Starting phenix.real_space_refine on Thu Mar 5 13:04:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7scz_25043/03_2026/7scz_25043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7scz_25043/03_2026/7scz_25043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7scz_25043/03_2026/7scz_25043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7scz_25043/03_2026/7scz_25043.map" model { file = "/net/cci-nas-00/data/ceres_data/7scz_25043/03_2026/7scz_25043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7scz_25043/03_2026/7scz_25043.cif" } resolution = 3.5 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= 0.006 sd= 0.073 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: 6 Type Number sf(0) Gaussians P 294 5.49 5 S 19 5.16 5 C 7110 2.51 5 N 2388 2.21 5 O 2959 1.98 5 H 10435 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 18 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 23205 Number of models: 1 Model: "" Number of chains: 11 Chain: "I" Number of atoms: 4682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4682 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 4646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 4646 Classifications: {'DNA': 147} Modifications used: {'3*END': 1} Link IDs: {'rna3p': 146} Chain: "A" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1616 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 1271 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1271 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 1, 'TRANS': 75} Chain: "C" Number of atoms: 1733 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1733 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 1461 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 1461 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "E" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 1684 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 1459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 1459 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "G" Number of atoms: 1667 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1667 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "H" Number of atoms: 1450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 1450 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "K" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 1536 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Time building chain proxies: 4.03, per 1000 atoms: 0.17 Number of scatterers: 23205 At special positions: 0 Unit cell: (89.46, 121.41, 120.345, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 19 16.00 P 294 15.00 O 2959 8.00 N 2388 7.00 C 7110 6.00 H 10435 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.10 Conformation dependent library (CDL) restraints added in 562.8 milliseconds 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1588 Finding SS restraints... Secondary structure from input PDB file: 41 helices and 11 sheets defined 70.7% alpha, 3.9% beta 146 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 4.29 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.793A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.642A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 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 removed outlier: 3.501A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) 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 123 removed outlier: 3.644A pdb=" N SER D 123 " --> pdb=" O THR D 119 " (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 131 removed outlier: 3.633A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) 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: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.142A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 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 122 Processing helix chain 'K' and resid 404 through 415 Processing helix chain 'K' and resid 433 through 439 Processing helix chain 'K' and resid 440 through 449 Processing helix chain 'K' and resid 457 through 465 removed outlier: 3.766A pdb=" N ASP K 461 " --> pdb=" O ASP K 457 " (cutoff:3.500A) Processing helix chain 'K' and resid 468 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.967A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.647A 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 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.649A 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: 6.725A 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 'K' and resid 418 through 420 removed outlier: 6.351A pdb=" N CYS K 429 " --> pdb=" O VAL K 454 " (cutoff:3.500A) 444 hydrogen bonds defined for protein. 1302 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 374 hydrogen bonds 748 hydrogen bond angles 0 basepair planarities 146 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 2.