Starting phenix.real_space_refine on Sat Aug 23 13:29:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8v25_42898/08_2025/8v25_42898_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/8v25_42898/08_2025/8v25_42898.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2025/8v25_42898_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2025/8v25_42898_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2025/8v25_42898.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8v25_42898/08_2025/8v25_42898.map" } resolution = 3.32 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= 0.019 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 288 5.49 5 S 16 5.16 5 C 7063 2.51 5 N 2387 2.21 5 O 2935 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 17 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 12689 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 811 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "B" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 859 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 859 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 5, 'TRANS': 105} Chain: "D" Number of atoms: 764 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 764 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 94} Chain: "E" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 817 Classifications: {'peptide': 99} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 841 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 841 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 754 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 754 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 2, 'TRANS': 93} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 604 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 604 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N ARG K 74 " occ=0.95 ... (9 atoms not shown) pdb=" NH2 ARG K 74 " occ=0.95 residue: pdb=" N GLY K 75 " occ=0.65 ... (2 atoms not shown) pdb=" O GLY K 75 " occ=0.65 Time building chain proxies: 2.73, per 1000 atoms: 0.22 Number of scatterers: 12689 At special positions: 0 Unit cell: (101.85, 122.22, 119.31, 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 16 16.00 P 288 15.00 O 2935 8.00 N 2387 7.00 C 7063 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.22 Conformation dependent library (CDL) restraints added in 493.0 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1592 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 9 sheets defined 66.9% alpha, 4.2% beta 138 base pairs and 255 stacking pairs defined. Time for finding SS restraints: 2.05 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.520A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.803A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.860A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.622A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY A 132 " --> pdb=" O ARG A 128 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.099A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.656A pdb=" N GLN B 93 " --> pdb=" O ALA B 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 removed outlier: 3.649A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) 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 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 removed outlier: 3.588A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.558A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.599A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.607A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.533A 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 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.190A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.543A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.506A pdb=" N ASN G 73 " --> pdb=" O ALA G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.520A pdb=" N LEU G 83 " --> pdb=" O ILE G 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.611A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'K' and resid 22 through 34 Processing helix chain 'K' and resid 37 through 39 No H-bonds generated for 'chain 'K' and resid 37 through 39' Processing helix chain 'K' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.109A 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: 7.324A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.895A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.346A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'K' and resid 12 through 16 421 hydrogen bonds defined for protein. 1245 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 354 hydrogen bonds 708 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 255 stacking parallelities Total time for adding SS restraints: 2.64 Time building geometry restraints manager: 1.