Starting phenix.real_space_refine on Fri Jul 3 06:23:18 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9igj_52852/07_2026/9igj_52852.cif Found real_map, /net/cci-nas-00/data/ceres_data/9igj_52852/07_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_52852/07_2026/9igj_52852.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9igj_52852/07_2026/9igj_52852.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9igj_52852/07_2026/9igj_52852.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9igj_52852/07_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-dev-6108/lib/python3.11/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: 2.21, per 1000 atoms: 0.18 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: 0.84 Conformation dependent library (CDL) restraints added in 306.8 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: 1.51 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: 3.10 Time building geometry restraints manager: 1.05 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' DT J -72 " pdb=" N1 DT J -72 " ideal model delta sigma weight residual 1.468 1.549 -0.081 1.40e-02 5.10e+03 3.32e+01 bond pdb=" C1' DG I 58 " pdb=" N9 DG I 58 " ideal model delta sigma weight residual 1.468 1.388 0.080 1.40e-02 5.10e+03 3.27e+01 bond pdb=" C1' DC I 71 " pdb=" N1 DC I 71 " ideal model delta sigma weight residual 1.468 1.548 -0.080 1.40e-02 5.10e+03 3.26e+01 bond pdb=" C1' DA I 72 " pdb=" N9 DA I 72 " ideal model delta sigma weight residual 1.468 1.392 0.076 1.40e-02 5.10e+03 2.99e+01 bond pdb=" C1' DC I 70 " pdb=" N1 DC I 70 " ideal model delta sigma weight residual 1.468 1.543 -0.075 1.40e-02 5.10e+03 2.86e+01 ... (remaining 13262 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.18: 18655 3.18 - 6.36: 306 6.36 - 9.54: 14 9.54 - 12.72: 0 12.72 - 15.90: 2 Bond angle restraints: 18977 Sorted by residual: angle pdb=" O5' DT I -16 " pdb=" C5' DT I -16 " pdb=" C4' DT I -16 " ideal model delta sigma weight residual 109.40 115.28 -5.88 8.00e-01 1.56e+00 5.39e+01 angle pdb=" O4' DG J -56 " pdb=" C1' DG J -56 " pdb=" N9 DG J -56 " ideal model delta sigma weight residual 108.00 112.76 -4.76 7.00e-01 2.04e+00 4.62e+01 angle pdb=" O4' DG I 55 " pdb=" C1' DG I 55 " pdb=" N9 DG I 55 " ideal model delta sigma weight residual 108.00 112.42 -4.42 7.00e-01 2.04e+00 3.98e+01 angle pdb=" O5' DC J 7 " pdb=" C5' DC J 7 " pdb=" C4' DC J 7 " ideal model delta sigma weight residual 109.40 114.05 -4.65 8.00e-01 1.56e+00 3.38e+01 angle pdb=" O5' DG J -70 " pdb=" C5' DG J -70 " pdb=" C4' DG J -70 " ideal model delta sigma weight residual 109.40 113.62 -4.22 8.00e-01 1.56e+00 2.78e+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 - 0.119: 2022 0.119 - 0.238: 97 0.238 - 0.357: 9 0.357 - 0.477: 0 0.477 - 0.596: 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 2.34 -2.93 -0.60 2.00e-01 2.50e+01 8.87e+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 2.34 -2.87 -0.53 2.00e-01 2.50e+01 7.08e+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 2.34 -2.86 -0.52 2.00e-01 2.50e+01 6.86e+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: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.040 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:1.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6530 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 : 0.008 0.081 13267 Z= 0.707 Angle : 1.008 15.902 18977 Z= 0.819 Chirality : 0.071 0.596 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/Z covalent geometry : bond 0.00820 / 0.71 (13267) covalent geometry : angle 1.00774 / 0.82 (18977) hydrogen bonds : bond 0.13008 / 8.63 ( 805) hydrogen bonds : angle 4.52164 / 3.28 ( 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 : 0.351 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: 0.1307 time to fit residues: 63.8385 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 : 0.363 ------------------------------------------------------------------------------- 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: 30.0000 chunk 49 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 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: 50.0000 chunk 106 optimal weight: 20.0000 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN D 63 ASN E 113 HIS F 25 ASN F 93 GLN G 73 ASN G 104 GLN K 232 GLN K 283 GLN K 288 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.036528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.028724 restraints weight = 133149.650| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.029526 restraints weight = 68956.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.030073 restraints weight = 44428.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.030424 restraints weight = 32378.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.030638 restraints weight = 25950.647| |-----------------------------------------------------------------------------| r_work (final): 0.2952 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8090 moved from start: 0.2795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 13267 Z= 0.191 Angle : 0.805 12.455 18977 Z= 0.451 Chirality : 0.049 0.207 2139 Planarity : 0.006 0.108 1531 Dihedral : 29.390 99.120 3758 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 12.