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.88 - 1.07: 2390 1.07 - 1.26: 9404 1.26 - 1.45: 5394 1.45 - 1.63: 6804 1.63 - 1.82: 33 Bond restraints: 24025 Sorted by residual: bond pdb=" N LEU K 478 " pdb=" H LEU K 478 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" N SER K 479 " pdb=" H SER K 479 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" C6 DC J 69 " pdb=" H6 DC J 69 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" NH1 ARG G 88 " pdb="HH11 ARG G 88 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.70e+01 bond pdb=" C6 DC I -58 " pdb=" H6 DC I -58 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 24020 not shown) Histogram of bond angle deviations from ideal: 0.00 - 6.26: 43131 6.26 - 12.51: 448 12.51 - 18.77: 1 18.77 - 25.02: 0 25.02 - 31.28: 3 Bond angle restraints: 43583 Sorted by residual: angle pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 77.72 31.28 3.00e+00 1.11e-01 1.09e+02 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 110.00 79.30 30.70 3.00e+00 1.11e-01 1.05e+02 angle pdb=" CB ARG F 17 " pdb=" CA ARG F 17 " pdb=" HA ARG F 17 " ideal model delta sigma weight residual 109.00 79.95 29.05 3.00e+00 1.11e-01 9.38e+01 angle pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" C ARG F 17 " ideal model delta sigma weight residual 109.52 123.02 -13.50 1.55e+00 4.16e-01 7.58e+01 angle pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 110.00 120.05 -10.05 1.50e+00 4.44e-01 4.49e+01 ... (remaining 43578 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.32: 8370 35.32 - 70.64: 1611 70.64 - 105.96: 39 105.96 - 141.28: 1 141.28 - 176.60: 3 Dihedral angle restraints: 10024 sinusoidal: 7285 harmonic: 2739 Sorted by residual: dihedral pdb=" C ARG F 17 " pdb=" N ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual -122.60 -142.09 19.49 0 2.50e+00 1.60e-01 6.08e+01 dihedral pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CA ARG F 17 " pdb=" CB ARG F 17 " ideal model delta harmonic sigma weight residual 122.80 141.32 -18.52 0 2.50e+00 1.60e-01 5.49e+01 dihedral pdb=" CA SER K 431 " pdb=" C SER K 431 " pdb=" N THR K 432 " pdb=" CA THR K 432 " ideal model delta harmonic sigma weight residual 180.00 152.38 27.62 0 5.00e+00 4.00e-02 3.05e+01 ... (remaining 10021 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.163: 2105 0.163 - 0.326: 114 0.326 - 0.489: 12 0.489 - 0.652: 0 0.652 - 0.815: 1 Chirality restraints: 2232 Sorted by residual: chirality pdb=" CA ARG F 17 " pdb=" N ARG F 17 " pdb=" C ARG F 17 " pdb=" CB ARG F 17 " both_signs ideal model delta sigma weight residual False 2.51 1.70 0.81 2.00e-01 2.50e+01 1.66e+01 chirality pdb=" C3' DG I -44 " pdb=" C4' DG I -44 " pdb=" O3' DG I -44 " pdb=" C2' DG I -44 " both_signs ideal model delta sigma weight residual False -2.66 -2.26 -0.40 2.00e-01 2.50e+01 3.91e+00 chirality pdb=" CB THR B 82 " pdb=" CA THR B 82 " pdb=" OG1 THR B 82 " pdb=" CG2 THR B 82 " both_signs ideal model delta sigma weight residual False 2.55 2.17 0.39 2.00e-01 2.50e+01 3.71e+00 ... (remaining 2229 not shown) Planarity restraints: 2501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DT J 38 " -0.301 2.00e-02 2.50e+03 1.63e-01 7.98e+02 pdb=" N1 DT J 38 " -0.094 2.00e-02 2.50e+03 pdb=" C2 DT J 38 " 0.051 2.00e-02 2.50e+03 pdb=" O2 DT J 38 " 0.285 2.00e-02 2.50e+03 pdb=" N3 DT J 38 " -0.035 2.00e-02 2.50e+03 pdb=" C4 DT J 38 " -0.100 2.00e-02 2.50e+03 pdb=" O4 DT J 38 " -0.257 2.00e-02 2.50e+03 pdb=" C5 DT J 38 " 0.035 2.00e-02 2.50e+03 pdb=" C7 DT J 38 " 0.193 2.00e-02 2.50e+03 pdb=" C6 DT J 38 " 0.028 2.00e-02 2.50e+03 pdb=" H3 DT J 38 " 0.087 2.00e-02 2.50e+03 pdb=" H6 DT J 38 " 0.107 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG J 47 " -0.369 2.00e-02 2.50e+03 1.34e-01 6.26e+02 pdb=" N9 DG J 47 " 0.012 2.00e-02 2.50e+03 pdb=" C8 DG J 47 " 0.096 2.00e-02 2.50e+03 pdb=" N7 DG J 47 " 0.103 2.00e-02 2.50e+03 pdb=" C5 DG J 47 " 0.057 2.00e-02 2.50e+03 pdb=" C6 DG J 47 " -0.034 2.00e-02 2.50e+03 pdb=" O6 DG J 47 " -0.218 2.00e-02 2.50e+03 pdb=" N1 DG J 47 " 0.021 2.00e-02 2.50e+03 pdb=" C2 DG J 47 " 0.077 2.00e-02 2.50e+03 pdb=" N2 DG J 47 " 0.084 2.00e-02 2.50e+03 pdb=" N3 DG J 47 " 0.091 2.00e-02 2.50e+03 pdb=" C4 DG J 47 " 0.080 2.00e-02 2.50e+03 pdb=" H8 DG J 47 " 0.085 2.00e-02 2.50e+03 pdb=" H1 DG J 47 " -0.084 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DT J 55 " 0.349 2.00e-02 2.50e+03 1.42e-01 6.07e+02 pdb=" N1 DT J 55 " -0.040 2.00e-02 2.50e+03 pdb=" C2 DT J 55 " -0.108 2.00e-02 2.50e+03 pdb=" O2 DT J 55 " -0.200 2.00e-02 2.50e+03 pdb=" N3 DT J 55 " -0.026 2.00e-02 2.50e+03 pdb=" C4 DT J 55 " 0.045 2.00e-02 2.50e+03 pdb=" O4 DT J 55 " 0.211 2.00e-02 2.50e+03 pdb=" C5 DT J 55 " -0.050 2.00e-02 2.50e+03 pdb=" C7 DT J 55 " -0.093 2.00e-02 2.50e+03 pdb=" C6 DT J 55 " -0.064 2.00e-02 2.50e+03 pdb=" H3 DT J 55 " 0.035 2.00e-02 2.50e+03 pdb=" H6 DT J 55 " -0.059 2.00e-02 2.50e+03 ... (remaining 2498 not shown) Histogram of nonbonded