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2639 1.33 - 1.45: 4191 1.45 - 1.57: 6065 1.57 - 1.69: 576 1.69 - 1.81: 27 Bond restraints: 13498 Sorted by residual: bond pdb=" C1' DG J -70 " pdb=" N9 DG J -70 " ideal model delta sigma weight residual 1.460 1.389 0.071 2.00e-02 2.50e+03 1.26e+01 bond pdb=" C1' DG I -70 " pdb=" N9 DG I -70 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N THR K 55 " pdb=" CA THR K 55 " ideal model delta sigma weight residual 1.455 1.487 -0.032 1.25e-02 6.40e+03 6.36e+00 bond pdb=" N ARG K 72 " pdb=" CA ARG K 72 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.24e-02 6.50e+03 5.94e+00 bond pdb=" N LEU K 56 " pdb=" CA LEU K 56 " ideal model delta sigma weight residual 1.458 1.485 -0.027 1.27e-02 6.20e+03 4.41e+00 ... (remaining 13493 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.27: 19259 2.27 - 4.53: 176 4.53 - 6.80: 27 6.80 - 9.06: 3 9.06 - 11.33: 1 Bond angle restraints: 19466 Sorted by residual: angle pdb=" C3' DG J 71 " pdb=" O3' DG J 71 " pdb=" P DA J 72 " ideal model delta sigma weight residual 120.20 108.87 11.33 1.50e+00 4.44e-01 5.71e+01 angle pdb=" C3' DG I 71 " pdb=" O3' DG I 71 " pdb=" P DA I 72 " ideal model delta sigma weight residual 120.20 112.34 7.86 1.50e+00 4.44e-01 2.74e+01 angle pdb=" C3' DC J 70 " pdb=" O3' DC J 70 " pdb=" P DG J 71 " ideal model delta sigma weight residual 120.20 113.10 7.10 1.50e+00 4.44e-01 2.24e+01 angle pdb=" C3' DT J 69 " pdb=" O3' DT J 69 " pdb=" P DC J 70 " ideal model delta sigma weight residual 120.20 114.19 6.01 1.50e+00 4.44e-01 1.60e+01 angle pdb=" C ASP F 24 " pdb=" CA ASP F 24 " pdb=" CB ASP F 24 " ideal model delta sigma weight residual 111.40 116.33 -4.93 1.29e+00 6.01e-01 1.46e+01 ... (remaining 19461 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.81: 6017 35.81 - 71.62: 1378 71.62 - 107.44: 8 107.44 - 143.25: 4 143.25 - 179.06: 1 Dihedral angle restraints: 7408 sinusoidal: 4945 harmonic: 2463 Sorted by residual: dihedral pdb=" CA MET K 1 " pdb=" C MET K 1 " pdb=" N GLN K 2 " pdb=" CA GLN K 2 " ideal model delta harmonic sigma weight residual -180.00 -151.83 -28.17 0 5.00e+00 4.00e-02 3.17e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 39.06 -179.06 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J 54 " pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sinusoidal sigma weight residual 220.00 94.61 125.39 1 3.50e+01 8.16e-04 1.24e+01 ... (remaining 7405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.098: 2165 0.098 - 0.196: 48 0.196 - 0.294: 0 0.294 - 0.392: 0 0.392 - 0.490: 6 Chirality restraints: 2219 Sorted by residual: chirality pdb=" P DG J 71 " pdb=" OP1 DG J 71 " pdb=" OP2 DG J 71 " pdb=" O5' DG J 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.84 -0.49 2.00e-01 2.50e+01 6.00e+00 chirality pdb=" P DT J 69 " pdb=" OP1 DT J 69 " pdb=" OP2 DT J 69 " pdb=" O5' DT J 69 " both_signs ideal model delta sigma weight residual True 2.35 -2.80 -0.46 2.00e-01 2.50e+01 5.27e+00 chirality pdb=" P DG I 71 " pdb=" OP1 DG I 71 " pdb=" OP2 DG I 71 " pdb=" O5' DG I 71 " both_signs ideal model delta sigma weight residual True 2.35 -2.79 -0.45 2.00e-01 2.50e+01 5.04e+00 ... (remaining 2216 not shown) Planarity restraints: 1463 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP F 24 " 0.013 2.00e-02 2.50e+03 2.52e-02 6.33e+00 pdb=" C ASP F 24 " -0.044 2.00e-02 2.50e+03 pdb=" O ASP F 24 " 0.017 2.00e-02 2.50e+03 pdb=" N ASN F 25 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 47 " 0.025 2.00e-02 2.50e+03 1.03e-02 3.15e+00 pdb=" N9 DG I 47 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DG I 47 " -0.004 2.00e-02 2.50e+03 pdb=" C5 DG I 47 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 47 " 0.004 2.00e-02 2.50e+03 pdb=" O6 DG I 47 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 47 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 47 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 47 " -0.005 2.00e-02 2.50e+03 pdb=" N3 DG I 47 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 47 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS A 37 " 0.026 5.00e-02 4.00e+02 3.85e-02 2.37e+00 pdb=" N PRO A 38 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " 0.022 5.00e-02 4.00e+02 ... (remaining 1460 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2675 2.81 - 3.33: 10636 3.33 - 3.85: 22521 3.85 - 4.38: 26626 4.38 - 4.90: 38325 Nonbonded interactions: 100783 Sorted by model distance: nonbonded pdb=" OE1 GLU K 51 " pdb=" OH TYR K 59 " model vdw 2.287 3.040 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 65 " model vdw 2.303 3.040 nonbonded pdb=" O ASP F 24 " pdb=" OD1 ASP F 24 " model vdw 2.309 3.040 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.313 3.120 nonbonded pdb=" O THR E 58 " pdb=" OG1 THR E 58 " model vdw 2.315 3.040 ... (remaining 100778 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 37 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 10 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 26 through 121) 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=0.62 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.790 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: 0.020 Extract box with map and model: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.420 Find NCS groups from input model: 0.100 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:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.740 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8751 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 : 0.004 0.071 13498 Z= 0.189 Angle : 0.600 11.331 19466 Z= 0.360 Chirality : 0.042 0.490 2219 Planarity : 0.004 0.038 1463 Dihedral : 27.354 179.059 5816 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 0.42 % Allowed : 20.34 % Favored : 79.