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Rotamer: Outliers : 2.96 % Allowed : 22.91 % Favored : 74.13 % 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: 1.49 (0.27), residues: 900 helix: 1.60 (0.20), residues: 637 sheet: -2.37 (0.90), residues: 32 loop : -0.09 (0.38), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 39 TYR 0.024 0.003 TYR B 88 PHE 0.036 0.003 PHE H 65 TRP 0.013 0.002 TRP L 211 HIS 0.003 0.001 HIS D 109 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.19 (13267) covalent geometry : angle 0.80546 / 0.45 (18977) hydrogen bonds : bond 0.05559 / 3.70 ( 805) hydrogen bonds : angle 3.84118 / 2.83 ( 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 256 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 233 time to evaluate : 0.386 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: A 81 ASP cc_start: 0.7376 (t0) cc_final: 0.7052 (t0) REVERT: A 105 GLU cc_start: 0.8952 (mm-30) cc_final: 0.8716 (mm-30) REVERT: B 44 LYS cc_start: 0.9360 (tttt) cc_final: 0.9003 (ttpt) REVERT: C 92 GLU cc_start: 0.8772 (mm-30) cc_final: 0.8436 (mt-10) REVERT: D 63 ASN cc_start: 0.9095 (OUTLIER) cc_final: 0.8855 (t0) REVERT: D 68 ASP cc_start: 0.9265 (t0) cc_final: 0.7707 (t0) REVERT: D 71 GLU cc_start: 0.9019 (tm-30) cc_final: 0.8768 (pp20) REVERT: D 102 LEU cc_start: 0.9340 (tp) cc_final: 0.9114 (tp) REVERT: E 52 ARG cc_start: 0.9535 (OUTLIER) cc_final: 0.9027 (mtm-85) REVERT: E 94 GLU cc_start: 0.8736 (tp30) cc_final: 0.8281 (tp30) REVERT: E 120 MET cc_start: 0.8849 (mtp) cc_final: 0.8001 (mpp) REVERT: F 24 ASP cc_start: 0.8571 (t0) cc_final: 0.8225 (t0) REVERT: F 74 GLU cc_start: 0.8737 (pp20) cc_final: 0.8246 (pp20) REVERT: H 42 TYR cc_start: 0.8733 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: H 95 GLN cc_start: 0.9257 (pt0) cc_final: 0.8276 (pp30) REVERT: H 105 GLU cc_start: 0.9108 (tp30) cc_final: 0.8801 (tp30) REVERT: L 264 MET cc_start: 0.8851 (ppp) cc_final: 0.8450 (ppp) REVERT: K 229 LYS cc_start: 0.8406 (OUTLIER) cc_final: 0.7551 (mmmt) REVERT: K 264 MET cc_start: 0.9653 (ttp) cc_final: 0.9158 (mtt) outliers start: 23 outliers final: 12 residues processed: 245 average time/residue: 0.1357 time to fit residues: 44.7930 Evaluate side-chains 210 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 87 SER 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 E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 248 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 71 optimal weight: 9.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 94 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 85 optimal weight: 8.9990 chunk 8 optimal weight: 1.9990 chunk 44 optimal weight: 3.9990 chunk 4 optimal weight: 9.9990 chunk 102 optimal weight: 30.0000 overall best weight: 3.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 68 GLN A 108 ASN D 63 ASN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 84 ASN K 232 GLN K 255 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.034755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2843 r_free = 0.2843 target = 0.026903 restraints weight = 137382.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.027663 restraints weight = 71080.386| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2891 r_free = 0.2891 target = 0.028140 restraints weight = 45662.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2905 r_free = 0.2905 target = 0.028486 restraints weight = 33839.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.028704 restraints weight = 27060.375| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8143 moved from start: 0.3506 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13267 Z= 0.202 Angle : 0.758 11.384 18977 Z= 0.426 Chirality : 0.047 0.218 2139 Planarity : 0.006 0.090 1531 Dihedral : 29.488 102.364 3758 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 12.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.22 % Allowed : 22.39 % Favored : 74.39 % 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: 1.55 (0.28), residues: 900 helix: 1.64 (0.20), residues: 643 sheet: -2.35 (0.91), residues: 32 loop : -0.06 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG H 99 TYR 0.036 0.002 TYR B 88 PHE 0.035 0.002 PHE H 65 TRP 0.012 0.002 TRP L 211 HIS 0.007 0.001 HIS H 82 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (13267) covalent geometry : angle 0.75806 / 0.43 (18977) hydrogen bonds : bond 0.05619 / 3.74 ( 805) hydrogen bonds : angle 3.86136 / 2.83 ( 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 238 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.334 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: A 81 ASP cc_start: 0.7487 (t0) cc_final: 0.7272 (t0) REVERT: A 94 GLU cc_start: 0.9012 (tp30) cc_final: 0.8776 (tt0) REVERT: B 44 LYS cc_start: 0.9355 (tttt) cc_final: 0.8976 (ttpt) REVERT: B 74 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8608 (tm-30) REVERT: B 77 LYS cc_start: 0.9196 (mmmm) cc_final: 0.8898 (mmmt) REVERT: B 91 LYS cc_start: 0.8997 (tmmt) cc_final: 0.8404 (pttm) REVERT: D 63 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8791 (t0) REVERT: D 76 GLU cc_start: 0.8938 (tp30) cc_final: 0.8503 (tp30) REVERT: D 83 TYR cc_start: 0.8694 (m-80) cc_final: 0.8228 (m-80) REVERT: D 102 LEU cc_start: 0.9374 (tp) cc_final: 0.9008 (tp) REVERT: E 52 ARG cc_start: 0.9503 (OUTLIER) cc_final: 0.9066 (mtm-85) REVERT: E 120 MET cc_start: 0.8998 (mtp) cc_final: 0.8550 (mtp) REVERT: G 24 GLN cc_start: 0.8851 (mm-40) cc_final: 0.8638 (mp10) REVERT: G 39 TYR cc_start: 0.8823 (m-80) cc_final: 0.8609 (m-10) REVERT: H 42 TYR cc_start: 0.8760 (OUTLIER) cc_final: 0.8451 (m-80) REVERT: H 76 GLU cc_start: 0.8955 (mm-30) cc_final: 0.8600 (mm-30) REVERT: H 79 ARG cc_start: 0.9228 (mmp80) cc_final: 0.9007 (mmm160) REVERT: H 105 GLU cc_start: 0.9091 (tp30) cc_final: 0.8730 (tp30) REVERT: L 264 MET cc_start: 0.9040 (ppp) cc_final: 0.8781 (ppp) REVERT: K 227 TYR cc_start: 0.9446 (m-10) cc_final: 0.8986 (m-10) REVERT: K 238 PHE cc_start: 0.8804 (p90) cc_final: 0.8041 (p90) REVERT: K 264 MET cc_start: 0.9488 (ttp) cc_final: 0.8881 (mtm) outliers start: 25 outliers final: 14 residues processed: 222 average time/residue: 0.1180 time to fit residues: 35.7762 Evaluate side-chains 205 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 188 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 B residue 37 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 ILE 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 E residue 125 GLN Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 74 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 5 optimal weight: 10.0000 chunk 72 optimal weight: 6.9990 chunk 99 optimal weight: 50.0000 chunk 64 optimal weight: 4.9990 chunk 34 optimal weight: 0.0270 chunk 73 optimal weight: 8.9990 chunk 103 optimal weight: 40.0000 chunk 6 optimal weight: 0.9990 chunk 16 optimal weight: 7.9990 overall best weight: 4.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 63 ASN G 24 GLN ** G 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 232 GLN K 283 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3115 r_free = 0.3115 target = 0.033771 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2809 r_free = 0.2809 target = 0.026045 restraints weight = 137965.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.026742 restraints weight = 71962.731| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.027210 restraints weight = 46499.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.027565 restraints weight = 34541.789| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.027787 restraints weight = 27717.543| |-----------------------------------------------------------------------------| r_work (final): 0.2862 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3950 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.068 13267 Z= 0.202 Angle : 0.718 10.225 18977 Z= 0.410 Chirality : 0.045 0.216 2139 Planarity : 0.005 0.060 1531 Dihedral : 29.575 102.680 3758 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.35 % Allowed : 22.14 % Favored : 74.52 % 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: 1.54 (0.28), residues: 900 helix: 1.67 (0.20), residues: 637 sheet: -2.41 (0.90), residues: 32 loop : -0.15 (0.37), residues: 231 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG K 233 TYR 0.040 0.002 TYR B 88 PHE 0.050 0.002 PHE H 65 TRP 0.019 0.003 TRP K 230 HIS 0.006 0.001 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00399 / 0.20 (13267) covalent geometry : angle 0.71840 / 0.41 (18977) hydrogen bonds : bond 0.05307 / 3.54 ( 805) hydrogen bonds : angle 3.81981 / 2.81 ( 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 228 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 202 time to evaluate : 0.363 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: 0.8602 (tp-100) cc_final: 0.8265 (tm-30) REVERT: A 94 GLU cc_start: 0.8997 (tp30) cc_final: 0.8686 (tt0) REVERT: A 105 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8376 (mm-30) REVERT: B 44 LYS cc_start: 0.9400 (tttt) cc_final: 0.9016 (ttpt) REVERT: B 64 ASN cc_start: 0.9356 (m-40) cc_final: 0.9028 (m-40) REVERT: B 74 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8589 (tm-30) REVERT: B 77 LYS cc_start: 0.9240 (mmmm) cc_final: 0.8979 (mmmt) REVERT: B 91 LYS cc_start: 0.9106 (tmmt) cc_final: 0.8567 (pttm) REVERT: D 63 ASN cc_start: 0.9207 (OUTLIER) cc_final: 0.8898 (t0) REVERT: D 68 ASP cc_start: 0.9104 (t0) cc_final: 0.7585 (t0) REVERT: D 71 GLU cc_start: 0.8937 (tm-30) cc_final: 0.8728 (pp20) REVERT: D 79 ARG cc_start: 0.9266 (ttm-80) cc_final: 0.8981 (mtm-85) REVERT: D 102 LEU cc_start: 0.9386 (tp) cc_final: 0.9006 (tp) REVERT: E 120 MET cc_start: 0.8950 (mtp) cc_final: 0.8511 (mtp) REVERT: G 39 TYR cc_start: 0.8792 (m-80) cc_final: 0.8555 (m-10) REVERT: G 89 ASN cc_start: 0.9538 (m-40) cc_final: 0.9220 (m-40) REVERT: H 42 TYR cc_start: 0.8817 (OUTLIER) cc_final: 0.8587 (m-80) REVERT: H 113 GLU cc_start: 0.9366 (tt0) cc_final: 0.8862 (mt-10) REVERT: L 264 MET cc_start: 0.9100 (ppp) cc_final: 0.8864 (ppp) REVERT: K 232 GLN cc_start: 0.8874 (tp-100) cc_final: 0.8522 (tm-30) REVERT: K 238 PHE cc_start: 0.8959 (p90) cc_final: 0.8148 (p90) REVERT: K 264 MET cc_start: 0.9422 (ttp) cc_final: 0.8831 (mtm) REVERT: K 292 MET cc_start: 0.3902 (ttp) cc_final: 0.3181 (mtp) outliers start: 26 outliers final: 15 residues processed: 215 average time/residue: 0.1229 time to fit residues: 36.2993 Evaluate side-chains 201 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 ILE 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 E residue 125 GLN Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 67 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 110 optimal weight: 30.0000 chunk 80 optimal weight: 3.9990 chunk 95 optimal weight: 30.0000 chunk 12 optimal weight: 8.9990 chunk 45 optimal weight: 0.0270 chunk 96 optimal weight: 30.0000 overall best weight: 5.6046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 63 ASN G 68 ASN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.032705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.024895 restraints weight = 140215.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.025632 restraints weight = 72064.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.2815 r_free = 0.2815 target = 0.026113 restraints weight = 46539.899| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.026438 restraints weight = 34318.