interaction distances: 1.58 - 2.18: 1155 2.18 - 2.79: 36628 2.79 - 3.39: 62947 3.39 - 4.00: 89620 4.00 - 4.60: 128365 Nonbonded interactions: 318715 Sorted by model distance: nonbonded pdb=" OP1 DA I 28 " pdb=" HG1 THR B 80 " model vdw 1.578 2.450 nonbonded pdb=" OP1 DG J 28 " pdb=" HG1 THR F 80 " model vdw 1.611 2.450 nonbonded pdb=" HG1 THR D 90 " pdb=" OE1 GLU D 93 " model vdw 1.617 2.450 nonbonded pdb=" OD2 ASP D 68 " pdb=" HH TYR F 98 " model vdw 1.621 2.450 nonbonded pdb=" HG1 THR H 90 " pdb=" OE1 GLU H 93 " model vdw 1.628 2.450 ... (remaining 318710 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' selection = (chain 'E' and resid 38 through 133) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 25 through 101) } ncs_group { reference = (chain 'C' and resid 15 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 33 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.090 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: 0.110 Extract box with map and model: 0.220 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 25.270 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 : 0.014 0.065 13590 Z= 0.757 Angle : 1.915 13.497 19596 Z= 1.269 Chirality : 0.088 0.815 2232 Planarity : 0.035 0.172 1456 Dihedral : 27.439 176.605 5861 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 0.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.13 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.09 (0.26), residues: 832 helix: 0.25 (0.19), residues: 580 sheet: -0.58 (1.52), residues: 6 loop : -0.05 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG C 77 TYR 0.124 0.021 TYR C 57 PHE 0.049 0.012 PHE D 70 TRP 0.068 0.027 TRP K 481 HIS 0.014 0.004 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.01353 (13590) covalent geometry : angle 1.91481 (19596) hydrogen bonds : bond 0.13010 ( 818) hydrogen bonds : angle 6.36587 ( 2050) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 0.356 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 108 ASN cc_start: 0.8343 (t0) cc_final: 0.8023 (t0) REVERT: B 98 TYR cc_start: 0.8484 (m-10) cc_final: 0.8270 (m-10) REVERT: C 40 SER cc_start: 0.7653 (p) cc_final: 0.7293 (p) REVERT: C 90 ASP cc_start: 0.6953 (t70) cc_final: 0.6674 (t70) REVERT: D 59 MET cc_start: 0.8395 (tpp) cc_final: 0.8195 (tpp) REVERT: D 89 ILE cc_start: 0.9266 (mt) cc_final: 0.8903 (mt) REVERT: E 97 GLU cc_start: 0.7227 (mt-10) cc_final: 0.6935 (mt-10) REVERT: G 61 GLU cc_start: 0.8342 (tp30) cc_final: 0.8059 (tp30) REVERT: H 88 THR cc_start: 0.9138 (m) cc_final: 0.8859 (p) outliers start: 0 outliers final: 0 residues processed: 304 average time/residue: 0.3444 time to fit residues: 134.2938 Evaluate side-chains 196 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 196 time to evaluate : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 49 optimal weight: 0.8980 chunk 97 optimal weight: 3.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 0.9980 chunk 100 optimal weight: 8.9990 chunk 106 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 476 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3556 r_free = 0.3556 target = 0.094868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.066434 restraints weight = 67413.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.069585 restraints weight = 23792.125| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.071569 restraints weight = 13906.368| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.072663 restraints weight = 10620.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.073275 restraints weight = 9280.848| |-----------------------------------------------------------------------------| r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 13590 Z= 0.208 Angle : 0.721 5.249 19596 Z= 0.442 Chirality : 0.043 0.409 2232 Planarity : 0.005 0.046 1456 Dihedral : 31.312 171.580 4153 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer: Outliers : 2.09 % Allowed : 12.71 % Favored : 85.20 % Cbeta Deviations : 0.13 % 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: 1.98 (0.28), residues: 832 helix: 1.96 (0.21), residues: 585 sheet: -1.93 (1.31), residues: 11 loop : -0.11 (0.36), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 116 TYR 0.013 0.002 TYR F 98 PHE 0.019 0.002 PHE A 67 TRP 0.006 0.002 TRP K 481 HIS 0.008 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00452 (13590) covalent geometry : angle 0.72130 (19596) hydrogen bonds : bond 0.05008 ( 818) hydrogen bonds : angle 3.47353 ( 2050) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 208 time to evaluate : 0.