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.59 (0.30), residues: 831 helix: 3.13 (0.22), residues: 523 sheet: 1.31 (0.88), residues: 26 loop : -1.14 (0.35), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS K 68 Details of bonding type rmsd covalent geometry : bond 0.00386 (13498) covalent geometry : angle 0.60048 (19466) hydrogen bonds : bond 0.12257 ( 775) hydrogen bonds : angle 3.86195 ( 1953) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 131 time to evaluate : 0.484 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 133 average time/residue: 0.1894 time to fit residues: 32.5636 Evaluate side-chains 129 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 127 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain F residue 85 ASP 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: 6.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 33 optimal weight: 4.9990 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 51 optimal weight: 0.0070 chunk 100 optimal weight: 10.0000 chunk 106 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3202 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 40 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.092490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.062626 restraints weight = 28894.944| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 1.95 r_work: 0.2659 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2658 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2658 r_free = 0.2658 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.62 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2657 r_free = 0.2657 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.2657 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8800 moved from start: 0.0726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.173 Angle : 0.538 5.973 19466 Z= 0.327 Chirality : 0.034 0.136 2219 Planarity : 0.004 0.042 1463 Dihedral : 29.404 178.915 4118 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.24 % Allowed : 19.21 % Favored : 78.54 % 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 aren not related in a simple way. whole: 2.71 (0.30), residues: 831 helix: 3.04 (0.22), residues: 550 sheet: 1.49 (0.88), residues: 26 loop : -1.15 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.007 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00370 (13498) covalent geometry : angle 0.53788 (19466) hydrogen bonds : bond 0.05839 ( 775) hydrogen bonds : angle 2.93980 ( 1953) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 133 time to evaluate : 0.330 Fit side-chains revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7905 (t0) cc_final: 0.7603 (t0) REVERT: B 27 GLN cc_start: 0.9168 (OUTLIER) cc_final: 0.8597 (mp10) REVERT: F 24 ASP cc_start: 0.7619 (p0) cc_final: 0.7301 (p0) REVERT: H 31 LYS cc_start: 0.8642 (mmmt) cc_final: 0.8366 (mmmt) REVERT: K 1 MET cc_start: 0.7268 (ppp) cc_final: 0.6998 (ppp) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.1781 time to fit residues: 32.3812 Evaluate side-chains 141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 127 time to evaluate : 0.372 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 8 optimal weight: 2.9990 chunk 65 optimal weight: 0.0970 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 6.9990 chunk 48 optimal weight: 3.9990 chunk 67 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 73 optimal weight: 10.0000 chunk 78 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 36 optimal weight: 0.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS ** K 31 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 = 0.3427 r_free = 0.3427 target = 0.092893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.062834 restraints weight = 28943.134| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.00 r_work: 0.2668 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2670 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2670 r_free = 0.2670 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2670 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8790 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13498 Z= 0.163 Angle : 0.521 5.910 19466 Z= 0.318 Chirality : 0.033 0.136 2219 Planarity : 0.004 0.048 1463 Dihedral : 29.348 178.438 4114 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.24 % Allowed : 19.92 % Favored : 77.84 % 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 aren not related in a simple way. whole: 2.84 (0.30), residues: 831 helix: 3.16 (0.22), residues: 554 sheet: 1.34 (0.85), residues: 26 loop : -1.20 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.007 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd covalent geometry : bond 0.00348 (13498) covalent geometry : angle 0.52144 (19466) hydrogen bonds : bond 0.05482 ( 775) hydrogen bonds : angle 2.81829 ( 1953) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 135 time to evaluate : 0.306 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.8014 (t0) cc_final: 0.7731 (t0) REVERT: B 27 GLN cc_start: 0.9138 (OUTLIER) cc_final: 0.8591 (mp10) REVERT: F 24 ASP cc_start: 0.7682 (p0) cc_final: 0.7477 (p0) REVERT: F 92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8414 (mtp85) REVERT: H 65 ASP cc_start: 0.9139 (t0) cc_final: 0.8854 (t0) REVERT: K 1 MET cc_start: 0.7299 (ppp) cc_final: 0.6750 (ppp) outliers start: 16 outliers final: 9 residues processed: 145 average time/residue: 0.1792 time to fit residues: 33.4180 Evaluate side-chains 143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 132 time to evaluate : 0.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain K residue 70 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 31 optimal weight: 0.8980 chunk 65 optimal weight: 0.5980 chunk 26 optimal weight: 6.9990 chunk 69 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 75 optimal weight: 6.9990 chunk 88 optimal weight: 8.9990 chunk 54 optimal weight: 9.9990 chunk 57 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.093293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.063542 restraints weight = 28696.845| |-----------------------------------------------------------------------------| r_work (start): 0.2854 rms_B_bonded: 1.89 r_work: 0.2691 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2691 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2691 r_free = 0.2691 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2691 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8762 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13498 Z= 0.153 Angle : 0.524 8.145 19466 Z= 0.319 Chirality : 0.033 0.146 2219 Planarity : 0.004 0.059 1463 Dihedral : 29.342 178.478 4114 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.95 % Allowed : 19.92 % Favored : 77.14 % 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 aren not related in a simple way. whole: 2.93 (0.30), residues: 831 helix: 3.26 (0.22), residues: 554 sheet: 1.05 (0.83), residues: 26 loop : -1.20 (0.37), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 83 TYR 0.007 0.001 TYR K 59 PHE 0.014 0.001 PHE K 45 HIS 0.002 0.000 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00317 (13498) covalent geometry : angle 0.52395 (19466) hydrogen bonds : bond 0.05204 ( 775) hydrogen bonds : angle 2.76969 ( 1953) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 133 time to evaluate : 0.352 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 24 ASP cc_start: 0.7999 (t0) cc_final: 0.7755 (t0) REVERT: B 27 GLN cc_start: 0.9125 (OUTLIER) cc_final: 0.8604 (mp10) REVERT: F 92 ARG cc_start: 0.9051 (OUTLIER) cc_final: 0.8405 (mtp85) REVERT: H 65 ASP cc_start: 0.9119 (t0) cc_final: 0.8801 (t0) REVERT: K 1 MET cc_start: 0.7508 (ppp) cc_final: 0.6804 (ppp) outliers start: 21 outliers final: 14 residues processed: 145 average time/residue: 0.1631 time to fit residues: 30.7789 Evaluate side-chains 147 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 131 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 59 LYS Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 94 optimal weight: 7.9990 chunk 44 optimal weight: 5.9990 chunk 78 optimal weight: 6.9990 chunk 9 optimal weight: 10.0000 chunk 57 optimal weight: 0.2980 chunk 10 optimal weight: 3.9990 chunk 63 optimal weight: 6.9990 chunk 49 optimal weight: 0.9980 chunk 105 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 overall best weight: 1.8584 ------------------------------------------------------------------------------- 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 = 0.3399 r_free = 0.3399 target = 0.091091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.060982 restraints weight = 28778.841| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 1.88 r_work: 0.2629 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8832 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13498 Z= 0.194 Angle : 0.547 5.842 19466 Z= 0.331 Chirality : 0.035 0.150 2219 Planarity : 0.004 0.039 1463 Dihedral : 29.402 178.717 4114 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 5.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.66 % Allowed : 19.78 % Favored : 77.