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.026631 restraints weight = 27721.805| |-----------------------------------------------------------------------------| r_work (final): 0.2822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.4422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13267 Z= 0.232 Angle : 0.737 9.412 18977 Z= 0.419 Chirality : 0.045 0.229 2139 Planarity : 0.005 0.049 1531 Dihedral : 29.684 102.410 3758 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 14.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 4.25 % Allowed : 22.14 % Favored : 73.62 % 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: 1.53 (0.28), residues: 900 helix: 1.69 (0.21), residues: 626 sheet: -2.44 (0.89), residues: 32 loop : -0.14 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 226 TYR 0.051 0.002 TYR D 83 PHE 0.047 0.002 PHE H 65 TRP 0.011 0.002 TRP L 211 HIS 0.008 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00452 / 0.23 (13267) covalent geometry : angle 0.73650 / 0.42 (18977) hydrogen bonds : bond 0.06109 / 4.11 ( 805) hydrogen bonds : angle 3.96392 / 2.91 ( 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 226 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 193 time to evaluate : 0.364 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: A 68 GLN cc_start: 0.8601 (tp-100) cc_final: 0.8241 (tm-30) REVERT: A 94 GLU cc_start: 0.8980 (tp30) cc_final: 0.8729 (tt0) REVERT: A 105 GLU cc_start: 0.8860 (mm-30) cc_final: 0.8488 (mm-30) REVERT: B 44 LYS cc_start: 0.9419 (tttt) cc_final: 0.8971 (ttpt) REVERT: B 53 GLU cc_start: 0.8238 (mt-10) cc_final: 0.7973 (pt0) REVERT: B 64 ASN cc_start: 0.9354 (m-40) cc_final: 0.9018 (m-40) REVERT: B 74 GLU cc_start: 0.9002 (tm-30) cc_final: 0.8456 (tm-30) REVERT: B 88 TYR cc_start: 0.9119 (m-10) cc_final: 0.8863 (m-10) REVERT: B 91 LYS cc_start: 0.9129 (tmmt) cc_final: 0.8896 (pptt) REVERT: D 68 ASP cc_start: 0.9135 (t0) cc_final: 0.7759 (t0) REVERT: D 71 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8748 (pp20) REVERT: D 102 LEU cc_start: 0.9397 (tp) cc_final: 0.9016 (tp) REVERT: E 52 ARG cc_start: 0.9506 (OUTLIER) cc_final: 0.9048 (mtm-85) REVERT: E 94 GLU cc_start: 0.8406 (tp30) cc_final: 0.7798 (tp30) REVERT: E 120 MET cc_start: 0.8963 (mtp) cc_final: 0.8495 (mtp) REVERT: G 39 TYR cc_start: 0.8950 (m-80) cc_final: 0.8728 (m-80) REVERT: G 56 GLU cc_start: 0.9081 (tt0) cc_final: 0.8181 (tt0) REVERT: G 89 ASN cc_start: 0.9594 (m-40) cc_final: 0.9332 (m-40) REVERT: H 42 TYR cc_start: 0.8927 (OUTLIER) cc_final: 0.8558 (m-80) REVERT: H 82 HIS cc_start: 0.9457 (t-90) cc_final: 0.9077 (t-90) REVERT: H 93 GLU cc_start: 0.9291 (mp0) cc_final: 0.9058 (mp0) REVERT: H 113 GLU cc_start: 0.9353 (tt0) cc_final: 0.8966 (mt-10) REVERT: L 227 TYR cc_start: 0.9293 (m-80) cc_final: 0.8276 (m-80) REVERT: L 264 MET cc_start: 0.9181 (ppp) cc_final: 0.8957 (ppp) REVERT: K 229 LYS cc_start: 0.8366 (OUTLIER) cc_final: 0.7666 (mmmt) REVERT: K 238 PHE cc_start: 0.9094 (p90) cc_final: 0.8308 (p90) REVERT: K 264 MET cc_start: 0.9395 (ttp) cc_final: 0.8796 (mtm) REVERT: K 292 MET cc_start: 0.4956 (ttp) cc_final: 0.3102 (mtp) outliers start: 33 outliers final: 22 residues processed: 211 average time/residue: 0.1350 time to fit residues: 38.9862 Evaluate side-chains 204 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 179 time to evaluate : 0.309 ------------------------------------------------------------------------------- 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 37 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 B residue 93 GLN Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 94 ILE 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 E residue 125 GLN Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 222 ASN Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 233 ARG Chi-restraints excluded: chain K residue 241 VAL Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 26 optimal weight: 0.3980 chunk 81 optimal weight: 7.9990 chunk 95 optimal weight: 30.0000 chunk 58 optimal weight: 6.9990 chunk 97 optimal weight: 40.0000 chunk 36 optimal weight: 8.9990 chunk 18 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 50 optimal weight: 7.9990 chunk 107 optimal weight: 30.0000 chunk 79 optimal weight: 30.0000 overall best weight: 4.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN D 63 ASN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 283 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.032647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2764 r_free = 0.2764 target = 0.024823 restraints weight = 139288.551| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025566 restraints weight = 71326.788| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.026051 restraints weight = 45956.967| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.026378 restraints weight = 33855.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2836 r_free = 0.2836 target = 0.026587 restraints weight = 27325.804| |-----------------------------------------------------------------------------| r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8234 moved from start: 0.4670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 13267 Z= 0.195 Angle : 0.724 8.156 18977 Z= 0.412 Chirality : 0.044 0.229 2139 Planarity : 0.005 0.053 1531 Dihedral : 29.727 102.815 3758 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.86 % Allowed : 24.32 % 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: 1.51 (0.28), residues: 900 helix: 1.67 (0.21), residues: 626 sheet: -2.44 (0.85), residues: 32 loop : -0.16 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.052 0.002 TYR D 83 PHE 0.055 0.002 PHE H 65 TRP 0.010 0.002 TRP K 230 HIS 0.007 0.001 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00384 / 0.20 (13267) covalent geometry : angle 0.72398 / 0.41 (18977) hydrogen