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8323 (mt-10) cc_final: 0.8022 (mt-10) REVERT: A 73 GLU cc_start: 0.7926 (tp30) cc_final: 0.7650 (tp30) REVERT: B 74 GLU cc_start: 0.8807 (tt0) cc_final: 0.8193 (mt-10) REVERT: D 35 GLU cc_start: 0.7100 (mt-10) cc_final: 0.6851 (mt-10) REVERT: E 50 GLU cc_start: 0.8561 (mt-10) cc_final: 0.8081 (tt0) REVERT: E 73 GLU cc_start: 0.8583 (tm-30) cc_final: 0.7917 (tm-30) REVERT: E 94 GLU cc_start: 0.8287 (mm-30) cc_final: 0.7986 (tp30) REVERT: E 108 ASN cc_start: 0.8684 (t0) cc_final: 0.8228 (t0) REVERT: F 25 ASN cc_start: 0.8536 (m110) cc_final: 0.8260 (m110) REVERT: G 61 GLU cc_start: 0.8608 (tp30) cc_final: 0.8407 (tp30) REVERT: G 92 GLU cc_start: 0.8918 (mp0) cc_final: 0.8639 (mp0) REVERT: H 68 ASP cc_start: 0.8524 (t0) cc_final: 0.8224 (t0) outliers start: 15 outliers final: 13 residues processed: 219 average time/residue: 0.2846 time to fit residues: 84.2839 Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 184 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 47 SER Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 64 optimal weight: 2.9990 chunk 106 optimal weight: 20.0000 chunk 90 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 chunk 42 optimal weight: 4.9990 chunk 20 optimal weight: 4.9990 chunk 1 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 85 optimal weight: 0.6980 chunk 21 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 108 ASN H 82 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.091450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.063271 restraints weight = 69157.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.066202 restraints weight = 25015.524| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.068073 restraints weight = 14958.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.069032 restraints weight = 11509.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069673 restraints weight = 10153.122| |-----------------------------------------------------------------------------| r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8057 moved from start: 0.4656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 13590 Z= 0.267 Angle : 0.675 5.020 19596 Z= 0.415 Chirality : 0.045 0.369 2232 Planarity : 0.004 0.050 1456 Dihedral : 31.080 171.075 4153 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 3.35 % Allowed : 14.11 % Favored : 82.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.07 (0.28), residues: 832 helix: 2.19 (0.21), residues: 579 sheet: -1.99 (1.38), residues: 11 loop : -0.48 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG F 45 TYR 0.015 0.002 TYR G 57 PHE 0.011 0.001 PHE A 67 TRP 0.002 0.001 TRP K 481 HIS 0.005 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00581 (13590) covalent geometry : angle 0.67549 (19596) hydrogen bonds : bond 0.04680 ( 818) hydrogen bonds : angle 3.46390 ( 2050) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 218 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 194 time to evaluate : 0.465 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8491 (mt-10) cc_final: 0.8210 (mt-10) REVERT: B 74 GLU cc_start: 0.8873 (tt0) cc_final: 0.8532 (mt-10) REVERT: C 76 THR cc_start: 0.8909 (p) cc_final: 0.8697 (t) REVERT: D 35 GLU cc_start: 0.7629 (mt-10) cc_final: 0.7390 (mt-10) REVERT: D 42 TYR cc_start: 0.7585 (t80) cc_final: 0.7248 (t80) REVERT: D 59 MET cc_start: 0.8546 (tpp) cc_final: 0.8312 (tpp) REVERT: E 94 GLU cc_start: 0.8274 (mm-30) cc_final: 0.7763 (tp30) REVERT: E 125 GLN cc_start: 0.8777 (mm-40) cc_final: 0.8557 (mm-40) REVERT: H 113 GLU cc_start: 0.9091 (mm-30) cc_final: 0.8880 (tp30) REVERT: K 409 LYS cc_start: 0.8268 (tttt) cc_final: 0.8036 (pttp) outliers start: 24 outliers final: 23 residues processed: 210 average time/residue: 0.2741 time to fit residues: 78.7034 Evaluate side-chains 206 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 183 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 27 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 66 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 27 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 51 optimal weight: 2.9990 chunk 98 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 67 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 81 optimal weight: 2.9990 chunk 69 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 27 optimal weight: 4.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN C 24 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.091936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2993 r_free = 0.2993 target = 0.063881 restraints weight = 68718.213| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.066791 restraints weight = 24686.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.068643 restraints weight = 14680.186| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.069686 restraints weight = 11302.289| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.070215 restraints weight = 9905.542| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.5039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13590 Z= 0.227 Angle : 0.643 7.506 19596 Z= 0.393 Chirality : 0.042 0.361 2232 Planarity : 0.004 0.052 1456 Dihedral : 30.918 171.911 4153 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.21 % Allowed : 15.08 % Favored : 81.