cc_start: 0.8946 (t0) cc_final: 0.7994 (t0) REVERT: D 71 GLU cc_start: 0.9136 (tm-30) cc_final: 0.8749 (pp20) REVERT: D 72 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.8868 (mmm-85) REVERT: D 83 TYR cc_start: 0.9146 (m-10) cc_final: 0.8914 (m-80) REVERT: E 52 ARG cc_start: 0.9475 (OUTLIER) cc_final: 0.9087 (mtm-85) REVERT: E 94 GLU cc_start: 0.8806 (mm-30) cc_final: 0.8570 (mm-30) REVERT: E 115 LYS cc_start: 0.8976 (mppt) cc_final: 0.8738 (mppt) REVERT: E 120 MET cc_start: 0.8626 (mpp) cc_final: 0.8022 (mpp) REVERT: F 84 MET cc_start: 0.9359 (mmm) cc_final: 0.8799 (mmm) REVERT: G 56 GLU cc_start: 0.9078 (OUTLIER) cc_final: 0.8559 (mt-10) REVERT: H 42 TYR cc_start: 0.8917 (OUTLIER) cc_final: 0.8557 (m-80) REVERT: H 68 ASP cc_start: 0.9447 (t0) cc_final: 0.9144 (t0) REVERT: H 76 GLU cc_start: 0.9184 (mm-30) cc_final: 0.8690 (tp30) REVERT: H 80 LEU cc_start: 0.9678 (mp) cc_final: 0.9431 (mt) REVERT: K 238 PHE cc_start: 0.8952 (p90) cc_final: 0.8281 (p90) REVERT: K 264 MET cc_start: 0.8912 (mmm) cc_final: 0.8633 (mmm) REVERT: K 292 MET cc_start: 0.3519 (ttp) cc_final: 0.2444 (mtm) outliers start: 24 outliers final: 15 residues processed: 200 average time/residue: 0.1333 time to fit residues: 36.2969 Evaluate side-chains 200 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 179 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 104 GLN Chi-restraints excluded: chain D residue 72 ARG Chi-restraints excluded: chain D residue 109 HIS Chi-restraints excluded: chain D residue 112 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain L residue 210 LEU Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain K residue 214 LEU Chi-restraints excluded: chain K residue 229 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 30.0000 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 102 optimal weight: 10.0000 chunk 58 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 111 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 62 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2971 r_free = 0.2971 target = 0.028952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.021584 restraints weight = 152680.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.022260 restraints weight = 78996.348| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.2690 r_free = 0.2690 target = 0.022692 restraints weight = 50911.778| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2704 r_free = 0.2704 target = 0.022989 restraints weight = 37481.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 19)----------------| | r_work = 0.2714 r_free = 0.2714 target = 0.023169 restraints weight = 30114.528| |-----------------------------------------------------------------------------| r_work (final): 0.2696 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8432 moved from start: 0.8044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.056 13267 Z= 0.302 Angle : 0.780 9.889 18977 Z= 0.435 Chirality : 0.040 0.207 2139 Planarity : 0.005 0.065 1531 Dihedral : 29.896 87.458 3758 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.96 % Allowed : 28.96 % Favored : 68.08 % 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: 1.51 (0.28), residues: 900 helix: 1.56 (0.21), residues: 635 sheet: -2.46 (1.14), residues: 20 loop : -0.03 (0.36), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 226 TYR 0.059 0.002 TYR K 261 PHE 0.018 0.002 PHE A 67 TRP 0.016 0.002 TRP K 250 HIS 0.006 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00669 (13267) covalent geometry : angle 0.77984 (18977) hydrogen bonds : bond 0.06585 ( 805) hydrogen bonds : angle 4.04399 ( 2063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2167.80 seconds wall clock time: 38 minutes 4.17 seconds (2284.17 seconds total)