bonds : bond 0.05208 / 3.50 ( 805) hydrogen bonds : angle 3.93983 / 2.87 ( 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 225 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 195 time to evaluate : 0.361 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: A 68 GLN cc_start: 0.8639 (tp-100) cc_final: 0.8243 (tm-30) REVERT: A 94 GLU cc_start: 0.8980 (tp30) cc_final: 0.8711 (tt0) REVERT: A 105 GLU cc_start: 0.8947 (mm-30) cc_final: 0.8682 (mm-30) REVERT: B 26 ILE cc_start: 0.9136 (tt) cc_final: 0.8932 (tp) REVERT: B 44 LYS cc_start: 0.9423 (tttt) cc_final: 0.8954 (ttpt) REVERT: B 46 ILE cc_start: 0.9601 (tp) cc_final: 0.9367 (tp) REVERT: B 53 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7984 (pt0) REVERT: B 64 ASN cc_start: 0.9353 (m-40) cc_final: 0.9038 (m-40) REVERT: B 91 LYS cc_start: 0.9139 (tmmt) cc_final: 0.8875 (pptt) REVERT: D 79 ARG cc_start: 0.9451 (ttm110) cc_final: 0.8939 (ttm110) REVERT: D 102 LEU cc_start: 0.9388 (tp) cc_final: 0.9012 (tp) REVERT: E 52 ARG cc_start: 0.9520 (OUTLIER) cc_final: 0.9052 (mtm-85) REVERT: E 94 GLU cc_start: 0.8448 (tp30) cc_final: 0.8107 (tp30) REVERT: E 120 MET cc_start: 0.8908 (mtp) cc_final: 0.8529 (mpp) REVERT: G 39 TYR cc_start: 0.8928 (m-80) cc_final: 0.8534 (m-80) REVERT: G 56 GLU cc_start: 0.9183 (tt0) cc_final: 0.8791 (mt-10) REVERT: G 110 ASN cc_start: 0.9136 (t0) cc_final: 0.8687 (m110) REVERT: H 39 ILE cc_start: 0.9483 (OUTLIER) cc_final: 0.9105 (tp) REVERT: H 42 TYR cc_start: 0.8851 (OUTLIER) cc_final: 0.8510 (m-80) REVERT: H 68 ASP cc_start: 0.9223 (t0) cc_final: 0.8966 (t0) REVERT: H 71 GLU cc_start: 0.9391 (tp30) cc_final: 0.9165 (tp30) REVERT: H 72 ARG cc_start: 0.9463 (mmm-85) cc_final: 0.9166 (mtt90) REVERT: H 82 HIS cc_start: 0.9433 (t-90) cc_final: 0.9181 (t-90) REVERT: H 93 GLU cc_start: 0.9325 (mp0) cc_final: 0.9074 (mp0) REVERT: L 264 MET cc_start: 0.9310 (ppp) cc_final: 0.9053 (ppp) REVERT: K 229 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.7836 (tppt) REVERT: K 238 PHE cc_start: 0.8999 (p90) cc_final: 0.8208 (p90) REVERT: K 264 MET cc_start: 0.9375 (ttp) cc_final: 0.8774 (mtm) REVERT: K 292 MET cc_start: 0.5142 (ttp) cc_final: 0.3081 (mtp) outliers start: 30 outliers final: 20 residues processed: 213 average time/residue: 0.1333 time to fit residues: 39.0041 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 : 0.416 ------------------------------------------------------------------------------- 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 37 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 C residue 76 THR Chi-restraints excluded: chain D residue 73 ILE Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR 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 E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 12 optimal weight: 0.9990 chunk 74 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 45 optimal weight: 0.0980 chunk 4 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 37 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 85 optimal weight: 8.9990 chunk 28 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 overall best weight: 1.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 288 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 = 0.3093 r_free = 0.3093 target = 0.033052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2785 r_free = 0.2785 target = 0.025407 restraints weight = 139407.500| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.026140 restraints weight = 71760.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.026617 restraints weight = 46349.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.026913 restraints weight = 34061.380| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.027129 restraints weight = 27702.673| |-----------------------------------------------------------------------------| r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8211 moved from start: 0.4840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 13267 Z= 0.164 Angle : 0.726 8.354 18977 Z= 0.412 Chirality : 0.044 0.220 2139 Planarity : 0.005 0.052 1531 Dihedral : 29.639 103.612 3758 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.35 % Allowed : 26.64 % 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: 1.39 (0.28), residues: 900 helix: 1.56 (0.20), residues: 639 sheet: -1.99 (1.11), residues: 22 loop : -0.40 (0.36), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG L 226 TYR 0.067 0.002 TYR B 88 PHE 0.047 0.002 PHE H 65 TRP 0.010 0.002 TRP K 230 HIS 0.007 0.001 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00325 / 0.16 (13267) covalent geometry : angle 0.72586 / 0.41 (18977) hydrogen bonds : bond 0.04306 / 2.86 ( 805) hydrogen bonds : angle 3.83859 / 2.81 ( 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 229 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 203 time to evaluate : 0.373 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: A 68 GLN cc_start: 0.8575 (tp-100) cc_final: 0.8021 (tp-100) REVERT: A 105 GLU cc_start: 0.8930 (mm-30) cc_final: 0.8592 (mm-30) REVERT: A 106 ASP cc_start: 0.9314 (m-30) cc_final: 0.9016 (m-30) REVERT: A 126 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8638 (tp) REVERT: B 26 ILE cc_start: 0.9131 (tt) cc_final: 0.8928 (tp) REVERT: B 44 LYS cc_start: 0.9425 (tttt) cc_final: 0.8994 (ttpt) REVERT: B 46 ILE cc_start: 0.9644 (tp) cc_final: 0.9428 (tp) REVERT: B 53 GLU cc_start: 0.8209 (mt-10) cc_final: 0.7979 (pt0) REVERT: B 59 LYS cc_start: 0.9492 (ttpp) cc_final: 0.8966 (tmmt) REVERT: B 64 ASN cc_start: 0.9329 (m-40) cc_final: 0.9013 (m-40) REVERT: C 92 GLU cc_start: 0.9117 (mm-30) cc_final: 0.8737 (mm-30) REVERT: D 68 ASP cc_start: 0.9151 (t0) cc_final: 0.8121 (t0) REVERT: D 71 GLU cc_start: 0.8982 (tm-30) cc_final: 0.8743 (pp20) REVERT: D 79 ARG cc_start: 0.9381 (ttm110) cc_final: 0.9085 (ttm110) REVERT: D 102 LEU cc_start: 0.9375 (tp) cc_final: 0.8997 (tp) REVERT: E 52 ARG cc_start: 0.9508 (OUTLIER) cc_final: 0.8953 (mtm-85) REVERT: E 120 MET cc_start: 0.8924 (mtp) cc_final: 0.8595 (mpp) REVERT: G 39 TYR cc_start: 0.8896 (m-80) cc_final: 0.8600 (m-80) REVERT: G 56 GLU cc_start: 0.9160 (tt0) cc_final: 0.8714 (mt-10) REVERT: G 110 ASN cc_start: 0.9265 (t0) cc_final: 0.8834 (m110) REVERT: H 39 ILE cc_start: 0.9281 (OUTLIER) cc_final: 0.8817 (tp) REVERT: H 42 TYR cc_start: 0.8815 (OUTLIER) cc_final: 0.8501 (m-80) REVERT: H 68 ASP cc_start: 0.9216 (t0) cc_final: 0.8939 (t0) REVERT: H 72 ARG cc_start: 0.9492 (mmm-85) cc_final: 0.9192 (mtt90) REVERT: H 82 HIS cc_start: 0.9365 (t-90) cc_final: 0.9145 (t-90) REVERT: L 283 GLN cc_start: 0.8569 (mm-40) cc_final: 0.8332 (mp10) REVERT: K 229 LYS cc_start: 0.8431 (OUTLIER) cc_final: 0.7706 (tppt) REVERT: K 238 PHE cc_start: 0.8918 (p90) cc_final: 0.8093 (p90) REVERT: K 264 MET cc_start: 0.9315 (ttp) cc_final: 0.8738 (mtm) REVERT: K 292 MET cc_start: 0.4905 (ttp) cc_final: 0.3086 (mtp) outliers start: 26 outliers final: 16 residues processed: 216 average time/residue: 0.1291 time to fit residues: 38.4520 Evaluate side-chains 204 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 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 D residue 82 HIS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain E residue 52 ARG Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 37 LEU Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 84 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 73 optimal weight: 40.0000 chunk 29 optimal weight: 10.0000 chunk 83 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN A 108 ASN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.031932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.024182 restraints weight = 139568.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2770 r_free = 0.2770 target = 0.024911 restraints weight = 71788.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.025388 restraints weight = 46167.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.2803 r_free = 0.2803 target = 0.025683 restraints weight = 34046.079| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.2813 r_free = 0.2813 target = 0.025908 restraints weight = 27698.916| |-----------------------------------------------------------------------------| r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.5217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 13267 Z= 0.219 Angle : 0.772 9.361 18977 Z= 0.435 Chirality : 0.044 0.234 2139 Planarity : 0.005 0.043 1531 Dihedral : 29.745 103.116 3758 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 3.73 % Allowed : 27.28 % 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: 1.35 (0.27), residues: 900 helix: 1.48 (0.20), residues: 630 sheet: -1.81 (1.07), residues: 22 loop : -0.21 (0.37), residues: 248 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG L 226 TYR 0.083 0.003 TYR D 83 PHE 0.035 0.002 PHE H 65 TRP 0.008 0.002 TRP L 211 HIS 0.009 0.002 HIS E 113 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.22 (13267) covalent geometry : angle 0.77224 / 0.44 (18977) hydrogen bonds : bond 0.06203 / 4.18 ( 805) hydrogen bonds : angle 4.04040 / 2.94 ( 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 221 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 0.372 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: A 68 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8091 (tp-100) REVERT: A 106 ASP cc_start: 0.9304 (m-30) cc_final: 0.8999 (m-30) REVERT: B 44 LYS cc_start: 0.9465 (tttt) cc_final: 0.9087 (ttpt) REVERT: B 46 ILE cc_start: 0.9669 (tp) cc_final: 0.9464 (tp) REVERT: B 53 GLU cc_start: 0.8251 (mt-10) cc_final: 0.8021 (pt0) REVERT: B 64 ASN cc_start: 0.9359 (m-40) cc_final: 0.9081 (m110) REVERT: C 92 GLU cc_start: 0.9036 (mm-30) cc_final: 0.8754 (mm-30) REVERT: C 110 ASN cc_start: 0.8901 (t0) cc_final: 0.8513 (p0) REVERT: D 35 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7617 (tp30) REVERT: D 68 ASP cc_start: 0.9224 (t0) cc_final: 0.8309 (t0) REVERT: D 71 GLU cc_start: 0.9017 (tm-30) cc_final: 0.8786 (pp20) REVERT: D 76 GLU cc_start: 0.9361 (tp30) cc_final: 0.8992 (tp30) REVERT: D 79 ARG cc_start: 0.9315 (ttm110) cc_final: 0.8998 (ttp-110) REVERT: D 102 LEU cc_start: 0.9395 (tp) cc_final: 0.9132 (tp) REVERT: E 59 GLU cc_start: 0.8705 (pm20) cc_final: 0.8468 (pm20) REVERT: E 94 GLU cc_start: 0.8533 (tp30) cc_final: 0.8273 (tp30) REVERT: E 120 MET cc_start: 0.8946 (mtp) cc_final: 0.8487 (mpp) REVERT: F 53 GLU cc_start: 0.8122 (pp20) cc_final: 0.7674 (pp20) REVERT: G 56 GLU cc_start: 0.9110 (tt0) cc_final: 0.8645 (mt-10) REVERT: H 42 TYR cc_start: 0.8990 (OUTLIER) cc_final: 0.8614 (m-80) REVERT: H 59 MET cc_start: 0.9142 (tpt) cc_final: 0.8894 (tpt) REVERT: H 68 ASP cc_start: 0.9350 (t0) cc_final: 0.9096 (t0) REVERT: H 82 HIS cc_start: 0.9400 (t-90) cc_final: 0.9132 (t-90) REVERT: H 109 HIS cc_start: 0.9209 (m170) cc_final: 0.8777 (m90) REVERT: L 264 MET cc_start: 0.8583 (ppp) cc_final: 0.8126 (ppp) REVERT: L 283 GLN cc_start: 0.8595 (mm-40) cc_final: 0.8391 (mp10) REVERT: K 229 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.7831 (tppt) REVERT: K 238 PHE cc_start: 0.8964 (p90) cc_final: 0.8188 (p90) REVERT: K 264 MET cc_start: 0.9237 (ttp) cc_final: 0.8723 (mtm) outliers start: 29 outliers final: 18 residues processed: 208 average time/residue: 0.1259 time