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.22 (0.28), residues: 832 helix: 2.30 (0.21), residues: 579 sheet: -1.67 (1.43), residues: 11 loop : -0.41 (0.35), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG K 452 TYR 0.013 0.001 TYR G 57 PHE 0.014 0.001 PHE K 458 TRP 0.002 0.001 TRP K 481 HIS 0.005 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00485 (13590) covalent geometry : angle 0.64317 (19596) hydrogen bonds : bond 0.03922 ( 818) hydrogen bonds : angle 3.23002 ( 2050) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 188 time to evaluate : 0.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8426 (mt-10) cc_final: 0.8159 (mt-10) REVERT: A 94 GLU cc_start: 0.7925 (mm-30) cc_final: 0.7715 (mm-30) REVERT: B 74 GLU cc_start: 0.8976 (tt0) cc_final: 0.8488 (mt-10) REVERT: C 92 GLU cc_start: 0.8375 (mp0) cc_final: 0.7857 (mp0) REVERT: D 35 GLU cc_start: 0.7740 (mt-10) cc_final: 0.7437 (mt-10) REVERT: D 42 TYR cc_start: 0.7612 (t80) cc_final: 0.7332 (t80) REVERT: D 47 GLN cc_start: 0.8623 (mt0) cc_final: 0.8369 (tt0) REVERT: H 93 GLU cc_start: 0.8263 (mp0) cc_final: 0.7428 (mp0) REVERT: K 409 LYS cc_start: 0.8315 (tttt) cc_final: 0.8064 (pttp) outliers start: 23 outliers final: 20 residues processed: 203 average time/residue: 0.2659 time to fit residues: 73.9881 Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 177 time to evaluate : 0.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 33 optimal weight: 2.9990 chunk 68 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 96 optimal weight: 0.0870 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 overall best weight: 2.2166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN A 108 ASN E 76 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.091102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.063700 restraints weight = 68391.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.066566 restraints weight = 24362.259| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.068354 restraints weight = 14487.504| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.069319 restraints weight = 11151.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3114 r_free = 0.3114 target = 0.069693 restraints weight = 9829.689| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 13590 Z= 0.233 Angle : 0.632 4.928 19596 Z= 0.388 Chirality : 0.043 0.358 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.767 171.801 4153 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Rotamer: Outliers : 2.93 % Allowed : 17.46 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.31 (0.28), residues: 832 helix: 2.38 (0.21), residues: 580 sheet: -1.51 (1.49), residues: 11 loop : -0.46 (0.36), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.010 0.001 TYR G 57 PHE 0.013 0.001 PHE A 67 TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00501 (13590) covalent geometry : angle 0.63213 (19596) hydrogen bonds : bond 0.03991 ( 818) hydrogen bonds : angle 3.21871 ( 2050) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 183 time to evaluate : 0.495 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: B 74 GLU cc_start: 0.8975 (tt0) cc_final: 0.8491 (mt-10) REVERT: D 47 GLN cc_start: 0.8596 (mt0) cc_final: 0.8382 (tt0) REVERT: E 50 GLU cc_start: 0.8738 (mt-10) cc_final: 0.8342 (tt0) REVERT: E 59 GLU cc_start: 0.8095 (pm20) cc_final: 0.7822 (pm20) REVERT: E 125 GLN cc_start: 0.8853 (mm-40) cc_final: 0.8601 (mm-40) REVERT: G 110 ASN cc_start: 0.8822 (t0) cc_final: 0.8248 (p0) REVERT: H 93 GLU cc_start: 0.8267 (OUTLIER) cc_final: 0.7436 (mp0) REVERT: K 409 LYS cc_start: 0.8349 (tttt) cc_final: 0.8054 (pttm) outliers start: 21 outliers final: 20 residues processed: 196 average time/residue: 0.2663 time to fit residues: 71.8575 Evaluate side-chains 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 180 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 71 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 chunk 107 optimal weight: 9.9990 chunk 79 optimal weight: 0.9980 chunk 103 optimal weight: 20.0000 chunk 61 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.091474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2988 r_free = 0.2988 target = 0.063708 restraints weight = 69037.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.066585 restraints weight = 24896.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.068376 restraints weight = 14877.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.069354 restraints weight = 11513.