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.75 (0.30), residues: 831 helix: 3.16 (0.22), residues: 552 sheet: 0.88 (0.84), residues: 26 loop : -1.31 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR K 59 PHE 0.009 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00428 (13498) covalent geometry : angle 0.54674 (19466) hydrogen bonds : bond 0.06426 ( 775) hydrogen bonds : angle 2.95145 ( 1953) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 132 time to evaluate : 0.402 Fit side-chains REVERT: A 59 GLU cc_start: 0.8391 (OUTLIER) cc_final: 0.7605 (pm20) REVERT: B 27 GLN cc_start: 0.9140 (OUTLIER) cc_final: 0.8595 (mp10) REVERT: F 92 ARG cc_start: 0.9069 (OUTLIER) cc_final: 0.8440 (mtp85) REVERT: H 31 LYS cc_start: 0.8748 (mmmt) cc_final: 0.8267 (mmtm) REVERT: K 1 MET cc_start: 0.7447 (ppp) cc_final: 0.6889 (ppp) outliers start: 19 outliers final: 12 residues processed: 144 average time/residue: 0.1883 time to fit residues: 34.9572 Evaluate side-chains 139 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 124 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 98 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 105 optimal weight: 30.0000 chunk 26 optimal weight: 5.9990 chunk 72 optimal weight: 0.8980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.8980 chunk 34 optimal weight: 2.9990 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.092223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2851 r_free = 0.2851 target = 0.062290 restraints weight = 28610.173| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 1.88 r_work: 0.2659 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2660 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2660 r_free = 0.2660 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2660 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 13498 Z= 0.156 Angle : 0.536 7.396 19466 Z= 0.326 Chirality : 0.034 0.156 2219 Planarity : 0.004 0.053 1463 Dihedral : 29.380 178.512 4114 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 3.51 % Allowed : 20.06 % Favored : 76.44 % 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 aren not related in a simple way. whole: 2.84 (0.30), residues: 831 helix: 3.22 (0.22), residues: 552 sheet: 0.85 (0.96), residues: 20 loop : -1.22 (0.36), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 72 TYR 0.008 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.002 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00318 (13498) covalent geometry : angle 0.53635 (19466) hydrogen bonds : bond 0.05741 ( 775) hydrogen bonds : angle 2.81471 ( 1953) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.390 Fit side-chains REVERT: B 24 ASP cc_start: 0.7876 (t0) cc_final: 0.7673 (t0) REVERT: B 27 GLN cc_start: 0.9102 (OUTLIER) cc_final: 0.8578 (mp10) REVERT: F 24 ASP cc_start: 0.8017 (p0) cc_final: 0.7812 (p0) REVERT: F 92 ARG cc_start: 0.9061 (OUTLIER) cc_final: 0.8381 (mtp85) REVERT: G 42 ARG cc_start: 0.8888 (OUTLIER) cc_final: 0.8069 (mtm180) REVERT: H 31 LYS cc_start: 0.8750 (mmmt) cc_final: 0.8426 (mmmt) REVERT: H 65 ASP cc_start: 0.9132 (t0) cc_final: 0.8755 (t0) REVERT: K 1 MET cc_start: 0.7698 (ppp) cc_final: 0.6843 (ppp) outliers start: 25 outliers final: 18 residues processed: 146 average time/residue: 0.1895 time to fit residues: 35.3763 Evaluate side-chains 150 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 129 time to evaluate : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 37 LYS Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 72 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 101 optimal weight: 20.0000 chunk 51 optimal weight: 0.0060 chunk 73 optimal weight: 10.0000 chunk 13 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 82 optimal weight: 7.9990 chunk 6 optimal weight: 2.9990 chunk 28 optimal weight: 9.9990 chunk 61 optimal weight: 0.9990 overall best weight: 1.3802 ------------------------------------------------------------------------------- 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 = 0.3420 r_free = 0.3420 target = 0.092406 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.062460 restraints weight = 28726.734| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 1.89 r_work: 0.2666 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2666 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8785 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13498 Z= 0.169 Angle : 0.527 6.347 19466 Z= 0.320 Chirality : 0.033 0.157 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.340 178.476 4114 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.23 % Allowed : 20.06 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.87 (0.30), residues: 831 helix: 3.26 (0.22), residues: 553 sheet: 0.99 (0.98), residues: 20 loop : -1.25 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.010 0.001 TYR K 59 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00365 (13498) covalent geometry : angle 0.52658 (19466) hydrogen bonds : bond 0.05595 ( 775) hydrogen bonds : angle 2.79972 ( 1953) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.228 Fit side-chains REVERT: A 59 GLU cc_start: 0.8340 