to fit residues: 36.5202 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 : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 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 D residue 35 GLU Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 58 optimal weight: 7.9990 chunk 66 optimal weight: 6.9990 chunk 7 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 108 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 40 optimal weight: 7.9990 chunk 75 optimal weight: 0.0470 chunk 41 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 39 optimal weight: 4.9990 overall best weight: 5.4086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 108 ASN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.031610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.023875 restraints weight = 142914.926| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.2754 r_free = 0.2754 target = 0.024592 restraints weight = 72934.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.025083 restraints weight = 46996.219| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.025402 restraints weight = 34495.235| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2798 r_free = 0.2798 target = 0.025586 restraints weight = 27779.223| |-----------------------------------------------------------------------------| r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8280 moved from start: 0.5536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 13267 Z= 0.231 Angle : 0.798 12.607 18977 Z= 0.450 Chirality : 0.046 0.240 2139 Planarity : 0.005 0.039 1531 Dihedral : 29.892 102.956 3758 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.22 % Favored : 97.78 % Rotamer: Outliers : 3.73 % Allowed : 28.96 % Favored : 67.31 % 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: 1.31 (0.28), residues: 900 helix: 1.59 (0.21), residues: 615 sheet: -1.93 (0.86), residues: 32 loop : -0.43 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG L 226 TYR 0.072 0.003 TYR D 83 PHE 0.027 0.002 PHE H 65 TRP 0.010 0.002 TRP L 211 HIS 0.010 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00467 / 0.23 (13267) covalent geometry : angle 0.79774 / 0.45 (18977) hydrogen bonds : bond 0.05875 / 3.95 ( 805) hydrogen bonds : angle 4.19990 / 3.06 ( 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 210 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 181 time to evaluate : 0.372 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8654 (tp-100) cc_final: 0.8106 (tp-100) REVERT: A 126 LEU cc_start: 0.9238 (OUTLIER) cc_final: 0.8879 (tp) REVERT: B 44 LYS cc_start: 0.9460 (tttt) cc_final: 0.9032 (ttpt) REVERT: B 53 GLU cc_start: 0.8300 (mt-10) cc_final: 0.8065 (pt0) REVERT: B 59 LYS cc_start: 0.9516 (ttpp) cc_final: 0.9031 (tmmt) REVERT: B 64 ASN cc_start: 0.9403 (m-40) cc_final: 0.9152 (m-40) REVERT: C 110 ASN cc_start: 0.8954 (t0) cc_final: 0.8561 (p0) REVERT: D 68 ASP cc_start: 0.9214 (t0) cc_final: 0.8333 (t0) REVERT: D 71 GLU cc_start: 0.9033 (tm-30) cc_final: 0.8823 (pp20) REVERT: D 79 ARG cc_start: 0.9364 (ttm110) cc_final: 0.9114 (ttm110) REVERT: D 102 LEU cc_start: 0.9402 (tp) cc_final: 0.9088 (tp) REVERT: E 59 GLU cc_start: 0.8866 (pm20) cc_final: 0.8595 (pm20) REVERT: E 94 GLU cc_start: 0.8709 (tp30) cc_final: 0.8218 (tp30) REVERT: E 120 MET cc_start: 0.9004 (mtp) cc_final: 0.8582 (mpp) REVERT: G 30 VAL cc_start: 0.9301 (t) cc_final: 0.9099 (p) REVERT: G 56 GLU cc_start: 0.9159 (tt0) cc_final: 0.8685 (mt-10) REVERT: H 39 ILE cc_start: 0.9307 (OUTLIER) cc_final: 0.8836 (tp) REVERT: H 42 TYR cc_start: 0.9030 (OUTLIER) cc_final: 0.8709 (m-80) REVERT: H 59 MET cc_start: 0.9219 (tpt) cc_final: 0.8962 (tpt) REVERT: H 68 ASP cc_start: 0.9384 (t0) cc_final: 0.9096 (t0) REVERT: H 82 HIS cc_start: 0.9405 (t-90) cc_final: 0.9091 (t-90) REVERT: H 105 GLU cc_start: 0.9225 (tp30) cc_final: 0.8941 (tp30) REVERT: L 264 MET cc_start: 0.8487 (ppp) cc_final: 0.8184 (ppp) REVERT: K 229 LYS cc_start: 0.8544 (OUTLIER) cc_final: 0.7819 (mmmt) REVERT: K 238 PHE cc_start: 0.8978 (p90) cc_final: 0.8189 (p90) REVERT: K 259 MET cc_start: 0.5465 (OUTLIER) cc_final: 0.4805 (tpp) REVERT: K 264 MET cc_start: 0.9243 (ttp) cc_final: 0.8862 (mtt) REVERT: K 292 MET cc_start: 0.3072 (ttp) cc_final: 0.2590 (mtp) outliers start: 29 outliers final: 20 residues processed: 196 average time/residue: 0.1203 time to fit residues: 33.0507 Evaluate side-chains 196 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 LEU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain D residue 82 HIS Chi-restraints excluded: chain D residue 87 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 106 LEU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 90 optimal weight: 30.0000 chunk 38 optimal weight: 8.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 5.9990 chunk 78 optimal weight: 10.0000 chunk 109 optimal weight: 30.0000 chunk 65 optimal weight: 0.3980 chunk 62 optimal weight: 30.0000 chunk 86 optimal weight: 8.9990 chunk 43 optimal weight: 0.6980 chunk 68 optimal weight: 4.9990 overall best weight: 3.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 93 GLN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.031853 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.024063 restraints weight = 141471.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.024789 restraints weight = 72123.210| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.025277 restraints weight = 46510.893| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.2793 r_free = 0.2793 target = 0.025598 restraints weight = 34202.