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.069968 restraints weight = 10136.525| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 13590 Z= 0.229 Angle : 0.627 4.848 19596 Z= 0.384 Chirality : 0.042 0.357 2232 Planarity : 0.004 0.052 1456 Dihedral : 30.676 172.328 4153 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.07 % Allowed : 17.18 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.37 (0.28), residues: 832 helix: 2.44 (0.21), residues: 580 sheet: -1.19 (1.57), residues: 11 loop : -0.50 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.013 0.001 TYR D 40 PHE 0.014 0.001 PHE K 458 TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00491 (13590) covalent geometry : angle 0.62686 (19596) hydrogen bonds : bond 0.03903 ( 818) hydrogen bonds : angle 3.16501 ( 2050) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 183 time to evaluate : 0.449 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: B 74 GLU cc_start: 0.8933 (tt0) cc_final: 0.8590 (mt-10) REVERT: D 35 GLU cc_start: 0.7742 (mt-10) cc_final: 0.7457 (mt-10) REVERT: E 59 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7897 (pm20) REVERT: G 84 GLN cc_start: 0.8553 (tp40) cc_final: 0.8301 (tp-100) REVERT: G 110 ASN cc_start: 0.8804 (t0) cc_final: 0.8266 (p0) REVERT: H 59 MET cc_start: 0.9026 (tpp) cc_final: 0.8733 (tpp) REVERT: H 93 GLU cc_start: 0.8266 (OUTLIER) cc_final: 0.7453 (mp0) REVERT: K 409 LYS cc_start: 0.8342 (tttt) cc_final: 0.8026 (pttp) outliers start: 22 outliers final: 16 residues processed: 195 average time/residue: 0.2710 time to fit residues: 72.5553 Evaluate side-chains 200 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 182 time to evaluate : 0.493 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 41 optimal weight: 0.9980 chunk 50 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 79 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 107 optimal weight: 8.9990 chunk 51 optimal weight: 2.9990 chunk 27 optimal weight: 5.9990 chunk 67 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 88 optimal weight: 2.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** F 75 HIS ** 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 = 0.3530 r_free = 0.3530 target = 0.091682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.064467 restraints weight = 69837.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.067332 restraints weight = 24803.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.069135 restraints weight = 14727.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.070195 restraints weight = 11336.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070710 restraints weight = 9886.056| |-----------------------------------------------------------------------------| r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8012 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13590 Z= 0.214 Angle : 0.621 5.169 19596 Z= 0.380 Chirality : 0.042 0.357 2232 Planarity : 0.004 0.052 1456 Dihedral : 30.591 172.646 4153 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 2.79 % Allowed : 18.02 % Favored : 79.19 % 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: 2.48 (0.29), residues: 832 helix: 2.51 (0.21), residues: 583 sheet: -0.76 (1.75), residues: 11 loop : -0.46 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG H 92 TYR 0.013 0.001 TYR D 40 PHE 0.013 0.001 PHE K 458 TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00461 (13590) covalent geometry : angle 0.62067 (19596) hydrogen bonds : bond 0.03811 ( 818) hydrogen bonds : angle 3.09852 ( 2050) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 191 time to evaluate : 0.445 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: B 74 GLU cc_start: 0.8926 (tt0) cc_final: 0.8590 (mt-10) REVERT: D 35 GLU cc_start: 0.7785 (mt-10) cc_final: 0.7542 (mt-10) REVERT: E 37 LYS cc_start: 0.8494 (pttm) cc_final: 0.8272 (pttt) REVERT: E 50 GLU cc_start: 0.8725 (mt-10) cc_final: 0.8328 (tt0) REVERT: E 59 GLU cc_start: 0.8100 (OUTLIER) cc_final: 0.7827 (pm20) REVERT: G 110 ASN cc_start: 0.8808 (t0) cc_final: 0.8292 (p0) REVERT: H 93 GLU cc_start: 0.8256 (mp0) cc_final: 0.7448 (mp0) REVERT: H 121 TYR cc_start: 0.9018 (t80) cc_final: 0.8755 (t80) REVERT: K 409 LYS cc_start: 0.8356 (tttt) cc_final: 0.8036 (pttp) outliers start: 20 outliers final: 15 residues processed: 202 average time/residue: 0.2569 time to fit residues: 71.7354 Evaluate side-chains 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 185 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 111 VAL Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 30.0000 chunk 37 optimal weight: 0.6980 chunk 84 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 98 optimal weight: 3.9990 chunk 1 optimal weight: 5.9990 chunk 73 optimal weight: 0.5980 chunk 70 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 39 optimal weight: 2.9990 overall best weight: 1.2642 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN ** F 75 HIS ** 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 = 0.3552 r_free = 0.3552 target = 0.092939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.065680 restraints weight = 69347.507| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.068594 restraints weight = 24409.