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: B 27 GLN cc_start: 0.9128 (OUTLIER) cc_final: 0.8600 (mp10) REVERT: F 24 ASP cc_start: 0.8077 (p0) cc_final: 0.7867 (p0) REVERT: F 92 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8323 (mtp85) REVERT: G 42 ARG cc_start: 0.8856 (OUTLIER) cc_final: 0.8027 (mtm180) REVERT: H 31 LYS cc_start: 0.8803 (mmmt) cc_final: 0.8539 (mmmt) REVERT: H 65 ASP cc_start: 0.9149 (t0) cc_final: 0.8771 (t0) REVERT: K 1 MET cc_start: 0.7672 (ppp) cc_final: 0.6927 (ppp) outliers start: 23 outliers final: 16 residues processed: 145 average time/residue: 0.1595 time to fit residues: 30.0981 Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 45 optimal weight: 0.9980 chunk 9 optimal weight: 9.9990 chunk 35 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 73 optimal weight: 10.0000 chunk 102 optimal weight: 5.9990 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 62 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.091677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2838 r_free = 0.2838 target = 0.061693 restraints weight = 28498.891| |-----------------------------------------------------------------------------| r_work (start): 0.2814 rms_B_bonded: 1.87 r_work: 0.2646 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2647 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2647 r_free = 0.2647 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2647 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8818 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 13498 Z= 0.184 Angle : 0.545 6.198 19466 Z= 0.328 Chirality : 0.034 0.165 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.355 178.504 4114 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 2.81 % Allowed : 21.32 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.81 (0.30), residues: 831 helix: 3.20 (0.22), residues: 553 sheet: 0.87 (0.97), residues: 20 loop : -1.24 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.007 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00406 (13498) covalent geometry : angle 0.54493 (19466) hydrogen bonds : bond 0.06011 ( 775) hydrogen bonds : angle 2.84592 ( 1953) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.347 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7569 (pm20) REVERT: B 27 GLN cc_start: 0.9107 (OUTLIER) cc_final: 0.8573 (mp10) REVERT: D 30 ARG cc_start: 0.8211 (mtp85) cc_final: 0.7850 (mtt180) REVERT: F 92 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8353 (mtp85) REVERT: G 42 ARG cc_start: 0.8910 (OUTLIER) cc_final: 0.8084 (mtm180) REVERT: H 31 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8571 (mmmt) REVERT: H 65 ASP cc_start: 0.9161 (t0) cc_final: 0.8789 (t0) REVERT: K 1 MET cc_start: 0.7950 (ppp) cc_final: 0.7225 (ppp) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 0.1832 time to fit residues: 32.6824 Evaluate side-chains 143 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 124 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 63 optimal weight: 0.0770 chunk 62 optimal weight: 1.9990 chunk 84 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 103 optimal weight: 8.9990 chunk 37 optimal weight: 7.9990 chunk 25 optimal weight: 3.9990 chunk 59 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 1.1942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 2 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 = 0.3412 r_free = 0.3412 target = 0.091971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2844 r_free = 0.2844 target = 0.062021 restraints weight = 28677.869| |-----------------------------------------------------------------------------| r_work (start): 0.2820 rms_B_bonded: 1.89 r_work: 0.2652 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2654 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2654 r_free = 0.2654 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2654 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8811 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.166 Angle : 0.541 6.528 19466 Z= 0.326 Chirality : 0.033 0.165 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.358 178.538 4114 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.81 % Allowed : 21.60 % Favored : 75.60 % 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 aren not related in a simple way. whole: 2.84 (0.30), residues: 831 helix: 3.22 (0.22), residues: 553 sheet: 1.08 (1.03), residues: 20 loop : -1.25 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 83 TYR 0.008 0.001 TYR H 37 PHE 0.008 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00353 (13498) covalent geometry : angle 0.54082 (19466) hydrogen bonds : bond 0.05824 ( 775) hydrogen bonds : angle 2.81767 ( 1953) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 125 time to evaluate : 0.231 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.7562 (pm20) REVERT: B 27 GLN cc_start: 0.9097 (OUTLIER) cc_final: 0.8564 (mp10) REVERT: D 30 ARG cc_start: 0.8208 (mtp85) cc_final: 0.7850 (mtt180) REVERT: F 92 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8355 (mtp85) REVERT: G 42 ARG cc_start: 0.8905 (OUTLIER) cc_final: 0.8077 (mtm180) REVERT: H 31 LYS cc_start: 0.8844 (mmmt) cc_final: 0.8573 (mmmt) REVERT: H 65 ASP cc_start: 0.9146 (t0) cc_final: 0.8765 (t0) REVERT: K 1 MET cc_start: 0.7726 (ppp) cc_final: 0.6990 (ppp) outliers start: 20 outliers final: 15 residues processed: 139 average time/residue: 0.1726 time to fit residues: 30.7682 Evaluate side-chains 144 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 125 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 53 optimal weight: 3.9990 chunk 97 optimal weight: 6.9990 chunk 75 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 15 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 35 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 2 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 = 0.3413 r_free = 0.3413 target = 0.091965 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.061916 restraints weight = 28915.386| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 1.90 r_work: 0.2653 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.2653 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2659 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2659 r_free = 0.2659 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2659 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 13498 Z= 0.179 Angle : 0.544 6.584 19466 Z= 0.327 Chirality : 0.034 0.163 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.334 178.417 4114 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 2.52 % Allowed : 21.74 % Favored : 75.74 % 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 aren not related in a simple way. whole: 2.82 (0.30), residues: 831 helix: 3.22 (0.22), residues: 553 sheet: 0.88 (1.02), residues: 20 loop : -1.28 (0.36), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.008 0.001 TYR H 37 PHE 0.009 0.001 PHE F 61 HIS 0.004 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00393 (13498) covalent geometry : angle 0.54350 (19466) hydrogen bonds : bond 0.05811 ( 775) hydrogen bonds : angle 2.80897 ( 1953) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 123 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8333 (OUTLIER) cc_final: 0.7561 (pm20) REVERT: B 27 GLN cc_start: 0.9108 (OUTLIER) cc_final: 0.8574 (mp10) REVERT: D 30 ARG cc_start: 0.8178 (mtp85) cc_final: 0.7919 (mtt180) REVERT: F 92 ARG cc_start: 0.9066 (OUTLIER) cc_final: 0.8367 (mtp85) REVERT: G 42 ARG cc_start: 0.8862 (OUTLIER) cc_final: 0.8034 (mtm180) REVERT: H 31 LYS cc_start: 0.8834 (mmmt) cc_final: 0.8536 (mmmt) REVERT: H 65 ASP cc_start: 0.9153 (t0) cc_final: 0.8765 (t0) REVERT: K 1 MET cc_start: 0.8182 (ppp) cc_final: 0.7513 (ppp) outliers start: 18 outliers final: 14 residues processed: 135 average time/residue: 0.1777 time to fit residues: 31.0749 Evaluate side-chains 140 residues out of total 713 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 GLU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain F residue 96 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 83 ARG Chi-restraints excluded: chain H residue 88 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain H residue 116 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 108 random chunks: chunk 54 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 48 optimal weight: 0.4980 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 3.9990 chunk 60 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 89 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 107 optimal weight: 0.0040 chunk 9 optimal weight: 9.9990 overall best weight: 3.0998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** K 2 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 = 0.3360 r_free = 0.3360 target = 0.088902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.058442 restraints weight = 28713.664| |-----------------------------------------------------------------------------| r_work (start): 0.2744 rms_B_bonded: 1.89 r_work: 0.2571 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8882 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13498 Z= 0.270 Angle : 0.610 6.997 19466 Z= 0.364 Chirality : 0.038 0.161 2219 Planarity : 0.004 0.038 1463 Dihedral : 29.448 179.287 4114 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.95 % Allowed : 21.74 % Favored : 75.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.42 (0.30), residues: 831 helix: 2.96 (0.22), residues: 547 sheet: 0.63 (1.01), residues: 20 loop : -1.43 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.009 0.001 TYR D 39 PHE 0.014 0.002 PHE H 67 HIS 0.003 0.001 HIS F 75 Details of bonding type rmsd covalent geometry : bond 0.00621 (13498) covalent geometry : angle 0.61033 (19466) hydrogen bonds : bond 0.07737 ( 775) hydrogen bonds : angle 3.16142 ( 1953) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2711.16 seconds wall clock time: 47 minutes 6.80 seconds (2826.80 seconds total)