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.2802 r_free = 0.2802 target = 0.025794 restraints weight = 27632.310| |-----------------------------------------------------------------------------| r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8274 moved from start: 0.5704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.118 13267 Z= 0.194 Angle : 0.788 12.702 18977 Z= 0.443 Chirality : 0.045 0.234 2139 Planarity : 0.005 0.035 1531 Dihedral : 29.885 103.476 3758 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 3.22 % Allowed : 29.47 % Favored : 67.31 % 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: 1.33 (0.28), residues: 900 helix: 1.55 (0.21), residues: 614 sheet: -1.44 (1.17), residues: 22 loop : -0.38 (0.37), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 79 TYR 0.072 0.003 TYR D 83 PHE 0.024 0.002 PHE H 65 TRP 0.007 0.002 TRP K 230 HIS 0.008 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00401 / 0.19 (13267) covalent geometry : angle 0.78790 / 0.44 (18977) hydrogen bonds : bond 0.04991 / 3.33 ( 805) hydrogen bonds : angle 4.16492 / 3.05 ( 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 207 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 182 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 68 GLN cc_start: 0.8641 (tp-100) cc_final: 0.8094 (tp-100) REVERT: B 44 LYS cc_start: 0.9480 (tttt) cc_final: 0.8924 (ttpt) REVERT: B 53 GLU cc_start: 0.8313 (mt-10) cc_final: 0.8048 (pt0) REVERT: B 59 LYS cc_start: 0.9501 (ttpp) cc_final: 0.9141 (tmmt) REVERT: B 64 ASN cc_start: 0.9408 (m-40) cc_final: 0.9155 (m110) REVERT: C 110 ASN cc_start: 0.8976 (t0) cc_final: 0.8598 (p0) REVERT: D 68 ASP cc_start: 0.9184 (t0) cc_final: 0.8272 (t0) REVERT: D 71 GLU cc_start: 0.9015 (tm-30) cc_final: 0.8802 (pp20) REVERT: D 76 GLU cc_start: 0.9350 (tp30) cc_final: 0.9135 (tp30) REVERT: D 79 ARG cc_start: 0.9387 (ttm110) cc_final: 0.9128 (ttm110) REVERT: D 102 LEU cc_start: 0.9414 (tp) cc_final: 0.9211 (tp) REVERT: F 53 GLU cc_start: 0.8110 (pp20) cc_final: 0.7660 (pp20) REVERT: G 30 VAL cc_start: 0.9318 (t) cc_final: 0.9109 (p) REVERT: G 56 GLU cc_start: 0.9131 (tt0) cc_final: 0.8628 (mt-10) REVERT: H 39 ILE cc_start: 0.9299 (OUTLIER) cc_final: 0.8828 (tp) REVERT: H 42 TYR cc_start: 0.8995 (OUTLIER) cc_final: 0.8679 (m-80) REVERT: H 76 GLU cc_start: 0.9284 (mm-30) cc_final: 0.9058 (mm-30) REVERT: H 82 HIS cc_start: 0.9363 (t-90) cc_final: 0.9044 (t-90) REVERT: H 105 GLU cc_start: 0.9219 (tp30) cc_final: 0.8937 (tp30) REVERT: L 264 MET cc_start: 0.8374 (ppp) cc_final: 0.8030 (ppp) REVERT: K 238 PHE cc_start: 0.8974 (p90) cc_final: 0.8241 (p90) REVERT: K 259 MET cc_start: 0.5207 (OUTLIER) cc_final: 0.4600 (tpp) REVERT: K 264 MET cc_start: 0.9233 (ttp) cc_final: 0.8859 (mtt) REVERT: K 292 MET cc_start: 0.2675 (ttp) cc_final: 0.2158 (mtp) outliers start: 25 outliers final: 18 residues processed: 193 average time/residue: 0.1171 time to fit residues: 31.6720 Evaluate side-chains 195 residues out of total 777 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 120 MET Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 37 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 D residue 82 HIS Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 42 TYR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 108 LYS Chi-restraints excluded: chain K residue 229 LYS Chi-restraints excluded: chain K residue 255 ASN Chi-restraints excluded: chain K residue 259 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 112 random chunks: chunk 100 optimal weight: 50.0000 chunk 5 optimal weight: 0.7980 chunk 25 optimal weight: 8.9990 chunk 71 optimal weight: 6.9990 chunk 102 optimal weight: 40.0000 chunk 58 optimal weight: 10.0000 chunk 73 optimal weight: 3.9990 chunk 111 optimal weight: 40.0000 chunk 36 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 62 optimal weight: 9.9990 overall best weight: 4.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 93 GLN ** L 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.031286 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.023517 restraints weight = 144789.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.2740 r_free = 0.2740 target = 0.024220 restraints weight = 74505.912| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.2760 r_free = 0.2760 target = 0.024685 restraints weight = 48274.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.2774 r_free = 0.2774 target = 0.024990 restraints weight = 35816.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.2783 r_free = 0.2783 target = 0.025203 restraints weight = 28969.610| |-----------------------------------------------------------------------------| r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8300 moved from start: 0.6014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13267 Z= 0.223 Angle : 0.800 11.270 18977 Z= 0.447 Chirality : 0.045 0.239 2139 Planarity : 0.005 0.062 1531 Dihedral : 29.961 103.485 3758 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.22 % Allowed : 29.73 % Favored : 67.05 % 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: 1.31 (0.28), residues: 900 helix: 1.56 (0.21), residues: 614 sheet: -1.79 (0.90), residues: 32 loop : -0.38 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG K 233 TYR 0.068 0.003 TYR D 83 PHE 0.033 0.002 PHE H 65 TRP 0.015 0.002 TRP L 230 HIS 0.009 0.002 HIS K 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00447 / 0.22 (13267) covalent geometry : angle 0.79969 / 0.45 (18977) hydrogen bonds : bond 0.06007 / 4.05 ( 805) hydrogen bonds : angle 4.21066 / 3.07 ( 2063) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2221.21 seconds wall clock time: 39 minutes 3.84 seconds (2343.84 seconds total)