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.070432 restraints weight = 14436.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.071436 restraints weight = 11087.287| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 53)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.072037 restraints weight = 9735.057| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.5749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13590 Z= 0.176 Angle : 0.615 7.943 19596 Z= 0.374 Chirality : 0.039 0.356 2232 Planarity : 0.004 0.051 1456 Dihedral : 30.475 173.216 4153 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 1.54 % Allowed : 19.27 % Favored : 79.19 % 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: 2.69 (0.29), residues: 832 helix: 2.68 (0.21), residues: 579 sheet: -0.70 (1.74), residues: 11 loop : -0.39 (0.37), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.014 0.001 TYR D 40 PHE 0.014 0.001 PHE K 458 TRP 0.001 0.000 TRP K 481 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00380 (13590) covalent geometry : angle 0.61468 (19596) hydrogen bonds : bond 0.03513 ( 818) hydrogen bonds : angle 2.94094 ( 2050) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 186 time to evaluate : 0.463 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: B 74 GLU cc_start: 0.8884 (tt0) cc_final: 0.8429 (mt-10) REVERT: D 35 GLU cc_start: 0.7771 (mt-10) cc_final: 0.7445 (mt-10) REVERT: E 37 LYS cc_start: 0.8504 (pttm) cc_final: 0.8267 (pttt) REVERT: E 59 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7885 (pm20) REVERT: G 84 GLN cc_start: 0.8542 (tp40) cc_final: 0.8296 (tp-100) REVERT: G 110 ASN cc_start: 0.8769 (t0) cc_final: 0.8349 (p0) REVERT: H 59 MET cc_start: 0.9027 (tpp) cc_final: 0.8775 (tpp) REVERT: H 93 GLU cc_start: 0.8182 (OUTLIER) cc_final: 0.7441 (mp0) REVERT: H 121 TYR cc_start: 0.9001 (t80) cc_final: 0.8708 (t80) outliers start: 11 outliers final: 8 residues processed: 193 average time/residue: 0.2639 time to fit residues: 69.9669 Evaluate side-chains 193 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 183 time to evaluate : 0.352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 55 optimal weight: 0.9990 chunk 15 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 47 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 11 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 76 GLN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3548 r_free = 0.3548 target = 0.093341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.065676 restraints weight = 70937.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.3108 r_free = 0.3108 target = 0.068623 restraints weight = 24547.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.070477 restraints weight = 14436.894| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.071513 restraints weight = 11069.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 49)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.072128 restraints weight = 9676.166| |-----------------------------------------------------------------------------| r_work (final): 0.3155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.5860 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13590 Z= 0.194 Angle : 0.620 7.867 19596 Z= 0.377 Chirality : 0.041 0.353 2232 Planarity : 0.004 0.052 1456 Dihedral : 30.428 173.556 4153 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 4.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.96 % Allowed : 19.27 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.71 (0.29), residues: 832 helix: 2.69 (0.21), residues: 582 sheet: -0.86 (1.66), residues: 11 loop : -0.39 (0.37), residues: 239 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.012 0.001 TYR D 40 PHE 0.016 0.001 PHE K 458 TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00419 (13590) covalent geometry : angle 0.62028 (19596) hydrogen bonds : bond 0.03665 ( 818) hydrogen bonds : angle 2.97641 ( 2050) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 187 time to evaluate : 0.544 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8685 (t160) cc_final: 0.8369 (t0) REVERT: B 74 GLU cc_start: 0.8881 (tt0) cc_final: 0.8429 (mt-10) REVERT: D 35 GLU cc_start: 0.7848 (mt-10) cc_final: 0.7576 (mt-10) REVERT: E 37 LYS cc_start: 0.8516 (pttm) cc_final: 0.8276 (pttt) REVERT: E 50 GLU cc_start: 0.8724 (mt-10) cc_final: 0.8046 (tt0) REVERT: E 59 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7901 (pm20) REVERT: G 84 GLN cc_start: 0.8563 (tp40) cc_final: 0.8323 (tp-100) REVERT: G 110 ASN cc_start: 0.8769 (t0) cc_final: 0.8351 (p0) REVERT: H 93 GLU cc_start: 0.8186 (OUTLIER) cc_final: 0.7458 (mp0) REVERT: H 121 TYR cc_start: 0.9008 (t80) cc_final: 0.8715 (t80) outliers start: 14 outliers final: 10 residues processed: 196 average time/residue: 0.2700 time to fit residues: 72.6507 Evaluate side-chains 198 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 186 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 93 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 85 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 4.9990 chunk 31 optimal weight: 0.8980 chunk 93 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 20 optimal weight: 4.9990 chunk 51 optimal weight: 2.9990 chunk 16 optimal weight: 5.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.092403 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.064719 restraints weight = 71567.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.067641 restraints weight = 24890.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.069464 restraints weight = 14612.791| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.070460 restraints weight = 11234.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.071074 restraints weight = 9859.280| |-----------------------------------------------------------------------------| r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.5899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 13590 Z= 0.241 Angle : 0.637 9.052 19596 Z= 0.386 Chirality : 0.043 0.353 2232 Planarity : 0.004 0.053 1456 Dihedral : 30.437 173.796 4153 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 5.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 1.54 % Allowed : 19.69 % Favored : 78.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.29), residues: 832 helix: 2.59 (0.21), residues: 580 sheet: -0.85 (1.74), residues: 11 loop : -0.47 (0.37), residues: 241 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.014 0.001 TYR D 40 PHE 0.015 0.001 PHE K 458 TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00520 (13590) covalent geometry : angle 0.63742 (19596) hydrogen bonds : bond 0.03949 ( 818) hydrogen bonds : angle 3.12646 ( 2050) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 180 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 108 ASN cc_start: 0.8708 (t160) cc_final: 0.8504 (t0) REVERT: B 74 GLU cc_start: 0.8881 (tt0) cc_final: 0.8417 (mt-10) REVERT: C 92 GLU cc_start: 0.8017 (mp0) cc_final: 0.7780 (mp0) REVERT: E 37 LYS cc_start: 0.8511 (pttm) cc_final: 0.8273 (pttt) REVERT: E 50 GLU cc_start: 0.8745 (mt-10) cc_final: 0.8356 (tt0) REVERT: E 59 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: G 84 GLN cc_start: 0.8593 (tp40) cc_final: 0.8354 (tp-100) REVERT: G 110 ASN cc_start: 0.8796 (t0) cc_final: 0.8335 (p0) REVERT: H 59 MET cc_start: 0.8994 (tpp) cc_final: 0.8760 (tpp) REVERT: H 93 GLU cc_start: 0.8222 (mp0) cc_final: 0.7435 (mp0) REVERT: K 409 LYS cc_start: 0.8376 (tttt) cc_final: 0.8032 (pttp) outliers start: 11 outliers final: 10 residues processed: 188 average time/residue: 0.2679 time to fit residues: 68.8776 Evaluate side-chains 189 residues out of total 716 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 178 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 74 ILE Chi-restraints excluded: chain E residue 107 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain H residue 55 SER Chi-restraints excluded: chain H residue 88 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 30.0000 chunk 82 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 81 optimal weight: 0.9990 chunk 102 optimal weight: 0.7980 chunk 103 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3573 r_free = 0.3573 target = 0.094009 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.066644 restraints weight = 69506.928| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3123 r_free = 0.3123 target = 0.069574 restraints weight = 24460.149| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.071444 restraints weight = 14439.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.072409 restraints weight = 11093.991| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.073053 restraints weight = 9787.347| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7971 moved from start: 0.6018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 13590 Z= 0.168 Angle : 0.617 9.226 19596 Z= 0.374 Chirality : 0.039 0.353 2232 Planarity : 0.004 0.050 1456 Dihedral : 30.312 173.644 4153 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 1.26 % Allowed : 20.25 % Favored : 78.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.82 (0.29), residues: 832 helix: 2.74 (0.21), residues: 583 sheet: -0.85 (1.71), residues: 11 loop : -0.28 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 86 TYR 0.015 0.001 TYR D 40 PHE 0.017 0.001 PHE K 458 TRP 0.001 0.000 TRP K 481 HIS 0.003 0.001 HIS A 39 Details of bonding type rmsd covalent geometry : bond 0.00368 (13590) covalent geometry : angle 0.61657 (19596) hydrogen bonds : bond 0.03451 ( 818) hydrogen bonds : angle 2.86923 ( 2050) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4047.11 seconds wall clock time: 69 minutes 23.44 seconds (4163.44 seconds total)